Phylogenetic and pathogenic description of Enterococcus faecalis at a Northern Chinese hospital

Enterococcus faecalis is one of the leading causes of bacterial infectious diseases. Describing this infection-inducing pathogen can facilitate evidence-based infection prevention and control. Yet clinical isolates of E. faecalis are difficult to structurally distinguish from non-clinical isolates, so a more precise and comprehensive typing assay is needed to equip us for this challenge. With its high accuracy and completeness, Whole-genome sequencing (WGS) has initiated a technological revolution in exploring the genetic variation of microbes. We aimed to investigate the use of WGS in characterizing the phylogenetic and pathogenic features of E. faecalis clinical isolates in the northern Chinese city of Tianjin. We analyzed these isolates' sequence types (STs), their phylogenetic relationship to their global counterparts, their possible domestic spread events, their genetic linkage and the possible within-hospital transmission. We also screened their profiles of antibiotic resistance genes (ARGs), virulence genes, pathogenicity islands (PAIs), and chromosome-encoded type IV secretion system (CE-T4SS). Furthermore, we verified the ARG profiles with the antimicrobial susceptibility results.

Among the 53 clinical E. faecalis isolates, we identified 15 known STs and reported 2 novel STs (ST1970 and ST1971). Three dominant STs exhibited different clustering patterns: ST16 isolates grouped with other Chinese isolates, ST745 isolates formed a separate cluster, and ST179 isolates overlapped with other global isolates. Isolates within some STs exhibited closer pairwise single nucleotide polymorphism (SNP) distances, but direct transmission was unlikely due to the lack of coincidence between the phylogenetically close isolates. Although local isolates generally carried a small number of ARGs and multiple virulence genes, isolates assigned to distinct STs varied in the distributions of ARGs, virulence genes, PAIs, and CE-T4SS. Also, the ARG profiles correlated well with their antibiotic-resistant phenotypes. We demonstrated for the first time the phylogenetic and pathogenic characterization of E. faecalis clinical isolates in the Tianjin area. Additionally, we revealed a robust correlation between these features and the STs of the isolates, indicating clinical isolates belonging to different STs might vary in pathogenic ability.

WGS exhibited excellent capabilities in characterizing local clinical E. faecalis, making it a potential tool for epidemiological studies and infection management. In the meantime, fully exploiting the use of genomic data from local clinical strains can enhance antimicrobial resistance surveillance and provide insights into potential pathogenicity, aiding the development of more effective treatment strategies.