A Core Genome Multilocus Sequence Typing Scheme for Enterococcus faecalis

J Clin Microbiol. 2019 Feb 27;57(3):e01686-18. doi: 10.1128/JCM.01686-18. Print 2019 Mar.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bacterial Proteins / genetics
  • Bacterial Typing Techniques / methods*
  • Enterococcus faecalis / classification
  • Enterococcus faecalis / genetics*
  • Enterococcus faecalis / isolation & purification
  • Environmental Microbiology
  • Genome, Bacterial / genetics*
  • Genotype
  • Gram-Positive Bacterial Infections / epidemiology
  • Gram-Positive Bacterial Infections / microbiology
  • Humans
  • Molecular Epidemiology
  • Multilocus Sequence Typing
  • One Health
  • Phylogeny
  • Polymorphism, Single Nucleotide


  • Bacterial Proteins