{"title":"印度焦特布尔一株罕见的耐碳青霉烯类抗生素 ST16 肺炎克雷伯氏菌在重症监护病房内出现最后抗菌药耐药性的基因组学启示。","authors":"Ardhendu Chakrabortty , Aastha Kapoor , Tamal Dey , Sharvika Subodh Khochare , Lavanya Arora , Vibhor Tak , Vijaya Lakshmi Nag , Pradeep Kumar Bhatia , Manoharan Shankar","doi":"10.1016/j.jgar.2024.05.008","DOIUrl":null,"url":null,"abstract":"<div><h3>Objectives</h3><p>To investigate the genomic differences between two extensively drug resistant, ST16 strains of <em>Klebsiella pneumoniae</em> recovered from patients in the same ICU, one of which was colistin resistant.</p></div><div><h3>Methods</h3><p>Antimicrobial susceptibilities of the isolates were determined using VITEK-2. Hybrid assemblies for both strains were generated using Oxford Nanopore and Illumina technologies. The sequence type, capsule type, O-locus type, antimicrobial resistance determinants and plasmids carried by the isolates were inferred from the genome sequence. The phylogenetic placement, antimicrobial resistance, and virulence determinants of the isolates relative to a collection (<em>n</em> = 871) of ST16 isolates were assessed.</p></div><div><h3>Results</h3><p>Both BC16, a colistin-resistant blood stream isolate and U23, a colistin-sensitive urinary isolate displayed near-identical antimicrobial resistance profiles and genome sequences with varying plasmid profiles. The BC16 genome only had 21 SNPs relative to U23 and belonged to the same capsule, O-antigen locus and multi-locus sequence types. The <em>mgrB</em> locus in BC16 was disrupted by an IS<em>5</em> element. Phylogenetically, U23 and BC16 were placed on a clade with 4 strains belonging to K-type K48 and O-type O2a as opposed to majority (<em>n</em> = 807) of the strains (K-type K51 and O-type O3b).</p></div><div><h3>Conclusions</h3><p>BC16 was a colistin resistant derivative of U23, which evolved colistin resistance by an IS<em>5</em>-mediated disruption of the <em>mgrB</em> locus, likely during treatment of the index patient with colistin in the ICU. The strains belong to a rare subtype of ST16 with unique capsular and O-antigen types underscoring the utility of genomic surveillance networks and open-access genomic surveillance data in tracking problem clones.</p></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":null,"pages":null},"PeriodicalIF":3.7000,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2213716524000961/pdfft?md5=1c22b3fbc46382da8c730977c5969533&pid=1-s2.0-S2213716524000961-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Genomic insights into in-ICU emergence of last-resort antimicrobial resistance in a rare, carbapenem resistant, ST16 Klebsiella pneumoniae strain from Jodhpur, India\",\"authors\":\"Ardhendu Chakrabortty , Aastha Kapoor , Tamal Dey , Sharvika Subodh Khochare , Lavanya Arora , Vibhor Tak , Vijaya Lakshmi Nag , Pradeep Kumar Bhatia , Manoharan Shankar\",\"doi\":\"10.1016/j.jgar.2024.05.008\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Objectives</h3><p>To investigate the genomic differences between two extensively drug resistant, ST16 strains of <em>Klebsiella pneumoniae</em> recovered from patients in the same ICU, one of which was colistin resistant.</p></div><div><h3>Methods</h3><p>Antimicrobial susceptibilities of the isolates were determined using VITEK-2. Hybrid assemblies for both strains were generated using Oxford Nanopore and Illumina technologies. The sequence type, capsule type, O-locus type, antimicrobial resistance determinants and plasmids carried by the isolates were inferred from the genome sequence. The phylogenetic placement, antimicrobial resistance, and virulence determinants of the isolates relative to a collection (<em>n</em> = 871) of ST16 isolates were assessed.</p></div><div><h3>Results</h3><p>Both BC16, a colistin-resistant blood stream isolate and U23, a colistin-sensitive urinary isolate displayed near-identical antimicrobial resistance profiles and genome sequences with varying plasmid profiles. The BC16 genome only had 21 SNPs relative to U23 and belonged to the same capsule, O-antigen locus and multi-locus sequence types. The <em>mgrB</em> locus in BC16 was disrupted by an IS<em>5</em> element. Phylogenetically, U23 and BC16 were placed on a clade with 4 strains belonging to K-type K48 and O-type O2a as opposed to majority (<em>n</em> = 807) of the strains (K-type K51 and O-type O3b).</p></div><div><h3>Conclusions</h3><p>BC16 was a colistin resistant derivative of U23, which evolved colistin resistance by an IS<em>5</em>-mediated disruption of the <em>mgrB</em> locus, likely during treatment of the index patient with colistin in the ICU. The strains belong to a rare subtype of ST16 with unique capsular and O-antigen types underscoring the utility of genomic surveillance networks and open-access genomic surveillance data in tracking problem clones.</p></div>\",\"PeriodicalId\":15936,\"journal\":{\"name\":\"Journal of global antimicrobial resistance\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.7000,\"publicationDate\":\"2024-05-21\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S2213716524000961/pdfft?md5=1c22b3fbc46382da8c730977c5969533&pid=1-s2.0-S2213716524000961-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of global antimicrobial resistance\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2213716524000961\",\"RegionNum\":3,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"INFECTIOUS DISEASES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of global antimicrobial resistance","FirstCategoryId":"3","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2213716524000961","RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"INFECTIOUS DISEASES","Score":null,"Total":0}
引用次数: 0
摘要
目的:研究从同一重症监护室的患者身上发现的两株具有广泛耐药性的 ST16 肺炎克雷伯菌的基因组差异:研究从同一重症监护室患者身上分离出的两株具有广泛耐药性的 ST16 型肺炎克雷伯菌(其中一株对可乐定耐药)之间的基因组差异:方法:使用 VITEK-2 测定分离菌株的抗菌药敏感性。使用牛津纳米孔和 Illumina 技术生成了这两种菌株的杂交组合。根据基因组序列推断了分离株的序列类型、胶囊类型、O-病灶类型、抗菌药耐药性决定因子和质粒。评估了分离株相对于 ST16 分离株集合(n=871)的系统发育位置、抗菌药耐药性和毒力决定因素:结果:耐秋水仙素的血流分离株 BC16 和对秋水仙素敏感的尿液分离株 U23 都显示出近乎相同的抗菌药耐药性特征和基因组序列,但质粒特征各不相同。BC16 基因组与 U23 相比只有 21 个 SNPs,属于相同的胶囊、O 抗原位点和多焦点序列类型。BC16 中的 mgrB 基因座被一个 IS5 元素破坏。在系统发育上,U23 和 BC16 与 4 株属于 K 型 K48 和 O 型 O2a 的菌株组成一个支系,而大多数(n=807)菌株(K 型 K51 和 O 型 O3b)则不属于 K 型 K48 和 O 型 O2a:结论:BC16是U23的耐秋水仙素衍生菌株,它通过IS5介导的mgrB基因座破坏进化出秋水仙素耐药性,很可能是在重症监护室用秋水仙素治疗该患者时产生的。这些菌株属于 ST16 的一种罕见亚型,具有独特的荚膜和 O 抗原类型,突出表明了基因组监控网络和开放式基因组监控数据在追踪问题克隆方面的实用性。
Genomic insights into in-ICU emergence of last-resort antimicrobial resistance in a rare, carbapenem resistant, ST16 Klebsiella pneumoniae strain from Jodhpur, India
Objectives
To investigate the genomic differences between two extensively drug resistant, ST16 strains of Klebsiella pneumoniae recovered from patients in the same ICU, one of which was colistin resistant.
Methods
Antimicrobial susceptibilities of the isolates were determined using VITEK-2. Hybrid assemblies for both strains were generated using Oxford Nanopore and Illumina technologies. The sequence type, capsule type, O-locus type, antimicrobial resistance determinants and plasmids carried by the isolates were inferred from the genome sequence. The phylogenetic placement, antimicrobial resistance, and virulence determinants of the isolates relative to a collection (n = 871) of ST16 isolates were assessed.
Results
Both BC16, a colistin-resistant blood stream isolate and U23, a colistin-sensitive urinary isolate displayed near-identical antimicrobial resistance profiles and genome sequences with varying plasmid profiles. The BC16 genome only had 21 SNPs relative to U23 and belonged to the same capsule, O-antigen locus and multi-locus sequence types. The mgrB locus in BC16 was disrupted by an IS5 element. Phylogenetically, U23 and BC16 were placed on a clade with 4 strains belonging to K-type K48 and O-type O2a as opposed to majority (n = 807) of the strains (K-type K51 and O-type O3b).
Conclusions
BC16 was a colistin resistant derivative of U23, which evolved colistin resistance by an IS5-mediated disruption of the mgrB locus, likely during treatment of the index patient with colistin in the ICU. The strains belong to a rare subtype of ST16 with unique capsular and O-antigen types underscoring the utility of genomic surveillance networks and open-access genomic surveillance data in tracking problem clones.
期刊介绍:
The Journal of Global Antimicrobial Resistance (JGAR) is a quarterly online journal run by an international Editorial Board that focuses on the global spread of antibiotic-resistant microbes.
JGAR is a dedicated journal for all professionals working in research, health care, the environment and animal infection control, aiming to track the resistance threat worldwide and provides a single voice devoted to antimicrobial resistance (AMR).
Featuring peer-reviewed and up to date research articles, reviews, short notes and hot topics JGAR covers the key topics related to antibacterial, antiviral, antifungal and antiparasitic resistance.