Thomson Project – High-throughput mutagenesis of diarrhoeal pathogens to understand human colonisation and environmental persistence
Supervisor: Nicholas Thomson
Diarrhoeal disease is ranked as the fourth most important cause of death worldwide and the second cause of years of productive life lost due to premature mortality or disability (160 million cases and 750,000 fatalities in the under-fives alone). A small number of bacterial pathogens, including Vibrio cholerae, Shigella spp, enterotoxigenic Escherichia coli, Salmonella spp. and Campylobacter spp., account for a significant percentage of all diarrhoeal diseases in these countries. Cholera alone accounts for 3-5 million cases of diarrhoea and 120,000 fatalities per annum. We have shown in several global phylogeographic surveys1-6 how diarrhoeal diseases are spreading globally. It’s clear from these data that functions important in both the human and the environmental phase of their transmission cycle and ecology are critical for their sustained transmission. We propose to use high-throughput mutagenesis to identify genes associated with colonisation and survival within a human infection model system, as well as comparing the differing ability of successful epidemic lineages, of key enteric pathogens, to survive and persist in the environment or the contaminated environment.
TraDIS offers enormous potential to combine high-throughput genomics with functional screening. In essence it assay the whole genome for genes linked to a range of phenotypes important for disease, colonistation or survival: either in a host or in the environment. We will prepare TraDIS libraries from isolates selected to represent the full diversity of their species, from those isolates that have been clinically successful globally to those linked only to sporadic disease localised disease. The ability to select isolates across the species to assay in this way will allow us to chart the evolutionary changes that define the emergence of these modern successful lineages, more specifically for diarrhoeal pathogens to define the boundaries of human and environmental adaptation.
1. Ankur Mutreja*, Dong Wook Kim*, Nicholas Thomson*, Thomas R Connor, Je Hee Lee, et al., Gordon Dougan (2011) Evidence for multiple global transmission events within the seventh cholera pandemic. Nature. 24th August 2011. PMID21866102 PMC3736323
2. François-Xavier Weill, Daryl Domman, Elisabeth Njamkepo, Chery Tarr, Jean Rauzier, et al., Nicholas R. Thomson. Genomic history of the seventh pandemic of cholera in Africa. Science. 2017 Nov 10;358(6364):785-789. doi: 10.1126/science.aad5901. PMID:29123067.
3. Daryl Domman, Marie-Laure Quilici, Matthew J. Dorman, Elisabeth Njamkepo, Ankur Mutreja, et al., Nicholas R. Thomson. Integrated view of Vibrio cholerae in the Americas. Science. 2017 Nov 10;358(6364):789-793. doi: 10.1126/science.aao2136. PMID: 29123068.
4. Holt KE, Thieu Nga TV, Thanh DP, Vinh H, Kim DW, Vu Tra MP, Campbell JI, Hoang NV, Vinh NT, Minh PV, et al., Parkhill J, Dougan G, Thomson NR, Baker S. Tracking the establishment of local endemic populations of an emergent enteric pathogen Proc Natl Acad Sci U S A. 2013 Oct 22;110(43):175227.
5. Kathryn E. Holt, Stephen Baker, François-Xavier Weill, Edward C. Holmes, Andrew Kitchen, Jun Yu, Vartul Sangal, Derek J. Brown, et al., Nicholas R. Thomson (2012) Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nature Genetics. 2012 Sep; 44(9):1056-9.
6. Gemma C. Langridge, Minh-Duy Phan, Daniel J. Turner, Timothy T. Perkins, Leopold Parts, et al., A. Keith Turner. (2009) Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res. 2009 Dec;19(12):2308-16.