High-Resolution Typing of Staphylococcus epidermidis Based on Core Genome Multilocus Sequence Typing To Investigate the Hospital Spread of Multidrug-Resistant Clones

Abstract

Staphylococcus epidermidis is a pathogen emerging worldwide as a leading cause of health care-associated infections. A standardized high-resolution typing method to document transmission and dissemination of multidrug-resistant S. epidermidis strains is needed. Our aim was to provide a core genome multilocus sequence typing (cgMLST) scheme for S. epidermidis to improve the international surveillance of S. epidermidis We defined a cgMLST scheme based on 699 core genes and used it to investigate the population structure of the species and the genetic relatedness of isolates recovered from infants hospitalized in several wards of a French hospital. Our results show the long-lasting endemic persistence of S. epidermidis clones within and across wards of hospitals and demonstrate the ability of our cgMLST approach to identify and track these clones. We made the scheme publicly available through the Institut Pasteur BIGSdb server (http://bigsdb.pasteur.fr/epidermidis/). This tool should enable international harmonization of the epidemiological surveillance of multidrug-resistant S. epidermidis clones. By comparing gene distribution among infection and commensal isolates, we also confirmed the association of the mecA locus with infection isolates and of the fdh gene with commensal isolates. (This study has been registered at ClinicalTrials.gov under registration no. NCT03374371.).

Keywords: Staphylococcus epidermidis; cgMLST; typing.

Copyright © 2021 American Society for Microbiology.

Figures

FIG 1

Distribution of gene presence and absence for mecA, ccrAB, ica, and fdh loci among 252 infection isolates and 194 commensal isolates from the BIGSdb. mecA encodes penicillin-binding protein 2 (PBP2); ccrA and ccrB encode cassette chromosome recombinase A and B, respectively; icaA and icaD genes are involved in polysaccharide intercellular adhesin (PIA) production; fdh encodes a formate dehydrogenase. There was a positive association between infection isolates and mecA, ccrA, and ccrB loci compared to commensal isolates (**, Fisher < 0.001), and there was a positive association between commensal isolates and fdh locus compared to infection isolates (*, Fisher < 0.005).

FIG 2

Comparison of cluster analysis based on cgMLST allelic profiles with phylogenetic analysis based on core gene alignments for 20 linezolid-resistant isolates. The minimum spanning tree based on cgMLST allelic profiles is shown on the left side. The tree was generated from allelic profiles of 699 core genes and visualized with PHYLOViZ. Each node represents an isolate and is colored according to the 7-locus ST. In silico MLST performed on the de novo assemblies revealed that isolates UCLA-Sa-LR-14 (497) and UCLA-Sa-LR-21 (503) had been erroneously assigned to ST24 and ST186-like, respectively, in the original publication (6). We found that in fact both strains belonged to ST186. Black numbers next to the nodes indicate the BIGSdb identifiers of each isolate. Red numbers on the connecting lines indicate the number of core gene allele differences between adjacent nodes. Link lengths are loosely related to the number of allelic differences. The tree based on 699 core gene sequence alignments is shown on the right side. The tip labels indicate the BIGSdb identifiers of each isolate. Clusters reported by Tewhey et al. based on the alignments of 2,093 core genes (6) are indicated by circles and letters (A, B, C, and D).

FIG 3

Comparison of clustering analyses based on cgMLST allelic profiles and on core gene sequences alignment for 25 S. epidermidis isolates sequenced in this study. The minimum spanning tree based on cgMLST allelic profiles is shown on the left side. The tree was generated from allelic profiles of 699 core genes. Each node represents an allelic profile and corresponds to a single isolate except the node corresponding to cluster VI where 2 isolates have the same profile. Nodes are colored according to the ward where patients were hospitalized. Black numbers next to the nodes indicate the BIGSdb identifiers of each isolate. Red numbers on the connecting lines indicate the number of core gene allele differences between adjacent nodes. Link lengths are not proportional to the number of allelic differences. Clusters of closely related genotypes (≤21 allele differences) are surrounded by circles and are numbered (I to VI). The tree based on 699 core gene alignment is shown on the right side. The tip labels indicate the BIGSdb identifiers and names of each isolate. Clusters are indicated by circles and are numbered (I to VI) as in the minimum spanning tree.

FIG 4

Timeline of the 21 hospitalized patients from which 24 S. epidermidis isolates were sequenced. The patient numbers indicated in the colored boxes and the patient isolate numbers indicated between brackets correspond to those in Table 1. The clusters to which isolates belong correspond to those in Fig. 3. The isolate sequence type (ST) is indicated on the right side of the graph.