Hybrid long-read sequencing reveals genomic homogeneity, blaZ copy-number variation, and phenotypic adaptation of the emerging Asian ST188 MSSA lineage from pediatric gut and vaginal colonization sites, Southern China

Abstract

Staphylococcus aureus ( S. aureus ) ST188 has emerged as an important methicillin-susceptible clonal lineage in Asia and is frequently associated with human colonization and community-acquired infections. This study investigates ST188 isolates from aerobic vaginitis and pediatric fecal colonization to elucidate molecular mechanisms underlying adaptation and low antimicrobial resistance. Nineteen ST188 S. aureus isolates were collected from vaginal secretions of patients with aerobic vaginitis ( n = 6) and fecal samples from children ( n = 13) in Shenzhen, China. Complete genomes were assembled using long-read sequencing and analyzed for core genome SNPs, virulence genes, antimicrobial resistance genes, and plasmids. Phenotypic characterization included antimicrobial susceptibility testing, biofilm formation, and agr typing. The global phylogenetic context was assessed using PathogenWatch, based on cgMLST. The isolates exhibited remarkable genomic homogeneity. Virulence genes were highly conserved, with the cap8 , isd , and ica gene clusters present in all strains, and low prevalence of superantigen genes ( seb , 5/19; sea , sec , selL , and tst , 1/19 each). Antimicrobial resistance was limited, with penicillin resistance in 12/19 isolates and blaZ carriage in 11/19 isolates; all blaZ -positive isolates were penicillin resistant. The tetracycline efflux gene tet(38) , the efflux pump genes mepA , norA , and lmrS , and the regulatory genes mepR , mgrA , arlS , and arlR were detected in all isolates. All blaZ genes were located on plasmids, and three types of plasmids were detected. Biofilm formation did not differ significantly between vaginal and fecal isolates under the tested laboratory conditions ( P = 0.0874). All strains belonged to agr group I. ST188 S. aureus in this cohort showed genomic variability and a restricted resistome dominated by plasmid-borne blaZ copy-number variation. The global analysis indicated that the study isolates did not form a single monophyletic cluster; therefore, these data do not support conclusions about niche-specific phenotypic adaptation.