A Genomic Snapshot of Antibiotic-ResistantEnterococcus faecalis within Public Hospital Environments in South Africa.

IF 1.1 Q4 PUBLIC, ENVIRONMENTAL & OCCUPATIONAL HEALTH
Global Health Epidemiology and Genomics Pub Date : 2023-06-12 eCollection Date: 2023-01-01 DOI:10.1155/2023/6639983
Christiana O Shobo, Daniel G Amoako, Mushal Allam, Arshad Ismail, Sabiha Y Essack, Linda A Bester
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Abstract

Enterococci are among the most common opportunistic hospital pathogens. This study used whole-genome sequencing (WGS) and bioinformatics to determine the antibiotic resistome, mobile genetic elements, clone and phylogenetic relationship of Enterococcus faecalis isolated from hospital environments in South Africa. This study was carried out from September to November 2017. Isolates were recovered from 11 frequently touched sites by patients and healthcare workers in different wards at 4 levels of healthcare (A, B, C, and D) in Durban, South Africa. Out of the 245 identified E. faecalis isolates, 38 isolates underwent whole-genome sequencing (WGS) on the Illumina MiSeq platform, following microbial identification and antibiotic susceptibility tests. The tet(M) (31/38, 82%) and erm(C) (16/38, 42%) genes were the most common antibiotic-resistant genes found in isolates originating from different hospital environments which corroborated with their antibiotic resistance phenotypes. The isolates harboured mobile genetic elements consisting of plasmids (n = 11) and prophages (n = 14) that were mostly clone-specific. Of note, a large number of insertion sequence (IS) families were found on the IS3 (55%), IS5 (42%), IS1595 (40%), and Tn3 transposons the most predominant. Microbial typing using WGS data revealed 15 clones with 6 major sequence types (ST) belonging to ST16 (n = 7), ST40 (n = 6), ST21 (n = 5), ST126 (n = 3), ST23 (n = 3), and ST386 (n = 3). Phylogenomic analysis showed that the major clones were mostly conserved within specific hospital environments. However, further metadata insights revealed the complex intraclonal spread of these E. faecalis major clones between the sampling sites within each specific hospital setting. The results of these genomic analyses will offer insights into antibiotic-resistantE. faecalis in hospital environments relevant to the design of optimal infection prevention strategies in hospital settings.

Abstract Image

南非公立医院环境中耐药粪肠球菌的基因组快照》(A Genomic Snapshot of Antibiotic-ResantEnterococcus faecalis within Public Hospital Environments in South Africa)。
肠球菌是最常见的机会性医院病原体之一。本研究利用全基因组测序(WGS)和生物信息学确定了从南非医院环境中分离的粪肠球菌的抗生素耐药性组、移动遗传因子、克隆和系统发育关系。本研究于 2017 年 9 月至 11 月进行。分离物是从南非德班 4 级医疗机构(A、B、C 和 D 级)不同病房的 11 个患者和医护人员经常接触的部位回收的。在鉴定出的 245 个粪肠球菌分离物中,有 38 个分离物在微生物鉴定和抗生素药敏试验后,在 Illumina MiSeq 平台上进行了全基因组测序(WGS)。tet(M) (31/38,82%)和erm(C) (16/38,42%)基因是来自不同医院环境的分离物中最常见的抗生素耐药基因,这与它们的抗生素耐药表型相吻合。分离物携带的移动遗传元件包括质粒(11 个)和噬菌体(14 个),它们大多具有克隆特异性。值得注意的是,在 IS3(55%)、IS5(42%)、IS1595(40%)和 Tn3 转座子上发现了大量插入序列(IS)家族。利用 WGS 数据进行的微生物分型显示,15 个克隆有 6 种主要序列类型 (ST),分别属于 ST16(n = 7)、ST40(n = 6)、ST21(n = 5)、ST126(n = 3)、ST23(n = 3)和 ST386(n = 3)。系统发生组分析表明,主要克隆大多在特定的医院环境中保持不变。不过,进一步的元数据分析显示,这些粪肠球菌主要克隆在每个特定医院环境中的采样点之间存在复杂的克隆内传播。这些基因组分析的结果将有助于深入了解医院环境中的耐抗生素粪肠球菌,从而设计出最佳的医院感染预防策略。
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来源期刊
Global Health Epidemiology and Genomics
Global Health Epidemiology and Genomics PUBLIC, ENVIRONMENTAL & OCCUPATIONAL HEALTH-
CiteScore
1.40
自引率
0.00%
发文量
10
审稿时长
20 weeks
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