title: Inconsistency of phenotypic and genomic characteristics of Campylobacter fetus subspecies requires reevaluation of current diagnostics.
abstract: Classifications of the Campylobacter fetus subspecies fetus and venerealis were first described in 1959 and were based on the source of isolation (intestinal versus genital) and the ability of the strains to proliferate in the genital tract of cows. Two phenotypic assays (1% glycine tolerance and H2S production) were described to differentiate the subspecies. Multiple molecular assays have been applied to differentiate the C. fetus subspecies, but none of these tests is consistent with the phenotypic identification methods. In this study, we defined the core genome and accessory genes of C. fetus, which are based on the closed genomes of five C. fetus strains. Phylogenetic analysis of the core genomes of 23 C. fetus strains of the two subspecies showed a division into two clusters. The phylogenetic core genome clusters were not consistent with the phenotypic classifications of the C. fetus subspecies. However, they were consistent with the molecular characteristics of the strains, which were determined by multilocus sequence typing, sap typing, and the presence/absence of insertion sequences and a type I restriction modification system. The similarity of the genome characteristics of three of the phenotypically defined C. fetus subsp. fetus strains to C. fetus subsp. venerealis strains, when considering the core genome and accessory genes, requires a critical evaluation of the clinical relevance of C. fetus subspecies identification by phenotypic assays.
authors.affiliation: Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands WHO Collaborating Centre for Campylobacter and OIE Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands.
authors.forename: Linda
authors.initials: L
authors.lastname: van der Graaf-van Bloois
authors.affiliation: Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA.
authors.forename: William G
authors.initials: WG
authors.lastname: Miller
authors.affiliation: Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA.
authors.forename: Emma
authors.initials: E
authors.lastname: Yee
authors.affiliation: VU University Medical Center, Department of Medical Microbiology and Infection Control, Amsterdam, the Netherlands.
authors.forename: Martine
authors.initials: M
authors.lastname: Rijnsburger
authors.affiliation: Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands WHO Collaborating Centre for Campylobacter and OIE Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands Central Veterinary Institute of Wageningen UR, Lelystad, the Netherlands.
authors.forename: Jaap A
authors.initials: JA
authors.lastname: Wagenaar
authors.affiliation: Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands WHO Collaborating Centre for Campylobacter and OIE Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands b.duim@uu.nl.
authors.forename: Birgitta
authors.initials: B
authors.lastname: Duim
mesh_terms: D000818:Animals; D001431:Bacteriological Techniques / Q000379:methods*; D002169:Campylobacter Infections / Q000175:diagnosis / Q000662:veterinary*; D002168:Campylobacter fetus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification* / Q000502:physiology; D002417:Cattle; D002418:Cattle Diseases / Q000175:diagnosis* / Q000382:microbiology*; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D005838:Genotype; D058889:Molecular Typing; D010641:Phenotype; D010802:Phylogeny
chemical_list: D004269:DNA, Bacterial