Isolation, identification, and whole genome sequencing of Bacillus cereus SCBCM001 from forest musk deer (Moschus berezovskii)

Abstract:

[Background] Bacterial diseases are major factors limiting the large-scale cultivation of forest musk deer. Bacillus cereus has been detected in abscesses of forest musk deer. However, there are few studies about the B. cereus from forest musk deer. [Objective] We isolated, identified, and sequenced the whole genome of a suspected B. cereus strain from the liver of a dead forest musk deer, aiming to provide a foundation for the prevention and treatment of diseases cause by B. cereus in forest musk deer. [Methods] After strain purification, we conducted biochemical tests, drug sensitivity tests, and mouse pathogenicity tests on the pathogen. We then employed the third-generation sequencing to reveal its whole genome and phylogenetic relationship. Furthermore, gene function annotation and genetic evolution analysis were conducted. [Results] The average nucleotide identity (ANI) and phylogenetic tree suggested that the pathogen belonged to the B. cereus group, and the biochemical test results of the strain conformed to the general characteristics of B. cereus. The isolate was thus named SCBCM001. The strain showed the median lethal dose of 8.3×10⁷ CFU for mice. It was resistant to most β-lactams, tetracycline, and sulfamethoxazole and sensitive to cephalexin, cefoperazone, imipenem, and aminoglycosides. The chromosome size of the strain was 5 292 570 bp, with the GC content of 35.37%. Multilocus sequence typing showed that SCBCM001 was a strain of ST427. The genome of SCBCM001 carried a variety of virulence genes such as hblA, hblC,hblD, nheA, nheB, clo, and cytK and the genes conferring the resistance to antibiotics such as β-lactams, vancomycin, and tetracycline, which were not completely consistent with the drug-resistant phenotype. In addition, the genome of strain SCBCM001 contained 6 plasmids, one of which had a relatively complete phage region. [Conclusion] The whole genome of a B. cereus strain isolated from forest musk deer was sequenced and analyzed, which provided a basis for the prevention and treatment of bacterial diseases in forest musk deer.