Genomic characterization of efflux pumps and putative small multidrug resistance (SMR)-like transporters in disinfectant-tolerant coagulase-negative staphylococci from a Vietnamese hospital

ABSTRACT Coagulase-negative staphylococci (CoNS) are common inhabitants of healthcare environments and can serve as reservoirs of antimicrobial resistance determinants. However, the relationship among disinfectant tolerance, efflux-associated phenotypes, and multidrug resistance in environmental CoNS remains incompletely defined. Here, 51 staphylococcal isolates were recovered from high-touch hospital surfaces in Hanoi, Vietnam, and 14 isolates showed elevated MICs to at least one disinfectant, including benzalkonium chloride, chlorhexidine gluconate, or hydrogen peroxide, relative to Staphylococcus aureus ATCC 25923. These isolates also displayed multidrug-resistant phenotypes. Moreover, ethidium bromide accumulation assays revealed a clear efflux-associated phenotype, and representative isolates exhibited biofilm-forming ability. Whole-genome sequencing of three representative isolates reclassified SDH.B1 and SDH.B3 as Staphylococcus nepalensis —a CoNS species rarely documented in hospital AMR surveillance—and confirmed SDH.B7 as Staphylococcus haemolyticus . To our knowledge, this is among the first reports of S. nepalensis carrying mecA together with the disinfectant efflux gene qacG , and a set of putative small multidrug resistance (SMR)-like transporters in a hospital environment from Southeast Asia. In addition, six putative SMR-like proteins were identified. Phylogenetic and structural analyses suggested relatedness to YkkC/YkkD-like systems, although their transport activity remains to be experimentally verified. These findings identify environmental CoNS as reservoirs of disinfectant tolerance and multidrug resistance in hospital settings and provide a basis for future functional investigation of putative SMR-like transporters. IMPORTANCE Hospital environmental CoNS are often dismissed as low-priority contaminants, yet they may persist under disinfectant pressure and carry clinically relevant resistance determinants. Here, disinfectant-tolerant CoNS recovered from a Vietnamese hospital combined multidrug resistance, efflux-associated phenotypes, and biofilm-related traits. Genome analysis further revealed known qac genes and six putative SMR-like proteins that merit functional testing. These findings support inclusion of environmental CoNS in infection-prevention surveillance and disinfectant stewardship programs.