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We investigated the antibiotic resistome, mobilome, virulome, and phylogenomic lineages of  Enterococcus  spp. obtained from a wastewater treatment plant and its associated waters using whole-genome sequencing (WGS) and bioinformatics tools. The whole genomes of  Enterococcus  isolates including  Enterococcus faecalis  ( n  = 4),  Enterococcus faecium  ( n  = 5),  Enterococcus hirae  ( n  = 2), and  Enterococcus durans  ( n  = 1) with similar resistance patterns from different sampling sites and time points were sequenced on an Illumina MiSeq machine. Multilocus sequence typing (MLST) analysis revealed two  E. faecalis  isolates that had a common sequence type ST179; the rest had unique sequence types ST841, and ST300. The  E. faecium  genomes belonged to 3 sequence types, ST94 ( n  = 2), ST361 ( n  = 2), and ST1096 ( n  = 1). Detected resistance genes included those encoding tetracycline [ tet (S),  tet (M), and  tet(L )], and macrolides [ msr (C),  msr(D) ,  erm(B) , and  mef (A)] resistance. Antibiotic resistance genes were associated with insertion sequences (IS6, ISL3, and IS982), and transposons (Tn3 and Tn6000). The  tet(M ) resistance gene was consistently found associated with a conjugative transposon protein (TcpC). A total of 20 different virulence genes were identified in  E. faecalis  and  E. faecium  including those encoding for sex pheromones ( cCF10, cOB1, cad , and  came ), adhesion ( ace, SrtA, ebpA, ebpC , and  efaAfs ), and cell invasion ( hylA  and  hylB ). Several virulence genes were associated with the insertion sequence IS256. No virulence genes were detected in  E. hirae  and  E. durans.  Phylogenetic analysis revealed that all  Enterococcus  spp. isolates were more closely related to animal and environmental isolates than clinical isolates.  Enterococcus  spp. with a diverse range of resistance and virulence genes as well as associated mobile genetic elements (MGEs) exist in the wastewater environment in South Africa.

Genomic Analysis of Enterococcus spp. Isolated From a Wastewater Treatment Plant and Its Associated Waters in Umgungundlovu District, South Africa