The field of monitoring and surveillance of pathogens, their characterization and subtyping as well as phylogeny and screening for antimicrobial resistance are highly relevant for Public Health and for professionals in the medical sectors. This also includes the veterinary field, the environment, pharmaceutical companies and private laboratories, especially those working with institutions or companies performing diagnostics, research or monitoring activities.
Whole genome sequencing of bacterial genomes - tools and applications
This online course includes video lectures about bacterial subtyping and applications of next generation technology to perform research and monitoring, and also demonstrations and guided exercises on the use of online tools.
The lectures provide a background for WGS analyses and present the Center for Genomic Epidemiology (CGE) tools which are available online and can be used widely and by non-bioinformaticians.
The lecturers in this course include both microbiologists and bioinformaticians and they are experienced in teaching E-learning courses. The lecturers themselves use the WGS technologies for both research and monitoring purposes and the bioinformaticians have been involved in building these tools and pipelines in addition to teaching common users in a very practical way.
The courses has the following videos:
Module 1
- General Principles of typing of bacteria
- Surveillance of Antimicrobial Resistance using whole genome sequencing
Module 2
- Application of Genomic tools- One technology takes it all
- Introduction to Next-Generation sequencing (NGS)
- De novo assembly- from raw reads to contigs: assembler tool description and application
Module 3
- Species identification: KmerFinder tool description and applications
- MLST Typing: MLST tool description and applications
- Resistance gene detection: Resfinder tool description and applications
Module 4
- Salmonella Serotype identification: SeqSero tool description and applications
- E. coli serotype identification: serotype finder tool description and applications
- Plasmid replicon identification and plasmid typing
Module 5
- Bacterial analysis pipeline- batch upload
- Phylogenetic relatedness: CSI Phylogeny tool description and applications
- Multipurpose detection of genetic markers- My Db finder tool description and applications