Angela Gomez-Simmonds, Medini K Annavajhala, Dwayne Seeram, Todd W Hokunson, Heekuk Park, Anne-Catrin Uhlemann
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Six hundred and five CRE isolates collected between 2009 and 2018 first underwent Illumina sequencing for genome-wide genotyping; 435 <i>bla</i> <sub>KPC</sub>-positive isolates were then successfully nanopore sequenced to generate hybrid assemblies including circularized <i>bla</i> <sub>KPC</sub>-harboring plasmids. Phylogenetic analysis and Mash clustering were used to define putative clonal and plasmid transmission clusters, respectively. Overall, CRE isolates belonged to 96 multilocus sequence types (STs) encoding <i>bla</i> <sub>KPC</sub> on 447 plasmids which formed 54 plasmid clusters. We found evidence for clonal transmission in 66% of CRE isolates, over half of which belonged to four clades comprising <i>K. pneumoniae</i> ST258. Plasmid-mediated acquisition of <i>bla</i> <sub>KPC</sub> occurred in 23%-27% of isolates. While most plasmid clusters were small, several plasmids were identified in multiple different species and STs, including a highly promiscuous IncN plasmid and an IncF plasmid putatively spreading <i>bla</i> <sub>KPC</sub> from ST258 to other clones. Overall, this points to both the continued dominance of <i>K. pneumoniae</i> ST258 and the dissemination of <i>bla</i> <sub>KPC</sub> across clones and species by diverse plasmid backbones. These findings support integrating long-read sequencing into genomic surveillance approaches to detect the hitherto silent spread of carbapenem resistance driven by mobile plasmids.</p>","PeriodicalId":12678,"journal":{"name":"Genome research","volume":null,"pages":null},"PeriodicalIF":6.2000,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of <i>bla</i> <sub>KPC</sub>.\",\"authors\":\"Angela Gomez-Simmonds, Medini K Annavajhala, Dwayne Seeram, Todd W Hokunson, Heekuk Park, Anne-Catrin Uhlemann\",\"doi\":\"10.1101/gr.279355.124\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Transmission of carbapenem-resistant Enterobacterales (CRE) in hospitals has been shown to occur through complex, multifarious networks driven by both clonal spread and horizontal transfer mediated by plasmids and other mobile genetic elements. We performed nanopore long-read sequencing on CRE isolates from a large urban hospital system to determine the overall contribution of plasmids to CRE transmission and identify specific plasmids implicated in the spread of <i>bla</i> <sub>KPC</sub> (the <i>Klebsiella pneumoniae</i> carbapenemase [KPC] gene). Six hundred and five CRE isolates collected between 2009 and 2018 first underwent Illumina sequencing for genome-wide genotyping; 435 <i>bla</i> <sub>KPC</sub>-positive isolates were then successfully nanopore sequenced to generate hybrid assemblies including circularized <i>bla</i> <sub>KPC</sub>-harboring plasmids. Phylogenetic analysis and Mash clustering were used to define putative clonal and plasmid transmission clusters, respectively. Overall, CRE isolates belonged to 96 multilocus sequence types (STs) encoding <i>bla</i> <sub>KPC</sub> on 447 plasmids which formed 54 plasmid clusters. We found evidence for clonal transmission in 66% of CRE isolates, over half of which belonged to four clades comprising <i>K. pneumoniae</i> ST258. Plasmid-mediated acquisition of <i>bla</i> <sub>KPC</sub> occurred in 23%-27% of isolates. While most plasmid clusters were small, several plasmids were identified in multiple different species and STs, including a highly promiscuous IncN plasmid and an IncF plasmid putatively spreading <i>bla</i> <sub>KPC</sub> from ST258 to other clones. Overall, this points to both the continued dominance of <i>K. pneumoniae</i> ST258 and the dissemination of <i>bla</i> <sub>KPC</sub> across clones and species by diverse plasmid backbones. 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引用次数: 0
摘要
耐碳青霉烯类肠杆菌(CRE)在医院中的传播已被证明是通过由质粒和其他移动遗传因子介导的克隆传播和水平转移所驱动的复杂而多样的网络进行的。我们对来自一个大型城市医院系统的 CRE 分离物进行了纳米孔长读数测序,以确定质粒对 CRE 传播的总体贡献,并识别与 bla KPC(肺炎克雷伯菌碳青霉烯酶 [KPC] 基因)传播有关的特定质粒。2009-2018 年间收集的 605 株 CRE 分离物首先进行了 Illumina 测序,以进行全基因组基因分型;然后对 435 株 bla KPC 阳性分离物进行了成功的纳米孔测序,以生成包括环化 bla KPC 携带质粒的杂交组合。系统发育分析和 Mash 聚类分别用于确定假定的克隆和质粒传播群。总体而言,CRE 分离物属于 96 个多焦点序列类型(ST),在 447 个质粒上编码 bla KPC,形成 54 个质粒群。我们在 66% 的 CRE 分离物中发现了克隆传播的证据,其中一半以上属于由肺炎克菌 ST258 组成的四个支系。23-27%的分离株通过质粒获得了 bla KPC。虽然大多数质粒群规模较小,但在多个不同物种和 ST 中发现了几种质粒,包括一种高度杂合的 IncN 质粒和一种可能将 bla KPC 从 ST258 传播到其他克隆的 IncF 质粒。总之,这表明肺炎克菌 ST258 仍处于优势地位,而 bla KPC 则通过不同的质粒骨架在克隆和物种间传播。这些发现支持将长读测序纳入基因组监测方法,以检测迄今为止由移动质粒驱动的碳青霉烯耐药性的无声传播。
Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of blaKPC.
Transmission of carbapenem-resistant Enterobacterales (CRE) in hospitals has been shown to occur through complex, multifarious networks driven by both clonal spread and horizontal transfer mediated by plasmids and other mobile genetic elements. We performed nanopore long-read sequencing on CRE isolates from a large urban hospital system to determine the overall contribution of plasmids to CRE transmission and identify specific plasmids implicated in the spread of blaKPC (the Klebsiella pneumoniae carbapenemase [KPC] gene). Six hundred and five CRE isolates collected between 2009 and 2018 first underwent Illumina sequencing for genome-wide genotyping; 435 blaKPC-positive isolates were then successfully nanopore sequenced to generate hybrid assemblies including circularized blaKPC-harboring plasmids. Phylogenetic analysis and Mash clustering were used to define putative clonal and plasmid transmission clusters, respectively. Overall, CRE isolates belonged to 96 multilocus sequence types (STs) encoding blaKPC on 447 plasmids which formed 54 plasmid clusters. We found evidence for clonal transmission in 66% of CRE isolates, over half of which belonged to four clades comprising K. pneumoniae ST258. Plasmid-mediated acquisition of blaKPC occurred in 23%-27% of isolates. While most plasmid clusters were small, several plasmids were identified in multiple different species and STs, including a highly promiscuous IncN plasmid and an IncF plasmid putatively spreading blaKPC from ST258 to other clones. Overall, this points to both the continued dominance of K. pneumoniae ST258 and the dissemination of blaKPC across clones and species by diverse plasmid backbones. These findings support integrating long-read sequencing into genomic surveillance approaches to detect the hitherto silent spread of carbapenem resistance driven by mobile plasmids.
期刊介绍:
Launched in 1995, Genome Research is an international, continuously published, peer-reviewed journal that focuses on research that provides novel insights into the genome biology of all organisms, including advances in genomic medicine.
Among the topics considered by the journal are genome structure and function, comparative genomics, molecular evolution, genome-scale quantitative and population genetics, proteomics, epigenomics, and systems biology. The journal also features exciting gene discoveries and reports of cutting-edge computational biology and high-throughput methodologies.
New data in these areas are published as research papers, or methods and resource reports that provide novel information on technologies or tools that will be of interest to a broad readership. Complete data sets are presented electronically on the journal''s web site where appropriate. The journal also provides Reviews, Perspectives, and Insight/Outlook articles, which present commentary on the latest advances published both here and elsewhere, placing such progress in its broader biological context.