A Core Genome Multilocus Sequence Typing Scheme for Enterococcus faecalis

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.

Comprehensive integrated NGS-based surveillance and contact-network modeling unravels transmission dynamics of vancomycin-resistant enterococci in a high-risk population within a tertiary care hospital

“…Other studies relied on SNP-based analyses only by using a proper and highly related reference genome to enhance the power of discrimination by this approach [60]. While these analyses provide results in high resolution, they are lacking comparability and transferability to other settings [41]. In our study, especially the combination of SNP-based and cgMLST-based results produced valid and comparable data.…”

“…The first parameter represents the tree topology and isolates clustering, while the second parameter examines the branch length which correlates with the phylogenetic distances between isolates. Using the normalized absolute difference of patristic distances of isolate pairs from each of the phylogenetic analyses, an isolate-by-isolate comparison was performed for all applied tree-building methods [41]. To generate distance values suitable to visual compare the different approaches, it was necessary to multiply the absolute differences by 1 x 10 9 and to transform the obtained values (logarithm with basis = 2).…”

“…This is bypassed by applying a so-called core genome MLST (cgMLST), which combines the extensive data generated by WGS with a gene target-based typing such as MLST, but on a scale of hundreds of gene targets. Thereby, a robust and expendable database and international nomenclature for genotyping are provided [33,41]. Although bioinformatics tools are a prerequisite to handle and interpret NGS-derived data, appropriate approaches of data analysis are still not standardized and under constant evaluation and discussion [40,42].…”

Development of a High-Resolution Single-Nucleotide Polymorphism Strain-Typing Assay Using Whole Genome-Based Analyses for the Lactobacillus acidophilus Probiotic Strain

“…By contrast, WGS-based strain typing uses a gene-by-gene approach, such as whole-genome MLST (wgMLST) or core-genome MLST (cgMLST), which entails the use of numerous gene loci to compare genomes [ 27 , 28 ]. These approaches provide resolutions superior to those of current subtyping techniques (including PFGE and multilocus variable-number tandem-repeat analysis (MLVA)) because they can discriminate between closely related strains of clinically relevant foodborne pathogens [ 29 , 30 , 31 ].…”

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“…Recentemente, uma abordagem de tipagem de sequência multilocus do core genoma (core genome MLST -cgMLST) foi proposta como um método patrão reproduzível para a diferenciação de linhagem baseada em WGS na investigação epidemiológica de diversos patógenos tais como Staphylococcus aureus, Campylobacter jejuni, Acinetobacter baumannii, Mycoplasma gallisepticum, Chlamydia trachomatis, Enterococcus faecalis e Brucella spp. (KOHL et al, 2014(KOHL et al, , 2018bCODY et al, 2017;HIGGINS et al, 2017;PARK et al, 2017;GHANEM et al, 2018;PATIÑO et al, 2018;SCHÜRCH et al, 2018;NEUMANN et al, 2019;SANKARASUBRAMANIAN et al, 2019).…”