A Genomic Snapshot of Enterococcus faecalis within Public Hospital Environments in South Africa

Enterococci are among the most common opportunistic hospital pathogens. This study used whole-genome sequencing (WGS) and bioinformatics to determine the antibiotic resistome, genetic support, clones and phylogenetic relationship of Enterococcus faecalis isolated from hospital environments in South Africa. Isolates were recovered from 11 frequently touched sites by patients and healthcare workers in different wards at 4 levels of healthcare (A, B, C and D) in Durban, South Africa. Following microbial identification and antibiotic susceptibility tests. Of the 245 E. faecalis isolates identified, 38 were subjected to WGS on the Illumina MiSeq platform. The tet(M) (31/38, 82%) and erm(C) (16/38, 42%) genes were the most common antibiotic resistome found in isolates originating from the different hospital environments which corroborated with their antibiotic resistance phenotypes. The isolates harboured mobile genetic elements consisting of plasmids (n=11) and prophages (n=14), that were mostly clone-specific. Of note, a large number insertion sequence (IS) families were found with the IS3 (55%), IS5 (42%), IS1595 (40%) and Tn3 Transposon been the most predominate. Microbial typing using WGS data revealed 15 clones with 6 major sequence types (ST) belonging to ST16 (n =7), ST40 (n = 6), ST21 (n =5), ST126 (n = 3), ST23 (n =3) and ST386 (n=3). Phylogenomic analysis showed that the major clones were mostly conserved within specific hospital environments. However, further metadata insights revealed the complex intra-clonal spread of these E. faecalis major clones between the sampling sites within each specific hospital setting. The results of these genomic analyses will offer insights into E. faecalis in the hospital environments relevant in the design of optimal infection prevention strategies in hospital settings.