Dataset Information

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.

SUBMITTER: Rossen JWA

PROVIDER: S-EPMC6440794 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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

Rossen John W A JWA Dombrecht Jill J Vanfleteren Diederik D De Bruyne Katrien K van Belkum Alex A Rosema Sigrid S Lokate Mariette M Bathoorn Erik E Reuter Sandra S Grundmann Hajo H Ertel Julia J Higgins Paul G PG Seifert Harald H

Journal of clinical microbiology 20190328 4

<i>Serratia marcescens</i> 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 <i>S. marcescens</i> Using a set of 299 publicly avail ...[more]

PMID: 30728192

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Project description:Whole-genome sequencing (WGS)-based typing methods have emerged as promising and highly discriminative epidemiological tools. In this study, we combined gene-by-gene allele calling and core genome single nucleotide polymorphism (cgSNP) approaches to investigate the genetic relatedness of a well-characterized collection of OXA-48-producing Klebsiella pneumoniae isolates. We included isolates from the predominant sequence type ST405 (n = 31) OXA-48-producing K. pneumoniae clone and isolates from ST101 (n = 3), ST14 (n = 1), ST17 (n = 1), and ST1233 (n = 1), obtained from eight Catalan hospitals. Core-genome multilocus sequence typing (cgMLST) schemes from Institut Pasteur's BIGSdb-Kp (634 genes) and SeqSphere+ (2,365 genes), and a SeqSphere+ whole-genome MLST (wgMLST) scheme (4,891 genes) were used. Allele differences or allelic mismatches and the genetic distance, as the proportion of allele differences, were used to interpret the results from a gene-by-gene approach, whereas the number of SNPs was used for the cgSNP analysis. We observed between 0-10 and 0-14 allele differences among the predominant ST405 using cgMLST and wgMLST from SeqSphere+, respectively, and <2 allelic mismatches when using Institut Pasteur's BIGSdb-Kp cgMLST scheme. For ST101, we observed 14 and 54 allele differences when using cgMLST and wgMLST SeqSphere+, respectively, and 2-5 allelic mismatches for BIGSdb-Kp cgMLST. A low genetic distance (<0.0035, a previously established threshold for epidemiological link) was generally in concordance with a low number of allele differences (<8) when using the SeqSphere+ cgMLST scheme. The cgSNP analysis showed 6-29 SNPs in isolates with identical allelic SeqSphere+ cgMLST profiles and 16-61 cgSNPs among ST405 isolates. Furthermore, comparison of WGS-based typing results with previously obtained MLST and pulsed-field gel electrophoresis (PFGE) data showed some differences, demonstrating the different molecular principles underlying these techniques. In conclusion, the use of the different WGS-based typing methods that were used to elucidate the genetic relatedness of clonal OXA-48-producing K. pneumoniae all led to the same conclusions. Furthermore, threshold parameters in WGS-based typing methods should be applied with caution and should be used in combination with clinical epidemiological data and population and species characteristics.

Project description:Abstract Background Outbreaks of pathogenic agents within healthcare facilities may have sporadic or nosocomial sources. Effective intervention requires distinguishing between these sources, which in turn requires epidemiological investigation in conjunction with typing of pathogen isolates. For the latter, established methods range from ribotyping and pulse-field gel electrophoresis to multilocus sequence typing and whole genome sequencing. Due to technical complexities and costs associated with these methods, however, typing is rarely pursued. Polymorphic locus sequence typing (PLST) addresses these issue by employing conventional PCR and Sanger sequencing; the key to PLST is its focus on a tandem repeat-containing locus exhibiting maximal variation due to combinations of single nucleotide polymorphisms and insertions/deletions. Serratia marcescens has been implicated in numerous nosocomial outbreaks, and relatedly has the ability to colonize the hospital environment (e.g., sinks), although few studies have definitively established an outbreak-environment link. Methods To extend PLST to S. marcescens, tandem repeats were bioinformatically identified in the genome sequence of strain WW4 (accession CP003959) and used with flanking sequences as queries in BLASTN searches of the GenBank nr/nt Serratia genome database including 97 S. marcescens strains. One locus designated SerMT1 (bp 243212-244195) was present in all strains and exhibited high variability associated with 6-16 copies of a PVVEPE-encoding repeat within signal recognition particle receptor gene ftsY. Results SerMT1 was downloaded from all 97 strains, aligned using Clustal Omega, and phylogenetically analyzed using DNA parsimony. This analysis resolved 91 total alleles and yielded an impressively high Simpson’s Diversity Index of 0.998. Six clusters of 2 to 4 strains shared SerMT1 sequence; their epidemiologic relatedness was supported by their GenBank annotations (e.g., UMH-10 and UMH-11 isolated the same month at the same facility). Conclusion SerMT1 PLST provides an affordable, user-friendly new tool for epidemiologic investigation of S. marcescens outbreaks. Disclosures Tom Edlind, PhD, MicrobiType LLC: Ownership Interest.

Dataset Information

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

Publications

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

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