Phylogenomic Analysis of Reveals a Clonal Structure of Insertion Element IS Positive Genomes.

Subspecies of the species are associated with specific host niches including mammals and reptiles. subsp. is a zoonotic pathogen infecting humans. Infections can vary from an acute intestinal illness to severe systemic infections, with sheep and cattle as major reservoirs. In contrast, subsp. causes bovine genital campylobacteriosis, which leads to abortion in cattle and a high economic burden for the farmers. Therefore, high-quality molecular subtyping is indispensable for interventional epidemiology. We used whole-genome sequencing (WGS) data of 283 strains from 18 countries and compared several methods for subtyping, including WGS, multilocus sequence typing, PCR assays, and the presence of the insertion element IS. We identified a highly clonal clade (designated as clade 1) that harbors the insertion sequence IS. The presence of this insertion sequence is an essential diagnostic tool for the identification of the subspecies subsp. , serving as a target for several PCR assays. However, we have found a high sequence variability for the IS besides the presence of IS-paralogues in certain other genomes ( = 7) which may cause incorrect diagnostic results. Clade 1 seems to be the cattle-specific clade of this species. We propose that only this clade might be designated as subsp. as it harbors the IS marker sequence, which is a major target for molecular methods currently used for subspecies identification. Fostering this proposal, we defined eleven stable nucleotide markers specific for this clade. Additionally, we developed a bioinformatics toolbox for the fast identification of this clade based on WGS data. In conclusion, our results demonstrate that WGS can be used for subtyping overcoming limitations of current PCR and MLST protocols.