Resistência aos antimicrobianos, virulência e genótipos de amostras de Staphylococcus aureus isoladas de pacientes internados em UTIs de um hospital do Rio de Janeiro na pandemia de COVID-19

Abstract

The COVID-19 pandemic has impacted the management of patients in Intensive Care Units (ICUs), making them more vulnerable to infection/colonization by clinically relevant pathogens. However, little is known about the phenotypic and molecular aspects of Staphylococcus aureus isolates that colonized these patients during the pandemic. This study aimed to characterize S. aureus isolates from surveillance swabs of patients admitted to two ICUs of a referral hospital for COVID-19 treatment in Rio de Janeiro, between September 2020 and September 2021. Antimicrobial resistance was assessed by disk diffusion testing. The isolates were evaluated for resistance and virulence genes by PCR, biofilm production by semiquantitative testing, and clonal profiles by PFGE, MLST, RM-PCR, and spa typing. Medical records were accessed to obtain clinical and demographic data. A total of 255 patients were colonized by S. aureus, with 79 (30.9%) in the cICU (COVID-19 ICU), whose patients had a higher use of antimicrobials during hospitalization (p < 0.01). A rate of 36.5% [41.7% in cICU and 34% in ncICU (non-COVID-19 ICU)] of MRSA was found. Higher rates of resistance were detected for erythromycin and clindamycin, as well as the iMLSB (inducible macrolide-lincosamide-streptogramin B resistance) phenotype and multidrug resistance in isolates from the cICU (p <0.05). SCCmec types II (22.6%) and IV (71%) were the most frequent, and the latter was more frequently found in the ncICU (p <0.01). More than 50% of the MRSA isolates carried the resistance genes ermC, msrA, mrsB, mphC aph3’-III3a and smr, and the virulence genes icaA, sasG, ebpS, fnbpB, can, scn and the egc cluster. Furthermore, ermC, smr and cna genes were more frequent among isolates from the cICU as well as strong biofilm-producing MRSA isolates (p < 0.05). Clonal complex (CC) 5 was prevalent (65.6%) and associated with the hospital clones USA800/ST5/SCCmecIV and USA100/ST105/ SCCmecII, which were most often found in ncICU (p < 0.05) and cICU, respectively. Community-associated clones, such as USA300/ST8/SCCmecIV and USA1100/ST30/SCCmec IV were associated with 25.8% of the MRSA isolates, while the CC398 was found in 104 (40.8%) of all S. aureus isolates, and prevalent among MSSA isolates (61.7%) and associated with the cICU (p < 0.05). Four of them were MRSA. High resistance rates were observed to penicillin, erythromycin, clindamycin, and gentamicin. The iMLSB phenotype was identified in 90% of isolates, and the virulence genes fnbA, fnbB, and cna, and the resistance genes ermT and ermC, were detected in over 90%. The HU clade was predominant (97.1% of isolates), while LA clade was identified in one MRSA isolate. The prevalent genotypic profile, MSSA t1451/ermC+/ermT+/PVL-/IEC type C, was found in 80.8% isolates belonging to the HU clade. The significant impact on antimicrobial resistance rates and the emergence of virulent lineages among S. aureus isolates during the COVID-19 pandemic highlights the high selective pressure exerted on microorganisms and the importance of continuous microbiological surveillance to mitigate the risks associated with future pandemics.