Speaker:  Professor Nick Thomson, Wellcome Trust Sanger Institute, will present seminar entitled: Demystifying cholera epidemiology using phylogenetic inference and next generation sequencing

Host: Ian Charles

Abstract
Cholera is thought by many to be a disease of the Victorian era. However, current reports from Yemen show that cholera continues to be a serious concern (one death per hour currently; >1 million cases annually; WHO statistics). Low-resolution tools and sparse sampling continue to confound our understanding of cholera transmission. We have applied high-resolution whole-genome approaches to study V. cholerae that represent every known significant cholera outbreak from across two continents, Latin America and Africa, over the last 50 years. In Africa we observe consistent and predictable patterns by which cholera spreads across the globe. In Latin America we provide phylogenetic clarity to what has been until now a confusing picture of pandemic disease. These studies explain how all significant reported cholera outbreaks within the seventh pandemic are related to one another. But more importantly that the current models of cholera do not accurately describe pandemic cholera or its transmission.

Biography
Historically Nick’s research has focused on pathogenic members of the Enterobacteriaceae including Salmonella, pathogenic E. coli, Shigella, Citrobacter, Yersinia and Proteus, although he has also studied the genetic makeup and diversity of non-enteric pathogens including Chlamydia. His work has progressed from generating reference genomes through to large-scale comparative phylogenomic projects, with his team now focusing largely on population-based studies including both national and international research projects. They have also focussed on defining the evolutionary signatures that mark long term evolution of whole Genera, in the case of Yersinia or lineages of Salmonella that have moved from being broad host range pathogens to becoming restricted to a particular host(s) or niche.

A strong theme in his work is the application of phylogeny to understand the contemporary or historical distribution of bacterial pathogens causing diarrheal disease or sexually transmitted pathogens, including Shigella sonnei (Nature Genetics, 2012) Shigella flexneri (eLife, 2015) and Vibrio cholerae (Nature, 2011), as well as antimicrobial resistance. In Salmonella we focused on the course of the epidemic of the zoonotic pathogen Salmonella Typhimurium DT104 in Scotland, isolated from both humans and farm animals over a 22-year period (Science, 2013).

Nick’s group has also developed different approaches to sequence high quality bacterial genomes directly from uncultured discarded clinical samples (Genome Res, 2013; Nature Protocols 2013) enabling his group to extend population based studies without the need for culture. This methodology has broad applications in clinical microbiology.

All staff from organisations on the Research Park are welcome to attend.