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

Abstract

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.

Characterization of KPC-Producing Serratia marcescens in an Intensive Care Unit of a Brazilian Tertiary Hospital

“…Serratia marcescens is a prominent opportunistic pathogen that frequently causes infections in intensive care, surgical and dialysis units (Krishnan et al, 1991;Martineau et al, 2018). In Brazil, there are only few studies on S. marcescens (Ribeiro et al, 2013;Silva et al, 2015).…”

Epidemiological Typing of Serratia marcescens Isolates by Whole-Genome Multilocus Sequence Typing

“…We were able to confirm their data using our wgMLST scheme (results not shown). In the examples brought forward by Martineau et al (24), a single outbreak was analyzed, whereas we have now taken the method to a higher level, including the development of a dedicated wgMLST WGS database and an informatics tool for the semiautomated analysis of potential outbreak scenarios. With turnaround calculation times of less than 30 min per sample and simultaneous processing of up to 24 samples, high-powered wgMLST performance is guaranteed.…”

Genomics of Serratia marcescens Isolates Causing Outbreaks in the Same Pediatric Unit 47 Years Apart: Position in an Updated Phylogeny of the Species

“…The most frequently used typing techniques for relevant human-related pathogens are PFGE and MLST; however, for S. marcescens, the MLST scheme has not yet been implemented (Martineau et al, 2018). Currently, WGS is a much better option given it is cost-effective in comparison with MLST and it reveals the composition of the accessory genome.…”