Serratia marcescens Outbreak in a Neonatal Intensive Care Unit: New Insights from Next-Generation Sequencing Applications.

is an environmental bacterium that is commonly associated with outbreaks in neonatal intensive care units (NICUs). Investigations of outbreaks require efficient recovery and typing of clinical and environmental isolates. In this study, we investigated how the use of next-generation sequencing applications, such as bacterial whole-genome sequencing (WGS) and bacterial community profiling, could improve outbreak investigations. Phylogenomic links and potential antibiotic resistance genes and plasmids in isolates were investigated using WGS, while bacterial communities and relative abundances of in environmental samples were assessed using sequencing of bacterial phylogenetic marker genes (16S rRNA and genes). Typing results obtained using WGS for the 10 isolates recovered during a NICU outbreak investigation were highly consistent with those obtained using pulsed-field gel electrophoresis (PFGE), the current standard typing method for this bacterium. WGS also allowed the identification of genes associated with antibiotic resistance in all isolates, while no plasmids were detected. Sequencing of the 16S rRNA and genes both showed greater relative abundances of at environmental sampling sites that were in close contact with infected babies. Much lower relative abundances of were observed following disinfection of a room, indicating that the protocol used was efficient. Variations in the bacterial community composition and structure following room disinfection and among sampling sites were also identified through 16S rRNA gene sequencing. Together, results from this study highlight the potential for next-generation sequencing tools to improve and to facilitate outbreak investigations.