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。

IF 3.7 3区 医学 Q2 INFECTIOUS DISEASES
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引用次数: 0

摘要

目的:尽管有关巴西肠杆菌属中 blaNDM 的报道越来越多,但全面的全基因组测序(WGS)数据仍然很少。为了填补这一知识空白,我们的研究重点是对巴西分离的一株产NDM-1的准肺炎克雷伯氏菌亚种(KQPN)临床菌株的基因组进行鉴定:方法:按照 BrCAST/EUCAST 的建议,通过琼脂稀释法或肉汤微量稀释法对 A-73.113 菌株进行抗菌药敏感性分析。使用 Illumina® NextSeq 平台进行了 WGS 分析,并使用 SPAdes 软件对生成的读数进行了组装。获得的序列被提交给生物信息学管道,以确定序列类型、抗性组、质粒组和病毒组:结果:A-73.113菌株被鉴定为KQPN,对多粘菌素(MICs,≤0.25 µg/mL)、替加环素(MIC,0.5 µg/mL)、环丙沙星(MIC,0.5 µg/mL)和左氧氟沙星(MIC,1 µg/mL)敏感。WGS 分析显示,存在对 β-内酰胺类(blaNDM-1、blaCTX-M-15、blaOXA-9、blaOKP-A-5、blaTEM-1)、氨基糖苷类[aph(3')-VI、aadA1、aac(6')-Ib]和氟喹诺酮类(ocqxAB、qnrS1、aac(6')-Ib-cr]产生耐药性的基因。此外,还验证了 Col(pHAD28)、IncFIA(HI1)、IncFIB(K) (pCAV1099-114)、IncFIB(pQil) 和 IncFII(K) 等质粒复制子以及毒力编码基因的存在:fimABCDEFGHIK(1 型缘膜)、pilW(IV 型纤毛)、iutA(气杆菌素)、entABCDEFS/fepABCDG/fes(Ent siderophores)、iroE(salmochelin)和 allABCDRS(尿囊素利用)。此外,我们还发现 A-73.113 株属于 ST1040:在此,我们报告了从巴西血液培养中分离出的一株产 NDM-1 的 KQPN ST1040 菌株的基因组特征。这些数据将有助于我们更好地理解该菌株是如何在巴西的病原环境中获取和传播 blaNDM-1 的。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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.

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来源期刊
Journal of global antimicrobial resistance
Journal of global antimicrobial resistance INFECTIOUS DISEASES-PHARMACOLOGY & PHARMACY
CiteScore
8.70
自引率
2.20%
发文量
285
审稿时长
34 weeks
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.
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