摘要
目标
在世界各地的医院环境中，对粘菌素和碳青霉烯耐药的肺炎克雷伯菌（CCR Kp）的分离正在增加，这与发病率、死亡率和医疗成本的增加有关。这项工作的目的是对来自阿根廷的广泛耐药（XDR）CCR Kp分离株进行全基因组测序（WGS）、基因组和系统发育分析以及结合分析。
方法
使用Illumina MiSeq-I对从血流感染中分离的菌株KpS26进行WGS，并使用SPAdes v.3.11实现从头组装。基于来自肺炎克雷伯菌分离株全基因组比对的核心基因组单核苷酸多态性，使用MEGA7创建了最大似然树，该分离株在计算机上被鉴定为序列类型15（ST15）。使用ResFinder、AMRFinderPlus、ISfinder、plasmidSPAdes、PlasmidFinder和IntegronFinder分析抗性组、质粒和整合子。进行标准接合。
后果
KpS26属于ST15，这比ST258、ST25和ST11更不常见，后者被全球报道为导致CCR Kp爆发的原因。检测到14个可转移的抗微生物耐药性基因（ARGs），包括通过偶联可转移的新型遗传平台中的blaKPC-2，对XDR表型有贡献。KpS26的pmrB基因编码的蛋白质中的氨基酸取代T157P也在该菌株中被鉴定，该蛋白先前被报道为是全球传播的肺炎克雷伯菌谱系对粘菌素耐药性的原因。
结论
这里分析的XDR CCR Kp分离物表明，ST15也在阿根廷与其他ARG一起传播blaKPC-2，这证明KPC流行病学继续受到复杂和多样的横向基因转移方式的影响。
ABSTRACT
Objectives
Isolation of colistin- and carbapenem-resistant Klebsiella pneumoniae (CCR-Kp) is increasing in hospital settings worldwide, which is related to increased morbidity, mortality and healthcare costs. The aim of this work was to perform whole-genome sequencing (WGS), genomic and phylogenetic analysis, and conjugation assays of an extensively drug-resistant (XDR) CCR-Kp isolate from Argentina.

Methods
WGS of strain KpS26 isolated from a bloodstream infection was performed using Illumina MiSeq-I, and de novo assembly was achieved using SPAdes v.3.11. A maximum likelihood tree was created using MEGA7 based on core genome single nucleotide polymorphisms from whole-genome alignment of K. pneumoniae isolates identified in silico as sequence type 15 (ST15). The resistome, plasmids and integrons were analysed using ResFinder, AMRFinderPlus, ISfinder, plasmidSPAdes, PlasmidFinder and IntegronFinder. Standard conjugation was performed.

Results
KpS26 belonged to ST15, which is less common than ST258, ST25 and ST11 that are globally reported as responsible for CCR-Kp outbreaks. Fourteen transferable antimicrobial resistance genes (ARGs), including blaKPC-2 in a novel genetic platform transferable by conjugation, were detected contributing to the XDR phenotype. The amino acid substitution T157P in the protein encoded by the pmrB gene of KpS26, previously reported as being responsible for resistance to colistin in K. pneumoniae lineages globally disseminated, was also identified in this strain.

Conclusion
The XDR CCR-Kp isolate analysed here shows that ST15 is also disseminating blaKPC-2 in Argentina alongside other ARGs, evidencing that KPC epidemiology continues to be shaped by intricate and assorted ways of lateral gene transfer.

https://www.sciencedirect.com/science/article/pii/S2213716521002666