Isolation, whole genome sequencing, and comparative genomics of Corynebacterium pseudotuberculosis to identify biovar ovis specific biomarkers.

BACKGROUND: Corynebacterium pseudotuberculosis, a gram-positive bacterium, causes caseous lymphadenitis in small ruminants (biovar ovis) and ulcerative lymphangitis in equines (biovar equi). Growing reports of C. pseudotuberculosis from various animals, including cattle, buffalo, pigs, deer, Iberian ibex, camel, llama, and alpaca. Since the host range is expanding, there is a need for biovar-specific identification of the organism. Hence, the present study was focused towards comparative genomics of C. pseudotuberculosis to identify biovar ovis specific markers. METHODS AND RESULTS: Corynebacterium pseudotuberculosis TN_CUL_1 was isolated from suspected cases of caseous lymphadenitis from small ruminants in an organized farm in Tamil Nadu, India. The C. pseudotuberculosis TN_CUL_1 strain was whole genome sequenced and was used for comparative genome analysis along with 157 C. pseudotuberculosis strains available in the NCBI genome database. Whole genome phylogeny showed a clear distinction between biovars equi and ovis, and the TN_CUL_1 strain was clustering in biovar ovis. Virulence gene pld was predicted in all the strains, while 9 strains isolated from buffalo had the tox gene coding for diphtheria toxin. Pangenome analysis indicated that the genome structure of C. pseudotuberculosis to be closed in nature as the pangenome curve attained a plateau. Biovar-specific genes like narT, narK, narY, narG, narX, moaC, moaA, mobA, and moeZ were predicted only in biovar equi, while yhaP was predicted only in biovar ovis strains. Further BLAST analysis indicated that the yhap gene coding for the ABC superfamily ATP binding cassette transporter binding protein was found only in biovar ovis strains. CONCLUSIONS: The study concludes that the yhap gene can be used as a biovar ovis-specific molecular marker.