Gene-By-Gene Comparison of Campylobacter jejuni Genomes to Identify Host Segregating Epidemiological Markers for Source Attribution

Campylobacter is a leading cause of bacterial gastroenteritis, worldwide, and is part of the commensal microbiota of numerous host species, which constitute potential sources of human infection. Molecular genotyping approaches, especially multi-locus sequence typing (MLST), have been used to identify the origin of human campylobacteriosis based on allelic variation at seven MLST loci, among isolates from animal reservoirs and human infections. The increasing availability of bacterial genomes provides data on allelic variation at loci across the genome, providing potential to improve the discriminatory power of data for source attribution. Here, we present a source attribution approach based on the identification of novel epidemiological markers among a reference pan-genome list of 1,810 genes identified using a gene-by-gene comparison of 884 genomes of Campylobacter jejuni isolates from animal reservoirs, the environment, and clinical cases. Fifteen loci were selected as host-segregating markers and used to attribute the source of French and UK, clinical C. jejuni isolates. Analyses performed on UK clinical isolates emphasized the importance of the chicken reservoir as an infection source in the UK; while in France, chicken and ruminant reservoirs appeared to be equally involved in clinical cases. The different proportions of French and UK clinical isolates attributed to each host reservoirs illustrate a potential role for local/national variations in C. jejuni transmission dynamics, indicating a benefit for further national-scale attribution modelling to account for differences in production, behaviour, and food consumption.