Longitudinal phylogenomic tracking of methicillin-resistant Staphylococcus aureus clones persisting over years in a neonatal intensive care unit.

INTRODUCTION

Infection control measures against methicillin-resistant Staphylococcus aureus (MRSA) are challenging in advanced neonatal intensive care units (NICUs) providing care for high-risk newborns. To design and implement better infection control strategies, it is necessary to identify endemic MRSA clones that are recurrently detected and understand how they survive and transmit in the NICU.

METHODS

We performed whole-genome sequencing (WGS) for all MRSA strains isolated in the level II-IV NICU in Kyushu University Hospital, Fukuoka, Japan, from March 2015 to December 2021. Strains within pairwise 250 allelic distances in core genome multi-locus sequence typing (cgMLST) were clustered as cgMLST250 clusters, which were further divided into subclusters within pairwise 30 single nucleotide polymorphism (SNP) distances in the core genome-based phylogenetic analysis (SNP30 clusters). SNP30 clusters were defined as persistently present when they were identified in ≥5 patients over 12 months.

RESULTS

A total of 235 strains from 226 patients were analysed. Three major clonal complexes (CC1, CC5, and CC8) accounted for 91.2% of the strains. Multi-step phylogenomic analyses identified eight putative persistent clones defined by SNP30 clustering, five of which contained 10-32 isolates. These five clones were isolated for 15-40 months, often without overlap of inpatient periods, and in several cases, with isolation intervals of over one year.

CONCLUSIONS

Unidentified long-term and/or multiple reservoirs and multiple/repeated MRSA re-introduction into the NICU may contribute to prolonged detection of transmissible MRSA clones in the NICU. Intensive control of these reservoirs and re-introduction may be mandatory, particularly in advanced NICUs.