Source attribution of Campylobacter jejuni shows variable importance of chicken and ruminants reservoirs in non-invasive and invasive French clinical isolates

• Published in: Scientific reports 2019-05, Vol.9 (1), p.8098, Article 8098
• Main Authors: Berthenet, Elvire, Thépault, Amandine, Chemaly, Marianne, Rivoal, Katell, Ducournau, Astrid, Buissonnière, Alice, Bénéjat, Lucie, Bessède, Emilie, Mégraud, Francis, Sheppard, Samuel K., Lehours, Philippe
• Format: Article
• Language: English
• Subjects: 45/23; 631/208/212/748; 631/326/2565/107; Animals; Bacterial Typing Techniques; Campylobacter; Campylobacter Infections - epidemiology; Campylobacter Infections - microbiology; Campylobacter jejuni; Campylobacter jejuni - genetics; Campylobacter jejuni - isolation & purification; Chickens; Chickens - microbiology; Clinical isolates; Datasets as Topic; Disease Reservoirs - microbiology; DNA, Bacterial - genetics; DNA, Bacterial - isolation & purification; Environmental DNA - genetics; Environmental DNA - isolation & purification; Epidemiological Monitoring - veterinary; Epidemiology; France - epidemiology; Gastroenteritis; Gastroenteritis - epidemiology; Gastroenteritis - microbiology; Genetic markers; Genetic Markers - genetics; Genome, Bacterial - genetics; Genomes; Humanities and Social Sciences; Humans; Infections; Life Sciences; Microbiota; Molecular Epidemiology; multidisciplinary; Multilocus Sequence Typing; Pathogens; Ruminants - microbiology; Science; Science (multidisciplinary); Strains (organisms); Whole Genome Sequencing
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-019-44454-2

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.