Drug resistance and molecular characteristics of Staphylococcus aureus strains from ICU environment based on whole genome sequencing

OBJECTIVE To investigate the distribution, drug resistance and molecular characteristics of the Staphylococcus aureus strains isolated from intensive care unit (ICU) environment in some hospitals of Shanghai Pudong New Area so as to provide bases for prevention and control of infections.

METHODS The specimens were collected from ICU environment of 8 medical institutions in Pudong District in 2019 and 2023, the S. aureus strains were isolated and identified. The drug susceptibility testing was performed by microbroth dilution method. The drug resistance genes and virulence genes were predicted based on virulence factors of bacterial pathogens, the comprehensive antibiotic resistance database (mcmaster.ca) and PubMLST, multilocus sequence typing (MLST) and phylogenetic analysis were performed.

RESULTS Totally 3408 samples were collected, and the isolated S. aureus strains accounted for 1.29%(44/3408);the isolated strains form both the shared articles and the articles that health care workers directly contact accounted for 20.45%. The drug resistance rate to penicillin was highest(72.73%, 32/44); the strains were completely susceptible to vancomycin, rifampicin, sulfamethoxazole-trimethoprim, daptomycin and nitrofurantoin. The methicillin-resistant Staphylococcus aureus (MRSA) strains accounted for 25.00%. The multi-drug resistance rate was 40.91%. The strains carried 26 types of drug resistance genes in total, covering 9 categories; the carrying rate of fluroquinolones resistance gene norA was 100.00%. The strains carried 12 types of enterotoxin genes, the carrying rate of sea gene was highest (50.00%, 22/44), some of the strains carried lukS-PV, lukF-PV and tsst gene. There were 14 types of sequence type (ST), dominated by ST7 (13/44, 29.55%), and novel ST type ST9342 was discovered. The phylogenetic analysis showed that all of the strains were divided into 2 major branches, and the strains with the same ST type were phylogenetically close on the evolutionary tree.

CONCLUSIONS The S.aureus strains are prevalent in ICU environment and are highly resistant to antibiotics. The strains exhibit various ST types, which, to a certain degree, is associated with the pathogenicity.