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Title: Whole genome sequence analysis indicates recent diversification of mammal-associated Campylobacter fetus and implicates a genetic factor associated with H2S production

Author
item VAN DER GRAFF, LINDA - Utrecht University
item DUIM, BIRGITTA - Utrecht University
item Miller, William - Bill
item FORBES, KENNETH - University Of Aberdeen
item WAGENAAR, JAAP - Utrecht University
item ZOMER, ALDERT - Utrecht University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/27/2016
Publication Date: 9/9/2016
Citation: Van der Graff, L., Duim, B., Miller, W.G., Forbes, K.J., Wagenaar, J.A., Zomer, A. 2016. Whole genome sequence analysis indicates recent diversification of mammal-associated Campylobacter fetus and implicates a genetic factor associated with H2S production. BMC Genomics. 17:713.

Interpretive Summary: The food-borne pathogen Campylobacter is a natural contaminant of most birds and livestock. Campylobacter fetus strains are associated normally with livestock disease and are one of the leading causes of abortions in cattle and sheep. Campylobacter fetus currently contains three defined subspecies: C. fetus subsp. fetus, C. fetus subsp. venerealis and C. fetus subsp. testudinum. These subspecies are distinguished by their host range and pathogenicity: C. f. fetus is isolated from different animals and occasionally food, C. f. venerealis is restricted to cattle and is a leading cause of abortions in cattle, and C. f. testudinum is isolated from reptiles and occasionally from human systemic infections. Although C. f. venerealis is a much more severe and agriculturally-relevant pathogen, the differences between these strains and the related C. fetus subsp. fetus are subtle and the tests that distinguish the two are often misinterpreted, leading to false positives or negatives. Also, although it is unclear if C. fetus subsp. fetus and C. fetus subsp. venerealis are in fact different subspecies, these labels still have important epidemiological and/or regulatory implications. This study indicates that C. fetus subsp. venerealis is a recent evolutionary branch of C. fetus, and that taxonomic distinctions rely apparently on unstable genomic markers, further complicating subspecies differentiation.

Technical Abstract: Campylobacter fetus can cause disease in both humans and animals. C. fetus has been divided into three subspecies: C. fetus subsp. fetus (Cff), C. fetus subsp. venerealis (Cfv) and C. fetus subsp. testudinum. Subspecies identification of C. fetus strains is crucial in the control of Bovine Genital Campylobacteriosis (BGC), a syndrome associated with Cfv. In this study, we describe the genome wide Single Nucleotide Polymorphism (SNP) analysis of both Cff and Cfv strains, which divided the strains into five different clades. Reconstruction of the phylogeny based on SNPs in the core genome showed that the Cfv clade and a Cff clade evolved relatively recently from a single Cff ancestor and that the genomes in the Cfv clade are under more diversifying selection than the Cff clades. Furthermore, we showed that H2S production, which separates Cfv from Cfv biovar intermedius strains, is tightly linked to the presence of two cysteine transporters. Phylogenetic reconstruction showed that deletion of cysteine transporter genes has occurred multiple times as independent events, suggesting that these genes are sensitive to deletion events. The presence of multiple C. fetus clades and instability of the H2S biochemical marker suggest closer evaluation of the current subspecies differentiation, considering that this differentiation is still applied in BGC control programs.