Abstract:
Vancomycin resistant enterococci (VRE) are a considerable burden on treatment,
and infection and transmission control. Studying the intricacies on the wholegenome
single nucleotide level is more informative than routine phenotypic
analysis. In this study, 21 clinical isolates of enterococci were first identified by
MALDI-TOF, and disk diffusion and E-test were used to determine antimicrobial
susceptibility profiles. Whole-genome sequencing (WGS) was conducted using
Illumina MiSeq platform. Resistance genes, ST-types, wgSNPs, cgSNPs, pangenomes
of coding and non-coding regions, as well as recombination hotspots were
evaluated for all the isolates using different bioinformatic approaches. The VRE
isolates clustered under two main ST types (ST80, ST203) with some isolates
having very similar whole-genome average nucleotide identities (wgANI). Pan
genome analysis revealed that the isolates were much more unique in their protein coding sequences and showed pronounced heterogeneity as a population. A closer
look at the resistance determinants, in particular, the vancomycin resistance genes
flanked by transposon fragments and recombination loci, revealed uniquely evolved features that emphasized the polyclonal spread of these pathogens. The vancomycinsusceptible
isolates also showed unique genomic features some of which had closely
related genomic profiles as that of the vancomycin-resistant clones of similar ST
types. A notable case was EF6 (vancomycin-susceptible), which was almost
identical (99.91% average nucleotide identity) to EF15 (vancomycin resistant)
except for the vancomycin resistance cassette. A few isolates were too diverse for
batched intergenomic comparative analyses, and one isolate harbored additional
antibiotic resistance determinants uncommon in the other enterococci. This study provided the first insights on the genomic diversity of vancomycinresistant
enterococci circulating in Lebanon. Our results demonstrated how an endto-
end whole-genome sequence-based outbreak surveillance, and resistance profiling
scheme could help in differentiating between closely related VRE isolates, whereas
phenotypic or even classical molecular approaches fail to highlight these
complexities.
