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.
Highlights
Among enterococci, Enterococcus faecalis occurs ubiquitously, with the highest incidence of human and animal infections
In due consideration of the importance of the human- and clinical-associated lineage sequence type 6 (ST6), which included most of the VRE, this genotype was more frequently represented in the collection (n ϭ 47, ϳ32%)
The scheme was implemented in the Ridom SeqSphereϩ software suite to generate highly concordant and comparable results and to provide a standardized nomenclature for the scientific community
Summary
Enterococcus faecalis occurs ubiquitously, with the highest incidence of human and animal infections. Exploiting hundreds of gene targets of the entire bacterial genome, thereby providing maximum resolution for multiple research and surveillance analyses [31, 32], is one of the greatest advantages of the cgMLST scheme Implementing this scheme in the SeqSphereϩ software (Ridom GmbH, Münster, Germany) allows the definition and curation of an international and standardized nomenclature, which has successfully been developed for other meaningful pathogens, such as Staphylococcus aureus, Listeria monocytogenes, and Enterococcus faecium [29, 33, 34]. We generated a powerful typing scheme for E. faecalis using the SeqSphereϩ software, providing an international standardized nomenclature that is suitable for surveillance approaches, outbreak investigations, and phylogenetic analyses
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