Development and Evaluation of a Core Genome Multilocus Sequencing Typing (cgMLST) Scheme for Serratia marcescens Molecular Surveillance and Outbreak Investigations

Abstract

Serratia marcescens can cause a range of severe infections and contributes to nosocomial outbreaks. Although whole-genome sequencing (WGS)-based typing is the standard method for molecular surveillance and outbreak investigation, there is no standardized analytic scheme for S. marcescens core genome multilocus sequence typing (cgMLST). Here, the development and evaluation of a S. marcescens cgMLST scheme is reported with the goal of enabling a standardized methodology and typing nomenclature. Four hundred ninety-one high-quality S. marcescens WGS data sets were extracted from public databases and-using the genomic sequence of NCBI reference strain S. marcescens Db11 (NZ_HG326223.1) as a starting point-all Db11 genes present in ≥97% data sets used to create a cgMLST scheme. The novel scheme was evaluated using WGS data from 24 outbreak investigations (n = 175 isolates) distributed over three continents. Analysis of Db11 genes within the 491 data sets identified 2,692 target genes present in ≥97% of genomes (mean, 99.1%; median, 99.9%). These genes formed the novel cgMLST scheme, covering 47.8% of nucleotides in the Db11 genome. Analyzing 175 isolates from 24 outbreaks using the novel scheme gave comparable results to previous typing efforts for both general groupings and allelic distances within clusters. In summary, a novel cgMLST scheme for S. marcescens was developed and evaluated. The scheme and its associated nomenclature will improve standardization of typing efforts for molecular surveillance and outbreak investigation, allowing better understanding of S. marcescens genomic epidemiology and facilitating interlaboratory comparisons.

Keywords: Serratia marcescens; cgMLST; outbreak investigation; typing; whole-genome sequencing.

FIG 1

Minimum spanning trees of 110 S. marcescens isolates from Rossen et al. (17) using the novel cgMLST scheme. Distances are based on the allelic profiles of up to 2,692 target genes, pairwise ignoring missing targets. The values on the connecting lines indicate the number of allelic differences between the connected isolates. Circle sizes are proportional to the numbers of isolates per genotype (i.e., the allelic profile). Related genotypes (≤12 alleles distance) are shaded in gray. Each tree represents the typing results of the different given cities (A) Groningen, (B) Freiburg, and (C) Cologne, and the genotypes are colored according to the cluster colors from the original publication and named identically for comparability.

FIG 2

Minimum spanning tree of 35 S. marcescens isolates using the novel cgMLST scheme from suspected clusters previously characterized by PFGE. Distances are based on the allelic profiles of up to 2,692 target genes, pairwise ignoring missing targets. Values on the connecting lines indicate the number of allelic differences between the connected isolates. Circle sizes are proportional to the numbers of isolates per genotype (i.e., the allelic profile). Related genotypes (≤12 alleles distance) are shaded in gray. The genotypes are colored according to the PGFE groups. Isolates with related PFGE types were grouped.

FIG 3

Minimum spanning tree of nine S. marcescens isolates using the novel cgMLST scheme from a suspected outbreak previously characterized by single nucleotide polymorphisms (SNPs) (19). Distances are based on the allelic profiles of up to 2,692 target genes, pairwise ignoring missing targets. The values on the connecting lines indicate the number of allelic differences between the connected isolates. Circle sizes are proportional to the numbers of isolates per genotype (i.e., the allelic profile). Related genotypes (≤12 alleles distance) are shaded in gray. Genotypes are named identically from the original publication for comparability.

FIG 4

Minimum spanning tree of 21 S. marcescens isolates using the novel cgMLST scheme previously characterized by MALDI-TOF MS clustering from suspected clusters (27). Distances are based on the allelic profiles of up to 2,692 target genes, pairwise ignoring missing targets. The values on the connecting lines indicate the number of allelic differences between the connected isolates. Circle sizes are proportional to the numbers of isolates per genotype (i.e., the allelic profile). Related genotypes (≤12 alleles distance) are shaded in gray. Genotypes are colored according to the MALDI-TOF MS pattern/cluster. Isolates with related MALDI-TOF MS types are grouped.