Abstract
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.
Highlights
MATERIALS AND METHODSThe efficiency of wastewater treatment plants (WWTPs) is critical to preventing the spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) into the environment (Karkman et al, 2017; Alexander et al, 2020)
Selected isolates consisted of E. faecalis (4 isolates), E. faecium (5), E. hirae (2), and E. durans (1) (Supplementary Table 1)
The resistance profile TET-SXT-STR was found in two isolates, one E. faecalis obtained from raw influent and one E. durans isolate from the influent
Summary
The efficiency of wastewater treatment plants (WWTPs) is critical to preventing the spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) into the environment (Karkman et al, 2017; Alexander et al, 2020). Enterococcus species are Gram positive non-sporulating organisms that mainly exist as commensals in the intestinal flora of healthy animals and humans. They can be excreted into environmental sources including soil and surface water as fecal matter and are commonly used as indicator organisms in water environments (Berendonk et al, 2013; Karkman et al, 2018). The application of WGS to antibiotic resistance surveillance remains largely confined to clinical and animal settings, with very little attention given to the environment (Hendriksen et al, 2019; Su et al, 2019; WHO, 2020). We assayed the role of the water environment in the dissemination of multi-drug resistant Enterococcus spp. which could be of clinical or veterinary importance
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