AUTHOR=Mbanga Joshua , Amoako Daniel G. , Abia Akebe L. K. , Allam Mushal , Ismail Arshad , Essack Sabiha Y. 

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

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.648454

DOI=10.3389/fmicb.2021.648454

ISSN=1664-302X

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