High colonization by multidrug-resistant and virulent Staphylococcus aureus genotypes among critically ill patients in the COVID-19 pandemic in a Brazilian hospital.

BACKGROUND

The COVID-19 pandemic has dramatically impacted in patients from Intensive Care Units (ICUs), making them more vulnerable to infection/colonization by clinically relevant pathogens. However, little is known about the Staphylococcus aureus isolates that colonized these patients during the pandemic.

METHODS

Consecutive S. aureus isolates from surveillance swabs of patients of two ICUs of a hospital in Rio de Janeiro, between September 2020 and September 2021, were evaluated for phenotypic antimicrobial resistance. Methicillin-resistant S. aureus (MRSA) isolates were evaluated for resistance and virulence genes, biofilm production, and their genotypic profiles. Medical records were accessed for clinical and demographic data.

RESULTS

Among 255 patients colonized by S. aureus, 79 (30.9%) were in the cICU (COVID-19 ICU) and 176 (69.1%) in the ncICU (non-COVID-19 ICU). COVID-19 patients made greater use of antimicrobials during hospitalization (p < 0.05). Higher rates of resistance for erythromycin and clindamycin, as well as the inducible macrolide-lincosamide-streptogramin B resistance phenotype and multidrug resistance were found in cICU isolates (p < 0.05). An overall rate of 36.5% of MRSA isolates was detected, with 41.7% in cICU and 34% in ncICU (p = 0.22). SCCmec types II (22.6%) and IV (71%) were the most found, and the latter was more frequent in the ncICU (p < 0.01). More than 50% of the isolates carried the resistance genes erm(C), msr(A), mrs(B), mph(C), aph(3')-III3a and smr, and the virulence genes icaA, sasG, ebpS, scn, egc cluster, fnbpB and cna. The cICU presented isolates that primarily carried the erm(C), smr, and cna genes and that showed strong biofilm production (p < 0.05). Clonal complex (CC) 5 was prevalent (65.6%) and associated with the hospital clones USA800/ST5-IV and USA100/ST105-II, which were most found in ncICU and cICU, respectively (p < 0.05). Community MRSA comprised 31.2% of isolates and mainly included the USA300/ST8-IV lineage (18.3%), with all isolates carrying the pvl genes.

CONCLUSIONS

The significant impact on antimicrobial resistance rates and the emergence of virulent lineages among S. aureus isolates during the COVID-19 pandemic highlights the close relationship between this disease and antimicrobial resistance and the importance of constant microbiological surveillance to reduce the risks associated with future pandemics.