{"title":"首次报告从北京一家三甲医院废水中分离出抗碳青霉烯类的密歇根克雷伯菌（Klebsiella michiganensis Co-Harboring bla KPC-2 and TmexCD2-ToprJ2）。","authors":"Jiamin Long, Jiali Chen, Yue Yuan, Shaozhen Yang, Xinya Xie, Xuelian Wu, Yuan Liu, Jinpeng Guo, Yong Chen, Changjun Wang, Xiong Liu","doi":"10.2147/IDR.S448256","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong><i>Klebsiella michiganensis</i> is an emerging human pathogen that causes nosocomial infections. Its prevalence and spread in the environment should not be ignored. This study identified and characterized <i>Klebsiella michiganensis</i> co-harboring <i>bla</i> <sub>KPC-2</sub> and <i>TmexCD2-ToprJ2</i> in hospital wastewater samples.</p><p><strong>Methods: </strong>Twelve <i>K. michiganensis</i> strains were isolated from wastewater samples collected at a tertiary hospital in Beijing, China. The genomic characteristics of <i>K. michiganensis</i> strains were analyzed using whole-genome sequences, providing information on the comparison between the genome of <i>K. michiganensis</i> strains and the reference genome, antibiotic resistance genes (ARGs), virulence genes, secretion systems, and mobile genetic elements (plasmids, insertion sequences [ISs], and prophages).</p><p><strong>Results: </strong>Genome analysis showed that the twelve multi-drug resistant (MDR) strains carried a variety of ARGs and virulence genes, as well as four macromolecular secretion systems (T1SS, T2SS, T5aSS, T5bSS, and T4aP). The genetic environments of both the <i>TmexCD2-ToprJ2</i> gene cluster and <i>bla</i> <sub>KPC-2</sub> gene contained ISs. The plasmids carrying <i>TmexCD2-ToprJ2</i> gene cluster of nine strains in clade 1 and two strains in clade 2 were annotated as IncR plasmid and rep_cluster_1254 type, respectively. The plasmids carrying <i>bla</i> <sub>KPC-2</sub> in 10 strains in clade 1 were identified as IncU, and the plasmids carrying <i>bla</i> <sub>KPC-2</sub> in the k11 and k12 strains in clade 2 were IncU and IncX6. The phylogenetic tree and heatmap revealed that the secretion system of type VI (T6SSi) existed in 10 strains in clade 1, and Type IV (T4SS) only existed in the k11 strain in clade 2. In addition, <i>K. michiganensis</i> strains carried 13 plasmids, 14 ISs, and 138 prophages.</p><p><strong>Conclusion: </strong>In this study, the whole genome sequencing demonstrated the diversity of <i>K. michiganensis</i> genome despite 12 <i>K. michiganensis</i> strains from a hospital wastewater, which lays the foundation for further genetic research and drug resistance gene transmission.</p>","PeriodicalId":13577,"journal":{"name":"Infection and Drug Resistance","volume":"17 ","pages":"5117-5128"},"PeriodicalIF":2.9000,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11589776/pdf/","citationCount":"0","resultStr":"{\"title\":\"First Report of Carbapenem-Resistant <i>Klebsiella michiganensis</i> Co-Harboring <i>bla</i> <sub>KPC-2</sub> and <i>TmexCD2-ToprJ2</i> Isolated from Wastewater at a Tertiary Hospital in Beijing.\",\"authors\":\"Jiamin Long, Jiali Chen, Yue Yuan, Shaozhen Yang, Xinya Xie, Xuelian Wu, Yuan Liu, Jinpeng Guo, Yong Chen, Changjun Wang, Xiong Liu\",\"doi\":\"10.2147/IDR.S448256\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong><i>Klebsiella michiganensis</i> is an emerging human pathogen that causes nosocomial infections. Its prevalence and spread in the environment should not be ignored. This study identified and characterized <i>Klebsiella michiganensis</i> co-harboring <i>bla</i> <sub>KPC-2</sub> and <i>TmexCD2-ToprJ2</i> in hospital wastewater samples.</p><p><strong>Methods: </strong>Twelve <i>K. michiganensis</i> strains were isolated from wastewater samples collected at a tertiary hospital in Beijing, China. The genomic characteristics of <i>K. michiganensis</i> strains were analyzed using whole-genome sequences, providing information on the comparison between the genome of <i>K. michiganensis</i> strains and the reference genome, antibiotic resistance genes (ARGs), virulence genes, secretion systems, and mobile genetic elements (plasmids, insertion sequences [ISs], and prophages).</p><p><strong>Results: </strong>Genome analysis showed that the twelve multi-drug resistant (MDR) strains carried a variety of ARGs and virulence genes, as well as four macromolecular secretion systems (T1SS, T2SS, T5aSS, T5bSS, and T4aP). The genetic environments of both the <i>TmexCD2-ToprJ2</i> gene cluster and <i>bla</i> <sub>KPC-2</sub> gene contained ISs. The plasmids carrying <i>TmexCD2-ToprJ2</i> gene cluster of nine strains in clade 1 and two strains in clade 2 were annotated as IncR plasmid and rep_cluster_1254 type, respectively. The plasmids carrying <i>bla</i> <sub>KPC-2</sub> in 10 strains in clade 1 were identified as IncU, and the plasmids carrying <i>bla</i> <sub>KPC-2</sub> in the k11 and k12 strains in clade 2 were IncU and IncX6. The phylogenetic tree and heatmap revealed that the secretion system of type VI (T6SSi) existed in 10 strains in clade 1, and Type IV (T4SS) only existed in the k11 strain in clade 2. In addition, <i>K. michiganensis</i> strains carried 13 plasmids, 14 ISs, and 138 prophages.</p><p><strong>Conclusion: </strong>In this study, the whole genome sequencing demonstrated the diversity of <i>K. michiganensis</i> genome despite 12 <i>K. michiganensis</i> strains from a hospital wastewater, which lays the foundation for further genetic research and drug resistance gene transmission.</p>\",\"PeriodicalId\":13577,\"journal\":{\"name\":\"Infection and Drug Resistance\",\"volume\":\"17 \",\"pages\":\"5117-5128\"},\"PeriodicalIF\":2.9000,\"publicationDate\":\"2024-11-21\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11589776/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Infection and Drug Resistance\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.2147/IDR.S448256\",\"RegionNum\":3,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q2\",\"JCRName\":\"INFECTIOUS DISEASES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Infection and Drug Resistance","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.2147/IDR.S448256","RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"INFECTIOUS DISEASES","Score":null,"Total":0}
引用次数: 0
摘要
背景：密歇根克雷伯氏菌是一种新出现的人类病原体，可引起医院内感染。它在环境中的流行和传播不容忽视。本研究发现并鉴定了医院废水样本中同时携带 bla KPC-2 和 TmexCD2-ToprJ2 的密歇根克雷伯氏菌：方法：从中国北京一家三甲医院采集的废水样本中分离出12株米奇根氏克雷伯菌。利用全基因组序列分析了K. michiganensis菌株的基因组特征，提供了K. michiganensis菌株基因组与参考基因组、抗生素耐药基因（ARGs）、毒力基因、分泌系统和移动遗传元件（质粒、插入序列[ISs]和噬菌体）之间的比较信息：基因组分析表明，12株多重耐药菌株携带多种ARGs和毒力基因，以及4种大分子分泌系统（T1SS、T2SS、T5aSS、T5bSS和T4aP）。TmexCD2-ToprJ2 基因簇和 bla KPC-2 基因的遗传环境都含有 ISs。携带TmexCD2-ToprJ2基因簇的质粒在支系1中有9株，在支系2中有2株，分别被注释为IncR质粒和rep_cluster_1254型。支系 1 中 10 株携带 bla KPC-2 的质粒被鉴定为 IncU，支系 2 中 k11 株和 k12 株携带 bla KPC-2 的质粒被鉴定为 IncU 和 IncX6。系统发生树和热图显示，支系 1 中的 10 株存在 VI 型分泌系统（T6SSi），支系 2 中的 k11 株只存在 IV 型分泌系统（T4SS）。此外，K. michiganensis 菌株还携带 13 个质粒、14 个 IS 和 138 个噬菌体：本研究通过对医院废水中的 12 株 K. michiganensis 进行全基因组测序，证明了 K. michiganensis 基因组的多样性，为进一步开展基因研究和耐药基因传播奠定了基础。
First Report of Carbapenem-Resistant Klebsiella michiganensis Co-Harboring blaKPC-2 and TmexCD2-ToprJ2 Isolated from Wastewater at a Tertiary Hospital in Beijing.
Background: Klebsiella michiganensis is an emerging human pathogen that causes nosocomial infections. Its prevalence and spread in the environment should not be ignored. This study identified and characterized Klebsiella michiganensis co-harboring blaKPC-2 and TmexCD2-ToprJ2 in hospital wastewater samples.
Methods: Twelve K. michiganensis strains were isolated from wastewater samples collected at a tertiary hospital in Beijing, China. The genomic characteristics of K. michiganensis strains were analyzed using whole-genome sequences, providing information on the comparison between the genome of K. michiganensis strains and the reference genome, antibiotic resistance genes (ARGs), virulence genes, secretion systems, and mobile genetic elements (plasmids, insertion sequences [ISs], and prophages).
Results: Genome analysis showed that the twelve multi-drug resistant (MDR) strains carried a variety of ARGs and virulence genes, as well as four macromolecular secretion systems (T1SS, T2SS, T5aSS, T5bSS, and T4aP). The genetic environments of both the TmexCD2-ToprJ2 gene cluster and blaKPC-2 gene contained ISs. The plasmids carrying TmexCD2-ToprJ2 gene cluster of nine strains in clade 1 and two strains in clade 2 were annotated as IncR plasmid and rep_cluster_1254 type, respectively. The plasmids carrying blaKPC-2 in 10 strains in clade 1 were identified as IncU, and the plasmids carrying blaKPC-2 in the k11 and k12 strains in clade 2 were IncU and IncX6. The phylogenetic tree and heatmap revealed that the secretion system of type VI (T6SSi) existed in 10 strains in clade 1, and Type IV (T4SS) only existed in the k11 strain in clade 2. In addition, K. michiganensis strains carried 13 plasmids, 14 ISs, and 138 prophages.
Conclusion: In this study, the whole genome sequencing demonstrated the diversity of K. michiganensis genome despite 12 K. michiganensis strains from a hospital wastewater, which lays the foundation for further genetic research and drug resistance gene transmission.
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