Multidrug-resistant Klebsiella pneumoniae (MDR Kp), in particular carbapenem-resistant Kp (CR-Kp), has become endemic in Italy, where alarming data have been reported on the spread of colistin-resistant CR-Kp (CRCR-Kp). During the period 2013-2014, 27 CRCR-Kp nosocomial strains were isolated within the Modena University Hospital Policlinico (MUHP) multidrug resistance surveillance program. We retrospectively investigated these isolates by whole-genome sequencing (WGS) analysis of the resistome, virulome, plasmid content, and core single nucleotide polymorphisms (cSNPs) in order to gain insights into their molecular epidemiology. The in silico WGS analysis of the resistome revealed the presence of genes, such as blaKPC, related to the phenotypically detected resistances to carbapenems. Concerning colistin resistance, the plasmidic genes mcr 1-9 were not detected, while known and new genetic variations in mgrB, phoQ, and pmrB were found. The virulome profile revealed the presence of type-3 fimbriae, capsular polysaccharide, and iron acquisition system genes. The detected plasmid replicons were classified as IncFIB(pQil), IncFIB(K), ColRNAI, IncX3, and IncFII(K) types. The cSNPs genotyping was consistent with the multi locus sequence typing (MLST) and with the distribution of mutations related to colistin resistance genes. In a nosocomial drug resistance surveillance program, WGS proved to be a useful tool for elucidating the spread dynamics of CRCR-Kp nosocomial strains and could help to limit their diffusion.

中文翻译：

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耐多药监测计划中分离出的碳青霉烯类和耐科力汀抗肺炎克雷伯菌的医院菌株的全基因组回顾性测序。

耐多药性肺炎克雷伯菌（MDR Kp），特别是耐碳青霉烯的Kp（CR-Kp）在意大利已成为地方病，据报道，关于大肠菌素耐药性CR-Kp（CRCR-Kp）的传播情况令人震惊。在2013-2014年期间，在摩德纳大学医院Policlinico（MUHP）多药耐药性监测计划中分离出27株CRCR-Kp医院菌株。我们通过对抵抗组，病毒组，质粒含量和核心单核苷酸多态性（cSNPs）进行全基因组测序（WGS）分析，对这些分离株进行了回顾性研究，以便深入了解其分子流行病学。电阻组的计算机WGS分析显示，存在与表型检测到的对碳青霉烯类抗性相关的基因，例如blaKPC。关于粘菌素抗性 未检测到质粒基因mcr 1-9，而在mgrB，phoQ和pmrB中发现了已知的新遗传变异。病毒组谱显示存在3型菌毛，荚膜多糖和铁捕获系统基因。检测到的质粒复制子被分类为IncFIB（pQil），IncFIB（K），ColRNAI，IncX3和IncFII（K）类型。cSNPs基因分型与多基因座序列分型（MLST）和与大肠菌素抗性基因相关的突变分布一致。在医院的耐药性监测程序中，WGS被证明是阐明CRCR-Kp医院菌株传播动态的有用工具，并且可以帮助限制它们的扩散。荚膜多糖和铁捕获系统的基因。检测到的质粒复制子被分类为IncFIB（pQil），IncFIB（K），ColRNAI，IncX3和IncFII（K）类型。cSNPs基因分型与多基因座序列分型（MLST）和与大肠菌素抗性基因相关的突变的分布一致。在医院的耐药性监测程序中，WGS被证明是阐明CRCR-Kp医院菌株传播动态的有用工具，并且可以帮助限制它们的扩散。荚膜多糖和铁捕获系统的基因。检测到的质粒复制子被分类为IncFIB（pQil），IncFIB（K），ColRNAI，IncX3和IncFII（K）类型。cSNPs基因分型与多基因座序列分型（MLST）和与大肠菌素抗性基因相关的突变分布一致。在医院的耐药监测程序中，WGS被证明是阐明CRCR-Kp医院菌株传播动态的有用工具，并且可以帮助限制其扩散。