{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,11]],"date-time":"2026-08-11T16:27:16Z","timestamp":1786465636204,"version":"build-2736575974"},"reference-count":44,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2021,6,14]],"date-time":"2021-06-14T00:00:00Z","timestamp":1623628800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>We investigated the antibiotic resistome, mobilome, virulome, and phylogenomic lineages of <jats:italic>Enterococcus<\/jats:italic> spp. obtained from a wastewater treatment plant and its associated waters using whole-genome sequencing (WGS) and bioinformatics tools. The whole genomes of <jats:italic>Enterococcus<\/jats:italic> isolates including <jats:italic>Enterococcus faecalis<\/jats:italic> (<jats:italic>n<\/jats:italic> = 4), <jats:italic>Enterococcus faecium<\/jats:italic> (<jats:italic>n<\/jats:italic> = 5), <jats:italic>Enterococcus hirae<\/jats:italic> (<jats:italic>n<\/jats:italic> = 2), and <jats:italic>Enterococcus durans<\/jats:italic> (<jats:italic>n<\/jats:italic> = 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 <jats:italic>E. faecalis<\/jats:italic> isolates that had a common sequence type ST179; the rest had unique sequence types ST841, and ST300. The <jats:italic>E. faecium<\/jats:italic> genomes belonged to 3 sequence types, ST94 (<jats:italic>n<\/jats:italic> = 2), ST361 (<jats:italic>n<\/jats:italic> = 2), and ST1096 (<jats:italic>n<\/jats:italic> = 1). Detected resistance genes included those encoding tetracycline [<jats:italic>tet<\/jats:italic>(S), <jats:italic>tet<\/jats:italic>(M), and <jats:italic>tet(L<\/jats:italic>)], and macrolides [<jats:italic>msr<\/jats:italic>(C), <jats:italic>msr(D)<\/jats:italic>, <jats:italic>erm(B)<\/jats:italic>, and <jats:italic>mef<\/jats:italic>(A)] resistance. Antibiotic resistance genes were associated with insertion sequences (IS6, ISL3, and IS982), and transposons (Tn3 and Tn6000). The <jats:italic>tet(M<\/jats:italic>) resistance gene was consistently found associated with a conjugative transposon protein (TcpC). A total of 20 different virulence genes were identified in <jats:italic>E. faecalis<\/jats:italic> and <jats:italic>E. faecium<\/jats:italic> including those encoding for sex pheromones (<jats:italic>cCF10, cOB1, cad<\/jats:italic>, and <jats:italic>came<\/jats:italic>), adhesion (<jats:italic>ace, SrtA, ebpA, ebpC<\/jats:italic>, and <jats:italic>efaAfs<\/jats:italic>), and cell invasion (<jats:italic>hylA<\/jats:italic> and <jats:italic>hylB<\/jats:italic>). Several virulence genes were associated with the insertion sequence IS256. No virulence genes were detected in <jats:italic>E. hirae<\/jats:italic> and <jats:italic>E. durans.<\/jats:italic> Phylogenetic analysis revealed that all <jats:italic>Enterococcus<\/jats:italic> spp. isolates were more closely related to animal and environmental isolates than clinical isolates. <jats:italic>Enterococcus<\/jats:italic> 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.<\/jats:p>","DOI":"10.3389\/fmicb.2021.648454","type":"journal-article","created":{"date-parts":[[2021,6,14]],"date-time":"2021-06-14T11:23:07Z","timestamp":1623669787000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":28,"title":["Genomic Analysis of Enterococcus spp. Isolated From a Wastewater Treatment Plant and Its Associated Waters in Umgungundlovu District, South Africa"],"prefix":"10.3389","volume":"12","author":[{"given":"Joshua","family":"Mbanga","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel G.","family":"Amoako","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akebe L. 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