Genomic Analysis of Enterococcus spp. Isolated From a Wastewater Treatment Plant and Its Associated Waters in Umgungundlovu District, South Africa
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 Enteroc...
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doaj-a8ea2c3e678e4f399ec317c8cc5fb9522021-06-14T11:23:03ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2021-06-011210.3389/fmicb.2021.648454648454Genomic Analysis of Enterococcus spp. Isolated From a Wastewater Treatment Plant and Its Associated Waters in Umgungundlovu District, South AfricaJoshua Mbanga0Joshua Mbanga1Daniel G. Amoako2Akebe L. K. Abia3Mushal Allam4Arshad Ismail5Sabiha Y. Essack6Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South AfricaDepartment of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, ZimbabweAntimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South AfricaAntimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South AfricaSequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South AfricaSequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South AfricaAntimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Durban, South AfricaWe 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.https://www.frontiersin.org/articles/10.3389/fmicb.2021.648454/fullEnterococcus spp.whole-genome sequencingwastewater treatment plantantibiotic resistanceSouth Africa |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Joshua Mbanga Joshua Mbanga Daniel G. Amoako Akebe L. K. Abia Mushal Allam Arshad Ismail Sabiha Y. Essack |
spellingShingle |
Joshua Mbanga Joshua Mbanga Daniel G. Amoako Akebe L. K. Abia Mushal Allam Arshad Ismail Sabiha Y. Essack Genomic Analysis of Enterococcus spp. Isolated From a Wastewater Treatment Plant and Its Associated Waters in Umgungundlovu District, South Africa Frontiers in Microbiology Enterococcus spp. whole-genome sequencing wastewater treatment plant antibiotic resistance South Africa |
author_facet |
Joshua Mbanga Joshua Mbanga Daniel G. Amoako Akebe L. K. Abia Mushal Allam Arshad Ismail Sabiha Y. Essack |
author_sort |
Joshua Mbanga |
title |
Genomic Analysis of Enterococcus spp. Isolated From a Wastewater Treatment Plant and Its Associated Waters in Umgungundlovu District, South Africa |
title_short |
Genomic Analysis of Enterococcus spp. Isolated From a Wastewater Treatment Plant and Its Associated Waters in Umgungundlovu District, South Africa |
title_full |
Genomic Analysis of Enterococcus spp. Isolated From a Wastewater Treatment Plant and Its Associated Waters in Umgungundlovu District, South Africa |
title_fullStr |
Genomic Analysis of Enterococcus spp. Isolated From a Wastewater Treatment Plant and Its Associated Waters in Umgungundlovu District, South Africa |
title_full_unstemmed |
Genomic Analysis of Enterococcus spp. Isolated From a Wastewater Treatment Plant and Its Associated Waters in Umgungundlovu District, South Africa |
title_sort |
genomic analysis of enterococcus spp. isolated from a wastewater treatment plant and its associated waters in umgungundlovu district, south africa |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2021-06-01 |
description |
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. |
topic |
Enterococcus spp. whole-genome sequencing wastewater treatment plant antibiotic resistance South Africa |
url |
https://www.frontiersin.org/articles/10.3389/fmicb.2021.648454/full |
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