Staphylococcus Aureus Cc398 as a Cause of Bloodstream Infection and Nasal Colonization Among Patients Hospitalized in a Hospital in Rio De Janeiro During the Covid-19 Pandemic

Methicillin-resistant Staphylococcus aureus (MRSA) of clonal complex (CC) 398 is commonly associated with livestock (LA clade – livestock-associated) and has been detected in invasive human infections. However, methicillin-susceptible CC398 (MSSA) strains not associated with livestock (HU clade – human-adapted) have also been increasingly reported in human infections. The objective of this study was to phenotypically and molecularly characterize CC398 isolates obtained from bloodstream infections (BSI) and surveillance swabs from patients with and without COVID-19 hospitalized during the pandemic in a hospital in Rio de Janeiro. The clonal complex was determined by RM-PCR and sequence type (ST) by MLST. Genes associated with adhesins (fnbB, fnbA, bbp, cna), toxins (pvl, sec, sed), macrolide resistance (ermA, ermC, ermT), HU clade markers (scn), LA clade markers (tetM, tetK), and Immune Evasion Cluster (IEC: scn, chp, sak, sea, or sep) typing were detected by PCR. Spa typing was performed by sequencing of the protein A gene. Between March 2020 and September 2021, a total of 318 S. aureus isolates were collected, of which 117 belonged to CC398 (ST398); 41% were obtained from patients with COVID-19. Among CC398 isolates, 13 were from bloodstream infections and 104 from nasal swabs, with four nasal isolates identified as MRSA. Adhesin genes fnbB, fnbA, and cna were detected in over 95% of isolates, while resistance genes ermT and ermC were present in 96.6% and 83.8%, respectively. All isolates were negative for ermA, pvl, sec, sed, and bbp. The HU clade was detected in 97.4% of isolates, with 50% classified as multidrug-resistant (resistant to clindamycin, erythromycin, gentamicin, and penicillin). Only one isolate belonged to the LA clade and one showed markers of both clades (LA/HU); both were MRSA. IEC type C, defined by the presence of scn and chp genes, was the most frequent (95.7%). Spa type t1451 was identified in 91.4% of isolates. No significant differences were observed between bloodstream infection and colonization isolates, or between patients with and without COVID-19. CC398 isolates belonging to the HU clade were frequent and exhibited resistance and virulence-related factors that may contribute to their dissemination.