Whole-Genome Sequencing Identified Co-Circulating VIM-Producing Serratia bockelmannii and Serratia sarumanii in a Neonatal Intensive Care Unit Cluster Investigation

Serratia marcescens complex bacteria are recognized causes of outbreaks in Neonatal Intensive Care Units (NICU). We investigated a cluster of VIM-producing Serratia spp. in the NICU of Santa Maria della Misericordia Hospital, Perugia, through a retrospective epidemiological and genomic analysis integrating clinical and surveillance data, antimicrobial susceptibility testing, environmental screening, and whole-genome sequencing (WGS). In November 2024, VIM-producing Serratia was isolated from eight neonates, of whom five developed clinical infections, including two bloodstream infections. Nine VIM-producing Serratia isolates recovered from these eight neonates and one non-VIM-producing isolate from a bloodstream infection (used for comparison) were analysed. Routine MALDI-TOF MS identified all isolates as S. marcescens, whereas WGS resolved them into two genomic lineages: seven S. bockelmannii ST388 isolates and three S. sarumanii ST382-like isolates. All VIM-producing Serratia carried blaVIM-1 and blaSHV-12 and showed multidrug-resistant phenotypes. Long-reads sequencing reconstructed complete, and almost identical, IncA-ST12 plasmids in all nine VIM-producing Serratia isolates; the plasmids carried blaVIM-1 and blaSHV-12 together with additional resistance determinants. Environmental, water, and healthcare-worker screening did not identify a Serratia reservoir. No new VIM-producing Serratia infections occurred after the November cluster. These findings show how WGS complements routine MALDI-TOF MS and rapid carbapenemase testing by providing the taxonomic, epidemiological, and plasmid-level resolution needed to investigate complex healthcare-associated outbreaks.