Multidrug-resistant CC3 Staphylococcus haemolyticus with increased vancomycin MIC among neonates in a Brazilian NICU

Staphylococcus haemolyticus has emerged as a cause of outbreaks in neonatal intensive care units (NICUs), particularly involving clonal complex (CC) 3 lineages. We investigated the prevalence and microbiological characteristics of S. haemolyticus colonizing neonates in a Brazilian NICU over two periods, spanning the onset of the COVID-19 pandemic. Nasal swabs were collected weekly between August 2019-March 2020 and between November 2020-April 2021. Isolates were identified by MALDI-TOF-MS and characterized by antimicrobial susceptibility testing, vancomycin minimum inhibitory concentration (MIC) determination, SCCmec typing, GTG5-PCR, and multilocus sequence typing (MLST). Among 108 neonates, 75 were colonized by S. haemolyticus and prematurity was the main cause of hospitalization (p=0.03). Colonization rates were similar between periods (71.2% vs. 67.3%; p=0.57), with no clinical or microbiological differences, except for reduced ampicillin-gentamicin use in the second period (p=0.048). Almost all isolates (96%) were multidrug-resistant, 78% presented increased vancomycin MIC (≥4 mg/L) and 52% carried the SCCmec type V. Molecular analysis revealed low genetic diversity, since >90% of isolates (70/75) clustered within a single predominant genotype shared with ten representative isolates confirmed as CC3-related lineages (ST1, ST3, ST25, and ST29) by MLST. No significant differences in resistance profiles or molecular characteristics were observed between periods. We demonstrate the circulation of multidrug-resistant CC3-related S. haemolyticus with increased vancomycin MIC in a Brazilian NICU. The epidemic ST29 lineage, subsequently associated with neonatal outbreaks in Europe, was already circulating in our NICU between 2019 and 2021. These findings highlight the need for enhanced surveillance of S. haemolyticus in neonatal settings.