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Title: Inconsistency of phenotypic and genomic characteristics of Campylobacter fetus subspecies requires re-evaluation of current diagnostics

item VAN DER GRAAF, LINDA - Utrecht University
item Miller, William - Bill
item Yee, Emma
item RIJNSBURGER, MARTINE - Vrije University
item WAGENAAR, JAAP - Utrecht University
item DUIM, BIRGITTA - Utrecht University

Submitted to: Journal of Clinical Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/10/2014
Publication Date: 9/17/2014
Citation: Van Der Graaf, L., Miller, W.G., Yee, E., Rijnsburger, M., Wagenaar, J.A., Duim, B. 2014. Inconsistency of phenotypic and genomic characteristics of Campylobacter fetus subspecies requires re-evaluation of current diagnostics. Journal of Clinical Microbiology. 52(12):4183-4188.

Interpretive Summary: Campylobacter fetus is a member of a bacterial group that also contains the established pathogens Campylobacter jejuni and Helicobacter pylori. Campylobacter fetus is currently divided into two groups, Campylobacter fetus fetus and Campylobacter fetus venerealis. C. fetus fetus has been isolated from food animals and multiple food sources and has also been associated with human illness, while C. fetus venerealis is exclusively a veterinary pathogen. A subtype of C. fetus venerealis has been described and termed ‘biovar intermedius’. This subtype can colonize the intestines of cattle as well as the genital tracts. Currently, these subspecies are identified based on chemical tests (such as tolerance of the amino acid glycine). However, these tests are not always precise and conclusive. This study sequenced the chromosomes of 23 C. fetus strains. The proteins common to all 23 strains were identified and compared. They fell into two classes that correlated with the presence of the fetus fetus strains or the fetus venerealis strains. However, some strains typed previously as C. fetus fetus were identified here as C. fetus venerealis, indicating that the current identification methods are error-prone and that novel typing and identification methodology is needed for this agriculturally-relevant pathogen.

Technical Abstract: Classification of the Campylobacter fetus subspecies fetus and venerealis was first described in 1959 and was based on the source of isolation (intestinal vs genital) and the ability of the strains to proliferate in 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 are consistent with the phenotypic identification. In this study, we defined the core genome and accessory genes of C. fetus, based on the closed genomes of five C. fetus strains. Phylogenetic analysis using the core genomes of 23 C. fetus strains of both subspecies showed a division into two clusters. The phylogenetic core genome clusters were not consistent with the phenotypic classification of the C. fetus subspecies. However, they were consistent with the molecular characteristics of the strains, determined by multilocus sequence typing, sap-typing, and the presence/absence of insertion sequences and a type I restriction-modification system. The fact that three of the phenotypically-defined C. fetus subsp. fetus strains clustered with 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.