{"title":"揭示携带 blaNDM-1 的准肺炎克雷伯氏菌临床分离株的基因组特征。","authors":"","doi":"10.1016/j.jgar.2024.05.022","DOIUrl":null,"url":null,"abstract":"<div><h3>Objective</h3><p>Despite the increasing reports of <em>bla</em><sub>NDM</sub> in <em>Enterobacterales</em> in Brazil, comprehensive whole genome sequencing (WGS) data remain scarce. To address this knowledge gap, our study focuses on the characterization of the genome of an New Delhi Metallo-β-lactamase (NDM)-1-producing <em>Klebsiella quasipneumoniae</em> subsp. <em>quasipneumoniae</em> (KQPN) clinical strain isolated in Brazil.</p></div><div><h3>Methods</h3><p>The antimicrobial susceptibility profile of the A-73.113 strain was performed by agar dilution or broth microdilution following the Brazilian Antimicrobial Susceptibility Testing Committee/European Committee on Antimicrobial Susceptibility Testing recommendations. WGS was performed using the Illumina® NextSeq platform and the generated reads were assembled using the SPAdes software. The sequences obtained were submitted to the bioinformatics pipelines to determine the sequence type, resistome, plasmidome, and virulome.</p></div><div><h3>Results</h3><p>The A-73.113 strain was identified as KQPN and was susceptible to polymyxins (MICs, ≤0.25 µg/mL), tigecycline (MIC, 0.5 µg/mL), ciprofloxacin (MIC, 0.5 µg/mL), and levofloxacin (MIC, 1 µg/mL). WGS analysis revealed the presence of genes conferring resistance to β-lactams (<em>bla</em><sub>NDM-1</sub>, <em>bla</em><sub>CTX-M-15</sub>, <em>bla</em><sub>OXA-9</sub>, <em>bla</em><sub>OKP-A-5</sub>, <em>bla</em><sub>TEM-1</sub>), aminoglycosides [<em>aph(3′)-VI, aadA1, aac(6′)-Ib</em>], and fluoroquinolones (<em>oqxAB, qnrS1, aac(6′)-Ib-cr</em>]. Additionally, the presence of the plasmid replicons Col(pHAD28), IncFIA(HI1), IncFIB(K) (pCAV1099-114), IncFIB(pQil), and IncFII(K), as well as virulence-encoding genes <em>fimABCDEFGHIK</em> (type 1 fimbria), <em>pilW</em> (type IV pili), <em>iutA</em> (aerobactin), <em>entABCDEFS</em>/<em>fepABCDG</em>/<em>fes</em> (Ent siderophores), <em>iroE</em> (salmochelin), and <em>allABCDRS</em> (allantoin utilization) was verified. Furthermore, we found that the A-73.113 strain belongs to ST1040.</p></div><div><h3>Conclusions</h3><p>Here we report the genomic characteristics of an NDM-1-producing KQPN ST1040 strain isolated from blood cultures in Brazil. These data will enhance our comprehension of how this species contributes to the acquisition and dissemination of <em>bla</em><sub>NDM-1</sub> in Brazilian nosocomial settings.</p></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":null,"pages":null},"PeriodicalIF":3.7000,"publicationDate":"2024-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2213716524001103/pdfft?md5=12cf0fac85f82b861c677a2563aeface&pid=1-s2.0-S2213716524001103-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Unravelling the genomic characteristics of a Klebsiella quasipneumoniae clinical isolate carrying blaNDM-1\",\"authors\":\"\",\"doi\":\"10.1016/j.jgar.2024.05.022\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Objective</h3><p>Despite the increasing reports of <em>bla</em><sub>NDM</sub> in <em>Enterobacterales</em> in Brazil, comprehensive whole genome sequencing (WGS) data remain scarce. To address this knowledge gap, our study focuses on the characterization of the genome of an New Delhi Metallo-β-lactamase (NDM)-1-producing <em>Klebsiella quasipneumoniae</em> subsp. <em>quasipneumoniae</em> (KQPN) clinical strain isolated in Brazil.</p></div><div><h3>Methods</h3><p>The antimicrobial susceptibility profile of the A-73.113 strain was performed by agar dilution or broth microdilution following the Brazilian Antimicrobial Susceptibility Testing Committee/European Committee on Antimicrobial Susceptibility Testing recommendations. WGS was performed using the Illumina® NextSeq platform and the generated reads were assembled using the SPAdes software. The sequences obtained were submitted to the bioinformatics pipelines to determine the sequence type, resistome, plasmidome, and virulome.</p></div><div><h3>Results</h3><p>The A-73.113 strain was identified as KQPN and was susceptible to polymyxins (MICs, ≤0.25 µg/mL), tigecycline (MIC, 0.5 µg/mL), ciprofloxacin (MIC, 0.5 µg/mL), and levofloxacin (MIC, 1 µg/mL). WGS analysis revealed the presence of genes conferring resistance to β-lactams (<em>bla</em><sub>NDM-1</sub>, <em>bla</em><sub>CTX-M-15</sub>, <em>bla</em><sub>OXA-9</sub>, <em>bla</em><sub>OKP-A-5</sub>, <em>bla</em><sub>TEM-1</sub>), aminoglycosides [<em>aph(3′)-VI, aadA1, aac(6′)-Ib</em>], and fluoroquinolones (<em>oqxAB, qnrS1, aac(6′)-Ib-cr</em>]. Additionally, the presence of the plasmid replicons Col(pHAD28), IncFIA(HI1), IncFIB(K) (pCAV1099-114), IncFIB(pQil), and IncFII(K), as well as virulence-encoding genes <em>fimABCDEFGHIK</em> (type 1 fimbria), <em>pilW</em> (type IV pili), <em>iutA</em> (aerobactin), <em>entABCDEFS</em>/<em>fepABCDG</em>/<em>fes</em> (Ent siderophores), <em>iroE</em> (salmochelin), and <em>allABCDRS</em> (allantoin utilization) was verified. Furthermore, we found that the A-73.113 strain belongs to ST1040.</p></div><div><h3>Conclusions</h3><p>Here we report the genomic characteristics of an NDM-1-producing KQPN ST1040 strain isolated from blood cultures in Brazil. These data will enhance our comprehension of how this species contributes to the acquisition and dissemination of <em>bla</em><sub>NDM-1</sub> in Brazilian nosocomial settings.</p></div>\",\"PeriodicalId\":15936,\"journal\":{\"name\":\"Journal of global antimicrobial resistance\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.7000,\"publicationDate\":\"2024-06-07\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S2213716524001103/pdfft?md5=12cf0fac85f82b861c677a2563aeface&pid=1-s2.0-S2213716524001103-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/S2213716524001103\",\"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/S2213716524001103","RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"INFECTIOUS DISEASES","Score":null,"Total":0}
Unravelling the genomic characteristics of a Klebsiella quasipneumoniae clinical isolate carrying blaNDM-1
Objective
Despite the increasing reports of blaNDM in Enterobacterales in Brazil, comprehensive whole genome sequencing (WGS) data remain scarce. To address this knowledge gap, our study focuses on the characterization of the genome of an New Delhi Metallo-β-lactamase (NDM)-1-producing Klebsiella quasipneumoniae subsp. quasipneumoniae (KQPN) clinical strain isolated in Brazil.
Methods
The antimicrobial susceptibility profile of the A-73.113 strain was performed by agar dilution or broth microdilution following the Brazilian Antimicrobial Susceptibility Testing Committee/European Committee on Antimicrobial Susceptibility Testing recommendations. WGS was performed using the Illumina® NextSeq platform and the generated reads were assembled using the SPAdes software. The sequences obtained were submitted to the bioinformatics pipelines to determine the sequence type, resistome, plasmidome, and virulome.
Results
The A-73.113 strain was identified as KQPN and was susceptible to polymyxins (MICs, ≤0.25 µg/mL), tigecycline (MIC, 0.5 µg/mL), ciprofloxacin (MIC, 0.5 µg/mL), and levofloxacin (MIC, 1 µg/mL). WGS analysis revealed the presence of genes conferring resistance to β-lactams (blaNDM-1, blaCTX-M-15, blaOXA-9, blaOKP-A-5, blaTEM-1), aminoglycosides [aph(3′)-VI, aadA1, aac(6′)-Ib], and fluoroquinolones (oqxAB, qnrS1, aac(6′)-Ib-cr]. Additionally, the presence of the plasmid replicons Col(pHAD28), IncFIA(HI1), IncFIB(K) (pCAV1099-114), IncFIB(pQil), and IncFII(K), as well as virulence-encoding genes fimABCDEFGHIK (type 1 fimbria), pilW (type IV pili), iutA (aerobactin), entABCDEFS/fepABCDG/fes (Ent siderophores), iroE (salmochelin), and allABCDRS (allantoin utilization) was verified. Furthermore, we found that the A-73.113 strain belongs to ST1040.
Conclusions
Here we report the genomic characteristics of an NDM-1-producing KQPN ST1040 strain isolated from blood cultures in Brazil. These data will enhance our comprehension of how this species contributes to the acquisition and dissemination of blaNDM-1 in Brazilian nosocomial settings.
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.