Local genes for local bacteria: Evidence of allopatry in the genomes of transatlantic Campylobacter populations |
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| Authors: | Ben Pascoe Guillaume Méric Koji Yahara Helen Wimalarathna Susan Murray Matthew D. Hitchings Emma L. Sproston Catherine D. Carrillo Eduardo N. Taboada Kerry K. Cooper Steven Huynh Alison J. Cody Keith A. Jolley Martin C. J. Maiden Noel D. McCarthy Xavier Didelot Craig T. Parker Samuel K. Sheppard |
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| Affiliation: | 1. The Milner Centre for Evolution, Department of Biology and Biochemistry, Bath University, Claverton Down, Bath, UK;2. MRC CLIMB Consortium, Bath, UK;3. Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan;4. Swansea University Medical School, Swansea University, Swansea, UK;5. Department of Zoology, University of Oxford, Oxford, UK;6. Bureau of Microbial Hazards, Health Canada, Ottawa, ON, Canada;7. Canadian Food Inspection Agency, Ottawa, ON, Canada;8. National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, AB, Canada;9. Department of Biology, California State University Northridge, Northridge, CA, USA;10. Produce Safety and Microbiology Research Unit, Agricultural Research Service, US Department of Agriculture, Albany, CA, USA;11. NIHR Health Protection Research Unit in Gastrointestinal Infections, Oxford, UK;12. University of Warwick, Coventry, UK;13. Department of Infectious Disease Epidemiology, Imperial College London, London, UK |
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| Abstract: | The genetic structure of bacterial populations can be related to geographical locations of isolation. In some species, there is a strong correlation between geographical distance and genetic distance, which can be caused by different evolutionary mechanisms. Patterns of ancient admixture in Helicobacter pylori can be reconstructed in concordance with past human migration, whereas in Mycobacterium tuberculosis it is the lack of recombination that causes allopatric clusters. In Campylobacter, analyses of genomic data and molecular typing have been successful in determining the reservoir host species, but not geographical origin. We investigated biogeographical variation in highly recombining genes to determine the extent of clustering between genomes from geographically distinct Campylobacter populations. Whole‐genome sequences from 294 Campylobacter isolates from North America and the UK were analysed. Isolates from within the same country shared more recently recombined DNA than isolates from different countries. Using 15 UK/American closely matched pairs of isolates that shared ancestors, we identify regions that have frequently and recently recombined to test their correlation with geographical origin. The seven genes that demonstrated the greatest clustering by geography were used in an attribution model to infer geographical origin which was tested using a further 383 UK clinical isolates to detect signatures of recent foreign travel. Patient records indicated that in 46 cases, travel abroad had occurred <2 weeks prior to sampling, and genomic analysis identified that 34 (74%) of these isolates were of a non‐UK origin. Identification of biogeographical markers in Campylobacter genomes will contribute to improved source attribution of clinical Campylobacter infection and inform intervention strategies to reduce campylobacteriosis. |
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| Keywords: | allopatry
Campylobacter
genomics phylogeny recombination source attribution |
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