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

Abstract

Serratia marcescens is an opportunistic bacterial pathogen. It is notorious for its increasing antimicrobial resistance and its potential to cause outbreaks of colonization and infections, predominantly in neonatal intensive care units (NICUs). There, its spread requires rapid infection control response. To understand its spread, detailed molecular typing is key. We present a whole-genome multilocus sequence typing (wgMLST) method for S. marcescens. Using a set of 299 publicly available whole-genome sequences (WGS), we developed an initial wgMLST system consisting of 9,377 gene loci. This included 1,455 loci occurring in all reference genomes and 7,922 accessory loci. This closed system was validated using three geographically diverse collections of S. marcescens consisting of 111 clinical isolates implicated in nosocomial dissemination events in three hospitals. The validation procedure showed a full match between epidemiological data and the wgMLST analyses. We set the cutoff value for epidemiological (non)relatedness at 20 different alleles, though for the majority of outbreak-clustered isolates, this difference was limited to 4 alleles. This shows that the wgMLST system for S. marcescens provides prospects for successful future monitoring for the epidemiological containment of this opportunistic pathogen.

Detection of Serratia marcescens in neonatal intensive care units requires a rapid and comprehensive infection control response starting with the very first case

“…PFGE was used in this case. Sequencing-based methods are also emerging for Sm [ 5 ], [ 10 ]. One benefit of sequencing-based methods with a standardized nomenclature (e.g., core genome multilocus sequence typing) is that data generated from different settings (e.g., different outbreaks) can be compared quite easily.…”

Outbreak investigation of Serratia marcescens neurosurgical site infections associated with a contaminated shaving razors

“…The trimmed reads were mapped to the reference sequence using BWA-mem [11], and single nucleotide polymorphisms (SNPs) were detected using SAMtools and bcftools [12] using default parameters except the following: minimum mapping quality score 30, minimum base quality score 20, and ploidy 1. For comparison, using the same process, we processed two S. marcescens genome data, PRJEB28358 and PRJEB27112, publically available in the European Nucleotide Archive (ENA) database consisting of 19 and 17 isolates, derived from the outbreaks in Germany and India, respectively [13,14]. The core regions were defined as the genomic positions having depths from all 47 isolates ranging between mean depth ± 2 standard deviations.…”

Development and Validation of a High-Throughput Short Sequence Typing Scheme forSerratia marcescensPure Culture and Environmental DNA

“…Amongst Serratia species, Serratia marcescens is the most important opportunistic human pathogen, often multidrug resistant and involved in outbreaks of HAI in neonatal intensive care units (NICU) (16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26). No MLST scheme exists for the molecular typing of S. marcescens but other typing techniques have been used during previous epidemiological studies, such as pulsed-field gel electrophoresis (16,18,22), ribotyping (27) or more recently whole-genome MLST (28). Even though these techniques were proven efficient to distinguish strains, they are not tailored to epidemiological surveys involving large sample size because they are technically demanding due to upstream cultivation and isolation efforts.…”