Isolation, identification and whole-genome analysis of Bordetella bronchiseptica FMDBb1 from forest musk deer (Moschus berezovskii)

Abstract:

[Background] Respiratory diseases are common in captive musk deer, some of which are caused by Bordetella bronchiseptica (Bb). However, the research on Bb from forest musk deer (FMD) is insufficient. [Objective] To identify a strain of Bb isolated from the nasal mucus of FMD, analyze its whole-genome sequence and lay a foundation for the prevention and control of related diseases in FMD. [Methods] The pathogen was purified by culture method and preliminarily identified based on colony morphology and biochemical properties. Then, drug sensitivity test and mouse pathogenicity test were carried out to analyze the drug resistance and virulence phenotype. Finally, the whole genome was sequenced. The genetic relationship among species was evaluated based on average nucleotide identity (ANI) at the whole genome level. Meanwhile, gene function annotation and phylogenetic analysis were conducted. [Results] The ANI comparison demonstrated that the pathogen belonged to the classical Bordetella subspecies. According to the colony morphology and biochemical properties, the pathogen was identified as Bb and named FMDBb1. The strain was resistant to lincomycin, rifampicin and most β-lactam antibiotics, with LD₅₀=8.55×10⁶ CFU. The whole genome of the strain was 5 133 936 bp, and gene function annotation showed that it had strong metabolic capacity. In the genome, 65 classical Bordetella virulence factors and the resistance genes targeting pulvomycin and rifampicin were identified. Meanwhile, 19 insertion sequences and 1 phage region were found as well. The strain showed the sequence type 33 and the clone complex 6. The phylogenetic tree constructed based on the housekeeping genes showed that FMDBb1 had the highest homology with KVNON-570 isolated from Korean shorthair cat. [Conclusion] The whole genome of Bb isolated from FMD was sequenced and analyzed, which provided valuable information for the prevention and control of the pathogen infection.