Marais Gert, Moodley Clinton, Claassen-Weitz Shantelle, Patel Fadheela, Prentice Elizabeth, Tootla Hafsah, Nyakutira Nyasha, Lennard Katie, Reddy Kessendri, Bamford Colleen, Niehaus Abraham, Whitelaw Andrew, Brink Adrian
Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa.
National Health Laboratory Service Laboratory, Groote Schuur Hospital, Cape Town, Western Cape, South Africa.
JAC Antimicrob Resist. 2024 Mar 25;6(2):dlae050. doi: 10.1093/jacamr/dlae050. eCollection 2024 Apr.
The molecular epidemiology of carbapenem-resistant Enterobacterales in Cape Town remains largely unknown.
This study aimed to describe the molecular epidemiology, resistome, virulome and mobilome of carbapenem-resistant (CRKP) within Cape Town to guide therapy, antimicrobial stewardship and infection prevention and control practices.
Eighty-five CRKP isolates from hospitalized patients underwent WGS as part of a prospective, multicentre, cross-sectional study, conducted between 1 November 2020 and 30 November 2022, across public-sector and private-sector hospitals in Cape Town, South Africa.
MLST revealed three novel types, ST6785, ST6786 and ST6787, while the most common were ST219, ST307, ST17, ST13 and ST2497. Different predominant clones were noted in each hospital. The most common carbapenemase gene was , detected in 71% of isolates, with detected in 5%. Notably, co-detection of two carbapenemase genes ( and ) occurred in 13% of isolates. The yersiniabactin siderophore was detected in 73% of isolates, and was most commonly associated with the ICE5 mobile element. All carbapenemases were located on plasmids. The genes and colocalized with a ColKP3 replicon type on assembled contigs in 83% and 100% of cases, respectively.
CRKP epidemiology in Cape Town reflects institutionally dominant, rather than regional, clones. The most prevalent carbapenemase gene was , in keeping with CRKP epidemiology in South Africa in general. Emerging clones harbouring both and , such as ST17, ST2497 and the novel ST6787, are a concern due to the limited availability of appropriate antimicrobial agents in South Africa.
开普敦耐碳青霉烯类肠杆菌科细菌的分子流行病学情况仍大多未知。
本研究旨在描述开普敦耐碳青霉烯类肺炎克雷伯菌（CRKP）的分子流行病学、耐药基因组、毒力基因组和可移动基因组，以指导治疗、抗菌药物管理以及感染预防和控制措施。
作为一项前瞻性、多中心、横断面研究的一部分，对2020年11月1日至2022年11月30日期间南非开普敦公立和私立医院住院患者的85株CRKP分离株进行了全基因组测序（WGS）。
多位点序列分型（MLST）显示出三种新型类型，即ST6785、ST6786和ST6787，而最常见的是ST219、ST307、ST17、ST13和ST2497。每家医院都发现了不同的优势克隆。最常见的碳青霉烯酶基因是 ，在71%的分离株中检测到，5%的分离株中检测到 。值得注意的是，13%的分离株中同时检测到两种碳青霉烯酶基因（ 和 ）。73%的分离株中检测到耶尔森菌素铁载体，且最常与ICE5移动元件相关。所有碳青霉烯酶都位于质粒上。在83%和100%的病例中， 基因和 基因分别与组装重叠群上的ColKP3复制子类型共定位。
开普敦的CRKP流行病学反映的是机构主导的克隆，而非区域克隆。最普遍的碳青霉烯酶基因是 ，这与南非总体的CRKP流行病学情况一致。由于南非合适抗菌药物的供应有限，携带 和 的新兴克隆，如ST17、ST2497和新型ST6787，令人担忧。
