Niche segregation and genetic structure of Campylobacter jejuni populations from wild and agricultural host species

Abstract

Bacterial populations can display high levels of genetic structuring but the forces that influence this are incompletely understood. Here, by combining modelling approaches with multilocus sequence data for the zoonotic pathogen Campylobacter, we investigated how ecological factors such as niche (host) separation relate to population structure. We analysed seven housekeeping genes from published C. jejuni and C. coli isolate collections from a range of food and wild animal sources as well as abiotic environments. By reconstructing genetic structure and the patterns of ancestry, we quantified C. jejuni host association, inferred ancestral populations, investigated genetic admixture in different hosts and determined the host origin of recombinant C. jejuni alleles found in hybrid C. coli lineages. Phylogenetically distinct C. jejuni lineages were associated with phylogenetically distinct wild birds. However, in the farm environment, phylogenetically distant host animals shared several C. jejuni lineages that could not be segregated according to host origin using these analyses. Furthermore, of the introgressed C. jejuni alleles found in C. coli lineages, 73% were attributed to genotypes associated with food animals. Our results are consistent with an evolutionary scenario where distinct Campylobacter lineages are associated with different host species but the ecological factors that maintain this are different in domestic animals such that phylogenetically distant animals can harbour closely related strains.

Real-Time Genomic Epidemiological Evaluation of Human Campylobacter Isolates by Use of Whole-Genome Multilocus Sequence Typing

“…The analysis of the 52 rMLST (19) loci confirmed that MLST clonal complexes were genealogically coherent and it provided further information in two respects, (i) improved resolution within clonal complexes, enabling resolution of groups with greater discrimination than achieved with MLST, and (ii) information on the relationships among a number of clonal complexes, for example, the ST-21, ST-48, and ST-206 clonal complexes. The latter clonal complexes typically are isolated from livestock as well as from human patients and include Campylobacter strains that are adapted to the agricultural environment (29) (Fig. 2).…”

Genome-wide association study identifies vitamin B 5 biosynthesis as a host specificity factor in Campylobacter

“…Among wild birds, specific bird species most often harbor their own Campylobacter lineages (8,9). However, in agricultural animals, although there are host-associated lineages that are largely restricted to chickens or to ruminants, some of the most abundant lineages are found at high frequencies in chickens, cattle, and humans with food poisoning (8). This multihost lifestyle is curious because of the challenges of colonizing organisms with such distinct gastrointestinal tracts, diets, immune systems, and body temperatures.…”

“…The characterization of large numbers of C. jejuni and C. coli isolates from diverse sources and locations by multilocus sequence typing (MLST) has shown that there is genetic differentiation among sequence types (STs) associated with different hosts (8). Among wild birds, specific bird species most often harbor their own Campylobacter lineages (8,9).…”

“…The characterization of large numbers of C. jejuni and C. coli isolates from diverse sources and locations by multilocus sequence typing (MLST) has shown that there is genetic differentiation among sequence types (STs) associated with different hosts (8). Among wild birds, specific bird species most often harbor their own Campylobacter lineages (8,9). However, in agricultural animals, although there are host-associated lineages that are largely restricted to chickens or to ruminants, some of the most abundant lineages are found at high frequencies in chickens, cattle, and humans with food poisoning (8).…”

Scientific Opinion on the evaluation of molecular typing methods for major food‐borne microbiological hazards and their use for attribution modelling, outbreak investigation and scanning surveillance: Part 1 (evaluation of methods and applications)

“…Introgression of C. jejuni genes appears to be limited to clade 1, which comprises organisms mostly associated with poultry and human disease. Clades 2 and 3 are mostly found in wild animals and environmental sources, are not introgressed with C. jejuni genes, and are rarely associated with human disease (Sheppard et al, 2008;Sheppard et al, 2011a;Sheppard et al, 2013a). By contrast, C. jejuni comprises a large number of genetic types, with widespread evidence for recombination throughout the species.…”