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Subspecies of the species  Campylobacter fetus  are associated with specific host niches including mammals and reptiles.  Campylobacter fetus  subsp.  fetus  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,  Campylobacter fetus  subsp.  venerealis  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  Campylobacter fetus  strains from 18 countries and compared several methods for  Campylobacter fetus  subtyping, including WGS, multilocus sequence typing, PCR assays, and the presence of the insertion element IS Cfe1 . We identified a highly clonal clade (designated as clade 1) that harbors the insertion sequence IS Cfe1 . The presence of this insertion sequence is an essential diagnostic tool for the identification of the subspecies  Campylobacter fetus  subsp.  venerealis , serving as a target for several PCR assays. However, we have found a high sequence variability for the IS Cfe1  besides the presence of IS Cfe1 -paralogues in certain other genomes ( n  = 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  Campylobacter fetus  subsp.  venerealis  as it harbors the IS Cfe1  marker sequence, which is a major target for molecular methods currently used for  Campylobacter fetus  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  Campylobacter fetus  subtyping overcoming limitations of current PCR and MLST protocols.

Phylogenomic Analysis of Campylobacter fetus Reveals a Clonal Structure of Insertion Element ISCfe1 Positive Genomes