Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations
- Published
- Accepted
- Subject Areas
- Biogeography, Bioinformatics, Genomics, Microbiology, Epidemiology
- Keywords
- Allopatry, Campylobacter, Genomics, Source attribution, Recombination, Phylogenetics
- Copyright
- © 2017 Pascoe et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2017. Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations. PeerJ Preprints 5:e2638v2 https://doi.org/10.7287/peerj.preprints.2638v2
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 less than two 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.
Author Comment
Original PeerJ preprint has been modified to incorporate changes suggested during review. Article published in Molecular Ecology: http://onlinelibrary.wiley.com/doi/10.1111/mec.14176/full
Supplemental Information
Table S1
List of isolates used, including details of genome accession numbers.
Table S2
List of biogeographical epidemiological markers, including lists of highly recombining genes as determined by pairwise analysis of nucleotide diversity (more than 2% diversity); and genes used to model biogeographical segregation in structure (orange). Genes with a role in fluoroquinolone resistance are highlighted in yellow.