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.
Highlights
Geographical structure is well documented in bacteria and analysing genetic variation among isolates can provide information about the global spread of important pathogens
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
Sequence-based analyses have shown that populations of the main human disease-causing Campylobacter species, C. jejuni and C. coli, are highly structured into clusters of related lineages, which can be identified by MLST as clonal complexes (CC’s)
Summary
Geographical structure is well documented in bacteria and analysing genetic variation among isolates can provide information about the global spread of important pathogens. International trade, in agricultural animals including chicken and poultry products, provides a vehicle for global spread In this case, local phylogeographic signals can be weakened by the rapid movement of lineages around the world, and by genomic changes that occur within the reservoir host. In C. jejuni, hostassociated clonal complexes can be identified based upon the frequency with which particular genotypes are isolated from different hosts (Sheppard et al, 2011, Sheppard et al, 2014) Many of these lineages are globally distributed (Sheppard et al, 2010a) but despite this strong host signal, there is evidence for phylogeographic structuring and the proliferation of distinct lineages in different countries (McTavish et al, 2008, Asakura et al, 2012)
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