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A Core Genome Multilocus Sequence Typing Scheme for Enterococcus Faecalis

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A Core Genome Multilocus Sequence Typing Scheme for Enterococcus Faecalis

Bernd Neumann et al. J Clin Microbiol.

Abstract

Among enterococci, Enterococcus faecalis occurs ubiquitously, with the highest incidence of human and animal infections. The high genetic plasticity of E. faecalis complicates both molecular investigations and phylogenetic analyses. Whole-genome sequencing (WGS) enables unraveling of epidemiological linkages and putative transmission events between humans, animals, and food. Core genome multilocus sequence typing (cgMLST) aims to combine the discriminatory power of classical multilocus sequence typing (MLST) with the extensive genetic data obtained by WGS. By sequencing a representative collection of 146 E. faecalis strains isolated from hospital outbreaks, food, animals, and colonization of healthy human individuals, we established a novel cgMLST scheme with 1,972 gene targets within the Ridom SeqSphere+ software. To test the E. faecalis cgMLST scheme and assess the typing performance, different collections comprising environmental and bacteremia isolates, as well as all publicly available genome sequences from the NCBI and SRA databases, were analyzed. In more than 98.6% of the tested genomes, >95% good cgMLST target genes were detected (mean, 99.2% target genes). Our genotyping results not only corroborate the known epidemiological background of the isolates but exceed previous typing resolution. In conclusion, we have created a powerful typing scheme, hence providing an international standardized nomenclature that is suitable for surveillance approaches in various sectors, linking public health, veterinary public health, and food safety in a true One Health fashion.

Keywords: Enterococcus faecalis; core genome MLST; molecular surveillance; molecular typing; whole-genome sequencing.

Figures

FIG 1
FIG 1
Isolate collection for establishing the E. faecalis cgMLST scheme (n = 146). The phylogenetic tree is based on MLST analyses and was calculated with SeqSphere+. Sequence types (STs) were added and color-coded in the inner circle. Year of strain isolation was added and shaded as a gray circle (light gray to dark gray). Vancomycin resistance and the van genotype were also added as color-coded circles (see key, “VRE/VSE”). In the three outer circles (2 to 4), the origin of isolation was depicted (see key, “Origin”). Circle 2 depicts whether an isolate is of human (purple) or animal (yellow) origin. Circle 3 represents the origin of human isolates (blue, community; red, hospital associated). The outer circle, 4, shows whether an isolate was obtained from colonization (green) or was infection associated (pink). For some isolates, the data were not valid or were unknown (dark gray). Visualization was realized using iTOL.
FIG 2
FIG 2
The phylogenetic tree of 852 sequence types (STs) represents the distribution of STs used for cgMLST scheme development within the global ST population of E. faecalis and was generated using FastTree 2. (A) A radial overview and (B) a circular presentation of the main part of the tree are shown. STs represented in the strain collection for scheme definition are color coded in red. Blue color codes represent all STs available for this study. Visualization was realized using iTOL.
FIG 3
FIG 3
Isolate collection for establishing the E. faecalis cgMLST scheme (n = 146). The phylogenetic tree is based on cgMLST analyses and was calculated with SeqSphere+. Available data for sequence types (STs; inner circle) and complex types (CTs; outer circle) are depicted as colored circles. The collection comprised 41 different STs and 97 different CTs. Visualization was realized using iTOL.

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