Comparative Genome Analyses of Staphylococcus arlettae Isolated from Clinical Bovine Mastitis

Background: Staphylococcus arlettae is a coagulase-negative staphylococcal species increasingly recognized as a reservoir of antimicrobial resistance determinants in animal, human, and environmental. Methods: In the present study, a multidrug-resistant S. arlettae isolate (BVC_SA31) isolated from bovine mastitis milk was characterized by whole-genome sequencing and comparative pangenomic analyses. Results: Antimicrobial susceptibility testing revealed resistance to penicillin, oxacillin, clindamycin, and erythromycin. Whole-genome sequencing of isolate generated a high-quality draft genome comprising of 36 contigs, 2,521 coding sequences, 10 rRNA genes and 57 tRNA genes. Species identity was confirmed by average nucleotide identity and tetranucleotide correlation analysis. Isolate was assigned to sequence type ST1203 and harbored antimicrobial resistance genes, including mph(C), blaARL-2, vanT, vanY, sdrM, sepA, and norC. Mobile genetic elements like insertion sequences (49), genomic islands (4), CRISPR loci (2), and plasmid-associated recombination systems (2) were identified. Comparative genomic analysis of 74 S. arlettae genomes revealed an open and highly diverse pangenome comprising 10,153 gene clusters, including 547 core genes, 1,024 soft-core genes, 1,267 shell genes, and 7,315 cloud genes. ANI-based clustering and codon usage analyses grouped the genomes into four distinct clusters, while core proteome phylogeny characterised two major global evolutionary lineages. Diverse repertoire of plasmid replicons, rep7a, rep7b, rep7c, rep10, rep13, rep15, rep19c, rep20, rep21, rep22, rep24, rep39, repUS10, repUS12, and repUS19 were identified. A total 39 antimicrobial resistance genes were identified, with msr(A) (46.62%), blaARL-2 (25.9%), mph(C) (19.24%), blaARL-1 (18.5%), mecA (8.88%), aph(2'')-Ii (7.4%), erm(C) (7.4%), lnu(A) (7.4%), tet(K) (7.4%), and dfrG (6.66%) being the most prevalent, confer resistance to macrolides, β-lactams, aminoglycosides, lincosamides, tetracyclines, and trimethoprim. Only two strains were found to harbour SSCmecA elements. Conclusions: In conclusion two global lineages of S. arlettae were identified and global antimicrobial resistance profiling of S. arlettae, highlighting its potential role as an emerging reservoir of antimicrobial resistance genes were identified.