基于全基因组分析的肺炎克雷伯菌耐药性与流行病学特征分析

Drug resistance and epidemiological characteristics of Klebsiella pneumoniae based on whole genome sequencing analysis

目的了解肇庆市第二人民医院肺炎患者肺炎克雷伯菌(KP)分离株和医院环境KP分离株的病原学和分子流行病学特征。方法对该医院2021年收集的49株肺炎患者KP分离株和2株医院环境KP分离株进行抗菌药物敏感性试验鉴定其耐药表型;全基因组测序确定其质粒、分子血清型、多位点序列分型(MLST)、毒力基因与耐药基因等分子特征;基于core-SNPs构建发育进化树,分析优势流行型菌株的进化特征。结果感染KP的肺炎病患者大部分有基础病(87.76%),年龄>50岁(89.80%)。51株KP耐药表型以耐碳青霉烯肺炎克雷伯菌(CRKP)为主,存在优势耐药谱。携带的质粒主要为IncR、IncFⅡ(pHN7A8)和ColRNAⅠ,且IncFⅡ(pHN7A8)的pMLST为F33:A-:B-型。拥有优势分子血清型和MLST的菌株与优势耐药表型的菌株完全重合,为O_(2a)K_(64)-ST11 CRKP株。毒力基因和耐药基因显示,51株KP中2株菌株携带脲酶基因ureB。全部菌株携带耐药基因情况严重,且检测出10种不同亚型的β-内酰胺酶基因家族(bla_(CTX-M),bla_(ampC),bla_(OXA),bla_(LAP),bla_(KPC),bla_(LEN),bla_(SHV),bla_(SRT),bla_(TEM),bla_(OKP)),优势流行型菌株均携带bla KCP-2基因。系统发育树结果显示有26株优势流行菌株与我国泸州、衡阳的分离株属于一个克隆体,与北京、成都、巴黎的分离株属于一个克隆群。结论该医院感染KP的肺炎患者中存在一种优势流行的强耐药克隆体菌株(O_(2a)K_(64)-ST11 CRKP),且该型菌株已经出现在院内和社区的相互散播趋势。

Objective To investigate the pathogenic and molecular epidemiological characteristics of Klebsiella pneumoniae(KP)isolates from pneumonia patients and environments of Zhaoqing Second People′s Hospital.Methods Forty-nine KP isolates from pneumonia patients and two KP isolates from hospital environments were collected in 2021,and their drug resistance phenotypes were identified by the antimicrobial susceptibility test.Their plasmids,molecular serotypes,multilocus sequence typing(MLST),virulence genes and drug resistance genes were determined by whole genome sequencing,and the evolutionary characteristics of dominant epidemic strains were analyzed by constructing a developmental evolutionary tree based on core-SNPs.Results Most of the pneumonia patients infected with KP had basic diseases(87.76%),and 89.80%of patients were over 50 years old.Fifty-one strains of KP were mainly carbapenem-resistant Klebsiella pneumoniae(CRKP),and there was a dominant drug resistance spectrum.The plasmids carried were mainly IncR,IncFⅡ(pHN7A8)and ColRNAⅠ,and the pMLST of IncFⅡ(pHN7A8)was F33:A-:B-type.The strain with dominant molecular serotype and MLST completely coincided with the strain with dominant drug resistance phenotype as the O_(2a)K_(64)-ST11 CRKP strain.Virulence gene and drug resistance gene analysis showed that 2 of 51 KP strains carried urease gene ureB.All strains carried drug resistance genes seriously,and 10 different subtypes ofβ-lactamase gene family,including bla_(CTX-M),bla_(ampC),bla_(OXA),bla_(LAP),bla_(KPC),bla_(LEN),bla_(SHV),bla_(SRT),bla_(TEM)and bla_(OKP),were detected.All the dominant epidemic strains carried KCP-2 gene.Phylogenetic tree results showed that 26 dominant epidemic strains belonged to one clone with the isolates from Luzhou and Hengyang in China,and to one clone group with the isolates from Beijing,Chengdu and Paris.Conclusion There is a dominant and prevalent strong drug-resistant clonal strain,O_(2a)K_(64)-ST11 CRKP,in the pneumonia patients infected with KP in our hospital,and this type of strain has appeared the trend of mutual dissemination in hospitals and communities.