Cholera genomics

Welcome to our free online course on Vibrio cholerae genomics!

The aim of this course is to teach you about V. cholerae genomics, so that you can use genomics to perform analyses relevant to cholera public health, and extract meaningful insights from V. cholerae genomic data.

This course includes all you want to know about sequencing and analyses of V. cholerae genomes, including advanced bioinformatics topics relevant to V. cholerae genomics (e.g. genome assembly, phylogenetics, predicting antimicrobial resistance, etc.).

The course includes both theoretical material and bioinformatics teachings.

The course will teach how to carry out bioinformatics analyses using Vibriowatch, as well as other bioinformatics tools. If you already have cholera genomic data to analyse, and want to get going quickly, you may also be interested in our Vibriowatch tutorial.

Theoretical material in this course on topics relevant to V. cholerae genomics includes:

• The disease cholera and its epidemiology.

• The species Vibrio cholerae, and its geographic distribution.

• The history of cholera, and the history of global spread of the current pandemic lineage of V. cholerae (the 7PET lineage).

• Suggested strategies for sample collection and sequencing of V. cholerae.

• Isolates, lineages and sublineages of V. cholerae, their geographic distribution and role in cholera and diarrhoeal illness.

• Principal features of the V. cholerae genome.

• Potentially misleading results from surveilling presence/absence of marker genes and molecular/biochemical tests alone, in the absence of whole-genome sequencing data.

• Sublineages of 7PET, their geographic distribution, spread, and genomic/phenotypic features, and emergence of novel genetic variants in 7PET.

• Pathogenesis of cholera and genetic determinants of virulence, including new variants of concern and variants of interest.

• Cholera treatment and use of antimicrobials.

• Spread of antimicrobial resistance within key lineages of V. cholerae (e.g. within the 7PET lineage), as well as within V. cholerae, and also between other species of bacteria and V. cholerae.

• How genomics can play a role in public health decisions for cholera, and the potential of genomics as a platform to further refine cholera control strategies (e.g. vaccination strategies).

In each topic, learning will be enriched by examples of V. cholerae genome analysis, and practical bioinformatics exercises for learners, with an emphasis on analysing cholera genome data for public health.

Vibriowatch

In later modules of this course, you will learn how to carry out bioinformatics analyses using Vibriowatch, as well as other bioinformatics tools. If you already have cholera genomic data to analyse, and want to get going quickly, you may also be interested in our Vibriowatch tutorial.

Contact

I will be grateful if you will send me (Avril Coghlan) corrections or suggestions for improvements to my email address alc@sanger.ac.uk

Acknowledgements

Contributors to this course: Avril Coghlan, Matt Dorman, Ismail Bashir, Anne Bishop, Amber Barton, Stephanie McGimpsey, Jolynne Mokaya, Nisha Singh, Nick Thomson.

Contents

• Module 1.1: Cholera: Disease and Epidemiology
  • Introduction to Module 1.1
  • Acute Watery Diarrhoea, the Disease Cholera and its Epidemiology
  • Epidemic and Non-epidemic Lineages of Vibrio cholerae
  • The Geographic Distribution of V. cholerae and the Ecological Niche of Non-epidemic Lineages of V. cholerae
  • Diarrhoeal Illness Caused by Epidemic and Non-epidemic Lineages of V. cholerae
  • Cholera Vaccines
  • Brief Summary
  • Vibriowatch
  • Contact
  • Acknowledgements
• Module 1.2: Classification of Vibrio cholerae
  • Introduction to Module 1.2
  • Serogroups of V. cholerae
  • The Classical Biotype and the El Tor Biotype
  • Tracing the Evolutionary History of V. cholerae Lineages Using Whole Genome Sequencing (WGS) Data
  • Why is lineage more important than serogroup or biotype or production of cholera toxin, for epidemic potential?
  • The Revised GTFCC Definitions of Cholera Cases and Cholera-free Country Statuses
  • Brief Summary
  • Vibriowatch
  • Contact
  • Acknowledgements
• Module 1.3: The History of Cholera Pandemics and Cholera Spread
  • Introduction to Module 1.3
  • The History of Cholera: the Seven Historically Recorded Pandemics
  • John Snow and the 1854 Broad Street Cholera Outbreak
  • The History of 7PET’s Global Spread
  • Brief Summary
  • Vibriowatch
  • Contact
  • Acknowledgements
• Module 1.4: DNA, Genomes, Whole Genome Sequencing, Mutations, and Genome Evolution
  • Introduction to Module 1.4
  • The V. cholerae Genome and Whole-Genome Sequencing (WGS) of V. cholerae
  • Genes of V. cholerae
  • How Do Lineages Emerge at the Genetic Level?
  • Brief Summary
  • Vibriowatch
  • Contact
  • Acknowledgements
• Module 1: Glossary
  • Glossary of Key Terms for Module 1
  • Vibriowatch
  • Contact
  • Acknowledgements
• Module 1: Answers to Activity Questions
  • Answers to Questions in Module 1.1
  • Answers to Questions in Module 1.2
  • Answers to Questions in Module 1.3
  • Answers to Questions in Module 1.4
  • Vibriowatch
  • Contact
  • Acknowledgements
• Assemblies and assembly quality
  • Vibriowatch
• Vibrio cholerae lineage information
  • Vibriowatch
• Finding closely related isolates
  • Vibriowatch
• Predicting virulence genes, antimicrobial resistance genes, and plasmids
  • Vibriowatch