Kong Yingying, Sun Qingyang, Chen Hangfei, Draz Mohamed S, Xie Xinyou, Zhang Jun, Ruan Zhi
Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
Department of Clinical Laboratory, No. 903 Hospital of PLA Joint Logistic Support Force, Hangzhou, China.
Front Microbiol. 2021 Oct 7;12:736896. doi: 10.3389/fmicb.2021.736896. eCollection 2021.
The presence and dissemination of carbapenem-resistant (CRKP) often cause life-threatening infections worldwide, but the therapeutic option is limited. In this study, whole-genome sequencing (WGS) was applied to assess the epidemiological characteristics and transmission dynamics of CRKP isolates recovered from two fetal outbreaks of nosocomial infections. Between April 2016 and March 2018, a total of 70 isolates of were collected from sterile samples in a tertiary hospital in Hangzhou, China. The minimal inhibitory concentrations (MICs) of 21 antimicrobial agents were determined using the broth microdilution methods. Pulsed-field gel electrophoresis (PFGE) was performed on 47 CRKP isolates, and 16 clonally related isolates were further characterized by Illumina sequencing. In addition, the complete genome sequences of three representative isolates (KP12, KP36, and KP37) were determined by Oxford Nanopore sequencing. The isolates were recovered from patients diagnosed with pulmonary infection, cancer, or encephalopathy. For all CRKP isolates, PFGE separated three clusters among all strains. The most predominant PFGE cluster contained 16 isolates collected from patients who shared close hospital units and represented a potential outbreak. All 16 isolates showed an extremely high resistance level (≥87.5%) to 18 antimicrobials tested but remain susceptible to colistin (CST). Multiple antimicrobial resistance and virulence determinants, such as the carbapenem resistance gene , and genes encoding the virulence factor aerobactin and the regulator of the mucoid phenotype ( and ), were observed in the 16 CRKP isolates. These isolates belonged to sequence type 11 (ST11) and capsular serotype KL64. A core genome single nucleotide polymorphism (cgSNP)-based phylogenetic analysis indicated that the 16 CRKP isolates could be partitioned into two separate clades (≤15 SNPs), suggesting the two independent transmission scenarios co-occurred. Moreover, a high prevalence of IncFIB/IncHI1B type virulence plasmid with the locus deleted, and an IncFII/IncR type -bearing plasmid was co-harbored in ST11-KL64 CRKP isolates. In conclusion, our data indicated that the nosocomial dissemination of ST11-KL64 CRKP clone is a potential threat to anti-infective therapy. The development of novel strategies for surveillance, diagnosis, and treatment of this high-risk CRKP clone is urgently needed.
耐碳青霉烯类肺炎克雷伯菌（CRKP）的存在与传播在全球范围内常引发危及生命的感染，但治疗选择有限。在本研究中，应用全基因组测序（WGS）来评估从两起医院感染胎儿暴发中分离出的CRKP菌株的流行病学特征和传播动态。2016年4月至2018年3月期间，在中国杭州一家三级医院的无菌样本中总共收集了70株菌株。使用肉汤微量稀释法测定了21种抗菌药物的最低抑菌浓度（MIC）。对47株CRKP菌株进行了脉冲场凝胶电泳（PFGE），并通过Illumina测序对16株克隆相关菌株进行了进一步鉴定。此外，通过牛津纳米孔测序确定了三株代表性菌株（KP12、KP36和KP37）的完整基因组序列。这些菌株从被诊断患有肺部感染、癌症或脑病的患者中分离得到。对于所有CRKP菌株，PFGE在所有菌株中分离出三个簇。最主要的PFGE簇包含从共用紧密医院科室的患者中收集的16株菌株，代表一次潜在的暴发。所有16株菌株对18种测试抗菌药物均表现出极高的耐药水平（≥87.5%），但对黏菌素（CST）仍敏感。在16株CRKP菌株中观察到多种抗菌耐药和毒力决定因素，如碳青霉烯耐药基因 ，以及编码毒力因子气杆菌素和黏液样表型调节因子（ 和 ）的基因。这些菌株属于序列型11（ST11）和荚膜血清型KL64。基于核心基因组单核苷酸多态性（cgSNP）的系统发育分析表明，16株CRKP菌株可分为两个独立的进化枝（≤15个SNP），表明两种独立的传播情况同时发生。此外，在ST11-KL64 CRKP菌株中共存着高比例缺失 位点的IncFIB/IncHI1B型毒力质粒和携带 的IncFII/IncR型质粒。总之，我们的数据表明ST11-KL64 CRKP克隆在医院内的传播是抗感染治疗的潜在威胁。迫切需要制定针对这种高风险CRKP克隆的监测、诊断和治疗新策略。
