Abstract
Campylobacter jejuni is the most common cause of bacterial gastroenteritis worldwide. Mainly isolated from stool samples, C. jejuni can also become invasive. C. jejuni belongs to the commensal microbiota of a number of hosts, and infection by this bacterium can sometimes be traced back to exposure to a specific source. Here we genome sequenced 200 clinical isolates (2010–2016) and analyzed them with 701 isolate genomes from human infection, chicken, ruminants and the environment to examine the relative contribution of different reservoirs to non-invasive and invasive infection in France. Host-segregating genetic markers that can discriminate C. jejuni source were used with STRUCTURE software to probabilistically attribute the source of clinical strains. A self-attribution correction step, based upon the accuracy of source apportionment within each potential reservoir, improved attribution accuracy of clinical strains and suggested an important role for ruminant reservoirs in non-invasive infection and a potentially increased contribution of chicken as a source of invasive isolates. Structured sampling of Campylobacter in the clinic and from potential reservoirs provided evidence for variation in the contribution of different infection sources over time and an important role for non-poultry reservoirs in France. This provides a basis for ongoing genomic epidemiology surveillance and targeted interventions.
Highlights
Campylobacter jejuni is one of the most common bacterial enteropathogens in both high and low income countries[1,2]
An applied advantage of understanding the genomics of lineage-host association is that the origin of isolates from human infection can potentially be determined by comparison to genome sequenced isolates from putative reservoir sources, and quantitative probabilistic models have been developed for source attribution of clinical strains[23]
The continued importance of campylobacteriosis as a major preventable cause of gastroenteritis means that effective monitoring is a high priority in many countries
Summary
Campylobacter jejuni is one of the most common bacterial enteropathogens in both high and low income countries[1,2]. These ecological generalist strains cannot be assigned to one source as recent host transitions erode the signal of host association[26,27] While this remains a challenging, decreasing costs and increasing availability of large WGS datasets[28] is improving understanding of the genes and genetic elements that promote C. jejuni host adaptation[29,30] and survival[31,32] in particular niches. These elements represent candidate markers for source attribution studies and recent work analyzing the pan-genome of 4 C. jejuni reference strains in 884 genomes identified 15 host-segregating markers that were used for source attribution of specialist and generalist genotypes[33]. This clonal complex is less common in some other surveyed countries, including France[34], and it is unclear if particular lineages are over represented in invasive disease
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
