Staphylococcus aureus CC398 Lineage of the Human Clade Isolated from Bloodstream Infection and Colonization and Spread among Brazilian Patients Hospitalized during the COVID-19 Pandemic

Abstract Community lineages of Staphylococcus aureus emerging in hospitals, such as CC398, have raised concerns. S. aureus CC398 isolates from bloodstream infections (BSI) and nasal colonization of hospitalized patients, during the COVID-19 pandemic, between March/2020 and September/2021, were characterized for antimicrobial susceptibility by disk diffusion test. Spa types and Sequence Type (ST) were analyzed by PCR/sequencing, and genes of resistance, virulence, and human immune evasion cluster (IEC) were accessed by PCR. Of a total of 118 CC398 isolates, 104 were from nasal swabs (4 MRSA and 100 MSSA), and 14 MSSA were from BSI. Forty (33.9%) patients presented COVID-19, and prior antimicrobial use was common among those colonized ( p < 0.05). High resistance rates were found for penicillin (PEN, 92.4%), erythromycin (ERY, 95.8%), clindamycin (CLI, 90.7%) and gentamicin (GEN, 51.7%), and the iMLS B phenotype was commonly detected. All four nasal MRSA and 47.4% of MSSA isolates were multidrug-resistant. The CLI/ERY/GEN/PEN/ erm T/ erm C and CLI/ERY/ erm T resistance profiles were frequent in nasal (45.2%) and BSI (57.1%) isolates, respectively. The erm C gene was more found in nasal (93.3%) than in BSI (7.1%) isolates ( p < 0.05). Most of 95% of the isolates presented the fnbA , fnbB , cna , and ermT genes. The spa type t1451 was detected in 91.5% of isolates, and the human clade was associated with 98.3%, with IEC type C being prevalent. MSSA-CC398 isolates of the human clade were predominant among hospitalized patients during the pandemic. The increased selective pressure exerted on these isolates, previously resistant to macrolides, may have favored their dissemination in the environment.