Scientific publications

Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study
Janes et al. 2022

Semi-quantitative bacterial culture is the reference standard to diagnose urinary tract infection, but culture is time-consuming and can be unreliable if patients are receiving antibiotics. Metagenomics could increase diagnostic accuracy and speed by sequencing the microbiota and resistome directly from urine. We aimed to compare metagenomics to culture for semi-quantitative pathogen and resistome detection from urine.

We screened 529 urine samples of which 86 were sequenced (43 culture positive and 43 culture negative). The AUROC of the DNA concentration-based screening was 0·85 (95% CI 0·81–0·89). At a cutoff value of 6·0 ng/mL, culture positivity was ruled out with a negative predictive value of 91% (95% CI 87–93; 26 of 297 samples), reducing the number of samples requiring sequencing by 56% (297 of 529 samples). The AUROC of the diagnostic index was 0·87 (95% CI 0·79–0·95). A diagnostic index cutoff value of 17·2 yielded a positive predictive value of 93% (95% CI 85–97) and a negative predictive value of 69% (55–80), correcting for a culture-positive prevalence of 66%. Gram-positive pathogens explained eight (89%) of the nine false-negative metagenomic test results. Agreement of phenotypic and genotypic antimicrobial susceptibility testing varied between 71% (22 of 31 samples) and 100% (six of six samples), depending on the antibiotic tested.

DOI:   07-06-2022

Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns
Poulsen et al. 2021

Storage of biological specimens is crucial in the life and medical sciences. Storage conditions for samples can be different for a number of reasons, and it is unclear what effect this can have on the inferred microbiome composition in metagenomics analyses. Here, we assess the effect of common storage temperatures (deep freezer, −80°C; freezer, −20°C; refrigerator, 5°C; room temperature, 22°C) and storage times (immediate sample processing, 0 h; next day, 16 h; over weekend, 64 h; longer term, 4, 8, and 12 months) as well as repeated sample freezing and thawing (2 to 4 freeze-thaw cycles). We examined two different pig feces and sewage samples, unspiked and spiked with a mock community, in triplicate, respectively, amounting to a total of 438 samples (777 Gbp; 5.1 billion reads). Storage conditions had a significant and systematic effect on the taxonomic and functional composition of microbiomes.

DOI:   06-10-2021

Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation
Ingham et al. 2021

Patients undergoing allogeneic hematopoietic stem cell transplantation (HSCT) exhibit changes in their gut microbiota and are experiencing a range of complications, including acute graft-versus-host disease (aGvHD). It is unknown if, when, and under which conditions a re-establishment of microbial and immunological homeostasis occurs. It is also unclear whether microbiota long-term dynamics occur at other body sites than the gut such as the mouth or nose. Moreover, it is not known whether the patients’ microbiota prior to HSCT holds clues to whether the patient would suffer from severe complications subsequent to HSCT. Here, we take a holobiont perspective and performed an integrated host-microbiota analysis of the gut, oral, and nasal microbiota in 29 children undergoing allo-HSCT.

DOI:    28-06-2021

Meta-Ribosomalomics: RNA Sequencing Is an Unbiased Method for Parasite Detection of Different Sample Types
Wylezich et al. 2021

In this perspective article, we review the past use of ribosomal sequences to address scientific and diagnostic questions. We highlight a variety of sequencing approaches including metagenomics and DNA barcoding and their different demands and requirements. Meta-ribosomalomics is introduced as an unbiased approach to exploit high-throughput sequencing datasets for eukaryotic and prokaryotic ribosomal sequences. Prerequisites, benefits, drawbacks, and future perspectives are elaborated and compared to other sequencing approaches.

DOI:   21-06-2021

Rapid Open-Source SNP-Based Clustering Offers an Alternative to Core Genome MLST for Outbreak Tracing in a Hospital Setting
Szarvas et al. 2021

Traditional genotyping methods for infection control of antimicrobial-resistant bacteria in healthcare settings have been supplemented by whole-genome sequencing (WGS), often relying on a gene-based approach, e.g., core genome multilocus sequence typing (cgMLST), to cluster-related samples. In this study, we compared clusters of methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus faecium analyzed with the commercial cgMLST software Ridom SeqSphere+ and with an open-source single-nucleotide polymorphism (SNP)-based phylogenetic analysis pipeline (PAPABAC). A total of 5,655 MRSA and 2,572 E. faecium patient isolates, collected between 2013 and 2018, were processed. Clusters of 1,844 MRSA and 1,355 E. faecium isolates were compared to cgMLST results, and epidemiological data were included when available. The phylogenies inferred by the two different technologies were highly concordant, and the MRSA SNP tree re-captured known hospital-related outbreaks and epidemiologically linked samples. PAPABAC has the advantage over Ridom SeqSphere+ to generate stable, referable clusters without the need for sequence assembly, and it is a free-of-charge, open-source alternative to the commercial software.

DOI:     01-04-2021

Economic evaluation of whole genome sequencing for pathogen identification and surveillance – results of case studies in Europe and the Americas 2016 to 2019
Alleweldt et al. 2021

Whole genome sequencing (WGS) is increasingly used for pathogen identification and surveillance. We evaluated costs and benefits of routine WGS through case studies at eight reference laboratories in Europe and the Americas which conduct pathogen surveillance for avian influenza (two laboratories), human influenza (one laboratory) and food-borne pathogens (five laboratories). The evaluation focused on the institutional perspective, i.e. the ‘investment case’ for implementing WGS compared with conventional methods, based on costs and benefits during a defined reference period, mostly covering at least part of 2017. A break-even analysis estimated the number of cases of illness (for the example of Salmonella surveillance) that would need to be avoided through WGS in order to ‘break even’ on costs. On a per-sample basis, WGS was between 1.2 and 4.3 times more expensive than routine conventional methods. However, WGS brought major benefits for pathogen identification and surveillance, substantially changing laboratory workflows, analytical processes and outbreaks detection and control. Between 0.2% and 1.1% (on average 0.7%) of reported salmonellosis cases would need to be prevented to break even with respect to the additional costs of WGS. Even at cost levels documented here, WGS provides a level of additional information that more than balances the additional costs if used effectively. The substantial cost differences for WGS between reference laboratories were due to economies of scale, degree of automation, sequencing technology used and institutional discounts for equipment and consumables, as well as the extent to which sequencers are used at full capacity.

DOI:   04-03-2021

Extended-spectrum beta-lactamase-producing Escherichia coli and antimicrobial resistance in municipal and hospital wastewaters in Czech Republic: Culture-based and metagenomic approaches
Kutilova et al. 2020

Wastewaters serve as important hot spots for antimicrobial resistance and monitoring can be used to analyse the abundance and diversity of antimicrobial resistance genes at the level of large bacterial and human populations. In this study, whole genome sequencing of beta-lactamase-producing Escherichia coli and metagenomic analysis of whole-community DNA were used to characterize the occurrence of antimicrobial resistance in hospital, municipal and river waters in the city of Brno (Czech Republic).

DOI:  21-11-2020

Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset
Höper et al. 2020

Metagenomics-based high-throughput sequencing (HTS) enables comprehensive detection of all species comprised in a sample with a single assay and is becoming a standard method for outbreak investigation. However, unlike real-time PCR or serological assays, HTS datasets generated for pathogen detection do not easily provide yes/no answers. Rather, results of the taxonomic read assignment need to be assessed by trained personnel to gain information thereof. Proficiency tests are important instruments of validation, harmonization, and standardization. Within the European Union funded project COMPARE [COllaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks in Europe], we conducted a proficiency test to scrutinize the ability to assess diagnostic metagenomics data.

DOI:   04-11-2020

Setting a baseline for global urban virome surveillance in sewage
Nieuwenhuijse et al. 2020

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective.

DOI:   13-08-2020

ResFinder 4.0 for predictions of phenotypes from genotypes
Bortolaia et al. 2020

WGS-based antimicrobial susceptibility testing (AST) is as reliable as phenotypic AST for several antimicrobial/bacterial species combinations. However, routine use of WGS-based AST is hindered by the need for bioinformatics skills and knowledge of antimicrobial resistance (AMR) determinants to operate the vast majority of tools developed to date. By leveraging on ResFinder and PointFinder, two freely accessible tools that can also assist users without bioinformatics skills, we aimed at increasing their speed and providing an easily interpretable antibiogram as output.

The ResFinder code was re-written to process raw reads and use Kmer-based alignment. The existing ResFinder and PointFinder databases were revised and expanded. Additional databases were developed including a genotype-to-phenotype key associating each AMR determinant with a phenotype at the antimicrobial compound level, and species-specific panels for in silico antibiograms. ResFinder 4.0 was validated using Escherichia coli (n = 584), Salmonella spp. (n = 1081), Campylobacter jejuni (n = 239), Enterococcus faecium (n = 106), Enterococcus faecalis (n = 50) and Staphylococcus aureus (n = 163) exhibiting different AST profiles, and from different human and animal sources and geographical origins.

DOI:    11-08-2020

Thermus thermophilus DNA can be used as internal control for process monitoring of clinical metagenomic next-generation sequencing of urine samples
Janes et al. 2020

Metagenomics is increasingly considered for clinical diagnostics. In order for this technology to become integrated in the clinical microbiology laboratory, process controls are required. Molecular diagnostic tests typically integrate an internal control (IC) to detect potential sources of variation and technical failure. However, few studies report on the integration of an IC in metagenomics. Metagenomics is increasingly considered for clinical diagnostics. In order for this technology to become integrated in the clinical microbiology laboratory, process controls are required. Molecular diagnostic tests typically integrate an internal control (IC) to detect potential sources of variation and technical failure. However, few studies report on the integration of an IC in metagenomics.

DOI:     18-07-2020

Untargeted metagenomics shows a reliable performance for synchronous detection of parasites
Wylezich et al. 2020

Shotgun metagenomics with high-throughput sequencing (HTS) techniques is increasingly used for pathogen identification and characterization. While many studies apply targeted amplicon sequencing, here we used untargeted metagenomics to simultaneously identify protists and helminths in pre-diagnosed faecal and tissue samples. The approach starts from RNA and operates without an amplification step, therefore allowing the detection of all eukaryotes, including pathogens, since it circumvents the bias typically observed in amplicon-based HTS approaches. The generated metagenomics datasets were analysed using the RIEMS tool for initial taxonomic read assignment. Mapping analyses against ribosomal reference sequences were subsequently applied to extract 18S rRNA sequences abundantly present in the sequence datasets. The original diagnosis, which was based on microscopy and/or PCR, could be confirmed in nearly all cases using ribosomal RNA metagenomics. In addition to the pre-diagnosed taxa, we detected other intestinal eukaryotic parasites of uncertain pathogenicity (of the genera Dientamoeba, Entamoeba, Endolimax, Hymenolepis) that are often excluded from routine diagnostic protocols. The study clearly demonstrates the applicability of untargeted RNA metagenomics for the parallel detection of parasites.

DOI:    26-06-2020

Large scale automated phylogenomic analysis of bacterial isolates and the Evergreen Online platform
Szarvas et al. 2020

Public health authorities whole-genome sequence thousands of isolates each month for microbial diagnostics and surveillance of pathogenic bacteria. The computational methods have not kept up with the deluge of data and the need for real-time results. We have therefore created a bioinformatics pipeline for rapid subtyping and continuous phylogenomic analysis of bacterial samples, suited for large-scale surveillance.

DOI:   20-03-2020

Addressing Learning Needs on the Use of Metagenomics in Antimicrobial Resistance Surveillance
Duarte et al. 2020

One Health surveillance of antimicrobial resistance (AMR) depends on a harmonized method for detection of AMR. Metagenomics-based surveillance offers the possibility to compare resistomes within and between different target populations. Its potential to be embedded into policy in the future calls for a timely and integrated knowledge dissemination strategy. We developed a blended training (e-learning and a workshop) on the use of metagenomics in surveillance of pathogens and AMR. The objectives were to highlight the potential of metagenomics in the context of integrated surveillance, to demonstrate its applicability through hands-on training and to raise awareness to bias factors1. The target participants included staff of competent authorities responsible for AMR monitoring and academic staff. The training was organized in modules covering the workflow, requirements, benefits and challenges of surveillance by metagenomics. The training had 41 participants. The face-to-face workshop was essential to understand the expectations of the participants about the transition to metagenomics-based surveillance.

DOI:   25-02-2020

Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering
Ahrenfeldt et al. 2020

Knowledge about the difference in the global distribution of pathogens and non-pathogens is limited. Here, we investigate it using a multi-sample metagenomics phylogeny approach based on short-read metagenomic sequencing of sewage from 79 sites around the world. For each metagenomic sample, bacterial template genomes were identified in a non-redundant database of whole genome sequences. Reads were mapped to the templates identified in each sample. Phylogenetic trees were constructed for each template identified in multiple samples.

DOI:   20-02-2020

Prediction of Acquired Antimicrobial Resistance for Multiple Bacterial Species Using Neural Networks
Aytan-Aktug et al. 2020

Machine learning has proven to be a powerful method to predict antimicrobial resistance (AMR) without using prior knowledge for selected bacterial species-antimicrobial combinations. To date, only species-specific machine learning models have been developed, and to the best of our knowledge, the inclusion of information from multiple species has not been attempted. The aim of this study was to determine the feasibility of including information from multiple bacterial species to predict AMR for an individual species, since this may make it easier to train and update resistance predictions for multiple species and may lead to improved predictions.

DOI:   21-01-2020

The Risk of Infection by African Swine Fever Virus in European Swine Through Boar Movement and Legal Trade of Pigs and Pig Meat
Taylor et al. 2020

African swine fever (ASF) is currently spreading westwards throughout Europe and eastwards into China, with cases occurring in both wild boar and domestic pigs. A generic risk assessment framework is used to determine the probability of first infection with ASF virus (ASFV) at a fine spatial scale across European Union Member States. The framework aims to assist risk managers across Europe with their ASF surveillance and intervention activities. Performing the risk assessment at a fine spatial scale allows for hot-spot surveillance, which can aid risk managers by directing surveillance or intervention resources at those areas or pathways deemed most at risk, and hence enables prioritization of limited resources.

DOI:     10.3389/fvets.2019.00486     09-01-2020

The COMPARE Data Hubs
Amid et al. 2019

Data sharing enables research communities to exchange findings and build upon the knowledge that arises from their discoveries. Areas of public and animal health as well as food safety would benefit from rapid data sharing when it comes to emergencies. However, ethical, regulatory and institutional challenges, as well as lack of suitable platforms which provide an infrastructure for data sharing in structured formats, often lead to data not being shared or at most shared in form of supplementary materials in journal publications. Here, we describe an informatics platform that includes workflows for structured data storage, managing and pre-publication sharing of pathogen sequencing data and its analysis interpretations with relevant stakeholders.

DOI:    10.1093/database/baz136    23-12-2019

IS26-Mediated Transfer of blaNDM–1 as the Main Route of Resistance Transmission During a Polyclonal, Multispecies Outbreak in a German Hospital
Weber et al. 2019

One of the most demanding challenges in infection control is the worldwide dissemination of multidrug-resistant (MDR) bacteria in clinical settings. Especially the increasing prevalence of carbapenemase producing Gram-negative pathogens poses an urgent threat to public health, as these enzymes confer resistance to almost all β-lactam antibiotics including carbapenems. In this study, we report a prolonged nosocomial outbreak of various NDM-1-producing Enterobacterales species due to clonal spread and cross-species exchange of plasmids and possibly transposons.

DOI:   10.3389/fmicb.2019.02817     17-12-2019

Enzootic patterns of Middle East respiratory syndrome coronavirus in imported African and local Arabian dromedary camels: a prospective genomic study
El-Kafrawy et al. 2019

The Middle East respiratory syndrome coronavirus (MERS-CoV) is a lethal zoonotic pathogen endemic to the Arabian Peninsula. Dromedary camels are a likely source of infection and the virus probably originated in Africa. We studied the genetic diversity, geographical structure, infection prevalence, and age-associated prevalence among camels at the largest entry port of camels from Africa into the Arabian Peninsula.

DOI:   16-12-2019

Nosocomial infections caused by Crimean-Congo haemorrhagic fever virus
Tsergouli et al. 2019

Crimean-Congo haemorrhagic fever (CCHF) is an acute febrile illness, often accompanied by haemorrhagic manifestations, with high case fatality rate (CFR). The causative agent is CCHF virus (CCHFV) and is transmitted to humans mainly through tick bites or exposure to blood or tissues of viremic patients or livestock. Human-to-human transmission usually occurs in hospital settings and health care workers (HCWs) are mainly affected. A review on nosocomial CCHFV infections was performed to elucidate the routes and circumstances of CCHFV transmission in hospital settings.

DOI:   10.1016/j.jhin.2019.12.001   09-12-2019

Source Attribution of Salmonella in Macadamia Nuts to Animal and Environmental Reservoirs in Queensland, Australia
Munck et al. 2019

Salmonella enterica is a common contaminant of macadamia nut kernels in the subtropical state of Queensland (QLD), Australia. We hypothesized that nonhuman sources in the plantation environment contaminate macadamia nuts. We applied a modified Hald source attribution model to attribute Salmonella serovars and phage types detected on macadamia nuts from 1998 to 2017 to specific animal and environmental sources. Potential sources were represented by Salmonella types isolated from avian, companion animal, biosolids-soil-compost, equine, porcine, poultry, reptile, ruminant, and wildlife samples by the QLD Health reference laboratory. Two attribution models were applied: model 1 merged data across 1998–2017, whereas model 2 pooled data into 5-year time intervals.

DOI:  04-12-2019

Detection of flaviviruses and alphaviruses in mosquitoes in Central Macedonia, Greece, 2018
Papa et al. 2019

Culex mosquitoes are vectors of several flaviviruses and alphaviruses posing a potential risk to public and veterinary health. In order to gain an insight into the flaviviruses and alphaviruses circulating in the five regional units of Central Macedonia in northern Greece, 17,470 female Culex spp. mosquitoes collected during 2018 were tested for these viruses. Among 229 mosquito pools, West Nile virus (WNV) was detected in 10 (4.4%) pools, while insect-specific flavi- and alphaviruses were detected in 2 (0.9%) and 8 (3.5%) pools, respectively.

DOI:    20-11-2019

Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale
Vila Nova et al. 2019

Salmonella enterica subsp. enterica is a public health issue related to food safety, and its adaptation to animal sources remains poorly described at the pangenome scale. Firstly, serovars presenting potential mono- and multi-animal sources were selected from a curated and synthetized subset of Enterobase. The corresponding sequencing reads were downloaded from the European Nucleotide Archive (ENA) providing a balanced dataset of 440 Salmonella genomes in terms of serovars and sources (i).

DOI:   06-11-2019

Application of different DNA extraction procedures, library preparation protocols and sequencing platforms: impact on sequencing results
Pasquali et al. 2019

In this study three DNA extraction procedures, two library preparation protocols and two sequencing platforms were applied to analyse six bacterial cultures and their corresponding DNA obtained as part of a proficiency test. The impact of each variable on sequencing results was assessed using the following parameters: reads quality, assembly and alignment statistics; number of single nucleotide polymorphisms (SNPs), detected applying assembly- and alignment-based strategies; antimicrobial resistance genes (ARGs), identified on de novo assemblies of all sequenced genomes.

DOI:    10.1016/j.heliyon.2019.e02745    01-11-2019

Transmission dynamics between infected waterfowl and terrestrial poultry: Differences between the transmission and tropism of H5N8 highly pathogenic avian influenza virus (clade among ducks, chickens and turkeys
Puranik et al. 2019

H5N8 highly-pathogenic avian influenza viruses (HPAIVs, clade have spread globally via migratory waterfowl. Pekin ducks infected with a UK virus (H5N8-2014) served as the donors of infection in three separate cohousing experiments to attempt onward transmission chains to sequentially introduced groups of contact ducks, chickens and turkeys. Efficient transmission occurred among ducks and turkeys up to the third contact stage, with all (100%) birds becoming infected.

DOI:   31-10-2019

A Simple and Robust Statistical Method to Define Genetic Relatedness of Samples Related to Outbreaks at the Genomic Scale – Application to Retrospective Salmonella Foodborne Outbreak Investigations
Radomski et al. 2019

The investigation of foodborne outbreaks (FBOs) from genomic data typically relies on inspecting the relatedness of samples through a phylogenomic tree computed on either SNPs, genes, kmers, or alleles (i.e., cgMLST and wgMLST). The phylogenomic reconstruction is often time-consuming, computation-intensive and depends on hidden assumptions, pipelines implementation and their parameterization. In the context of FBO investigations, robust links between isolates are required in a timely manner to trigger appropriate management actions. Here, we propose a non-parametric statistical method to assert the relatedness of samples (i.e., outbreak cases) or whether to reject them (i.e., non-outbreak cases).

DOI:    24-10-2019

Metavirome Sequencing to Evaluate Norovirus Diversity in Sewage and Related Bioaccumulated Oysters
Strubbia et al. 2019

Metagenomic sequencing is a promising method to determine the virus diversity in environmental samples such as sewage or shellfish. However, to identify the short RNA genomes of human enteric viruses among the large diversity of nucleic acids present in such complex matrices, method optimization is still needed. This work presents methodological developments focused on norovirus, a small ssRNA non-enveloped virus known as the major cause of human gastroenteritis worldwide and frequently present in human excreta and sewage.

DOI:   17-10-2019

Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach
Hendriksen et al. 2019

Worldwide, the number of emerging and re-emerging infectious diseases is increasing, highlighting the importance of global disease pathogen surveillance. Traditional population-based methods may fail to capture important events, particularly in settings with limited access to health care, such as urban informal settlements. In such environments, a mixture of surface water runoff and human feces containing pathogenic microorganisms could be used as a surveillance surrogate.

DOI:    10.1371/journal.pone.0222531   10-10-2019

Virus persistence in pig herds led to successive reassortment events between swine and human influenza A viruses, resulting in the emergence of a novel triple-reassortant swine influenza virus
Chastagner et al. 2019

This report describes the detection of a triple reassortant swine influenza A virus of H1avN2 subtype. It evolved from an avian-like swine H1avN1 that first acquired the N2 segment from a seasonal H3N2, then the M segment from a 2009 pandemic H1N1, in two reassortments estimated to have occurred 10 years apart. This study illustrates how recurrent influenza infections increase the co-infection risk and facilitate evolutionary jumps by successive gene exchanges. It recalls the importance of appropriate biosecurity measures inside holdings to limit virus persistence and interspecies transmissions, which both contribute to the emergence of new potentially zoonotic viruses.

DOI:     10.1186/s13567-019-0699-y   07-10-2019

An evolutionary divergent pestivirus lacking the Npro gene systemically infects a whale species
Jo et al. 2019

Pestiviruses typically infect members of the order Artiodactyla, including ruminants and pigs, although putative rat and bat pestiviruses have also been described. In the present study, we identified and characterized an evolutionary divergent pestivirus in the toothed whale species, harbour porpoise (Phocoena phocoena). We tentatively named the virus Phocoena pestivirus (PhoPeV). PhoPeV displays a typical pestivirus genome organization except for the unique absence of Npro, an N-terminal autoprotease that targets the innate host immune response. Evolutionary evidence indicates that PhoPeV emerged following an interspecies transmission event from an ancestral pestivirus that expressed Npro.

DOI:    17-09-2019

Genomic polymorphism of Mycoplasma flocculare revealed by a newly developed multilocus sequence typing scheme
Fourour et al. 2019

Mycoplasma flocculare is genetically closely related to M. hyopneumoniae, the etiologic agent of porcine enzootic pneumonia, and is frequently isolated with this second species. In this article, we report on the development of the first multilocus sequence typing (MLST) scheme for M. flocculare, based on three genes (adk, rpoB and tpiA). In total, 5022 bp of sequence were analyzed. MLST was used to characterize seven M. flocculare isolates and the reference strain. Eight distinct sequence types were defined, showing the great intraspecies variability of M. flocculare, and the high discriminatory power of the new typing method.

DOI:    10.1016/j.vetmic.2019.108422     15-09-2019

Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation
Masche et al. 2019

Increasing evidence reveals the importance of the microbiome in health and disease and inseparable host-microbial dependencies. Host-microbe interactions are highly relevant in patients receiving allogeneic hematopoietic stem cell transplantation (HSCT), i.e., a replacement of the cellular components of the patients’ immune system with that of a foreign donor. HSCT is employed as curative immunotherapy for a number of non-malignant and malignant hematologic conditions, including cancers such as acute lymphoblastic leukemia. The procedure can be accompanied by severe side effects such as infections, acute graft-versus-host disease (aGvHD), and death.

DOI:    10.1186/s40168-019-0745-z    13-09-2019

Evolutionary dynamics of lineage 2 West Nile virus in Europe, 2004–2018: Phylogeny, selection pressure and phylogeography
Chaintoutis et al. 2019

West Nile virus (WNV) is an arbovirus causing neuroinvasive disease to humans and equines. Since 2004, lineage 2 WNV strains have been identified in Europe and have been implicated in severe outbreaks, with that of 2018 exceeding the total number from the previous seven years. The aim of this study was to explore the evolutionary process that shapes the genetic diversity of lineage 2 WNV strains (belonging to the Central European/Hungarian subclade) and reconstruct the origin and transmission routes in Europe, and especially in the Balkans. For this purpose, a high number of whole genome sequences (WGSs) were analyzed, along with newly characterized sequences, including strains from the 2018 WNV transmission season in Greece.

DOI:    10.1016/j.ympev.2019.106617    12-09-2019

Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers
Ingle et al. 2019

Salmonella enterica serovar Typhi (S. Typhi) is the causative agent of typhoid fever, a systemic human infection with a burden exceeding 20 million cases each year that occurs disproportionately among children in low and middle income countries. Antimicrobial therapy is the mainstay for treatment, but resistance to multiple agents is common. Here we report genotypes and antimicrobial resistance (AMR) determinants detected from routine whole-genome sequencing (WGS) of 533 S. Typhi isolates referred to Public Health England between April 2014 and March 2017, 488 (92%) of which had accompanying patient travel information obtained via an enhanced surveillance questionnaire.

DOI:    12-09-2019

A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences
Forth et al. 2019

African swine fever (ASF) is a severe disease of suids caused by African swine fever virus (ASFV). Its dsDNA genome (170–194 kbp) is scattered with homopolymers and repeats as well as inverted-terminal-repeats (ITR), which hamper whole-genome sequencing. To date, only a few genome sequences have been published and only for some are data on sequence quality available enabling in-depth investigations. Especially in Europe and Asia, where ASFV has continuously spread since its introduction into Georgia in 2007, a very low genetic variability of the circulating ASFV-strains was reported. Therefore, only whole-genome sequences can serve as a basis for detailed virus comparisons. Here, we report an effective workflow, combining target enrichment, Illumina and Nanopore sequencing for ASFV whole-genome sequencing.

DOI:     10.3390/v11090846    11-09-2019

Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next-Generation Sequencing
Strubbia et al. 2019

This study aimed to optimize a method to identify human enteric viruses in sewage and stool samples using random primed next-generation sequencing. We tested three methods, two employed virus enrichment based on the binding properties of the viral capsid using pig-mucin capture or by selecting viral RNA prior to library preparation through a capture using the SureSelect target enrichment. The third method was based on a non-specific biophysical precipitation with polyethylene glycol.

DOI:   24-08-2019

Worldwide human mitochondrial haplogroup distribution from urban sewage
Pipek et al. 2019

Community level genetic information can be essential to direct health measures and study demographic tendencies but is subject to considerable ethical and legal challenges. These concerns become less pronounced when analyzing urban sewage samples, which are ab ovo anonymous by their pooled nature. We were able to detect traces of the human mitochondrial DNA (mtDNA) in urban sewage samples and to estimate the distribution of human mtDNA haplogroups.

DOI:    10.1038/s41598-019-48093-5     12-08-2019

Metagenomics for broad and improved parasite detection: a proof-of-concept study using swine faecal samples
Wylezich et al. 2019

Efficient and reliable identification of emerging pathogens is crucial for the design and implementation of timely and proportionate control strategies. This is difficult if the pathogen is so far unknown or only distantly related with known pathogens. Diagnostic metagenomics – an undirected, broad and sensitive method for the efficient identification of pathogens – was frequently used for virus and bacteria detection, but seldom applied to parasite identification.

DOI:   10.1016/j.ijpara.2019.04.007    27-07-2019

Evolutionary Insights into the Tick Hologenome
Diaz-Sanchez et al. 2019

Recently, our knowledge of the composition and complexity of tick microbial communities has increased and supports microbial impact on tick biology. Results support a phylogenetic association between ticks and their microbiota across evolution; this is known as phylosymbiosis. Herein, using published datasets, we confirm the existence of phylosymbiosis between Ixodes ticks and their microbial communities.

DOI:   19-07-2019

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
Edwards et al. 2019

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world’s countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals.

DOI:   10.1038/s41564-019-0494-6    08-07-2019

Analysis of isolates from Bangladesh highlights multiple ways to carry resistance genes in Salmonella Typhi
Lima et al. 2019

Typhoid fever, caused by Salmonella Typhi, follows a fecal-oral transmission route and is a major global public health concern, especially in developing countries like Bangladesh. Increasing emergence of antimicrobial resistance (AMR) is a serious issue; the list of treatments for typhoid fever is ever-decreasing. In addition to IncHI1-type plasmids, Salmonella genomic island (SGI) 11 has been reported to carry AMR genes. Although reports suggest a recent reduction in multidrug resistance (MDR) in the Indian subcontinent, the corresponding genomic changes in the background are unknown.

DOI:   10.1186/s12864-019-5916-6    28-06-2019

Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) in bulk tank milk, livestock and dairy-farm personnel in north-central and north-eastern Greece: Prevalence, characterization and genetic relatedness
Papadopoulos et al. 2019

Recently, there has been an increased tendency towards raw-milk consumption, which may pose a consumer risk, due to the possible presence of human pathogenic microorganisms, such as Staphylococcus aureus and even methicillin-resistant S. aureus (MRSA). The prevalence of S. aureus and methicillin-resistant S. aureus (MRSA) was investigated in 40 dairy (cattle, sheep and goat) farms in northern Greece. S. aureus and MRSA were detected in 47.8% and 4.1% of the 387 samples (raw milk, farmers and animal samples) tested, respectively.

DOI:   10.1016/   22-06-2019

A PCR-based NGS protocol for whole genome sequencing of West Nile virus lineage 2 directly from biological specimens
Chaintoutis et al. 2019

Lineage 2 West Nile virus (WNV) strains have been implicated in severe encephalitis outbreaks in humans and equines residing in Europe. WNV molecular characterization is important for the development of diagnostic assays, as well as for obtaining molecular information, which is necessary for epidemiological investigations of virus transmission in areas at risk. For whole genome sequencing of lineage 2 WNV strains, directly from biological specimens, a PCR-based NGS protocol was developed.

DOI:  10.1016/j.mcp.2019.06.002     12-06-2019

Science-based wildlife disease response
Vicente et al. 2019

In 2007, the current outbreak of African swine fever (ASF), which severely affects wild boar populations and pigs, reached the Caucasus region. Since then, the virus has spread into eastern Europe and some places in central and western Europe (such as Belgium) through wild boar, domestic pigs, and human activities. The virus has raised serious concerns in countries with large pork industries, which may suffer economic losses due to trade restrictions (1). To control the outbreak, national authorities have taken drastic but likely ineffective measures that disregard the science of wildlife management.

DOI:   10.1126/science.aax4310    07-06-2019

How to value safety in economic evaluations in health care? A review of applications in different sectors
Perry-Duxbury et al. 2019

Improving (feelings of) safety is an important goal of many health systems, especially in the context of recurrent threats of pandemics, and natural disasters. Measures to improve safety should be cost-effective, raising the issue of how to value safety. This is a complex task due to the intangible nature of safety. We aim to synthesize the current empirical literature on the evaluation of safety to gain insights into current methodological practices. After a thorough literature search in two databases for papers from the fields of life sciences, social sciences, physical sciences and health sciences that empirically measure the value of increasing safety, 33 papers were found and summarized. The focus of the research was to investigate the methodologies used.

DOI:    10.1007/s10198-019-01076-9    06-06-2019

Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing datasets
Brinkmann et al. 2019

Quality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. Sensitivity and specificity of viral high-throughput sequence data analysis are highly affected by bioinformatics processing, using publicly available and custom tools and databases, and differ widely between individuals and institutions.

DOI:    10.1128/JCM.00466-19     05-06-2019

Genetic variability of porcine pegivirus in pigs from Europe and China and insights into tissue tropism
Kennedy et al. 2019

Pegiviruses belong to the family Flaviviridae and have been found in humans and other mammalian species. To date eleven different pegivirus species (Pegivirus A-K) have been described. However, little is known about the tissue tropism and replication of pegiviruses. In 2016, a so far unknown porcine pegivirus (PPgV, Pegivirus K) was described and persistent infection in the host, similar to human pegivirus, was reported. In this study, qRT-PCR, phylogenetic analyses and fluorescence in situ hybridization (FISH) were implemented to detect and quantify PPgV genome content in serum samples from domestic pigs from Europe and Asia, in tissue and peripheral blood mononuclear cell (PBMC) samples and wild boar serum samples from Germany.

DOI:    1038/s41598-019-44642-0     03-06-2019

Animals as Reservoir for Human Norovirus
Villabruna et al. 2019

Norovirus is the most common cause of non-bacterial gastroenteritis and is a burden worldwide. The increasing norovirus diversity is currently categorized into at least 10 genogroups which are further classified into more than 40 genotypes. In addition to humans, norovirus can infect a broad range of hosts including livestock, pets, and wild animals, e.g., marine mammals and bats.

DOI:   10.3390/v11050478     25-05-2019

Emergence and divergence of major lineages of Shiga-toxin-producing Escherichia coli in Australia
Ingle et al. 2019 b

Shiga-toxin-producing Escherichia coli (STEC) infection is an important global cause of foodborne disease. To date however, genomics-based studies of STEC have been predominately focused upon STEC collected in the Northern Hemisphere. Here, we demonstrate the population structure of 485 STEC isolates in Australia, and show that several clonal groups (CGs) common to Australia were infrequently detected in a representative selection of contemporary STEC genomes from around the globe. Further, phylogenetic analysis demonstrated that lineage II of the global O157:H7 STEC was most prevalent in Australia, and was characterized by a frameshift mutation in flgF, resulting in the H-non-motile phenotype.

DOI:    10.1099/mgen.0.000268    20-05-2019

Diagnostic approaches for Crimean-Congo hemorrhagic fever virus
Papa 2019

Crimean-Congo hemorrhagic fever (CCHF) is a potentially severe tick-borne viral disease endemic in several regions of Europe, Africa, and Asia. Rapid and reliable diagnosis is essential for early initiation of patient's treatment and for prompt implementation of appropriate precaution and infection control measures to prevent further spread of the disease.

DOI:   10.1080/14737159.2019.1615450    10-05-2019

Whole-genome sequencing reveals nosocomial Clostridioides difficile transmission and a previously unsuspected epidemic scenario
Garcia-Fernandez et al. 2019

To trace the routes and frequencies of transmission of Clostridioides difficile in a tertiary-care hospital in Madrid (Spain), we sequenced the genomes from all C. difficile isolates collected over 36 months (2014–2016) that were indistinguishable from any other isolate by PCR ribotyping. From a total of 589 C. difficile infection cases, we cultivated and PCR-ribotyped 367 C. difficile isolates (62%), of which 265 were genome-sequenced. Based on close relatedness of successively collected isolates (≤2 SNPs difference in their genomes), whole-genome sequencing revealed a total of 17 independent, putative transmission clusters, caused by various C. difficile strains and each containing 2 to 18 cases, none of which had been detected previously by standard epidemiological surveillance.

DOI:    10.1038/s41598-019-43464-4    06-05-2019

Mass Die-Off of Saiga Antelopes, Kazakhstan, 2015
Fereidouni et al. 2019

In 2015, a mass die-off of ≈200,000 saiga antelopes in central Kazakhstan was caused by hemorrhagic septicemia attributable to the bacterium Pasteurella multocida serotype B. Previous analyses have indicated that environmental triggers associated with weather conditions, specifically air moisture and temperature in the region of the saiga antelope calving during the 10-day period running up to the event, were critical to the proliferation of latent bacteria and were comparable to conditions accompanying historically similar die-offs in the same areas.

DOI:    10.3201/eid2506.180990     30-04-2019

A Field Recombinant Strain Derived from Two Type 1 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV-1) Modified Live Vaccines Shows Increased Viremia and Transmission in SPF Pigs
Eclercy et al. 2019

In Europe, modified live vaccines (MLV) are commonly used to control porcine reproductive and respiratory syndrome virus (PRRSV) infection. However, they have been associated with safety issues such as reversion to virulence induced by mutation and/or recombination. On a French pig farm, we identified a field recombinant strain derived from two PRRSV-1 MLV (MLV1). As a result, we aimed to evaluate its clinical, virological, and transmission parameters in comparison with both parental strains.

DOI:    10.3390/v11030296     23-04-2019

Co-circulation of genetically distinct highly pathogenic avian influenza A clade (H5N6) viruses in wild waterfowl and poultry in Europe and East Asia, 2017–18
Poen et al. 2019

Highly pathogenic avian influenza (HPAI) H5 clade viruses were first introduced into Europe in late 2014 and re-introduced in late 2016, following detections in Asia and Russia. In contrast to the 2014–15 H5N8 wave, there was substantial local virus amplification in wild birds in Europe in 2016–17 and associated wild bird mortality, with evidence for occasional gene exchange with low pathogenic avian influenza (LPAI) viruses. Since December 2017, several European countries have again reported events or outbreaks with HPAI H5N6 reassortant viruses in both wild birds and poultry, respectively.

DOI:    10.1093/ve/vez004    22-04-2019

Towards high quality real-time whole genome sequencing during outbreaks using Usutu virus as example
Oude Munnink et al. 2019

Recently, protocols for amplicon based whole genome sequencing using Nanopore technology have been described for Ebola virus, Zika virus, yellow fever virus and West Nile virus. However, there is some debate regarding reliability of sequencing using this technology, which is important for applications beyond diagnosis such as linking lineages to outbreaks, tracking transmission pathways and pockets of circulation, or mapping specific markers.

DOI:  10.1016/j.meegid.2019.04.015    18-04-2019

Genetic Characterization and Zoonotic Potential of Highly Pathogenic Avian Influenza Virus A(H5N6/H5N5), Germany, 2017–2018
Pohlmann et al. 2019

We genetically characterized highly pathogenic avian influenza virus A(H5N6) clade isolates found in Germany in 2017–2018 and assessed pathogenicity of representative H5N5 and H5N6 viruses in ferrets. These viruses had low pathogenicity; however, continued characterization of related isolates is warranted because of their high potential for reassortment.

DOI:    10.3201/eid2510.181931    09-04-2019

Bidirectional human-swine transmission of seasonal influenza A(H1N1)pdm09 virus in Pig Herd, France, 2018
Chastagner et al. 2019b

In 2018, a veterinarian became sick shortly after swabbing sows exhibiting respiratory syndrome on a farm in France. Epidemiologic data and genetic analyses revealed consecutive human-to-swine and swine-to-human influenza A(H1N1)pdm09 virus transmission, which occurred despite some biosecurity measures. Providing pig industry workers the annual influenza vaccine might reduce transmission risk.

DOI:    10.3201/eid2510.190068   09-04-2019

Emergence of West Nile virus lineage 2 belonging to the Eastern European subclade, Greece
Papa et al. 2019

West Nile virus (WNV) emerged in Greece in 2010 and since then human outbreaks occurred every year except 2015 and 2016. An early start and prolonged WNV transmission season was observed in 2018 with a record number of 316 reported cases and 47 fatalities. The Greek WNV strains detected during 2010-2018 clustered within the central European subclade of lineage 2. A novel WNV genetic variant was detected in August 2018 in one human case in the north-eastern region of Greece, at the land cross-border with Turkey and Bulgaria. The strain belongs to the Eastern European subclade of lineage 2 suggesting a new virus introduction in the country and the continuously changing epidemiology of the disease.

DOI:   10.1007/s00705-019-04243-8     05-04-2019

Hospital outbreak due to Clostridium difficile ribotype 018 (RT018) in Southern Germany
Berger et al. 2019

Clostridium (Clostridioides) difficile is the main cause of nosocomial diarrhoea. Ribotype 018 (RT018) has been recognized as the predominant strain responsible for C. difficile infection (CDI) in Italy, whereas in most other European countries only sporadic RT018 cases occur.

DOI:    10.1016/j.ijmm.2019.03.001    05-04-2019

Genetic Diversity of Salmonella Derby from the Poultry Sector in Europe
Sevellec et al. 2019

Salmonella Derby (S. Derby) is emerging in Europe as a predominant serovar in fattening turkey flocks. This serovar was recorded as being predominant in the turkey sector in 2014 in the United Kingdom (UK). Only two years later, in 2016, it was also recorded in the turkey and broiler sectors in Ireland and Spain. These S. Derby isolates were characterised as members of the multilocus sequence type (MLST) profile 71 (ST71). For the first time, we characterise by whole genome sequencing (WGS) analysis a panel of 90 S. Derby ST71 genomes to understand the routes of transmission of this emerging pathogen within the poultry/turkey food trade.

DOI:    04-04-2019

ND-GiST: A Novel Method for Disk-Resident k-mer Indexing
Szalai-Gindl et al. 2019

Several challenges are related to metagenomics, one of which is the data management. A related central concept is k-mer which means a possible subsequence of length k from a DNA (sub)sequence. In this work, the focus is on indexing k-mers and supporting box queries where a query string of length k might have multiple allowed nucleobases per position. A novel index structure: ND-GiST is introduced which has capability to handle box queries. Comparing it with full table scan and the traditional B-tree, the performance results of ND-GiST are encouraging.

DOI:    10.1007/978-3-030-16184-2_63    30-03-2019

Rapid cell division of Staphylococcus aureus during colonization of the human nose
Szafranska et al. 2019

Staphylococcus aureus is an important opportunistic pathogen and a commensal bacterium, thriving in the nasal cavities of 20% of the human population. Little is known about the dynamics of asymptomatic colonization and the occasional transition to infectious disease. In this study, we inferred that S. aureus cells replicate every one to three hours on average while colonizing the human nose, based on two independent lines of genomic evidence.

DOI:    10.1186/s12864-019-5604-6    20-03-2019

A retrospective molecular study of Cryptosporidium species and genotypes in HIV-infected patients from Thailand
Sannella et al. 2019

Opportunistic infections represent a serious health problem for HIV-infected people. Among enteric infections, cryptosporidiosis, a severe and life-threatening diarrheal disease, is of particular importance in low economic settings where access to anti-retroviral therapy is limited. Understanding transmission routes is crucial in establishing preventive measures, and requires the use of informative genotyping methods. In this study, we performed a retrospective analysis of Cryptosporidium species in 166 stool samples collected from 155 HIV-infected patients during 1999–2004 at the Siriraj Hospital in Bangkok, Thailand.

DOI:    10.1186/s13071-019-3348-4     12-03-2019

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage
Hendriksen et al. 2019 a

Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.

DOI:    10.1038/s41467-019-08853-3     08-03-2019

Identification of the novel class D β-lactamase OXA-679 involved in carbapenem resistance in Acinetobacter calcoaceticus
Tietgen et al. 2019

The aim of this study was to characterize the Acinetobacter calcoaceticus clinical isolate AC_2117 with the novel carbapenem-hydrolysing class D β-lactamase (CHDL) OXA-679.

DOI:    10.1093/jac/dkz080    07-03-2019

Use of Next Generation Sequencing to study two cowpox virus outbreaks
Antwerpen et al. 2019

Between 2008 and 2011 about 40 cases of human cowpox were reported from Germany and France. Infections had been acquired via close contact to infected, young pet rats. An identical and unique sequence of the hemagglutinin gene was found in various cowpox virus (CPXV) isolates pointing to a common source of infection. In a second CPXV outbreak in cats in a small animal clinic in Germany in 2015, four out of five hospitalized cats showed identical hemagglutinin sequences and thus, a hospital acquired transmission had been assumed. Next-Generation Sequencing was performed in order to re-investigate the outbreaks, as epidemiological data could not confirm all cases.

DOI:   10.7717/peerj.6561    01-03-2019

Global status of Middle East respiratory syndrome coronavirus in dromedary camels: a systematic review
Sikkema et al. 2019 a

Dromedary camels have been shown to be the main reservoir for human Middle East respiratory syndrome (MERS) infections. This systematic review aims to compile and analyse all published data on MERS-coronavirus (CoV) in the global camel population to provide an overview of current knowledge on the distribution, spread and risk factors of infections in dromedary camels. We included original research articles containing laboratory evidence of MERS-CoV infections in dromedary camels in the field from 2013 to April 2018.

DOI:    10.1017/S095026881800345X   21-02-2019

Microbiota analysis and microbiological hazard assessment in poultry carcasses from conventional and antibiotic free farms
De Desare et al. 2019

The aim of this study was to assess microbiota and microbiological hazards in poultry carcasses from animals reared in conventional (n=15) and antibiotic free (n=15) farms. An aliquot of neck and breast skin was obtained from each individual carcass at the end of the refrigeration tunnel and submitted to DNA extraction. Total DNA was sequenced in the 16S rRNA and reads analysed with MG-RAST to classify the colonising bacteria up to the genus level and compare each taxonomic group in terms of mean relative frequency of abundance in conventional and antibiotic free carcasses.

DOI:    11-02-2019

Whole genome sequencing based typing and characterisation of Shiga-toxin producing Escherichia coli strains belonging to O157 and O26 serotypes and isolated in dairy farms
Pasquali et al. 2019

In the present study, the genetic relationships as well as the virulome and resistome of newly sequenced O26 and O157 Shiga-toxin producing E. coli (STEC) isolates, collected from dairy farms in Italy, were investigated in comparison to publicly available genomes collected worldwide. The whole genome of Italian isolates was sequenced on Illumina MiSeq Platform.

DOI:    10.4081/ijfs.2018.7673    08-02-2019

Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in Australia
Ingle et al. 2019

In urban Australia, the burden of shigellosis is either in returning travelers from shigellosis-endemic regions or in men who have sex with men (MSM). Here, we combine genomic data with comprehensive epidemiological data on sexual exposure and travel to describe the spread of multidrug-resistant Shigella lineages.

DOI:    10.1093/cid/ciz005    07-01-2019

Drivers of MERS-CoV Emergence in Qatar
Farag et al. 2018

MERS-CoV (Middle East respiratory syndrome corona virus) antibodies were detected in camels since 1983, but the first human case was only detected in 2012. This study sought to identify and quantify possible drivers for the MERS-CoV emergence and spillover to humans. A list of potential human, animal and environmental drivers for disease emergence were identified from literature. Trends in possible drivers were analyzed from national and international databases, and through structured interviews with experts in Qatar.

DOI:     10.3390/v11010022    31-12-2018

A metaproteomics approach reveals changes in mandibular lymph node microbiota of wild boar naturally exposed to an increasing trend of Mycobacterium tuberculosis complex infection
Queiros et al. 2018

Constraints in the characterization of microbiota community that circulates in the host have limited the extent of co-infection studies in natural populations. In this study, we used a metaproteomics approach to characterize the mandibular lymph nodes microbiota of wild boar (Sus scrofa) naturally exposed to an increasing trend of Mycobacterium tuberculosis complex (MTC) infection. Our results showed a reduction in microbiota diversity and changes in the composition, structure and functionality of the microbiota community associated with an increase in tuberculosis prevalence, from 45% in 2002/06 to 83% in 2009/12.

DOI:   10.1016/    16-12-2018

Detection of distinct MERS-Coronavirus strains in dromedary camels from Kenya, 2017
Kiambi et al. 2018

MERS-Coronavirus (CoV) is a dromedary-transmitted zoonotic pathogen that is associated with severe viral pneumonia in humans. As of 28 September 2018, 2249 infections and 798 fatalities (36%) from 27 countries had been reported to the World Health Organization. Although the majority of dromedaries are found in Africa, zoonotic spillover events, nosocomial outbreaks, and human fatalities occurred predominantly in the Arabian Peninsula.

DOI:   10.1038/s41426-018-0193-z     28-11-2018

Machine Learning Methods as a Tool for Predicting Risk of Illness Applying Next‐Generation Sequencing Data
Njage et al. 2018 b

Next‐generation sequencing (NGS) data present an untapped potential to improve microbial risk assessment (MRA) through increased specificity and redefinition of the hazard. Most of the MRA models do not account for differences in survivability and virulence among strains. The potential of machine learning algorithms for predicting the risk/health burden at the population level while inputting large and complex NGS data was explored with Ias a case study.

DOI:     10.1111/risa.13239    21-11-2018

Lleida Bat Lyssavirus isolation in Miniopterus schreibersii in France
Picard-Meyer et al. 2018

Bat rabies cases are attributed in Europe to five different Lyssavirus species of 16 recognized Lyssavirus species causing rabies. One of the most genetically divergent Lyssavirus spp. has been detected in a dead Miniopterus schreibersii bat in France. Brain samples were found positive for the presence of antigen, infectious virus and viral RNA by classical virological methods and molecular methods respectively. The complete genome sequence was determined by next‐generation sequencing.

DOI:    10.1111/zph.12535     20-11-2018

Characterization of the bacterial microbiota in wild-caught Ixodes ventalloi
Diaz-Sanchez et al. 2019

Exploring the microbial diversity of ticks is crucial to understand geographical dispersion and pathogen transmission. Tick microbes participate in many biological processes implicated in the acquisition, maintenance, and transmission of pathogens, and actively promote host phenotypic changes, and adaptation to new environments. The microbial community of Ixodes ventalloi still remains unexplored. In this study, the bacterial microbiota of wild-caught I. ventalloi was characterized using shotgun-metagenomic sequencing in samples from unfed adults collected during December 2013-January 2014 in two locations from Sicily, Italy.

DOI:   10.1016/j.ttbdis.2018.11.014    19-11-2018

Improving hazard characterization in microbial risk assessment using next generation sequencing data and machine learning: Predicting clinical outcomes in shigatoxigenic Escherichia coli
Njage et al. 2018 a

The ever decreasing cost and increase in throughput of next generation sequencing (NGS) techniques have resulted in a rapid increase in availability of NGS data. Such data have the potential for rapid, reproducible and highly discriminative characterization of pathogens. This provides an opportunity in microbial risk assessment to account for variations in survivability and virulence among strains.

DOI:    10.1016/j.ijfoodmicro.2018.11.016    17-11-2018

Salmonella enterica Serovar Typhi in Bangladesh: Exploration of Genomic Diversity and Antimicrobial Resistance
Tanmoy et al. 2018

Typhoid fever, caused by Salmonella enterica serovar Typhi, is a global public health concern due to increasing antimicrobial resistance (AMR). Characterization of S. Typhi genomes for AMR and the evolution of different lineages, especially in countries where typhoid fever is endemic such as Bangladesh, will help public health professionals to better design and implement appropriate preventive measures.

DOI:   10.1128/mBio.02112-18    13-11-2018

Prevalence, antimicrobial susceptibility and characterization of Staphylococcus aureus and methicillin-resistant Staphylococcus aureus isolated from dairy industries in north-central and north-eastern Greece
Papadopoulos et al. 2018

Staphylococcus aureus is an important cause of food intoxication, whereas methicillin-resistant S. aureus (MRSA) constitutes a serious public-health concern due to its ability to colonize and infect humans and animals. S. aureus and MRSA have often been isolated from milk and dairy products. The objectives of this study were to estimate
the prevalence and the antimicrobial resistance of S. aureus and MRSA in four Greek dairy industries, to identify virulence factors of MRSA isolates and to describe their genetic diversity, in order to identify possible epidemiological links and evaluate the risk of MRSA dissemination to the community.

DOI:     10.1016/j.ijfoodmicro.2018.11.007    09-11-2018

Threats to timely sharing of pathogen sequence data
dos S. Ribeiro et al. 2018

Pathogen genome sequence databases are taking over important functions of physical collections of microbial and viral cultures (biobanks), adding functionalities for worldwide rapid sharing of pathogen genetic resources in support of research and outbreak response (1). But biobanks and databases also have to respect the ownership and rights of the sample and data providers, including the sovereign right of states to decide on the use of their resources [as stated in the Convention on Biological Diversity (CBD) (2)]. Where domestic or international regulation in this regard is absent or unclear, the integrity of databases and biobanks can be threatened by divergent interpretations, potentially leading to perceived violation of globally agreed sovereignty rights. In particular, the impact of the Nagoya Protocol (NP) to the CBD on public health and infectious disease control is highly debated and focused now on whether genetic sequence data (GSD) fall within the scope of the NP, which thus far has concentrated on access to physical samples.

DOI:     10.1126/science.aau5229    26-10-2018

Quantifying the contribution of four resistance mechanisms to ciprofloxacin MIC in Escherichia coli: a systematic review
van der Putten et al. 2018

Reviews assessing the genetic basis of ciprofloxacin resistance in Escherichia coli have mostly been qualitative. However, to predict resistance phenotypes based on genotypic characteristics, it is essential to quantify the contribution of genotypic determinants to resistance. We performed a systematic review to assess the relative contribution of known genomic resistance determinants to the MIC of ciprofloxacin in E. coli.

DOI:    10.1093/jac/dky417     23-10-2018

Vaccines, Apes, and Conspiracy
Mordini 2018

In their target article, Edwards, Norell, Illari, Clarke, and Neuhaus advocate for “a response to Ebola rooted in a One Health approach to infectious disease,” proposing to test the safety and effectiveness of novel vaccines in wild apes, employing what they call “a ‘pluralistic’ approach to evidence.”

DOI:     10.1080/15265161.2018.1516001    19-10-2018

Genome-wide identification of geographical segregated genetic markers in Salmonella enterica serovar Typhimurium variant 4,[5],12:i:-
Palma et al. 2018

Salmonella enterica ser. Typhimurium monophasic variant 4,[5],12:i:- has been associated with foodborne epidemics worldwide and swine appeared to be the main reservoir in most of the countries of isolation. However, the monomorphic nature of this serovar has, so far, hindered identifcation of the source due to expansion of clonal lineages in multiple hosts and food producing systems.

DOI:    10.1038/s41598-018-33266-5    15-10-2018

Attenuation of replication by a 29 nucleotide deletion in SARS-coronavirus acquired during the early stages of human-to-human transmission
Muth et al. 2018

A 29 nucleotide deletion in open reading frame 8 (ORF8) is the most obvious genetic change in severe acute respiratory syndrome coronavirus (SARS-CoV) during its emergence in humans. In spite of intense study, it remains unclear whether the deletion actually reflects adaptation to humans. Here we engineered full, partially deleted (−29 nt), and fully deleted ORF8 into a SARS-CoV infectious cDNA clone, strain Frankfurt-1. Replication of the resulting viruses was compared in primate cell cultures as well as Rhinolophus bat cells made permissive for SARS-CoV replication by lentiviral transduction of the human angiotensin-converting enzyme 2 receptor.

DOI:   11-10-2018

Novel composite SCCmec type III element in ST239 MRSA isolated from an Indian hospital
Coppens et al. 2018

MRSA causes hospital- and community-acquired infections across the world and is endemic in Indian hospitals with prevalence ranging from 19.5% to 81%.1–3 The highly recombinant and virulent clone ST239 and its single-locus variants [clonal complex 8 (CC8)] have been shown to be highly prevalent in Southern India.4 We recently demonstrated a remarkably higher base substitution and evolutionary rate among Indian ST239 that was in stark contrast to that of ST239 isolated from a Serbian hospital, explaining in part the clone’s success in the Asian continent.

DOI:   04-10-2018

LVQ-KNN: Composition-based DNA/RNA binning of short nucleotide sequences utilizing a prototype-based k-nearest neighbor approach
Belka et al. 2018

Unbiased sequencing is an upcoming method to gain information of the microbiome in a sample and for the detection of unrecognized pathogens. There are many software tools for a taxonomic classification of such metagenomics datasets available. Numerous of them have a satisfactory sensitivity and specificity for known organisms, but they fail if the sample contains unknown organisms, which cannot be detected by similarity-based classification employing available databases. However, recognition of unknowns is especially important for the detection of newly emerging pathogens, which are often RNA viruses. Here we present the composition-based analysis tool LVQ-KNN for binning unclassified nucleotide sequence reads into their provenance classes DNA or RNA.

DOI:    10.1016/j.virusres.2018.10.002     04-10-2018

Fatal Encephalitic Borna Disease Virus 1 in Solid-Organ Transplant Recipients
Schlottau et al. 2018

Borna disease virus 1 (BoDV-1; species Mammalian 1 orthobornavirus) causes progressive meningoencephalitis, mainly in horses and sheep. Evidence of BoDV-1 infection in humans is limited.1,2 However, after the identification of a bornavirus transmitted by exotic pet squirrels — the variegated squirrel bornavirus 1 (species Mammalian 2 orthobornavirus)3 — the zoonotic potential of mammalian bornaviruses should be considered. Here, we report evidence of donor-transmitted BoDV-1 infection occurring in three solid-organ transplant recipients, two of whom died.

DOI:    10.1056/NEJMc1803115     04-10-2018

Virus detection in high-throughput sequencing data without a reference genome of the host
Kruppa et al. 2018

Discovery of novel viruses in host samples is a multidisciplinary process which relies increasingly on next generation sequencing (NGS) followed by computational analysis. A crucial step in this analysis is to separate host sequence reads from the sequence reads of the virus to be discovered. This becomes especially difficult if no reference genome of the host is available. Furthermore, if the total number of viral reads in a sample is low, de novo assembly of a virus which is a requirement for most existing pipelines is hard to realize.

DOI:    10.1016/j.meegid.2018.09.026    03-10-2018

Spatio-temporal distribution and evolution of the A/H1N1 2009 pandemic virus in pigs in France from 2009 to 2017: identification of a potential swine-specific lineage
Chastagner et al. 2018

The H1N1 influenza virus responsible for the most recent pandemic in 2009 (H1N1pdm) has spread to swine populations worldwide while it replaced the previous seasonal H1N1 virus in humans. In France, surveillance of swine influenza A viruses in pig herds with respiratory outbreaks led to the detection of 44 H1N1pdm strains between 2009 and 2017, regardless of the season, and findings were not correlated to pig density. From these isolates, 17 whole genome sequences were obtained as well as 6 additional HA/NA sequences, in order to perform spatial and temporal analyses of the genetic diversity, and to compare evolutionary patterns of H1N1pdm in pigs to patterns for human strains.

DOI:    10.1128/JVI.00988-18      26-09-2018

A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection
Wylezich et al. 2018

Metagenomics is currently the only generic method for pathogen detection. Starting from RNA allows the assessment of the whole sample community including RNA viruses. Here we present our modular concerted protocol for sample processing for diagnostic metagenomics analysis of human, animal, and food samples. The workflow does not rely on dedicated amplification steps at any stage in the process and, in contrast to published methods, libraries prepared accordingly will yield only minute amounts of unclassifiable reads. We confirmed the performance of the approach using a spectrum of pathogen/matrix-combinations showing it has the potential to become a commonly usable analytical framework.

DOI:   10.1038/s41598-018-31496-1    30-08-2018

Crimean-Congo haemorrhagic fever in a Greek worker returning from Bulgaria, June 2018
Papa et al. 2018c

We report a tick-borne case of severe Crimean-Congo haemorrhagic fever (CCHF) imported into Greece from Bulgaria. The patient presented severe thrombocytopenia, hemophagocytosis, haemodynamic instability, large haematomas and altered mental status. Supportive treatment and ribavirin were administered. Symptoms started one day after the tick was removed; the patient was discharged from the hospital 26 days after symptom onset. No secondary cases were observed. Phylogenetically the CCHF virus strain belongs to clade Europe 1.

DOI:    10.2807/1560-7917.ES.2018.23.35.1800432       30-08-2018

Rapid and precise alignment of raw reads against redundant databases with KMA
Clausen et al. 2018

As the cost of sequencing has declined, clinical diagnostics based on next generation sequencing (NGS) have become reality. Diagnostics based on sequencing will require rapid and precise mapping against redundant databases because some of the most important determinants, such as antimicrobial resistance and core genome multilocus sequence typing (MLST) alleles, are highly similar to one another.

DOI:   10.1186/s12859-018-2336-6     29-08-2018

Further characterization of Bovine Hepacivirus: Antibody Response, Course of Infection, and Host Tropism
Baechlein et al. 2018

Bovine hepacivirus (BovHepV) is a recently added member to the growing genus Hepacivirus within the family Flaviviridae. Animal hepaciviruses are rarely characterized so far. Apart from norway rat hepacivirus which represents a promising HCV surrogate model, only equine hepaciviruses have been studied to some extent. BovHepV has been initially identified in bovine samples and was shown to establish persistent infections in cattle. However, consequences of those chronic infections, humoral immune response and the possibility of an extended host spectrum have not been explored so far. Therefore, we here investigated i. the presence of anti-NS3-antibodies and viral RNA in cattle herds in Germany, ii. the course of infection in cattle, and iii. the host tropism including zoonotic potential of bovine hepaciviruses.

DOI:    10.1111/tbed.12999     20-08-2018

A generic framework for spatial quantitative risk assessments of infectious diseases: Lumpy skin disease case study
Taylor et al. 2018

The increase in availability of spatial data and the technological advances to handle such data allow for subsequent improvements in our ability to assess risk in a spatial setting. We provide a generic framework for quantitative risk assessments of disease introduction that capitalizes on these new data. It can be adopted across multiple spatial scales, for any pathogen, method of transmission or location. The framework incorporates the risk of initial infection in a previously uninfected location due to registered movement (e.g., trade) and unregistered movement (e.g., daily movements of wild animals). We discuss the steps of the framework and the data required to compute it.

DOI:  10.1111/tbed.12993     13-08-2018

Characterization of plasmids harboring blaCTX-M genes in Escherichia coli from French pigs
Lucas et al. 2018

Resistance to extended-spectrum cephalosporins is prevalent in French pig E. coli isolates. The aim of this study was to characterize the plasmids and genes present in pathogenic and commensal extended-spectrum cephalosporins -resistant isolates. The resistance plasmids of 26 strains were sequenced and then analyzed to identify resistance and virulence genes.

DOI:    10.1016/j.vetmic.2018.08.005    03-08-2018

Interactomics and tick vaccine development: new directions for the control of tick-borne diseases
Artigas-Jerónimo et al. 2018

Ticks are obligate hematophagous arthropod ectoparasites that transmit pathogens responsible for a growing number of tick-borne diseases (TBDs) throughout the world. Vaccines have been shown to be the most efficient, cost-effective, and environmentally friendly approach for the control of ticks and the prevention of TBDs. Although at its infancy, interactomics has shown the possibilities that the knowledge of the interactome offers in understanding tick biology and the molecular mechanisms involved in pathogen infection and transmission. Furthermore, interactomics has provided information for the identification of candidate vaccine protective antigens.

DOI:   10.1080/14789450.2018.1506701    01-08-2018

Biotic and abiotic factors shape the microbiota of wild-caught populations of the arbovirus vector Culicoides imicola
Díaz-Sánchez et al. 2018

Biting midges of the genus Culicoides are known vectors of arboviruses affecting human and animal health. However, little is known about Culicoides imicola microbiota and its influence on this insect's biology. In this study, the impact of biotic and abiotic factors on C. imicola microbiota was characterized using shotgun-metagenomic sequencing of whole body DNA samples.

DOI:    10.1111/imb.12526     30-07-2018

Association of Batai Virus Infection and Encephalitis in Harbor Seals, Germany, 2016
Jo et al. 2018

We isolated Batai virus from the brain of a euthanized, 26-year-old, captive harbor seal with meningoencephalomyelitis in Germany. We provide evidence that this orthobunyavirus can naturally infect the central nervous system of a mammal. The full-genome sequence showed differences from a previously reported virus isolate from a mosquito in Germany.

DOI:     10.3201/eid2409.171829     25-07-2018

Comparison of Different In Situ Hybridization Techniques for the Detection of Various RNA and DNA Viruses
Pfankuche et al. 2018

In situ hybridization (ISH) is a technique to determine potential correlations between viruses and lesions. The aim of the study was to compare ISH techniques for the detection of various viruses in different tissues. Tested RNA viruses include atypical porcine pestivirus (APPV) in the cerebellum of pigs, equine and bovine hepacivirus (EqHV, BovHepV) in the liver of horses and cattle, respectively, and Schmallenberg virus (SBV) in the cerebrum of goats.

DOI:    10.3390/v10070384     20-07-2018

Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance
Roosenhoff et al. 2018

Influenza viruses can cause severe life threatening infections in high-risk patients, including young children, the elderly and patients with compromised immunity due to underlying medical conditions or immunosuppressive treatment. The impaired immunity of these patients causes prolonged virus infection and combined with antiviral treatment facilitates the emergence of viruses with resistance mutations. The diverse nature of their immune status makes them a challenging group to study the impact of influenza virus infection and the efficacy of antiviral therapy. Immunocompromised ferrets may represent a suitable animal model to assess influenza virus infection and antiviral treatment strategies in immunocompromised hosts.

DOI:     10.1371/journal.pone.0200849     19-07-2018

Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans
Mühlemann et al. 2018 b

The majority of viral genomic sequences available today are fewer than 50 years old. Parvovirus B19 (B19V) is a ubiquitous human pathogen causing fifth disease in children, as well as other conditions. By isolating B19V DNA from human remains between ∼0.5 and 6.9 thousand years old, we show that B19V has been associated with humans for thousands of years, which is significantly longer than previously thought. We also show that the virus has been evolving at a rate an order of magnitude lower than estimated previously.

DOI:   10.1073/pnas.1804921115    02-07-2018

Molecular epidemiology of Dobrava-Belgrade virus in Greece
Tsergouli et al. 2018

In order to gain an insight into the genetic relatedness of the Dobrava-Belgrade virus (DOBV) in Greece, a phylogenetic analysis was performed based on all currently available DOBV sequences obtained from hospitalized cases with hemorrhagic fever with renal syndrome (HFRS). Most cases occurred in northwestern and north central part of the country. Two sequence datasets consisted of 41 S and 12 M partial DOBV RNA segment sequences were analyzed.

DOI:     10.1016/j.meegid.2018.06.007    07-06-2018

From low to high pathogenicity—Characterization of H7N7 avian influenza viruses in two epidemiologically linked outbreaks
Dietze et al. 2018

The ability of low pathogenic (LP) avian influenza viruses (AIV) of the subtypes H5 and H7 to mutate spontaneously to highly pathogenic (HP) variants is the main reason for their stringent control. On‐the‐spot evidence from the field of mutations in LPAIV to render the virus into nascent HP variants is scarce. Epidemiological investigations and molecular characterization of two spatiotemporally linked outbreaks caused by LP, and subsequently, HPAIV H7N7 in two‐layer farms in Germany yielded such evidence.

DOI:    10.1111/tbed.12906    23-05-2018

Novel canine circovirus strains from Thailand: Evidence for genetic recombination
Piewbang et al. 2018

Canine circoviruses (CanineCV’s), belonging to the genus Circovirus of the Circoviridae family, were detected by next generation sequencing in samples from Thai dogs with respiratory symptoms. Genetic characterization and phylogenetic analysis of nearly complete CanineCV genomes suggested that natural recombination had occurred among different lineages of CanineCV’s. Similarity plot and bootscaning analyses indicated that American and Chinese viruses had served as major and minor parental viruses, respectively.

DOI:   10.1038/s41598-018-25936-1   14-05-2018

Ancient hepatitis B viruses from the Bronze Age to the Medieval period
Mühlemann et al. 2018 a

Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 × 10-6-1.51 × 10-5 nucleotide substitutions per site per year.

DOI:    10.1038/s41586-018-0097-z     09-05-2018

Convergent Loss of ABC Transporter Genes From Clostridioides difficile Genomes Is Associated With Impaired Tyrosine Uptake and p-Cresol Production
Steglich et al. 2018

We report the frequent, convergent loss of two genes encoding the substrate-binding protein and the ATP-binding protein of an ATP-binding cassette (ABC) transporter from the genomes of unrelated Clostridioides difficile strains. This specific genomic deletion was strongly associated with the reduced uptake of tyrosine and phenylalanine and production of derived Stickland fermentation products, including p-cresol, suggesting that the affected ABC transporter had been responsible for the import of aromatic amino acids. In contrast, the transporter gene loss did not measurably affect bacterial growth or production of enterotoxins.

DOI:    10.3389/fmicb.2018.00901     08-05-2018

Integrated metatranscriptomics and metaproteomics for the characterization of bacterial microbiota in unfed Ixodes ricinus
Hernandez-Jarguin et al. 2018

An innovative metaomics approach integrating metatranscriptomics and metaproteomics was used to characterize bacterial communities in the microbiota of the Lyme borreliosis spirochete vector, Ixodes ricinus (Acari: Ixodidae). Whole internal tissues and salivary glands from unfed larvae and female ticks, respectively were used. Reused I. ricinus RNA-sequencing data for metranscriptomics analysis together with metaproteomics provided a better characterization of tick bacterial microbiota by increasing bacteria identification and support for identified bacteria with putative functional implications.

DOI:     10.1016/j.ttbdis.2018.04.020     05-05-2018

How ownership rights over microorganisms affect infectious disease control and innovation: A root-cause analysis of barriers to data sharing as experienced by key stakeholders
Ribeiro et al. 2018

Genetic information of pathogens is an essential input for infectious disease control, public health and for research. Efficiency in preventing and responding to global outbreaks relies on timely access to such information. Still, ownership barriers stand in the way of timely sharing of genetic data from pathogens, frustrating efficient public health responses and ultimately the potential use of such resources in innovations. Under a One Health approach, stakeholders, their interests and ownership issues are manifold and need to be investigated.

DOI:   10.1371/journal.pone.0195885   02-05-2018

Overview of Virus Metagenomic Classification Methods and Their Biological Applications
Nooij et al. 2018

Metagenomics poses opportunities for clinical and public health virology applications by offering a way to assess complete taxonomic composition of a clinical sample in an unbiased way. However, the techniques required are complicated and analysis standards have yet to develop. This, together with the wealth of different tools and workflows that have been proposed, poses a barrier for new users. We evaluated 49 published computational classification workflows for virus metagenomics in a literature review.

DOI:     10.3389/fmicb.2018.00749     23-04-2018

Uukuniemi virus, Czech Republic
Papa et al. 2018b

Following the identification of severe fever with thrombocytopenia syndrome and Heartland viruses, the interest on tick-borne phleboviruses has increased rapidly. Uukuniemi virus has been proposed as a model for tick-borne phleboviruses. However, the number of available sequences is limited. In the current study we performed wholegenome sequencing on two Uukuniemi viral strains isolated in 2000 and 2004 from Ixodes ricinus ticks in the Czech Republic.

DOI:     10.1016/j.ttbdis.2018.04.011     20-04-2018

Wild ducks excrete highly pathogenic avian influenza virus H5N8 (2014–2015) without clinical or pathological evidence of disease
van den Brand et al. 2018

Highly pathogenic avian influenza (HPAI) is essentially a poultry disease. Wild birds have traditionally not been involved in its spread, but the epidemiology of HPAI has changed in recent years. After its emergence in southeastern Asia in 1996, H5 HPAI virus of the Goose/Guangdong lineage has evolved into several sub-lineages, some of which have spread over thousands of kilometers via long-distance migration of wild waterbirds. In order to determine whether the virus is adapting to wild waterbirds, we experimentally inoculated the HPAI H5N8 virus clade group A from 2014 into four key waterbird species—Eurasian wigeon (Anas penelope), common teal (Anas crecca), mallard (Anas platyrhynchos), and common pochard (Aythya ferina)—and compared virus excretion and disease severity with historical data of the HPAI H5N1 virus infection from 2005 in the same four species.

DOI:   10.1038/s41426-018-0070-9    18-04-2018

Case of seasonal reassortant A(H1N2) influenza virus infection, the Netherlands, March 2018
Meijer et al. 2018

A seasonal reassortant A(H1N2) influenza virus harbouring genome segments from seasonal influenza viruses A(H1N1) pdm09 (HA and NS) and A(H3N2) (PB2, PB1, PA, NP, NA and M) was identified in March 2018 in a 19-months-old patient with influenza-like illness (ILI) who presented to a general practitioner participating in the routine sentinel surveillance of ILI in the Netherlands.

DOI:     10.2807/1560-7917.ES.2018.23.15.18-00160       12-04-2018

Infectivity and RNA Persistence of a Norovirus Surrogate, the Tulane Virus, in Oysters
Polo et al. 2018

Oysters, being filter feeders, can accumulate some human pathogens such as norovirus, a highly infectious calicivirus, most common cause of acute gastroenteritis worldwide. Accumulated virus decays over a period of days to weeks, possibly rendering contaminated oysters safe again. Sensitive molecular methods have been set up for shellfish analysis but without answering the question of infectious virus detection. Using the Tulane virus (TV), a norovirus surrogate that recognizes the same ligand as human norovirus in oyster tissues, the genome and infectious virus decay rates were estimated using inverse linear regression in a Bayesian framework for genome copies.

DOI:   10.3389/fmicb.2018.00716     12-04-2018

Emergence and multiple reassortments of French 2015-2016 highly pathogenic H5 avian influenza viruses
Briand et al. 2018

From November 2015 to August 2016, 81 outbreaks of highly pathogenic (HP) H5 avian influenza virus were detected in poultry farms from South-Western France. These viruses were mainly detected in farms raising waterfowl, but also in chicken or guinea fowl flocks, and did not induce severe signs in waterfowl although they did meet the HP criteria. Three different types of neuraminidases (N1, N2 and N9) were associated with the HP H5 gene.

DOI:   10.1016/j.meegid.2018.04.007    09-04-2018

Microbiological profile of chicken carcasses: A comparative analysis using shotgun metagenomic sequencing
De Cesare et al. 2018

In the last few years metagenomic and 16S rRNA sequencing have completly changed the microbiological investigations of food products. In this preliminary study, the microbiological profile of chicken carcasses collected from animals fed with different diets were tested by using shotgun metagenomic sequencing. A total of 15 carcasses have been collected at the slaughetrhouse at the end of the refrigeration tunnel from chickens reared for 35 days and fed with a control diet (n=5), a diet supplemented with 1500 FTU/kg of commercial phytase (n=5) and a diet supplemented with 1500 FTU/kg of commercial phytase and 3g/kg of inositol (n=5).

DOI:   10.4081/ijfs.2018.6923    11-04-2018

Listeria monocytogenes Sequence Types 121 and 14 Repeatedly Isolated Within One Year of Sampling in a Rabbit Meat Processing Plant: Persistence and Ecophysiology
Pasquali et al. 2018

Listeria monocytogenes is a foodborne pathogen adapted to survive and persist in multiple environments. Following two previous studies on prevalence and virulence of L. monocytogenes ST121 and ST14 repeatedly collected in a the same rabbit-meat processing plant, the research questions of the present study were to: (1) assess persistence of L. monocytogenes isolates from the rabbit-plant; (2) select genes associated to physiological adaptation to the food-processing environment; (3) compare presence/absence/truncation of these genes in newly sequenced and publicly available ST121 and ST14 genomes.

DOI:    10.3389/fmicb.2018.00596     29-03-2018

Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid
Kirstahler et al. 2018

Advances in genomics have the potential to revolutionize clinical diagnostics. Here, we examine the microbiome of vitreous (intraocular body fuid) from patients who developed endophthalmitis following cataract surgery or intravitreal injection. Endophthalmitis is an infammation of the intraocular cavity and can lead to a permanent loss of vision. As controls, we included vitreous from endophthalmitisnegative patients, balanced salt solution used during vitrectomy and DNA extraction blanks.

DOI:     10.1038/s41598-018-22416-4       07-03-2018

Full-length genome sequences of porcine epidemic diarrhoea virus strain CV777; Use of NGS to analyse genomic and sub-genomic RNAs
Rasmussen et al. 2018

Porcine epidemic diarrhoea virus, strain CV777, was initially characterized in 1978 as the causative agent of a disease first identified in the UK in 1971. This coronavirus has been widely distributed among laboratories and has been passaged both within pigs and in cell culture. To determine the variability between different stocks of the PEDV strain CV777, sequencing of the full-length genome (ca. 28kb) has been performed in 6 different laboratories, using different protocols.

DOI:    10.1371/journal.pone.0193682      01-03-2018

Isolation and whole-genome sequencing of a Crimean-Congo hemorrhagic fever virus strain, Greece
Papa et al. 2018a

Crimean-Congo hemorrhagic fever virus (CCHFV) was isolated from a pool of two adult Rhipicephalus bursa ticks removed from a goat in 2015 in Greece. The strain clusters into lineage Europe 2 representing the second available whole-genome sequenced isolate of this lineage. CCHFV IgG antibodies were detected in 8 of 19 goats of the farm. Currently CCHFV is not associated with disease in mammals other than humans. Studies in animal models are needed to investigate the pathogenicity level of lineage Europe 2 and compare it with that of other lineages.

DOI:     10.1016/j.ttbdis.2018.02.024     01-03-2018

Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak Scenario
Becker et al. 2018

Extended-spectrum beta-lactamase (ESBL) producing Klebsiella pneumoniae pose an important threat of infection with increased morbidity and mortality, especially for immunocompromised patients. Here, we use the rise of multidrug-resistant K. pneumoniae in a German neurorehabilitation center from April 2015 to April 2016 to dissect the benefit of whole genome sequencing (WGS) for outbreak analyses. In total, 53 isolates were obtained from 52 patients and examined using WGS.

DOI:    10.3389/fmicb.2018.00322     23-02-2018

Epidemiological characteristics of human-infective RNA viruses
Woolhouse et al. 2018

RNA viruses are a major threat to human health. Here, based on extensive literature searches carried out over a period of 18 years, we provide a catalogue of all 214 known human-infective RNA virus species. We link these viruses to metadata for a number of traits that influence their epidemiology, including the date of the first report of human infection, transmissibility in human populations, transmission route(s) and host range. This database can be used in comparative studies of human-infective RNA viruses to identify the characteristics of viruses most likely to pose the greatest public health threat, both now and in the future.

DOI:    10.1038/sdata.2018.17      20-02-2018

SCCmecFinder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus Using Whole-Genome Sequence Data
Kaya et al. 2018

Typing of methicillin-resistant Staphylococcus aureus (MRSA) is important in infection control and surveillance. The current nomenclature of MRSA includes the genetic background of the S. aureus strain determined by multilocus sequence typing (MLST) or equivalent methods like spa typing and typing of the mobile genetic element staphylococcal cassette chromosome mec (SCCmec), which carries the mecA or mecC gene. Whereas MLST and spa typing are relatively simple, typing of SCCmec is less trivial because of its heterogeneity. Whole-genome sequencing (WGS) provides the essential data for typing of the genetic background and SCCmec, but so far, no bioinformatic tools for SCCmec typing have been available.

DOI:    10.1128/mSphere.00612-17     14-02-2018

Canine Bocavirus Type 2 Infection Associated With Intestinal Lesions
Piewbang et al. 2018

Bocaviruses are small nonenveloped DNA viruses belonging to the Bocaparvovirus genus of the Parvoviridae family and have been linked to both respiratory and enteric disease in humans and animals. To date, 3 bocaviruses, canine bocaviruses 1 to 3 (CBoV-1-3), have been shown to affect dogs with different disease manifestations reported for infected animals. We used next-generation sequencing to identify a novel strain of canine CBoV-2 (CBoV TH-2016) in a litter of puppies that died in Thailand from acute dyspnea and hemoptysis, for which no causal pathogen could be identified in routine assays.

DOI:   10.1177/0300985818755253      08-02-2018

Draft genome sequences of Anaplasma phagocytophilum, A. marginale, and A. ovis isolates from different hosts
Diaz et al. 2018

Here, we report the draft genome sequences of isolates of Anaplasma phagocytophilum, Anaplasma marginale, and Anaplasma ovis. The genomes of A. phagocytophilum (human), A. marginale (cattle), and A. ovis (goat) isolates from the United States were sequenced and characterized. This is the first report of an A. ovis genome sequence.

DOI:   10.1128/genomeA.01503-17      01-02-2018

Local amplification of highly pathogenic avian influenza H5N8 viruses in wild birds in the Netherlands, 2016 to 2017
Poen et al. 2018

Highly pathogenic avian influenza (HPAI) viruses of subtype H5N8 were re-introduced into the Netherlands by late 2016, after detections in southeast Asia and Russia. This second H5N8 wave resulted in a large number of outbreaks in poultry farms and the deaths of large numbers of wild birds in multiple European countries. Methods: Here we report on the detection of HPAI H5N8 virus in 57 wild birds of 12 species sampled during active (32/5,167) and passive (25/36) surveillance activities, i.e. in healthy and dead animals respectively, in the Netherlands between 8 November 2016 and 31 March 2017.

DOI:    10.2807/1560-7917.ES.2018.23.4.17-00449     25-01-2018

Zoonotic Infection With Pigeon Paramyxovirus Type 1 Linked to Fatal Pneumonia
Kuiken et al. 2018

The characteristics and risk factors of pigeon paramyxovirus type 1 (PPMV-1) infection in humans are poorly known. We performed virological, pathological, and epidemiological analyses of a Dutch case, and compared the results with those of a US case. Both infections occurred in transplant patients under immunosuppressive therapy and caused fatal respiratory failure. Both virus isolates clustered with PPMV-1, which has pigeons and doves as reservoir.

DOI:   10.1093/infdis/jiy036      24-01-2018

Swarm incursions of reassortants of highly pathogenic avian influenza virus strains H5N8 and H5N5, clade, Germany, winter 2016/17
Pohlmann et al. 2018

The outbreak of highly pathogenic avian influenza H5Nx viruses in winter 2016/2017 was the most severe HPAI epizootic ever reported in Germany. The H5N8 and H5N5 viruses detected in birds in Germany in 2016/2017 represent a reassortant swarm of at least five distinct genotypes, which carried closely related HA segments derived from clade The genotypes of these viruses and their spatio-temporal distribution indicated a unique situation with multiple independent entries of HPAIV into Germany.

DOI:   10.1038/s41598-017-16936-8     08-01-2018

Cross-border outbreak of listeriosis caused by cold-smoked salmon, revealed by integrated surveillance and whole genome sequencing (WGS), Denmark and France, 2015 to 2017
Schjørring et al. 2017

In August 2017, an outbreak of six listeriosis cases in Denmark was traced to cold-smoked salmon, using epidemiological investigations and whole-genome sequencing (WGS) analyses. Exchange of genome sequences allowed identification in France of a food isolate from a salmon-derived product and a human isolate from 2016 within the same cgMLST cluster as the Danish isolates (L2-SL8-ST8-CT771). The salmon product came from a third European Union country. WGS can rapidly link human cases and food isolates across Europe.

DOI:    10.2807/1560-7917.ES.2017.22.50.17-00762   14-12-2017

Atypical Cowpox Virus Infection in a Series of Cats
Jungwirth et al. 2017

Within 4 weeks, five cats with skin lesions affecting the hindlimbs and mainly consisting of oedema, hyperaemia and plaque-like alterations were presented to the same veterinary clinic. The cats were suffering from lameness, trauma, renal insufficiency or complicated tail amputation.

DOI:   10.1016/j.jcpa.2017.12.003    08-12-2017

Human Clade A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets
Herst et al. 2017

Since their emergence in 1997, A/H5N1 influenza viruses of the A/goose/Guangdong/1/96 lineage have diversified in multiple genetic and antigenic clades upon continued circulation in poultry in several countries in Eurasia and Africa. Since 2009, reassortant viruses carrying clade hemagglutinin (HA) and internal and neuraminidase (NA) genes of influenza A viruses of different avian origin have been detected, yielding various HA-NA combinations, such as A/H5N1, A/H5N2, A/H5N3, A/H5N5, A/H5N6, and A/H5N8.

DOI:    10.1128/mSphere.00405-17     04-12-2017

Second International Conference on Crimean-Congo Hemorrhagic Fever
Spengler et al. 2017

The Second International Conference on Crimean-Congo Hemorrhagic Fever (CCHF) was held in Thessaloniki, Greece, from September 10-13, 2017, and brought together international public health professionals, clinicians, ecologists, and basic laboratory researchers. Nearly 100 participants, representing 24 countries and the World Health Organization (WHO), were in attendance.

DOI:   10.1016/j.antiviral.2017.11.019    02-12-2017

First gene-ontology enrichment analysis based on bacterial coregenome variants: insights into adaptations of Salmonella serovars to mammalian- and avian-hosts
Felten et al. 2017

Many of the bacterial genomic studies exploring evolution processes of the host adaptation focus on the accessory genome describing how the gains and losses of genes can explain the colonization of new habitats. Consequently, we developed a new approach focusing on the coregenome in order to describe the host adaptation of Salmonella serovars.

DOI:   10.1186/s12866-017-1132-1   28-11-2017

Acute viral infections of the central nervous system, 2014-2016, Greece
Papa A, Papadopoulou E. 2017

In order to investigate the viral etiology of acute infections of central nervous system (CNS), multiplex and single PCRs combined with serology for arboviruses were applied on samples from 132 hospitalized patients in Greece during May 2014‐December 2016. A viral pathogen was detected in 52 of 132 (39.4%) cases with acute CNS infection. Enteroviruses predominated (15/52, 28.8%), followed by West Nile virus (9/52, 17.3%).

DOI:   10.1002/jmv.24997     23-11-2017

Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics
Brinkmann et al. 2017

We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing (NGS)-based identification of viral hemorrhagic fever (VHF) agents and assess the feasibility of this approach in diagnostics.

DOI:    10.1371/journal.pntd.0006075    20-11-2017

New Avian Hepadnavirus in Palaeognathous Bird, Germany
Jo et al. 2017

In 2015, we identified an avian hepatitis B virus associated with hepatitis in a group of captive elegant-crested tinamous (Eudromia elegans) in Germany. The full-length genome of this virus shares <76% sequence identity with other avihepadnaviruses. The virus may therefore be considered a new extant avian hepadnavirus.

DOI:   10.3201/eid2312.161634      16-11-2017

Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction
Matamoros et al. 2017

To understand the dynamics behind the worldwide spread of the mcr-1 gene, we determined the population structure of Escherichia coli and of mobile genetic elements (MGEs) carrying the mcr-1 gene. After a systematic review of the literature we included 65 E. coli whole genome sequences (WGS), adding 6 recently sequenced travel related isolates, and 312 MLST profiles. We included 219 MGEs described in 7 Enterobacteriaceae species isolated from human, animal and environmental samples.

DOI:   10.1038/s41598-017-15539-7      10-11-2017

Next‑generation sequencing of fve new avian paramyxoviruses 8 isolates from Kazakhstan indicates a low genetic evolution rate over four decades
Fereidouni et al. 2017

Five avian paramyxoviruses of serotype 8 (APMV-8) were isolated during a study monitoring wild birds in Kazakhstan in 2013 and each was further characterized. The viruses were isolated from three White-fronted geese (Anser albifrons), one Whooper swan (Cygnus cygnus), and one Little stint (Calidris minuta). Before our study, only two complete APMV-8 sequences had been reported
worldwide since their discovery in the USA and Japan in the 1970s.

DOI:     10.1007/s00705-017-3593-9     22-10-2017

Identification and molecular characterization of spotted fever group rickettsiae in ticks collected from farm ruminants in Lebanon
Fernandez de Mera et al. 2017

Tick-borne diseases have become a world health concern, emerging with increasing incidence in recent decades. Spotted fever group (SFG) rickettsiae are tick-borne pathogens recognized as important agents of human tickborne diseases worldwide. In this study, 88 adult ticks from the species Hyalomma anatolicum, Rhipicephalus
annulatus, Rh. bursa, Rh. sanguineus sensu lato, and Rh. turanicus, were collected from farm ruminants in Lebanon, and SFG rickettsiae were molecularly identified and characterized in these ticks.

DOI:    10.1016/j.ttbdis.2017.10.001    12-10-2017

Whole genome sequencing for typing and characterisation of Listeria monocytogenes isolated in a rabbit meat processing plant
Palma et al. 2017

Listeria monocytogenes is a food-borne pathogen able to survive and grow in different environments including food processing plants where it can persist for month or years. In the present study the discriminatory power of Whole Genome Sequencing (WGS)-based analysis (cgMLST) was compared to that of molecular typing methods on 34 L. monocytogenes isolates collected over one year in the same rabbit meat processing plant and belonging to three genotypes (ST14, ST121, ST224). Each genotype included isolates indistinguishable by standard molecular typing methods. The virulence potential of all isolates was assessed by Multi Virulence-Locus Sequence Typing (MVLST) and the investigation of a representative database of virulence determinant genes.

DOI:    10.4081/ijfs.2017.6879      28-09-2017

Loeffler 4.0: Diagnostic Metagenomics
Höper et al. 2017

A new world of possibilities for "virus discovery" was opened up with high-throughput sequencing becoming available in the last decade. While scientifically metagenomic analysis was established before the start of the era of high-throughput sequencing, the availability of the first second-generation sequencers was the kick-off for diagnosticians to use sequencing for the detection of novel pathogens. Today, diagnostic metagenomics is becoming the standard procedure for the detection and genetic characterization of new viruses or novel virus variants. Here, we provide an overview about technical considerations of high-throughput sequencing-based diagnostic metagenomics together with selected examples of "virus discovery" for animal diseases or zoonoses and metagenomics for food safety or basic veterinary research.

DOI:  10.1016/bs.aivir.2017.08.001    21-09-2017

Molecular detection of Crimean-Congo hemorrhagic fever virus in ticks, Greece, 2012–2014
Papa et al. 2017

Crimean-Congo hemorrhagic fever virus (CCHFV) is transmitted to humans mainly through the bite of infected ticks. In Greece, only one clinical case has been observed, in 2008, but the seroprevalence in humans is relatively high (4.2%). To have a first insight into the circulation of CCHFV in Greece, 2000 ticks collected from livestock during 2012–2014 were tested.

DOI:    10.1007/s00436-017-5616-6   17-09-2017

Characterization of Posa and Posa-like virus genomes in fecal samples from humans, pigs, rats, and bats collected from a single location in Vietnam
Oude Munnink et al. 2017

Porcine stool-associated RNA virus (posavirus), and Human stool-associated RNA virus (husavirus) are viruses in the order Picornavirales recently described in porcine and human fecal samples. The tentative group (Posa and Posa-like viruses: PPLVs) also includes fish stool-associated RNA virus (fisavirus) as well as members detected in insects (Drosophila subobscura and Anopheles sinensis) and parasites (Ascaris suum). As part of an agnostic deep sequencing survey of animal and human viruses in Vietnam, we detected three husaviruses in human fecal samples, two of which share 97–98% amino acid identity to Dutch husavirus strains and one highly divergent husavirus with only 25% amino acid identity to known husaviruses.

DOI:  10.1093/ve/vex022      23-08-2017

Crimean-Congo hemorrhagic fever virus in ticks collected from livestock in Albania
Papa et al. 2017b

Albania is a Balkan country endemic for Crimean-Congo hemorrhagic fever (CCHF). It was shown previously that CCHF virus (CCHFV) sequences from Albanian patients cluster into Europe 1 clade. Aim of the present study was to test for CCHFV ticks collected in several regions of Albania, and to determine the genetic lineage(s) of the CCHFV strains in relation with their geographic distribution.

DOI:     19-08-2017

Global Spread of Norovirus GII.17 Kawasaki 308, 2014–2016
Chan et al. 2017

Analysis of complete capsid sequences of the emerging norovirus GII.17 Kawasaki 308 from 13 countries demonstrated that they originated from a single haplotype since the initial emergence in China in late 2014. Global spread of a sublineage SL2 was identified. A new sublineage SL3 emerged in China in 2016.

DOI:  10.3201/eid2308.161138     01-08-2017

Prevalence of Staphylococcus aureus and of methicillin-resistant S-aureus (MRSA) along the production chain of dairy products in north-western Greece
Papadopoulos et al. 2017

The objective of this study was to estimate the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in the production chain of dairy products. Of 367 tested samples (36 bulk tank milk (BTM), 19 dairy products, 72 human, 185 animal, 55 equipment), 212 (57.8%) were found positive for S. aureus. Almost all isolates (99.6%) were resistant to at least one antimicrobial and 13.3% were multi-drug resistant (MDR), exhibiting resistance to three or more antibiotic classes.

DOI:  10.1016/    28-07-2017

Genome Target Evaluator (GTEvaluator): A workflow exploiting genome dataset to measure the sensitivity and specificity of genetic markers
Felton et al. 2017

Most of the bacterial typing methods used to discriminate isolates in medical or food safety microbiology are based on genetic markers used as targets in PCR or hybridization experiments. These DNA typing methods are important tools for studying prevalence and epidemiology, for conducting surveillance, investigations and control of biological hazard sources. In that perspective, it is crucial to insure that the chosen genetic markers have the greatest specificity and sensitivity.

DOI:  10.1371/journal.pone.0182082     27-07-2017

Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study
van Ingen et al. 2017

Since 2013, over 100 cases of Mycobacterium chimaera prosthetic valve endocarditis and disseminated disease were notified in Europe and the USA, linked to contaminated heater–cooler units (HCUs) used during cardiac surgery. We did a molecular epidemiological investigation to establish the source of these patients' disease.

DOI:  10.1016/S1473-3099(17)30324-9     12-07-2017

Ιnfluenza A(H3N2) genetic variants in vaccinated patients in northern Greece
Melidou et al. 2017

Influenza A(H3N2) viruses predominated during the influenza 2016/2017 season and showed extensive genetic diversification. A high vaccination failure rate was noticed during the 2016/17 season in Greece, especially among the elderly.

DOI:  10.1016/j.jcv.2017.07.003      08-07-2017

Porcine Epidemic Diarrhea in Europe: In-Detail Analyses of Disease Dynamics and Molecular Epidemiology
Hanke et al. 2017

Porcine epidemic diarrhea (PED) is an acute and highly contagious enteric disease of swine caused by the eponymous virus (PEDV) which belongs to the genus Alphacoronavirus within the Coronaviridae virus family. Following the disastrous outbreaks in Asia and the United States, PEDV has been detected also in Europe. In order to better understand the overall situation, the molecular epidemiology, and factors that might influence the most variable disease impact; 40 samples from swine feces were collected from different PED outbreaks in Germany and other European countries and sequenced by shot-gun next-generation sequencing.

DOI:  10.3390/v9070177    06-07-2017

Microarray-Based Gene Expression Analysis for Veterinary Pathologists: A Review
Raddatz et al. 2017

High-throughput, genome-wide transcriptome analysis is now commonly used in all fields of life science research and is on the cusp of medical and veterinary diagnostic application. Transcriptomic methods such as microarrays and next-generation sequencing generate enormous amounts of data. The pathogenetic expertise acquired from understanding of general pathology provides veterinary pathologists with a profound background, which is essential in translating transcriptomic data into meaningful biological knowledge, thereby leading to a better understanding of underlying disease mechanisms. The scientific literature concerning high-throughput data-mining techniques usually addresses mathematicians or computer scientists as the target audience. In contrast, the present review provides the reader with a clear and systematic basis from a veterinary pathologist’s perspective.

DOI:    10.1177/0300985817709887     23-06-2017

A single amino acid change in the non-structural NV protein impacts the virulence phenotype of Viral hemorrhagic septicemia virus in trout
Baillon et al. 2017

Novirhabdoviruses like the Viral hemorrhagic septicemia virus (VHSV) are rhabdoviruses infecting fish. In the current study, RNA genomes of different VHSV field isolates classified as high, medium or low virulent phenotypes have been sequenced by next-generation sequencing and compared. Various amino acid changes, depending on the VHSV phenotype, have been identified in all the VHSV proteins. As a starting point, we focused our study on the non-virion (NV) non-structural protein in which an arginine residue (R116) is present in all the virulent isolates and replaced by a serine/asparagine residue S/N116 in the attenuated isolates.

DOI:  10.1099/jgv.0.000830    22-06-2017

Rapid and Consistent Evolution of Colistin Resistance in Extensively Drug-Resistant Pseudomonas aeruginosa during Morbidostat Culture
Doesselmann et al. 2017

Colistin is a last-resort antibiotic commonly used against multidrug-resistant strains of Pseudomonas aeruginosa. To investigate the potential for in situ evolution of resistance against colistin and to map the molecular targets of colistin resistance, we exposed two P. aeruginosa isolates to colistin using a continuous-culture device known as a morbidostat. As a result, colistin resistance reproducibly increased 10-fold within 10 days and 100-fold within 20 days, along with highly stereotypic yet strain-specific mutation patterns. The majority of mutations hit the pmrAB two-component signaling system and genes involved in lipopolysaccharide (LPS) synthesis, including lpxC, pmrE, and migA.

DOI:  10.1128/AAC.00043-17      19-06-2017

PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance
Nadon et al. 2017

PulseNet International is a global network dedicated to laboratory-based surveillance for food-borne diseases. The network comprises the national and regional laboratory networks of Africa, Asia Pacific, Canada, Europe, Latin America and the Caribbean, the Middle East, and the United States. The PulseNet International vision is the standardised use of whole genome sequencing (WGS) to identify and subtype food-borne bacterial pathogens worldwide, replacing traditional methods to strengthen preparedness and response, reduce global social and economic disease burden, and save lives. To meet the needs of real-time surveillance, the PulseNet International network will standardise subtyping via WGS using whole genome multilocus sequence typing (wgMLST), which delivers sufficiently high resolution and epidemiological concordance, plus unambiguous nomenclature for the purposes of surveillance. Standardised protocols, validation studies, quality control programmes, database and nomenclature development, and training should support the implementation and decentralisation of WGS. Ideally, WGS data collected for surveillance purposes should be publicly available, in real time where possible, respecting data protection policies.

DOI:  10.2807/1560-7917.ES.2017.22.23.30544     08-06-2017          

Multiple detection of zoonotic variegated squirrel bornavirus 1 RNA in different squirrel species suggests a possible unknown origin for the virus
Schlottau et al. 2017

The recently discovered variegated squirrel bornavirus 1 (VSBV-1) caused the death of three squirrel breeders in Germany. Subsequent first screening of squirrels with in vivo collected swab samples and a VSBV-1-specific RT-qPCR revealed not only variegated squirrel infections (Sciurus variegatoides), but also Prevost's squirrels (Callosciurus prevostii) as positive for VSBV-1 genome. In this study, 328 squirrels were tested using the established RT-qPCR assays.

DOI:  10.1007/s00705-017-3432-z    07-06-2017

PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens
Zankari et al. 2017

Background Antibiotic resistance is a major health problem, as drugs that were once highly effective no longer cure bacterial infections. WGS has previously been shown to be an alternative method for detecting horizontally acquired antimicrobial resistance genes. However, suitable bioinformatics methods that can provide easily interpretable, accurate and fast results for antimicrobial resistance associated with chromosomal point mutations are still lacking. Methods Phenotypic antimicrobial susceptibility tests were performed on 150 isolates covering three different bacterial species: Salmonella enterica, Escherichia coli and Campylobacter jejuni. The web-server ResFinder-2.1 was used to identify acquired antimicrobial resistance genes and two methods, the novel PointFinder (using BLAST) and an in-house method (mapping of raw WGS reads), were used to identify chromosomal point mutations.

DOI:    10.1093/jac/dkx217     07-06-2017

Crimean-Congo Hemorrhagic Fever: Tick-Host-Virus Interactions
Papa et al. 2017c

Crimean-Congo hemorrhagic fever virus (CCHFV) is transmitted to humans by bite of infected ticks or by direct contact with blood or tissues of viremic patients or animals. It causes to humans a severe disease with fatality up to 30%. The current knowledge about the vector-host-CCHFV interactions is very limited due to the high-level containment required for CCHFV studies.

DOI:  10.3389/fcimb.2017.00213    26-05-2017

Zika virus evolution and spread in the Americas
Metsky et al. 2017

Although the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects have attracted a great deal of attention1,2, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part owing to a lack of genomic data. Here we address this gap in knowledge by using multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak.

DOI:  10.1038/nature22402    24-05-2017

Genomic epidemiology reveals multiple introductions of Zika virus into the United States
Grubaugh et al. 2017

Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital abnormalities1,2. In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States; since then, hundreds of locally acquired infections have been reported in Florida3,4. To gain insights into the timing, source, and likely route(s) of ZIKV introduction, we tracked the virus from its first detection in Florida by sequencing ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We show that at least 4 introductions, but potentially as many as 40, contributed to the outbreak in Florida and that local transmission is likely to have started in the spring of 2016—several months before its initial detection.

DOI:  10.1038/nature22400   24-05-2017

Establishment and cryptic transmission of Zika virus in Brazil and the Americas
Faria et al. 2017

Transmission of Zika virus (ZIKV) in the Americas was first confirmed in May 2015 in northeast Brazil1. Brazil has had the highest number of reported ZIKV cases worldwide (more than 200,000 by 24 December 20162) and the most cases associated with microcephaly and other birth defects (2,366 confirmed by 31 December 20162). Since the initial detection of ZIKV in Brazil, more than 45 countries in the Americas have reported local ZIKV transmission, with 24 of these reporting severe ZIKV-associated disease3. However, the origin and epidemic history of ZIKV in Brazil and the Americas remain poorly understood, despite the value of this information for interpreting observed trends in reported microcephaly. Here we address this issue by generating 54 complete or partial ZIKV genomes, mostly from Brazil, and reporting data generated by a mobile genomics laboratory that travelled across northeast Brazil in 2016.

DOI:  10.1038/nature22401   24-05-2017

The challenge of detecting indels in bacterial genomes from short-read sequencing data
Steglich and Nübel 2017

We tested the capabilities of four different software tools to detect insertions and deletions (indels) in a bacterial genome on the basis of short sequencing reads. We included tools applying the gapped-alignment (VarScan, FreeBayes) or split-read (Pindel) methods, respectively, and a combinatorial approach with local de-novo assembly (ScanIndel). Tests were performed with 151-basepair, paired-end sequencing reads simulated from a bacterial (Clostridioides difficile R20291) genome sequence with predefined indels (indel length, 1–2321 bp). Results achieved with the different tools varied widely, and the specific sensitivity and false-discovery rates strongly depended on indel size.

DOI:   10.1016/j.jbiotec.2017.02.026     20-05-2017

First molecular investigation of Cryptosporidium spp. in young calves in Algeria
Benhouda et al. 2017

To date, no information is available on the prevalence and genetic identity of Cryptosporidium spp. in cattle in Algeria. In this study, 17 dairy farms in the province of Batna, located in the northeast of the country, were visited to collect 132 fecal samples from young calves (< 8 weeks old). Samples were examined microscopically using the modified Ziehl-Neelsen acid-fast staining method, and at least one sample per farm was submitted for molecular analysis.

DOI:  10.1051/parasite/2017014       12-05-2017

Virus genomes reveal factors that spread and sustained the Ebola epidemic
Dudas et al. 2017

The 2013-2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. We test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic 'gravity' model, with intense dispersal between larger and closer populations.

DOI:  10.1038/nature22040      12-04-2017

Pathological findings in the red fox (Vulpes vulpes), stone marten (Martes foina) and raccoon dog (Nyctereutes procyonoides), with special emphasis on infectious and zoonotic agents in Northern Germany
Lempp et al. 2017

Anthropogenic landscape changes contributed to the reduction of availability of habitats to wild animals. Hence, the presence of wild terrestrial carnivores in urban and peri-urban sites has increased considerably over the years implying an increased risk of interspecies spill-over of infectious diseases and the transmission of zoonoses. The present study provides a detailed characterisation of the health status of the red fox (Vulpes vulpes), stone marten (Martes foina) and raccoon dog (Nyctereutes procyonoides) in their natural rural and peri-urban habitats in Schleswig-Holstein, Germany between November 2013 and January 2016 with focus on zoonoses and infectious diseases that are potentially threatening to other wildlife or domestic animal species.

DOI:  10.1371/journal.pone.0175469     11-04-2017

Modelling the impact of curtailing antibiotic usage in food animals on antibiotic resistance in humans
van Bunnik et al. 2017

Consumption of antibiotics in food animals is increasing worldwide and is approaching, if not already surpassing, the volume consumed by humans. It is often suggested that reducing the volume of antibiotics consumed by food animals could have public health benefits. Although this notion is widely regarded as intuitively obvious there is a lack of robust, quantitative evidence to either support or contradict the suggestion. As a first step towards addressing this knowledge gap, we develop a simple mathematical model for exploring the generic relationship between antibiotic consumption by food animals and levels of resistant bacterial infections in humans.

DOI:  10.1098/rsos.161067               05-04-2017

Developing a framework to assess the cost-effectiveness of COMPARE - a global platform for the exchange of sequence-based pathogen data
Allewedlt et al. 2017

Analysing the genomic data of pathogens with the help of next-generation sequencing (NGS) is an increasingly important part of disease outbreak investigations and helps guide responses. While this technology has already been successfully employed to elucidate and control disease outbreaks, wider implementation of NGS also depends on its cost-effectiveness.

DOI:  10.20506/rst.36.1.2631      01-04-2017

Outbreaks among Wild Birds and Domestic Poultry Caused by Reassorted Influenza A(H5N8) Clade Viruses, Germany, 2016
Pohlmann et al. 2017

In November 2016, an influenza A(H5N8) outbreak caused deaths of wild birds and domestic poultry in Germany. Clade virus was closely related to viruses detected at the Russia–Mongolia border in 2016 but had new polymerase acidic and nucleoprotein segments. These new strains may be more efficiently transmitted to and shed by birds.

DOI:  10.3201/eid2304.161949      01-04-2017

Emerging arboviral human diseases in Southern Europe
Papa 2017

Southern Europe is characterized by unique landscape and climate which attract tourists, but also arthropod vectors, some of them carrying pathogens. Among several arboviral diseases that emerged in the region during the last decade, West Nile fever accounted for high number of human cases and fatalities, while Crimean-Congo hemorrhagic fever expanded its geographic distribution, and is considered as a real threat for Europe.

DOI:   10.1002/jmv.24803      22-03-2017

Yellow fever in a traveller returning from Suriname to the Netherlands, March 2017
Wouthuyzen-Baker et al. 2017

A Dutch traveller returning from Suriname in early March 2017, presented with fever and severe acute liver injury. Yellow fever was diagnosed by (q)RT-PCR and sequencing. During hospital stay, the patient’s condition deteriorated and she developed hepatic encephalopathy requiring transfer to the intensive care. Although yellow fever has not been reported in the last four decades in Suriname, vaccination is recommended by the World Health Organization for visitors to this country.

DOI:  10.2807/1560-7917.ES.2017.22.11.30488       16-03-2017

Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease
Joensen et al. 2017

The accurate microbiological diagnosis of diarrhoea involves numerous laboratory tests and, often, the pathogen is not identified in time to guide clinical management. With next-generation sequencing (NGS) becoming cheaper, it has huge potential in routine diagnostics. The aim of this study was to evaluate the potential of NGS-based diagnostics through direct sequencing of faecal samples.

DOI:   10.1007/s10096-017-2947-2    11-03-2017

Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis
Agoti et al. 2017

Detailed information on the source, spread and evolution of respiratory syncytial virus (RSV) during seasonal community outbreaks remains sparse. Molecular analyses of attachment (G) gene sequences from hospitalized cases suggest that multiple genotypes and variants co-circulate during epidemics and that RSV persistence over successive seasons is characterized by replacement and multiple new introductions of variants. No studies have defined the patterns of introduction, spread and evolution of RSV at the local community and household level.

DOI:          11-03-2017

Effect of blood type on anti-α-Gal immunity and the incidence of infectious diseases
Cabezas-Cruz et al. 2017

The identification of factors affecting the susceptibility to infectious diseases is essential toward reducing their burden on the human population. The ABO blood type correlates with susceptibility to malaria and other infectious diseases. Due to the structural similarity between blood antigen B and Galα1-3Galβ1-(3)4GlcNAc-R (α-Gal), we hypothesized that self-tolerance to antigen B affects the immune response to α-Gal, which in turn affects the susceptibility to infectious diseases caused by pathogens carrying α-Gal on their surface.

DOI:  10.1038/emm.2016.164       10-03-2017

Discordant detection of avian influenza virus subtypes in time and space between poultry and wild birds; Towards improvement of surveillance programs
Verhagen et al. 2017

Avian influenza viruses from wild birds can cause outbreaks in poultry, and occasionally infect humans upon exposure to infected poultry. Identification and characterization of viral reservoirs and transmission routes is important to develop strategies that prevent infection of poultry, and subsequently virus transmission between poultry holdings and to humans. Based on spatial, temporal and phylogenetic analyses of data generated as part of intense and large-scale influenza surveillance programs in wild birds and poultry in the Netherlands from 2006 to 2011, we demonstrate that LPAIV subtype distribution differed between wild birds and poultry, suggestive of host-range restrictions.

DOI:   10.1371/journal.pone.0173470     09-03-2017

Variegated Squirrel Bornavirus 1 in Squirrels, Germany and the Netherlands
Schlottau et al. 2017

We screened squirrels in Germany and the Netherlands for the novel zoonotic variegated squirrel bornavirus 1 (VSBV-1). The detection of VSBV-1 in 11 squirrels indicates a considerable risk for transmission to humans handling those animals. Therefore, squirrels in contact with humans should routinely be tested for VSBV-1.

DOI:   10.3201/eid2303.161061    01-03-2017

Zoonotic Transmission of mcr-1 Colistin Resistance Gene from Small-Scale Poultry Farms, Vietnam
Trung et al. 2017

We investigated the consequences of colistin use in backyard chicken farms in Vietnam by examining the prevalence of mcr-1 in fecal samples from chickens and humans. Detection of mcr-1–carrying bacteria in chicken samples was associated with colistin use and detection in human samples with exposure to mcr-1–positive chickens.

DOI:    10.3201/eid2303.161553    01-03-2017

A novel astrovirus associated with encephalitis and ganglionitis in domestic sheep
Pfaff et al. 2017b

In June 2013, a 4-year-old Welsh Mountain ewe and in March 2014 a 10-day-old lamb of the same breed and the same flock presented progressive neurological signs including depressed sensorium, tremor, and unusual behaviour. Neuropathological examination of the brain and spinal cord detected non-suppurative polioencephalomyelitis and dorsal root ganglionitis, characteristic of a neurotropic viral agent in both sheep. Metagenomic analysis of different tissue samples from both animals identified a novel Ovine Astrovirus (OvAstV).

DOI:  10.1111/tbed.12623   22-02-2017

A novel alphaherpesvirus associated with fatal diseases in banded Penguins
Pfaff et al. 2017a

A novel avian alphaherpesvirus, preliminarily designated sphenicid alphaherpesvirus 1 (SpAHV-1), has been independently isolated from juvenile Humboldt and African penguins (Spheniscus humboldti and Spheniscus demersus) kept in German zoos suffering from diphtheroid oropharyngitis/laryngotracheitis and necrotizing enteritis (collectively designated as penguin-diphtheria-like disease). High-throughput sequencing was used to determine the complete genome sequences of the first two SpAHV-1 isolates.

DOI:  10.1099/jgv.0.000698    20-02-2017

Human influence and biotic homogenization drive the distribution of Escherichia coli virulence genes in natural habitats
Cabal et al. 2017

Cattle are the main reservoirs for Shiga-toxin-producing Escherichia coli (STEC), the only known zoonotic intestinal E. coli pathotype. However, there are other intestinal pathotypes that can cause disease in humans, whose presence has been seldom investigated. Thus, our aim was to identify the effects of anthropic pressure and of wild and domestic ungulate abundance on the distribution and diversity of the main human E. coli pathotypes and nine of their representative virulence genes (VGs).

DOI:  10.1002/mbo3.445     18-02-2017

Metagenomic Sequencing for Surveillance of Food- and Waterborne Viral Diseases
David F. Nieuwenhuijse and Marion P. G. Koopmans 2017

A plethora of viruses can be transmitted by the food- and waterborne route. However, their recognition is challenging because of the variety of viruses, heterogeneity of symptoms, the lack of awareness of clinicians, and limited surveillance efforts. Classical food- and waterborne viral disease outbreaks are mainly caused by caliciviruses, but the source of the virus is often not known and the foodborne mode of transmission is difficult to discriminate from human-to-human transmission. Atypical food- and waterborne viral disease can be caused by viruses such as hepatitis A and hepatitis E. In addition, a source of novel emerging viruses with a potential to spread via the food- and waterborne route is the repeated interaction of humans with wildlife. Wildlife-to-human adaptation may give rise to self- limiting outbreaks in some cases, but when fully adjusted to the human host can be devastating. Metagenomic sequencing has been investigated as a promising solution for surveillance purposes as it detects all viruses in a single protocol, delivers additional genomic information for outbreak tracing, and detects novel unknown viruses.

DOI:  10.3389/fmicb.2017.00230    15-02-2017

Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST
Baele et al. 2017

Advances in sequencing technology continue to deliver increasingly large molecular sequence datasets that are often heavily partitioned in order to accurately model the underlying evolutionary processes. In phylogenetic analyses, partitioning strategies involve estimating conditionally independent models of molecular evolution for different genes and different positions within those genes, requiring a large number of evolutionary parameters that have to be estimated, leading to an increased computational burden for such analyses.

DOI:   10.1093/bioinformatics/btx088    13-02-2017

Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut
Pipek et al. 2017

Detection of somatic mutations is one of the main goals of next generation DNA sequencing. A wide range of experimental systems are available for the study of spontaneous or environmentally induced mutagenic processes. However, most of the routinely used mutation calling algorithms are not optimised for the simultaneous analysis of multiple samples, or for non-human experimental model systems with no reliable databases of common genetic variations. Most standard tools either require numerous in-house post filtering steps with scarce documentation or take an unpractically long time to run. To overcome these problems, we designed the streamlined IsoMut tool which can be readily adapted to experimental scenarios where the goal is the identification of experimentally induced mutations in multiple isogenic samples.

DOI:  10.1186/s12859-017-1492-4      31-01-2017

Widespread activity of multiple lineages of Usutu virus, western Europe, 2016
Cadar et al. 2017

In the summer of 2016, Belgium, France, Germany and the Netherlands reported widespread Usutu virus (USUV) activity based on live and dead bird surveillance. The causative USUV strains represented four lineages, of which two putative novel lineages were most likely recently introduced into Germany and spread to other western European countries. The spatial extent of the outbreak area corresponded with R-O values > 1. The occurrence of the outbreak, the largest USUV epizootic registered so far in Europe, allowed us to gain insight in how a recently introduced arbovirus with potential public health implications can spread and become a resident pathogen in a naive environment.

DOI:  10.2807/1560-7917.ES.2017.22.4.30452      26-01-2017

Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing
Hjelmsø et al. 2017

Viral sewage metagenomics is a novel field of study used for surveillance, epidemiological studies, and evaluation of waste water treatment efficiency. In raw sewage human waste is mixed with household, industrial and drainage water, and virus particles are, therefore, only found in low concentrations. This necessitates a step of sample concentration to allow for sensitive virus detection. Additionally, viruses harbor a large diversity of both surface and genome structures, which makes universal viral genomic extraction difficult. Current studies have tackled these challenges in many different ways employing a wide range of viral concentration and extraction procedures. However, there is limited knowledge of the efficacy and inherent biases associated with these methods in respect to viral sewage metagenomics, hampering the development of this field. By the use of next generation sequencing this study aimed to evaluate the efficiency of four commonly applied viral concentrations techniques (precipitation with polyethylene glycol, organic flocculation with skim milk, monolithic adsorption filtration and glass wool filtration) and extraction methods (Nucleospin RNA XS, QIAamp Viral RNA Mini Kit, NucliSENS® miniMAG®, or PowerViral® Environmental RNA/DNA Isolation Kit) to determine the viriome in a sewage sample.

DOI:  10.1371/journal.pone.0170199      18-01-2017

Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods
Ahrenfeldt et al. 2017

Whole genome sequencing (WGS) is increasingly used in diagnostics and surveillance of infectious diseases. A major application for WGS is to use the data for identifying outbreak clusters, and there is therefore a need for methods that can accurately and efficiently infer phylogenies from sequencing reads. In the present study we describe a new dataset that we have created for the purpose of benchmarking such WGS-based methods for epidemiological data, and also present an analysis where we use the data to compare the performance of some current methods.

DOI:    10.1186/s12864-016-3407-6   05-01-2017

Norovirus Infection in Harbor Porpoises
de Graaf et al. 2017

A norovirus was detected in harbor porpoises, a previously unknown host for norovirus. This norovirus had low similarity to any known norovirus. Viral RNA was detected primarily in intestinal tissue, and specific serum antibodies were detected in 8 (24%) of 34 harbor porpoises from the North Sea.

DOI:  10.3201/eid2301.161081      01-01-2017

Genome Sequences of a Novel Vietnamese Bat Bunyavirus
Oude Munnink et al. 2016

To document the viral zoonotic risks in Vietnam, fecal samples were systematically collected from a number of mammals in southern Vietnam and subjected to agnostic deep sequencing. We describe here novel Vietnamese bunyavirus sequences detected in bat feces. The complete L and S segments from 14 viruses were determined.

DOI:   10.1128/genomeA.01366-16   22-12-2016

Chronic norovirus infection among solid organ recipients in a tertiary care hospital, the Netherlands, 2006-2014
van Beek et al. 2016

OBJECTIVES: Immunocompromised patients can suffer prolonged norovirus symptoms and virus shedding for many years. Little is known about the prevalence of chronic norovirus infection among solid organ transplant (SOT) recipients. In this study, 2182 SOT recipients were retrospectively tested for chronic norovirus infection.

DOI:  10.1016/j.cmi.2016.12.010       18-12-2016

Assessing the Epidemic Potential of RNA and DNA Viruses
Woolhouse et al. 2016

Many new and emerging RNA and DNA viruses are zoonotic or have zoonotic origins in an animal reservoir that is usually mammalian and sometimes avian. Not all zoonotic viruses are transmissible (directly or by an arthropod vector) between human hosts. Virus genome sequence data provide the best evidence of transmission.

DOI:          12-12-2016

Digital PCR for Quantifying Norovirus in Oysters Implicated in Outbreaks, France
Polo et al. 2016

Using samples from oysters clearly implicated in human disease, we quantified norovirus levels by using digital PCR. Concentrations varied from 43 to 1,170 RNA copies/oyster. The analysis of frozen samples from the production area showed the presence of norovirus 2 weeks before consumption.

DOI:  10.3201/eid2212.160841           01-12-2016    

Dual Emergence of Usutu Virus in Common Blackbirds, Eastern France, 2015
Lecollinet et al. 2016

Usutu virus (USUV) is a mosquitoborne flavivirus amplified in an enzootic cycle involving passeriform and strigiform birds as reservoir hosts and Culex mosquitos as vectors (1). Although originating from Africa, USUV has been introduced at least twice into central and western Europe, leading to substantial bird fatalities in central Europe (particularly in Austria, Hungary, Italy, Germany, and Switzerland) since 1996.

DOI:  10.3201/eid2212.161272    01-12-2016

Severe acute respiratory infection caused by swine influenza virus in a child necessitating extracorporeal membrane oxygenation (ECMO), the Netherlands, October 2016
Fraaij et al. 2016

In October 2016, a severe infection with swine influenza A(H1N1) virus of the Eurasian avian lineage occurred in a child with a previous history of eczema in the Netherlands, following contact to pigs. The patient’s condition deteriorated rapidly and required life support through extracorporeal membrane oxygenation. After start of oseltamivir treatment and removal of mucus plugs, the patient fully recovered. Monitoring of more than 80 close unprotected contacts revealed no secondary cases.

DOI:   10.2807/1560-7917.ES.2016.21.48.30416     01-12-2016

One Health training and research activities in Western Europe
Reina Sikkema and Marion Koopmans 2016

The increase in emerging human infectious diseases that have a zoonotic origin and the increasing resistance of microorganisms to antimicrobial drugs have shown the need for collaborations between the human, animal and environmental health sectors. The One Health concept increasingly receives recognition from policy makers and researchers all over the world.

DOI: 10.3402/iee.v6.33703          29-11-2016

European Nucleotide Archive in 2016
Toribio et al. 2016

The European Nucleotide Archive (ENA; offers a rich platform for data sharing, publishing and archiving and a globally comprehensive data set for onward use by the scientific community. With a broad scope spanning raw sequencing reads, genome assemblies and functional annotation, the resource provides extensive data submission, search and download facilities across web and programmatic interfaces. Here, we outline ENA content and major access modalities, highlight major developments in 2016 and outline a number of examples of data reuse from ENA.

DOI: 10.1093/nar/gkw1106        28-11-2016

Epidemiological and Molecular Analysis of an Outbreak of Highly Pathogenic Avian Influenza H5N8 clade in a German Zoo: Effective Disease Control with Minimal Culling
Globig et al. 2016

Outbreaks of highly pathogenic avian influenza A virus (HPAIV) subtype H5N8, clade, were first reported in January 2014 from South Korea. These viruses spread rapidly to Europe and the North American continent during autumn 2014 and caused, in Germany, five outbreaks in poultry holdings until February 2015. In addition, birds kept in a zoo in north-eastern Germany were affected. Only a few individual white storks (Ciconia ciconia) showed clinical symptoms and eventually died in the course of the infection, although subsequent in-depth diagnostic investigations showed that other birds kept in the same compound of the white storks were acutely positive for or had undergone asymptomatic infection with HPAIV H5N8.

DOI:   10.1111/tbed.12570      15-11-2016

Next-generation sequencing and norovirus
Matthew Cotten and Marion Koopmans 2016

Noroviruses (NoVs) are highly transmissible viruses and the most common cause of diarrhea and vomiting. While illness in most infected persons is relatively mild and self-limiting, severe complications and death may ensue in risk groups, including the extremes of age and persons with reduced immunocompetence due to a range of diseases and treatments.

DOI:  10.2217/fvl-2016-0099      11-11-2016

Novel phlebovirus detected in Haemaphysalis parva ticks in a Greek Island
Papa et al. 2016

During the last decade the number of novel tick-borne phleboviruses has increased rapidly, especially after the identification of severe fever with thrombocytopenia syndrome and Heartland viruses which can cause severe disease in humans. A novel virus, Antigone virus was recently detected in ticks collected from the mainland of Greece. The aim of the present study was to investigate the presence of tick-borne phleboviruses in an island in Greece.

DOI:  10.1016/j.ttbdis.2016.10.012   29-10-2016

Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition
Knudsen et al. 2016

Explorations of complex microbiomes using genomics greatly enhance our understanding about their diversity, biogeography, and function. The isolation of DNA from microbiome specimens is a key prerequisite for such examinations, but challenges remain in obtaining sufficient DNA quantities required for certain sequencing approaches, achieving accurate genomic inference of microbiome composition, and facilitating comparability of findings across specimen types and sequencing projects. These aspects are particularly relevant for the genomics-based global surveillance of infectious agents and antimicrobial resistance from different reservoirs.

DOI:  10.1128/mSystems.00095-16             18-10-2016

Role for migratory wild birds in the global spread of avian influenza H5N8
The Global Consortium for H5N8 and Related Influenza Viruses

Avian influenza viruses affect both poultry production and public health. A subtype H5N8 (clade virus, following an outbreak in poultry in South Korea in January 2014, rapidly spread worldwide in 2014–2015. Our analysis of H5N8 viral sequences, epidemiological investigations, waterfowl migration, and poultry trade showed that long-distance migratory birds can play a major role in the global spread of avian influenza viruses.

DOI:  10.1126/science.aaf8852                    14-10-2016

The evolution of Ebola virus: Insights from the 2013–2016 epidemic
Holmes et al. 2016

The 2013-2016 epidemic of Ebola virus disease in West Africa was of unprecedented magnitude and changed our perspective on this lethal but sporadically emerging virus. This outbreak also marked the beginning of large-scale real-time molecular epidemiology. Here, we show how evolutionary analyses of Ebola virus genome sequences provided key insights into virus origins, evolution and spread during the epidemic.

DOI:   10.1038/nature19790    12-10-2016

Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection
Phan et al. 2016

Coordinated and synchronous surveillance for zoonotic viruses in both human clinical cases and animal reservoirs provides an opportunity to identify interspecies virus movement. Rotavirus (RV) is an important cause of viral gastroenteritis in humans and animals. In this study, we document the RV diversity within co-located humans and animals sampled from the Mekong delta region of Vietnam using a primer-independent, agnostic, deep sequencing approach.

DOI:   10.1093/ve/vew027     03-10-2016

Bacterial pathogens and endosymbionts in ticks
Papa et al. 2016

Ticks collected from goats in northern Greece were tested for the presence of tick-borne bacteria. Among adult ticks, 37 (57.8%) were Rhipicephalus bursa, 11 (17.2%) Dermacentor marginatus, 10 (15.6%) Ixodes ricinus, 3 (4.7%) Rhipicephalus sanguineus sensu lato and 2 (3.1%) Haemaphysalis parva; one (1.6%) Rhipicephalus spp. tick was nymph. Rickettsia monacensis, Rickettsia massilae, Anaplasma phagocytophilum and Anaplasma platys were detected in I. ricinus and Rh. bursa ticks. A variety of Coxiella-like endosymbionts were detected in all tick genera tested, forming distinct clades from Coxiella burnetii in the phylogenetic tree based on the 16S rRNA gene.

DOI:      23-09-2016

Lack of virological and serological evidence for continued circulation of highly pathogenic avian influenza H5N8 virus in wild birds in the Netherlands, 14 November 2014 to 31 January 2016
Poen et al. 2016

In 2014, H5N8 clade highly pathogenic avian influenza (HPAI) viruses of the A/Goose/Guangdong/1/1996 lineage emerged in poultry and wild birds in Asia, Europe and North America. Here, wild birds were extensively investigated in the Netherlands for HPAI H5N8 virus (real-time polymerase chain reaction targeting the matrix and H5 gene) and antibody detection (haemagglutination inhibition and virus neutralisation assays) before, during and after the first virus detection in Europe in late 2014. Between 21 February 2015 and 31 January 2016, 7,337 bird samples were tested for the virus.

DOI: 10.2807/1560-7917.ES.2016.21.38.30349          22-09-2016

Comparison of norovirus genogroup I, II and IV seroprevalence among children in the Netherlands, 1963, 1983 and 2006
van Beek et al. 2016

Noroviruses are a major cause of acute gastroenteritis worldwide and are a genetically diverse group of viruses. Since 2002, an increasing number of norovirus outbreaks have been reported globally, but it is not clear whether this increase has been caused by a higher awareness or reflects the emergence of new genogroup II genotype 4 (GII.4) variants. The hypothesis that norovirus prevalence has increased post-2002 and is related to the emergence of GII.4 is tested in this study.

DOI:  10.1099/jgv.0.000533      01-09-2016

Bluetongue virus serotype 27: Detection and characterization of two novel variants in Corsica, France
Schulz et al. 2016

During the compulsory vaccination program against bluetongue virus serotype 1 (BTV-1) in Corsica (France) in 2014, a BTV strain belonging to a previously uncharacterised
serotype (BTV-27) was isolated from asymptomatic goats. The present study describes the detection and molecular characterisation of two additional distinct BTV-27 variants
found in goats in Corsica in 2014 and 2015.

DOI:  10.1099/jgv.0.000557                         01-09-2016

Infections shared with wildlife: an updated perspective
Gortazar et al. 2016

Infections shared with wildlife matter because many are zoonotic, because of their impact on animal health and in consequence on livestock production, and due to their adverse effects on conservation and on the sustainable use of wildlife. We describe recent environmental and societal changes that contribute to explain the current wildlife disease scenario, propose an updated list and ranking of relevant shared disease agents, illustrate key risk factors which often underlay shared infections, and provide a summary of recent progress in wildlife monitoring and disease control. We conclude, first, that there is a need for a better understanding of population dynamics and for good baseline data on wildlife population trends.

DOI:  10.1007/s10344-016-1033-x         05-08-2016

Challenges in laboratory diagnosis of acute viral central nervous system infections in the era of emerging infectious diseases: the syndromic approach
Papa et al. 2016b

Many acute viral infections of the central nervous system (CNS) remain without etiological diagnosis. Specific treatment is available for only few of them; however, accurate diagnosis is essential for patient’s life and public Health.

DOI:   10.1080/14787210.2016.1215914        31-07-2016

Influenza A (H10N7) Virus Causes Respiratory Tract Disease in Harbor Seals and Ferrets
van den Brand er al. 2016

Avian influenza viruses sporadically cross the species barrier to mammals, including humans, in which they may cause epidemic disease. Recently such an epidemic occurred due to the emergence of avian influenza virus of the subtype H10N7 (Seal/H10N7) in harbor seals (Phoca vitulina). This epidemic caused high mortality in seals along the north-west coast of Europe and represented a potential risk for human health. To characterize the spectrum of lesions and to identify the target cells and viral distribution, findings in 16 harbor seals spontaneously infected with Seal/H10N7 are described.

DOI: 10.1371/journal.pone.0159625              22-07-2016

Identification of a novel plasmid-mediated colistin-resistance gene, mcr-2, in Escherichia coli, Belgium, June 2016
Xavier et al. 2016

We identified a novel plasmid-mediated colistinresistance gene in porcine and bovine colistin-resistant Escherichia coli that did not contain mcr-1. The gene, termed mcr-2, a 1,617 bp phosphoethanolamine transferase harboured on an IncX4 plasmid, has 76.7% nucleotide identity to mcr-1. Prevalence of mcr-2 in porcine colistin-resistant E. coli (11/53) in Belgium was higher than that of mcr-1 (7/53). These data call for an immediate introduction of mcr-2 screening in ongoing molecular epidemiological surveillance of colistin-resistant Gram-negative pathogens.

DOI:               07-07-2016

Porcine Bocavirus Infection Associated with Encephalomyelitis in a Pig, Germany
Pfankuche et al. 2016

In 2013, a 6-week-old female piglet kept in a flatdeck cage had coughing, growth retardation, and diarrhea and was taken to a local veterinarian in Hannover, Germany; the piglet was euthanized. After necropsy at the University of Veterinary Medicine in Hannover, histologic investigation found interstitial pneumonia; a mild, multifocal, lymphohistiocytic panencephalitis that affected the cerebrum and cerebellum, including brain stem and medulla oblongata; and a mild, multifocal, lymphohistiocytic panmyelitis. Results from screening for typical neurotropic viruses (classical swine fever virus, suid herpesvirus 1, rabies virus, teschovirus, porcine enterovirus 8, 9, and 10) were negative; Mycoplasma hyorhinis was detected by multiplex PCR (Institute of Virology, University of Veterinary Medicine Hannover) within the lung and pulmonary lymph nodes. Cerebral tissue from the pig was processed for viral metagenomics by random RNA and DNA virus screening and next-generation sequencing (NGS) with the 454 sequencing platform (GS Junior; Roche, Basel, Switzerland), as described (1), and 21,359 reads were obtained. Analysis by using blastn and blastx (2) showed 10 reads had >97% nt identity with porcine bocavirus (PBoV) KU14. No other viral sequences were detected.

DOI:                  01-07-2016

Hepatitis E Virus Infection in Dromedaries, North and East Africa, United Arab Emirates, and Pakistan, 1983-2015
Rasche et al. 2016

A new hepatitis E virus (HEV-7) was recently found in dromedaries and 1 human from the United Arab Emirates. We screened 2,438 dromedary samples from Pakistan, the United Arab Emirates, and 4 African countries. HEV-7 is long established, diversified and geographically widespread. Dromedaries may constitute a neglected source of zoonotic HEV infections.

DOI:                  01-07-2016

Crimean-Congo hemorrhagic fever virus lineages Europe 1 and Europe 2 in Bulgarian ticks 
Panayotova et al. 2016

Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne human viral disease with fatality rate up to 30%. Two genetic lineages of CCHF virus (CCHFV) are present in Europe – lineage Europe 1 which contains pathogenic CCHFV strains, and lineage Europe 2 consisting of AP92 and AP92-like strains. In order to investigate CCHFV distribution and potential risk for humans, ticks were collected from livestock in the five districts where CCHF cases have been reported in the last five years in Bulgaria. CCHFV lineage Europe 1 was detected in 39 of 623 H. marginatum ticks (6.3%; range per village 2.7 - 15.2%), while CCHFV lineage Europe 2 was detected for the first time in Bulgaria in 49 of 415 R. sanguineus sensu lato ticks (11.8%; range 0 - 58.3%). The present study shows that both Europe 1 and Europe 2 CCHFV lineages are present in Bulgaria. The pathogenic role of the AP92-like strains remains to be elucidated.

DOI:      01-07-2016

Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases
Arias et al. 2016

To end the largest known outbreak of Ebola virus disease (EVD) in West Africa and to prevent new transmissions, rapid epidemiological tracing of cases and contacts was required. The ability to quickly identify unknown sources and chains of transmission is key to ending the EVD epidemic and of even greater importance in the context of recent reports of Ebola virus (EBOV) persistence in survivors.

DOI:  10.1093/ve/vew016                             22-06-2016

Comparison of six commercial kits to extract bacterial chromosome and plasmid DNA for MiSeq sequencing 
Becker et al. 2016

We compared commercial kits for extraction of genomic DNA from the Gram-negative bacterium Klebsiella pneumoniae for subsequent Miseq sequencing. Purification of DNA was based on matrix binding (silica or anion exchange resin) or differential precipitation (salting out), respectively. The choice of extraction kit had little effect on sequencing quality and coverage across drastically different replicons, except for an apparent depletion of small plasmids (<5 kb) during precipitation-based extractions. Sequencing coverage provided copy-number estimates for small plasmids that were consistently higher than those from quantitative real-time PCR.

DOI: 10.1038/srep28063                              17-06-2016

A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance
Thomsen et al. 2016

Recent advances in whole genome sequencing have made the technology available for routine use in microbiological laboratories. However, a major obstacle for using this technology is the availability of simple and automatic bioinformatics tools. Based on previously published and already available web-based tools we developed a single pipeline for batch uploading of whole genome sequencing data from multiple bacterial isolates.

DOI:          21-06-2016

High Prevalence of Highly Variable Atypical Porcine Pestiviruses Found in Germany
Beer et al. 2016

Recently, a novel atypical porcine pestivirus (APPV) with significant distribution was described in the USA. Subsequent screening of the German pig sector showed a high prevalence of APPV with high variability among strains. First indication of a cell culture isolate is provided which will allow further investigations like pathogenesis studies.

DOI:  10.1111/tbed.12532                            14-06-2016

Presence of atypical porcine pestivirus (APPV) genomes in newborn piglets correlates with congenital tremor 
Postel et al. 2016

Pestiviruses are highly variable RNA viruses belonging to the continuously growing family Flaviviridae. A genetically very distinct pestivirus was recently discovered in the USA, designated atypical porcine pestivirus (APPV). Here, a screening of 369 sera from apparently healthy adult pigs demonstrated the existence of APPV in Germany with an estimated individual prevalence of 2.4% and ~10% at farm level. Additionally, APPV genomes were detected in newborn piglets affected by congenital tremor (CT), but genomes were absent in unaffected piglets. High loads of genomes were identified in glandular epithelial cells, follicular centers of lymphoid organs, the inner granular cell layer of the cerebellum, as well as in the trigeminal and spinal ganglia. Retrospective analysis of cerebellum samples from 2007 demonstrated that APPV can be found in piglets with CT of unsolved aetiology. Determination of the first European APPV complete polyprotein coding sequence revealed 88.2% nucleotide identity to the APPV sequence from the USA. APPV sequences derived from different regions in Germany demonstrated to be highly variable. Taken together, the results of this study strongly suggest that the presence of APPV genomes in newborn piglets correlates with CT, while no association with clinical disease could be observed in viremic adult pigs.

DOI: 10.1038/srep27735                              13-06-2016

The Biodefense Field
Emilio Mordini, 2016

On April 20, 2016, in Karachi, Pakistan, seven police officers were killed while escorting health workers involved in polio vaccination (Pakistan is one of three countries in the world where polio is still endemic). The Taliban claimed responsibility and promised future attacks. This news deserves to be read through the lens of a report published on October 28, 2015 by the Blue Ribbon Study Panel on Biodefense, a bipartisan commission sponsored by the Hudson Institute and the Potomac Institute for Policy Studies, two US think-tanks.

DOI: 10.1111/bioe.12269                             04-06-2016

Complete sequence of an IncFII plasmid harbouring the colistin resistance gene mcr-1 isolated from Belgian pig farms 
Xavier et al. 2016b

The monumental increase in antibiotic resistance among important bacterial pathogens, driven by inappropriate and appropriate use of ineffective drugs, is currently recognized as one of themost pressing threats to human health by the WHO.

DOI: 10.1093/jac/dkw191                             03-06-2016

Discovery and diagnosis of new viral pathogens: proposal for a generic workflow based on next-generation sequencing and new integrated data analysis approaches
Höper et al. 2016b

Diagnostic metagenomic analyses gained more impact for pathogen detection and discovery in recent years due to increasing opportunities for next-generation sequencing at simultaneously decreasing prices. However, as with all novel technologies, there is a lack of standardisation in this field. But, for day-to-day routine use in a diagnostic laboratory, standardisation is urgently required.

Euroreference, (1 June 2016), 58–62

Human norovirus transmission and evolution in a changing world 
de Graaf et al. 2016

Norovirus infections are a major cause of gastroenteritis, and outbreaks occur frequently. Several factors are currently increasing the challenge posed by norovirus infections to global health, notably the increasing number of infections in immunocompromised individuals, who are more susceptible to disease, and the globalization of the food industry, which enables large norovirus outbreaks to occur on an international scale. Furthermore, the rapid rate of the genetic and antigenic evolution of circulating noroviruses complicates the development of vaccines and therapies that are required to counter these challenges. In this Review, we describe recent advances in the study of the transmission, pathogenesis and evolution of human noroviruses, and consider the ongoing risk of norovirus outbreaks, together with the future prospects for therapeutics, in a rapidly changing world.

DOI: 10.1038/nrmicro.2016.48                                           23-05-2016

Detection of Hepatitis E Virus in Sewage After an Outbreak on a French Island 
Miura et al. 2016

A hepatitis E outbreak, which occurred on a small isolated island, provided an opportunity to evaluate the association between the number of hepatitis E cases in the community and the concentration of virus detected in sewage.

DOI: 10.1007/s12560-016-9241-9                  10-05-2016

SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes
Bielejec et al. 2016

Model-based phylogenetic reconstructions increasingly consider spatial or phenotypic traits in conjunction with sequence data to study evolutionary processes. Alongside parameter estimation, visualization of ancestral reconstructions represents an integral part of these analyses. Here, we present a complete overhaul of the spatial phylogenetic reconstruction of evolutionary dynamics software, now called SpreaD3 to emphasize the use of data-driven documents, as an analysis and visualization package that primarily complements Bayesian inference in BEAST ( , last accessed 9 May 2016). The integration of JavaScript D3 libraries ( , last accessed 9 May 2016) offers novel interactive web-based visualization capacities that are not restricted to spatial traits and extend to any discrete or continuously valued trait for any organism of interest.

DOI:  10.1093/molbev/msw082   23-04-2016

Using genomics data to reconstruct transmission trees during disease outbreaks
Hall et al. 2016a

Genetic sequence data from pathogens present a novel means to investigate the spread of infectious disease between infected hosts or infected premises, complementing traditional contact-tracing approaches, and much recent work has gone into developing methods for this purpose. The objective is to recover the epidemic transmission tree, which identifies who infected whom. This paper reviews the various approaches that have been taken.

DOI:                                          01-04-2016

Metagenomic approaches to identifying infectious agents
Höper et al. 2016a

Since the advent of next-generation sequencing (NGS) technologies, the untargeted screening of samples from outbreaks for pathogen identification using metagenomics has become technically and economically feasible. However, various aspects need to be considered in order to exploit the full potential of NGS for virus discovery. Here, the authors summarise those aspects of the main steps that have a significant impact, from sample selection through sample handling and processing, as well as sequencing and finally data analysis, with a special emphasis on existing pitfalls.

DOI:                                          01-04-2016

Sharing data for global infectious disease surveillance and outbreak detection 
Aarestrup and Koopmans 2016

Rapid global sharing and comparison of epidemiological and genomic data on infectious diseases would enable more rapid and efficient global outbreak control and tracking of diseases. Several barriers for global sharing exist but, in our opinion, the presumed magnitude of the problems appears larger than they are, and solutions can be found. 

DOI:                01-04-2016

Deletion Variants of Middle East Respiratory Syndrome Coronavirus from Humans, Jordan, 2015 
Lamers et al. 2016

We characterized Middle East respiratory syndrome coronaviruses from a hospital outbreak in Jordan in 2015. The viruses from Jordan were highly similar to isolates from Riyadh, Saudi Arabia, except for deletions in open reading frames 4a and 3. Transmissibility and pathogenicity of this strain remains to be determined.

DOI:                                        01-04-2016

Comparative Proteomics Identifies Host Immune System Proteins Affected by Infection with Mycobacterium bovis 
Lopez et al. 2016

Mycobacteria of the Mycobacterium tuberculosis complex (MTBC) greatly impact human and animal health worldwide. The mycobacterial life cycle is complex, and the mechanisms resulting in pathogen infection and survival in host cells are not fully understood. Eurasian wild boar (Sus scrofa) are natural reservoir hosts for MTBC and a model for mycobacterial infection and tuberculosis (TB). In the wild boar TB model, mycobacterial infection affects the expression of innate and adaptive immune response genes in mandibular lymph nodes and oropharyngeal tonsils, and biomarkers have been proposed as correlates with resistance to natural infection. However, the mechanisms used bymycobacteria tomanipulate host immune response are not fully characterized. Our hypothesis is that the immune system proteins under-represented in infected animals, when compared to uninfected controls, are used by mycobacteria to guarantee pathogen infection and transmission.

DOI: 10.1371/journal.pntd.0004541              30-03-2016

The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study
Hall et al. 2016b

The ongoing large-scale increase in the total amount of genetic data for viruses and other pathogens has led to a situation in which it is often not possible to include every available sequence in a phylogenetic analysis and expect the procedure to complete in reasonable computational time. This raises questions about how a set of sequences should be selected for analysis, particularly if the data are used to infer more than just the phylogenetic tree itself.

DOI:  10.1093/ve/vew003                             02-03-2016

Genetic Detection of Hantaviruses in Rodents, Albania 
Papa et al. 2016a

In order to have a first insight into the epidemiology of hantaviruses in Albania, 263 small mammals (248 rodents, 15 insectivores) were captured in 352 locations in 29 districts and tested for hantavirus infection. Dobrava– Belgrade virus (DOBV) was detected in 10 of 148 (6.7%) Apodemus flavicollis rodents. DOBV-positive A. flavicollis were detected in six districts (Diber, Korce, Kolonje, Librazhd, Pogradec, and Vlore). The obtained nucleotide sequences were highly similar to each other and to DOBV sequences from northwestern Greece. Understanding the epidemiology of hantaviruses and identifying the endemic foci enables the public health strategies to minimize the risk of human infection.

DOI: 10.1002/jmv.24486                              08-02-2016

Cross host transmission in the emergence of MERS coronavirus
Reusken et al. 2016

Coronaviruses (CoVs) able to infect humans emerge through cross-host transmission from animals. There is substantial evidence that the recent Middle East respiratory syndrome (MERS)-CoV outbreak is fueled by zoonotic transmission from dromedary camels. This is largely based on the fact that closely related viruses have been isolated from this but not any other animal species. Given the widespread geographical distribution of dromedaries found seropositive for MERS-CoV, continued transmission may likely occur in the future. Therefore, a further understanding of the cross host transmission of MERS-CoV is needed to limit the risks this virus poses to man.

DOI:  10.1016/j.coviro.2016.01.004     05-02-2016

Dissemination of the mcr-1 colistin resistance gene
Arcilla et al. 2016

Plasmid-mediated transferable colistin resistance encoded by the mcr-1 gene was described in Escherichia coli and Klebsiella pneumoniae isolates from pigs and chicken at a prevalence of around 20%, and in clinical isolates from human beings at a prevalence of around 1% in China.1 The prevalence of the mcr-1 gene in Enterobacteriaceae in other countries and in the
community is unknown. 

DOI:      01-02-2016

Consolidating and exploring antibiotic resistance gene data resources
Xavier et al. 2016

The unrestricted use of antibiotics has resulted in rapid acquisition of antibiotic resistance (AR) and spread of multi-drug-resistant (MDR) bacterial pathogens. With the advent of next generation sequencing technologies and their application in understanding MDR pathogen dynamics, it has become imperative to unify AR gene data resources for easy accessibility for researchers. However, due to the absence of a centralized platform for AR gene resources, availability, consistency and accuracy of information vary considerably across different databases. In this article, we sought to explore existing AR gene data resources in order to make them more visible to the clinical microbiology community, to identify their limitations, and to propose potential solutions. 

DOI: 10.1128/JCM.02717-15                        27-01-2016

Spatiotemporal analysis of the genetic diversity of seal influenza A(H10N7) virus, Northwestern Europe 
Bodewes et al. 2016

Influenza A viruses are major pathogens for humans, domestic animals and wildlife that cross the species barrier occasionally. In spring 2014, increased mortality of harbor seals (Phoca vitulina) was reported in Sweden and Denmark, associated with infection with an influenza A(H10N7) virus. Within a few months, this virus spread to seals of the coastal waters of Germany and the Netherlands, causing the death of thousands of animals. Genetic analysis of the hemagglutinin (HA) and neuraminidase (NA) genes of this seal influenza A(H10N7) virus revealed that it was most closely related to various avian influenza A(H10N7) viruses. The collection of samples from infected seals during the course of the outbreak provided an unique opportunity to follow the adaptation of this avian virus to its new seal host. Sequence data was obtained from samples collected from 41 different seals from four different countries between April 2014 and January 2015 using Sanger sequencing and next-generation sequencing to describe the molecular epidemiology of the seal influenza A(H10N7) virus. The majority of sequence variation occurred in the HA gene, and some mutations corresponded with amino acid changes not found in H10 viruses isolated from Eurasian birds. Also, sequence variation in the HA gene was greater at the beginning than at the end of the epidemic, when a number of the mutations observed earlier had been fixed. These results imply that when an avian influenza virus jumps the species barrier from birds to seals, amino acid changes in the HA may occur rapidly and are important for virus adaptation to its new mammalian host. 

DOI: 10.1128/JVI.03046-15                          27-01-2016

Immunolabelling of non-phosphorylated neurofilament indicates damage of spinal cord axons in TSE-infected goats 
Nadeem et al. 2016

TRANSMISSIBLE spongiform encephalopathies (TSEs) including bovine spongiform encephalopathy (BSE) are devastating neurodegenerative disorders caused by conversion of the normal cellular prion protein (PrPC) into an abnormal isoform (PrPSc; Prusiner, 1982, Chesebro, 2003). Following the discovery of goat BSE cases in the UK and France (Eloit and others 2005, Jeffrey and others 2006, Spiropoulos and others 2011) small ruminants were considered to pose a BSE infection risk/source for cattle, and human beings in particular.

DOI: 10.1136/vr.103425                               21-01-2016

Colistin-resistant Escherichia coli harbouring mcr-1 isolated from food animals in Hanoi, Vietnam 
Malhotra et al. 2016b

In The Lancet Infectious Diseases, Yi-Yun Liu and colleagues1 reported, for the first time, plasmid-mediated colistin resistance in Escherichia coli isolated from animals, food, and patients in China. We screened 24 extendedspectrum β-lactamase (ESBL, blaCTX-M) harbouring E coli isolated during 2014–15 from rectal swabs taken from chickens on two farms (n=11) in
the Van Lam district of the Hung Yen province, and from a pig farm (seven) and a pig slaughterhouse (four) located in the Hoai Duc region of the Hanoi province, Vietnam.

DOI:       08-01-2016

Colistin resistance gene mcr-1 harboured on a multidrug resistant plasmid 
Malhotra et al. 2016a

In The Lancet Infectious Diseases, Yi-Yun Liu and colleagues reported, for the fi rst time, plasmid-mediated colistin resistance in Escherichia coli isolated from animals, food, and patients in China.1 These data bring to the fore an as yet unknown facet of colistin resistance and yet again show the effect of antibiotic use in animal farming on human health.2,3

DOI:      08-01-2016

Emergence of a Clonal Lineage of Multidrug-Resistant ESBL-Producing Salmonella Infantis Transmitted from Broilers and Broiler Meat to Humans in Italy between 2011 and 2014 
Franco et al. 2015

We report the spread of a clone of multidrug-resistant (MDR), ESBL-producing (bla CTX-M-1) Salmonella enterica subsp. enterica serovar Infantis, in the Italian broiler chicken industry and along the food-chain. This was first detected in Italy in 2011 and led to human infection in Italy in 2013–2014.A set (n = 49) of extended-spectrum cephalosporin (ESC)-resistant (R) isolates of S. Infantis (2011–2014) from humans, food-producing animals and meat thereof, were studied along with a selected set of earlier and more recent ESC-susceptible (ESC-S) isolates (n = 42, 2001–2014). They were characterized by macrorestriction-PFGE analysis and genetic environment of ESC-resistance. Isolates representative of PFGE-patterns and origin were submitted to Whole Genome Sequencing. The emerging ESC-R clone, detected mainly from broiler chickens, broiler meat and humans, showed a minimum pattern of clinical resistance to cefotaxime, tetracycline, sulfonamides, and trimethoprim, beside ciprofloxacin microbiological resistance (MIC 0.25 mg/L). All isolates of this clone harbored a conjugative megaplasmid (~ 280–320 Kb), similar to that described in ESC-susceptible S. Infantis in Israel (pESI-like) in 2014. This megaplasmid carried the ESBL gene bla CTX-M-1, and additional genes [tet(A), sul1, dfrA1 and dfrA14] mediating cefotaxime, tetracycline, sulfonamide, and trimethoprim resistance. It also contained genes conferring enhanced colonization capability, virulence (fimbriae, yersiniabactin), resistance and fitness (qacE1, mer) in the intensive-farming environment. This emerging clone of S. Infantis has been causing infections in humans, most likely through the broiler industry. Since S. Infantis is among major serovars causing human infections in Europe and is an emerging non-typhoidal Salmonella globally, further spread of this lineage in primary productions deserves quick and thorough risk-management strategies.

DOI: 10.1371/journal.pone.0144802              30-12-2015

Seroprevalence of Antibodies against Seal Influenza A(H10N7) Virus in Harbor Seals and Gray Seals from the Netherlands 
Bodewes et al. 2015

In the spring and summer 2014, an outbreak of seal influenza A(H10N7) virus infection occurred among harbor seals (Phoca vitulina) off the coasts of Sweden and Denmark. This virus subsequently spread to harbor seals off the coasts of Germany and the Netherlands. While thousands of seals were reported dead in Sweden, Denmark and Germany, only a limited number of seals were found dead in the Netherlands. To determine the extent of exposure of seals in the Netherlands to influenza A/H10N7 virus, we measured specific antibody titers in serum samples from live-captured seals and seals admitted for rehabilitation in the Netherlands by use of a hemagglutination inhibition assay and an ELISA. In harbor seals in 2015, antibodies against seal influenza A(H10N7) virus were detected in 41% (32 out of 78) pups, 10% (5 out of 52) weaners, and 58% (7 out of 12) subadults or adults. In gray seals (Halichoerus grypus) in 2015, specific antibodies were not found in the pups (n = 26), but in 26% (5 out of 19) of the older animals. These findings indicate that, despite apparent low mortality, infection with seal influenza A(H10N7) virus was geographically widespread and also occurred in grey seals.

DOI: 10.1371/journal.pone.0144899              14-12-2015

Neurotropic virus infections as the cause of immediate and delayed neuropathology 
Ludlow et al. 2015

A wide range of viruses from different virus families in different geographical areas, may cause immediate or delayed neuropathological changes and neurological manifestations in humans and animals. Infection by neurotropic viruses as well as the resulting immune response can irreversibly disrupt the complex structural and functional architecture of the central nervous system, frequently leaving the patient or affected animal with a poor or fatal prognosis. Mechanisms that govern neuropathogenesis and immunopathogenesis of viral infections are highlighted, using examples of wellstudied virus infections that are associated with these alterations in different populations throughout the world. A better understanding of the molecular, epidemiological and biological characteristics of these infections and in particular of mechanisms that underlie their clinical manifestations may be expected to provide tools for the development of more effective intervention strategies and treatment regimens.

DOI: 10.1007/s00401-015-1511-3                  10-12-2015

Detection of mcr-1 encoding plasmid-mediated colistin-resistant Escherichia coli isolates from human bloodstream infection and imported chicken meat, Denmark 2015
Hasman et al. 2015

The plasmid-mediated colistin resistance gene, mcr-1, was detected in an Escherichia coli isolate from a Danish patient with bloodstream infection and in five E. coli isolates from imported chicken meat. One isolate from chicken meat belonged to the epidemic spreading sequence type ST131. In addition to IncN2, an incX4 replicon was found to be linked to mcr-1. This report follows a recent detection of mcr-1 in E. coli from animals, food and humans in China. 

DOI:               10-12-2015

Comparative Genomics of Field Isolates of Mycobacterium bovis and M. caprae Provides Evidence for Possible Correlates with Bacterial Viability and Virulence 
de la Fuente et al. 2015b

Mycobacteria of the Mycobacterium tuberculosis complex (MTBC) greatly affect humans and animals worldwide. The life cycle of mycobacteria is complex and the mechanisms resulting in pathogen infection and survival in host cells are not fully understood. Recently, comparative genomics analyses have provided new insights into the evolution and adaptation of the MTBC to survive inside the host. However, most of this information has been obtained using M. tuberculosis but not other members of the MTBC such as M. bovis and M. caprae. In this study, the genome of three M. bovis (MB1, MB3, MB4) and one M. caprae (MB2) field isolates with different lesion score, prevalence and host distribution phenotypes were sequenced. Genomesequence information was used for whole-genome and protein targeted comparative genomics analysis with the aim of finding correlates with phenotypic variation with potential implications for tuberculosis (TB) disease risk assessment and control.

DOI:10.1371/journal.pntd.0004232               19-11-2015

Biocuration of functional annotation at the European nucleotide archive 
Gibson et al. 2015

The European Nucleotide Archive (ENA; is a repository for the submission, maintenance and presentation of nucleotide sequence data and related sample and experimental information. In this article we report on ENA in 2015 regarding general activity, notable published data sets and major achievements. This is followed by a focus on sustainable biocuration of functional annotation, an area which has particularly felt the pressure of sequencing growth. The importance of functional annotation, how it can be submitted and the shifting role of the biocurator in the context of increasing volumes of data are all discussed.

DOI: 10.1093/nar/gkv1311                           09-11-2015

Evolutionary origins of hepatitis A virus in small mammals 
Drexler et al. 2015

Hepatitis A virus (HAV) is an ancient and ubiquitous human pathogen recovered previously only from primates. The sole species of the genus Hepatovirus, existing in both enveloped and nonenveloped forms, and with a capsid structure intermediate between that of insect viruses and mammalian picornaviruses, HAV is enigmatic in its origins. We conducted a targeted search for hepatoviruses in 15,987 specimens collected from 209 small mammal species globally and discovered highly diversified viruses in bats, rodents, hedgehogs, and shrews, which by pairwise sequence distance comprise 13 novel Hepatovirus species. Near-complete genomes from nine of these species show conservation of unique hepatovirus features, including predicted internal ribosome entry site structure, a truncated VP4 capsid protein lacking N-terminal myristoylation, a carboxyl- terminal pX extension of VP1, VP2 late domains involved in membrane envelopment, and a cis-acting replication element within the 3Dpol sequence. Antibodies in some bat sera immunoprecipitated and neutralized human HAV, suggesting conservation of critical antigenic determinants. Limited phylogenetic cosegregation among hepatoviruses and their hosts and recombination patterns are indicative of major hepatovirus host shifts in the past. Ancestral state reconstructions suggest a Hepatovirus origin in small insectivorous mammals and a rodent origin of human HAV. Patterns of infection in small mammals mimicked those of human HAV in hepatotropism, fecal shedding, acute nature, and extinction of the virus in a closed host population. The evolutionary conservation of epatovirus structure and pathogenesis provide novel insight into the origins of HAV and highlight the utility of analyzing animal reservoirs for risk assessment of emerging viruses.

DOI:                02-11-2015

Molecular Epidemiology of Crimean–Congo Hemorrhagic Fever in Bulgaria—An Update
Papa et al. 2015

Crimean–Congo hemorrhagic fever (CCHF) is endemic in Bulgaria. During 2013–2014, 11 confirmed CCHF cases have been reported in the country (seven in 2013 and four in 2014). The present study provides the CCHF molecular epidemiology in Bulgaria based on all currently available S, M, and L RNA segment nucleotide sequences spanning the years 1978–2014. A relatively low genetic difference (0–6%, the maximum seen in the M RNA segment) was seen among the CCHFV sequences suggesting that a slow evolving CCHFV strain belonging to “Europe 1” clade is present in Bulgaria. Although the virus emerged in new foci during the recent years, it is more active in the established endemic foci which seem to offer the most suitable ecosystem and environment. Understanding the CCHF epidemiology and virus evolution is the basis for public health programs and vaccine design.

DOI: 10.1002/jmv.24400                              15-10-2015

Genotypic anomaly in Ebola virus strains circulating in magazine wharf area, Freetown, Sierra Leone, 2015 
Smits et al. 2015 

The Magazine Wharf area, Freetown, Sierra Leone, was a focus of ongoing Ebola virus transmission from late June 2015. Viral genomes linked to this area contain a series of 13 T to C substitutions in a 150 base pair intergenic region downstream of viral protein 40 open reading frame, similar to the Ebolavirus/H.sapienswt/ SLE/2014/Makona-J0169 strain (J0169) detected in the same town in November 2014. This suggests that recently circulating viruses from Freetown descend from a J0169-like virus. 

DOI:                08-10-2015

Recovering full-length viral genomes from metagenomes 
Smits et al. 2-2015

Infectious disease metagenomics is driven by the question: “what is causing the disease?” in contrast to classical metagenome studies which are guided by “what is out there?” In case of a novel virus, a first step to eventually establishing etiology can be to recover a full-length viral genome from a metagenomic sample. However, retrieval of a full-length genome of a divergent virus is technically challenging and can be time-consuming and costly. Here we discuss different assembly and fragment linkage strategies such as iterative assembly, motif searches, k-mer frequency profiling, coverage profile binning, and other strategies used to recover genomes of potential viral pathogens in a timely and cost-effective manner.

DOI: 10.3389/fmicb.2015.01069                   01-10-2015

Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management
Woolhouse et al. 2015

The current Ebola virus disease outbreak in West Africa has revealed serious shortcomings in national and international capacity to detect, monitor, and respond to infectious disease outbreaks as they occur. Recent advances in diagnostics, risk mapping, mathematical modeling, pathogen genome sequencing, phylogenetics, and phylogeography have the potential to improve substantially the quantity and quality of information available to guide the public health response to outbreaks of all kinds.

DOI:  10.1126/scitranslmed.aab0191            30-09-2015

Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance
Petersen et al. 2015

Human populations worldwide are increasingly confronted with infectious diseases and antimicrobial resistance spreading faster and appearing more frequently. Knowledge regarding their occurrence and worldwide transmission is important to control outbreaks and prevent epidemics. Here, we performed shotgun sequencing of toilet waste from 18 international airplanes arriving in Copenhagen, Denmark, from nine cities in three world regions.

DOI:  10.1038/srep11444                             10-07-2015

Emergence of a novel GII.17 norovirus – End of the GII.4 era? 
de Graaf et al. 2015

In the winter of 2014/15 a novel GII.P17-GII.17 norovirus strain (GII.17 Kawasaki 2014) emerged, as a major cause of gastroenteritis outbreaks in China and Japan. Since their emergence these novel GII.P17-GII.17 viruses have replaced the previously dominant GII.4 genotype Sydney 2012 variant in some areas in Asia but were only detected in a limited number of cases on other continents. This perspective provides an overview of the available information on GII.17 viruses in order to gain insight in the viral and host characteristics of this norovirus genotype.             02-07-2015

Detection of Circovirus in Foxes with Meningoencephalitis, United Kingdom, 2009–2013 
Bexton et al. 2015

A fox circovirus was identified in serum samples from foxes with unexplained neurologic signs by using viral metagenomics. Fox circovirus nucleic acid was localized in histological lesions of the cerebrum by in situ hybridization. Viruses from the family Circoviridae may have neurologic tropism more commonly than previously anticipated. 

DOI:                  01-07-2015

Complete Genome Sequences of Field Isolates of Mycobacterium bovis and Mycobacterium caprae 
de la Fuente et al. 2015a

Here we report the complete genome sequences of field isolates of Mycobacterium bovis and the related mycobacterial species, Mycobacterium caprae. The genomes of three M. bovis (MB1, MB3, MB4) and one M. caprae (MB2) field isolates with different virulence, prevalence, and host distribution phenotypes were sequenced.

DOI: 10.1128/genomeA.00247-15                 25-06-2015

Low Virulence and Lack of Airborne Transmission of the Dutch Highly Pathogenic Avian Influenza Virus H5N8 in Ferrets 
Richard et al. 2015

Highly pathogenic avian influenza (HPAI) H5N8 viruses that emerged in poultry in East Asia spread to Europe and North America by late 2014. Here we show that the European HPAI H5N8 viruses differ from the Korean and Japanese HPAI H5N8 viruses by several amino acids and that a Dutch HPAI H5N8 virus had low virulence and was not transmitted via the airborne route in ferrets. The virus did not cross-react with sera raised against pre-pandemic H5 vaccine strains. This data is useful for public health risk assessments.

DOI: 10.1371/journal.pone.0129827              19-06-2015

Complete Genome Sequence of a Porcine Epidemic Diarrhea S Gene Indel Strain Isolated in France in December 2014
Grassland et al. 2015

We report the first and only case of a porcine epidemic diarrhea (PED) outbreak occurring in December 2014 in northern France, and we show using the full-length genome sequence of the French PED virus (PEDV) isolate that it was a PEDV indel strain close to German PEDV strains recently isolated.

DOI: 10.1128/genomeA.00535-15                 04-06-2015

Influenza A(H5N8) Virus Similar to Strain in Korea Causing Highly Pathogenic Avian Influenza in Germany
Harder et al. 2015

Highly pathogenic avian influenza (H5N8) virus, like the recently described H5N8 strain from Korea, was detected in November 2014 in farmed turkeys and in a healthy common teal (Anas crecca) in northeastern Germany. Infected wild birds possibly introduced this virus.

DOI:                  01-05-2015

Wild bird surveillance around outbreaks of highly pathogenic avian influenza A(H5N8) virus in the Netherlands, 2014, within the context of global flyways
Verhagen et al. 2015

Highly pathogenic avian influenza (HPAI) A(H5N8) viruses that emerged in poultry in east Asia since 2010 spread to Europe and North America by late 2014. Despite detections in migrating birds, the role of free-living wild birds in the global dispersal of H5N8 virus is unclear. Here, wild bird sampling activities in response to the H5N8 virus outbreaks in poultry in the Netherlands are summarised along with a review on ring recoveries. 

DOI:                 26-03-2015

One health, multiple challenges: The inter-species transmission of influenza A virus
Short et al. 2015

Influenza A viruses are amongst the most challenging viruses that threaten both human and animal health. Influenza
A viruses are unique in many ways. Firstly, they are unique in the diversity of host species that they infect.
This includes waterfowl (the original reservoir), terrestrial and aquatic poultry, swine, humans, horses, dog, cats,
whales, seals and several other mammalian species. Secondly, they are unique in their capacity to evolve and
adapt, following crossing the species barrier, in order to replicate and spread to other individuals within the
new species. Finally, they are unique in the frequency of inter-species transmission events that occur. Indeed,
the consequences of novel influenza virus strain in an immunologically naïve population can be devastating.

DOI: 10.1016/j.onehlt.2015.03.001          26-03-2015
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