Inconsistency of Phenotypic and Genomic Characteristics of Campylobacter fetus Subspecies Requires Reevaluation of Current Diagnostics

Abstract

e 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 H 2 S 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.

Chicken, beams, and Campylobacter: rapid differentiation of foodborne bacteria via vibrational spectroscopy and MALDI-mass spectrometry

“…92,93 There have also been several attempts to develop molecular assays ( predominantly PCR-based) for routine diagnostics, but most have been deemed unreliable upon further scrutiny. 94,95 It is perhaps worth noting that although the classification results achieved from all three analytical techniques were in general agreement, the results obtained from PC-DFA of the MALDI-TOF-MS and FT-IR spectral data, not only allowed for the differentiation of the Campylobacter spp., but they also provided the clear separation of C. fetus subsp. fetus from C. fetus subsp.…”

Bovine genital campylobacteriosis: isolation, identification and virulence profiling of Campylobacter fetus subsp. venerealis in a small animal model

“…venerealis are apparent in the literature, they are not routinely used for the diagnosis of BGC independently, but rather complimentarily or as a confirmatory test on culture (OIE 2012). Recent studies have demonstrated an ongoing lack of consistency between phenotypic and molecular characterisation, identifying the need for more definitive biochemical testing methodologies (van der Graaf-van Bloois, Miller et al 2014). …”

“…Hydrogen sulphide production causes a colour change on lead acetate paper in the presence on cysteine metabolism which is subjective in interpretation (Veron and Chatelain 1973). Current comparative research into phenotypic characterisation with molecular identification has shown that culture diagnosis is still inadequate compared to genomic identification and improvements are clearly required to continue its use as the gold standard (van der Graaf-van Bloois, Miller et al 2014). …”

Complete Genome Sequence of Type Strain Campylobacter fetus subsp. fetus ATCC 27374

“…fetus (4). The use of virulence genes to differentiate the C. fetus subspecies has been proposed (4–6); however, the small number of C. fetus subsp.…”

“…fetus (4). The use of virulence genes to differentiate the C. fetus subspecies has been proposed (4–6); however, the small number of C. fetus subsp. fetus genomes available for comparison precludes the identification of molecular targets with diagnosis potential and a full assessment of virulence factors that determine the specificity of infection.…”