Verdenskort - Updated 3. maj 2016

Global Sewage Surveillance Project

The project for global surveillance of infectious diseases and antimicrobial resistance from sewage has moved into the analytic phase, interpreting the sequencing and residue data of the collected 80 samples from 63 countries.

Please see the updates below.

With support from COMPARE and the World Health Organization, the global sewage surveillance project has moved into the analytic phase interpreting the results.

Update February 2017
A second phase of sampling for the Global Sewage Surveillance Project has now been opened with the addition of support funding from the Novo Nordisk Fund and continued support from the World Health Organization.

We wish to collect 2L of urban sewage four times in the study period, two times in 2017 and two times in 2018 from major cities around the world. The target is to enroll more than 100 countries and multiple cities within each country.

If you did not participate in the first phase of sampling and wish to join the Global Sewage Surveillance Project, please contact Rene Hendriksen (rshe@food.dtu.dk) for more information about the opportunities from participation.

Update December 2016

The National Food Institute, DTU (WHO Collaborating Centre and European Union Reference Laboratory for Antimicrobial Resistance in Foodborne Pathogens and Genomics) has spent the autumn 2016 interpreting the huge abundance of sequencing data generated. Antimicrobial resistance classes and genes have been identified for each of the samples. Various plots have been created to visually output the abundance profiles for each sample / country (read count matrixes). In conjunction with the identification of the antimicrobial resistance classes and genes, the epidemiological data captured through the survey have similarly undergone analysis categorizing the sample sites into groups.

National Institute for Public Health and the Environment, RIVM (WHO Collaborating Centre for Risk Assessment of Pathogens in Water and Food) has analyzed the samples for antimicrobial residues, which will be the proxy for inadequate global usage data.

Early in 2017, RIVM and DTU will jointly interpret all the data generated, the abundance of AMR genes, the residue data, the epidemiological data, and other health parameters to explain the findings.

Erasmus MC in the Netherlands is still working on sequencing the samples to identify viruses. We anticipate sharing the findings as soon as they become available.

Please contact Rene Hendriksen (rshe@food.dtu.dk) if you are interested to receive the read count abundances of identified resistance genes.

Preliminary results of identified antimicrobial resistance classes and genes for each of the samples.

Convex hulls 2 700

Ordination of Global Sewage resistomes. The read count matrix (genes by samples) was standardized using the Hellinger transformation. The Bray-Curtis dissimilarity indexes between all samples were calculated and principal coordinate analysis (PCoA) was used to project the data so that distances approximate inter-sample dissimilarities. Plotted samples are connected by convex hulls, highlighting geographical regions.

Box plot

Boxplots of Global Sewage resistance by drug class and region. The read count matrix (genes by samples) was adjusted for gene lengths and sample sequencing depths so that relative abundance (fragments per kilobase reference per million fragments, FPKM) was obtained. Gene abundances within the same drug class were summed and are shown here separated by geographical region.

Preliminary results of identified antimicrobial residues for each of the samples.

Overall concentrations

Results: Overall concentrations. This is a log-scale plot of antimicrobial residues. The highest concentrations are found often in open sewers.
Many compounds are not detected, such as beta lactams and cephalosporins, which are degraded before entering the sewers.

General Overview


A video on the project and the process involved is available for viewing.



Metagenomic sequencing of human sewage and quantification of antimicrobial resistance genes and residues combined with epidemiological data is a possible way to determine the occurrence and burden of resistance in defined healthy human populations.

Recent developments in high‐throughput sequencing offer the ability to rapidly identify nucleic acids from various organisms in clinical and environmental samples. Sewage systems are recognized as an important source of human pathogens, especially in crowded settings with poor infrastructure.

The project will serve as proof‐of‐concept for applying metagenomic approaches, which could initiate a global surveillance of human infectious diseases including antimicrobial resistance from sewage collected in major cities around the world to detect, control, prevent and predict human infectious diseases.

Along with The National Food Institute, DTU (WHO Collaborating Centre and European Union Reference Laboratory for Antimicrobial Resistance in Foodborne Pathogens), several other partners from COMPARE are involved in this joint study with WHO, including Erasmus MC, The Netherlands, and National Institute for Public Health and the Environment, RIVM (WHO Collaborating Centre for Risk Assessment of Pathogens in Water and Food).

Contact

Rene S. Hendriksen
Senior Reseacher
National Food Institute
+45 35 88 62 88
http://www.compare-europe.eu/Library/Global-Sewage-Surveillance-Project
22 NOVEMBER 2017