Clostridioides difficile hypervirulent strain ST1 isolated from clinical stool specimens obtained from three Provinces in South Africa.

IF 2.5 3区生物学 Q3 MICROBIOLOGY

Anaerobe Pub Date : 2024-11-28 DOI:10.1016/j.anaerobe.2024.102926

Hlambani Shirinda, Anthony M Smith, Ben Prinsloo, Marleen M Kock, Mishalan Moodley, Mohamed Said, Marthie M Ehlers

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引用次数: 0

Abstract

Objectives: Clostridioides difficile infection is a serious healthcare-associated infection linked to antimicrobial use. The severity of the disease can be associated with hypervirulent ribotypes such as RT027. The study aimed to investigate the molecular epidemiology and genomic characteristics of C. difficile isolates from private and public healthcare settings in South Africa.

Methods: One hundred clinical stool specimens were cultured on cycloserine-cefoxitin-fructose agar. Conventional multiplex polymerase chain reaction (M-PCR) assays were conducted for isolate identification and detection of toxin genes. Genomic characteristics of the isolates were determined using whole genome sequencing (WGS) and data was analysed using pubMLST, EnteroBase, Pathogenwatch and CARD.

Results: One hundred clinically presumptive C. difficile positive stool specimens were collected, of which 62 % (62/100) were confirmed as C. difficile by M-PCR assay. Among the 62 identified C. difficile isolates, 97 % (60/62) were toxigenic, with the most dominant toxin profile being A ⁺ B ⁺ CDT ⁺ according to the M-PCR assay. The results showed that 93 % (40/43) of the WGS analysed C. difficile strains clustered into clades 1 to 5. These 40 strains were categorized into 16 sequence types (STs), with ST1 (clade 2) being the most prevalent, representing 45 % (18/40), this strain is an RT027-associated strain previously epidemic hypervirulent strain. One major cluster (n = 18) comprising ST1 strains was identified in Gauteng Province and all the isolates associated with this cluster showed the same resistome (antimicrobial resistance genes and mutations: CDD-1, aac (6')-Ie-aph (2″)-Ia, PnimB^G and Thr82Ile). The study also identified one strain as ST11, this strain is well known for its zoonotic potential, and two strains were identified as ST37 known as an epidemic strain. Strains from public healthcare settings exhibited genetic similarity, while those from private settings showed greater genetic diversity.

Conclusion: The study reported, for the first time, hypervirulent strains ST1 in Africa and ST11 in South Africa, with a minimum spanning tree indicating an ongoing ST1 outbreak.

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从南非三个省的临床粪便标本中分离出难辨梭菌高毒株ST1。

目的：艰难梭菌感染是一种与抗菌药物使用相关的严重卫生保健相关感染。该疾病的严重程度可能与RT027等高毒性核型有关。该研究旨在调查南非私营和公共卫生机构分离的艰难梭菌的分子流行病学和基因组特征。方法：采用环丝氨酸-头孢西丁-果糖琼脂培养临床粪便标本100例。常规的多重聚合酶链反应（M-PCR）方法用于分离物的鉴定和毒素基因的检测。采用全基因组测序（WGS）确定分离株的基因组特征，利用pubMLST、EnteroBase、Pathogenwatch和CARD对数据进行分析。结果：收集临床推定难辨梭菌阳性粪便标本100份，其中62%（62/100）经M-PCR检测为难辨梭菌。在鉴定的62株艰难梭菌分离株中，97%（60/62）为产毒菌，其中A+B+CDT+为最主要的毒素谱。结果显示，93%（40/43）的WGS检测到艰难梭菌聚集在1 ~ 5枝。这40个菌株被划分为16个序列类型（STs），其中ST1（进化枝2）最为普遍，占45%(18/40)，该菌株是rt027相关的先前流行的高毒力菌株。在豪登省发现了一个由ST1菌株组成的主要聚类（n = 18），与该聚类相关的所有分离株均具有相同的耐药性组(耐药基因和突变：CDD-1、aac （6')-Ie-aph（2″）-Ia、PnimBG和Thr82Ile）。该研究还确定了一种菌株为ST11，这种菌株以其人畜共患的潜力而闻名，两种菌株被确定为ST37，被称为流行病菌株。来自公共医疗机构的菌株表现出遗传相似性，而来自私人医疗机构的菌株表现出更大的遗传多样性。结论：该研究首次在非洲报告了ST1高毒株，在南非报告了ST11高毒株，最小生成树表明正在发生ST1暴发。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Anaerobe 生物-微生物学

CiteScore

5.20

自引率

8.70%

发文量

137

审稿时长

76 days

期刊介绍： Anaerobe is essential reading for those who wish to remain at the forefront of discoveries relating to life processes of strictly anaerobes. The journal is multi-disciplinary, and provides a unique forum for those investigating anaerobic organisms that cause infections in humans and animals, as well as anaerobes that play roles in microbiomes or environmental processes. Anaerobe publishes reviews, mini reviews, original research articles, notes and case reports. Relevant topics fall into the broad categories of anaerobes in human and animal diseases, anaerobes in the microbiome, anaerobes in the environment, diagnosis of anaerobes in clinical microbiology laboratories, molecular biology, genetics, pathogenesis, toxins and antibiotic susceptibility of anaerobic bacteria.