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Rapid identification of a Serratia marcescens outbreak by massive third-generation nanopore sequencing in a neonatal intensive care unit

ABSTRACT: Serratia marcescens outbreak characterized by third-generation sequencing

PROVIDER: PRJEB55320 | ENA |

REPOSITORIES: ENA

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intensive care unit

Project description:intensive care unit Raw sequence reads

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Outbreak of extensively drug-resistant <i>Serratia marcescens</i> in an intensive care unit.

Project description:We present the investigation and control of an extensively drug-resistant Serratia marcescens outbreak in a 30-bed intensive care unit (ICU). Within 6 weeks, 4 critically ill trauma patients were infected by the same strain. Intensive containment measures limited the spread of this strain while sustaining the capacity of the trauma ICU.

| S-EPMC10654954 | biostudies-literature

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

Project description:Serratia marcescens is an environmental bacterium that is commonly associated with outbreaks in neonatal intensive care units (NICUs). Investigations of S. marcescens 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 S. marcescens outbreak investigations. Phylogenomic links and potential antibiotic resistance genes and plasmids in S. marcescens isolates were investigated using WGS, while bacterial communities and relative abundances of Serratia in environmental samples were assessed using sequencing of bacterial phylogenetic marker genes (16S rRNA and gyrB genes). Typing results obtained using WGS for the 10 S. marcescens 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 gyrB genes both showed greater relative abundances of Serratia at environmental sampling sites that were in close contact with infected babies. Much lower relative abundances of Serratia 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.

| S-EPMC6113457 | biostudies-literature

Outbreak of <i>Serratia marcescens</i> in the Neonatal Intensive Care Unit of a Tertiary Care Hospital in Mexico.

Project description:IntroductionWe describe an outbreak of Serratia marcescens (S. marcescens) infection in the neonatal intensive care unit at Women's Hospital in Sinaloa, Mexico.MethodsIn April 2021, an outbreak of S. marcescens infection was identified. A case was identified as any patient who tested positive for S. marcescens and showed signs of an infectious process.ResultsS. marcescens was isolated from the blood cultures of 15 neonates with clinical signs of neonatal sepsis. Statistical analysis showed that all neonates had an invasive medical device. The problem was controlled after hospital hygiene and sanitation measures were strengthened.ConclusionThe study provides evidence of an outbreak of nosocomial bacteremia due to the cross-transmission of S. marcescens. The findings highlight the need for hospitals to implement strict hygiene measures, especially regarding hand washing, to prevent future outbreaks.

| S-EPMC10539092 | biostudies-literature

Implementation of a PCR-based strategy to control an outbreak by Serratia marcescens in a Neonatal Intensive Care Unit.

Project description:ObjectivesTo evaluate the clinical and epidemiological impact of a new molecular surveillance strategy based on qPCR to control an outbreak by Serratia marcescens in a Neonatal Intensive Care Unit (NICU).MethodsWe design a specific qPCR for the detection of S. marcescens in rectal swabs of patients admitted to a NICU. We divided the surveillance study into two periods: (a) the pre-PCR, from the outbreak declaration to the qPCR introduction, and (b) the PCR period, from the introduction of the qPCR until the outbreak was solved. In all cases, S. marcescens isolates were recovered and their clonal relationship was analysed by PFGE. Control measures were implemented during the outbreak. Finally, the number of bloodstream infections (BSI) was investigated in order to evaluate the clinical impact of this molecular strategy.ResultsNineteen patients colonized/infected by S. marcescens were detected in the pre-PCR period (October 2020-April 2021). On the contrary, after the PCR implementation, 16 new patients were detected. The PFGE revealed 24 different pulsotypes belonging to 7 different clonal groups, that were not overlapping at the same time. Regarding the clinical impact, 18 months after the qPCR implementation, no more outbreaks by S. marcescens have been declared in the NICU of our hospital, and only 1 episode of BSI has occurred, compared with 11 BSI episodes declared previously to the outbreak control.ConclusionsThe implementation of this qPCR strategy has proved to be a useful tool to control the nosocomial spread of S. marcescens in the NICU.

| S-EPMC10714559 | biostudies-literature

Serratia marcescens outbreak

Project description:S. marcescens outbreak in Norway

| PRJEB87771 | ENA

Swab samples from a hospital neonatal intensive care unit (NICU)

Project description:Characterization of bacterial communities in a hospital NICU during a Serratia marcescens outbreak

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intensive care unit shotgun raw sequences

Project description:intensive care unit shotgun raw sequences Metagenome

| PRJNA562118 | ENA