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J Clin Microbiol. 2019 Jan 16. pii: JCM.01686-18. doi: 10.1128/JCM.01686-18. [Epub ahead of print]

A core genome multilocus sequence typing (cgMLST) scheme for Enterococcus faecalis.

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Robert Koch- Institute, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany.
Department of Periodontology and Restorative Dentistry, University Hospital Muenster, Muenster, Germany.
Robert Koch- Institute, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, Berlin, Germany.
Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany.
Friedrich Loeffler- Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany.
Department of Microbiology, St. Vincent's University Hospital and School of Medicine and Medical Science, University College Dublin, Dublin, Ireland.
Robert Koch-Institute, Berlin, Germany.


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 1972 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, and all publicly available genome sequences from NCBI and SRA 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.

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