基于全基因组测序的碳青霉烯类耐药肺炎克雷伯菌耐药机制及分子特征研究

Resistance mechanism and molecular epidemiological characteristics of carbapenem-resistant Klebsiella pneumoniae analyzed based on whole-genome sequencing

目的明确本地区碳青霉烯类耐药肺炎克雷伯菌(CRKP)的耐药特点和分子流行病学特征,为临床抗感染治疗提供依据。方法收集宁波大学附属第一医院和宁波市第二医院碳青霉烯类不敏感肺炎克雷伯菌92株。用VITEK2 Compact全自动微生物分析仪进行药敏试验;全基因组测序技术确定其荚膜血清型、多位点序列分型(MLST)与耐药基因等分子特征;使用PlasmidFinder确定菌株的质粒复制子类型;Parsnp进行细菌核心基因组系统发育分析。结果CRKP主要分离自病情较为危重的老年患者,标本以痰液居多(51.09%,47/92),其次是尿液(13.04%,12/92)和血液(8.70%,8/92),感染高发科室为重症监护病房(33.70%,31/92)。所有菌株对常用抗菌药物耐药率高,但对多黏菌素B耐药率较低(6.52%,6/92)。耐药基因以bla_(KPC-2)为主(78.26%,72/92),荚膜血清型以KL64为主(48.91%,45/92),MLST分型以ST11为主(54.35%,50/92)。ST11-KL64是优势克隆型,检出率高达46.74%(43/92),且携带多个质粒,以IncR和IncFⅡ型为主。结论本地区CRKP对临床常用抗菌药物高度耐药,主要携带bla_(KPC-2)耐药基因,克隆型ST11-KL64在本地区广泛克隆传播,两家医院流行的菌株存在相似性,应加强监控。

ObjectiveTo elucidate the drug resistance characteristics and molecular epidemiological features of carbapenem-resistant Klebsiella pneumoniae(CRKP)in this region,and to provide a basis for clinical anti-infective therapy.MethodsA total of 92 CRKP isolates were collected from the First Affiliated Hospital of Ningbo University and Ningbo No.2 Hospital.Antimicrobial susceptibility testing was performed using the VITEK2 Compact analyzer.Whole-genome sequencing was used to analyze their molecular characteristics including capsular serotypes,sequence types(multilocus sequencing typing)and resistance genes.Plasmid replicon types were identified using PlasmidFinder,and core genome phylogenetic analysis was performed with Parsnp.ResultsThe CRKP isolates were mainly isolated from critically ill elderly patients,with sputum(51.09%,47/92)and urine(13.04%,12/92)as the major specimen sources,followed by blood(8.70%,8/92).Most of the infections were reported in the intensive care unit(33.70%,31/92).All isolates showed high resistance to commonly used antibiotics,but lower resistance to polymyxin B(6.52%,6/92).The predominant resistance gene,capsule serotype and ST were bla_(KPC-2)(78.26%,72/92),KL64(48.91%,45/92),and ST11(54.35%,50/92),respectively.ST11-KL64 was the predominant clone,accounting for 46.74%(43/92)and carried multiple plasmids with IncR and IncFⅡas the major types.ConclusionsCRKP in this region mainly harbored the bla_(KPC-2) resistance gene and showed high resistance to commonly used antibiotics.The ST11-KL64 clone spread widely in this region and the strains circulating in the two hospitals were similar.Thus,the surveillance should be strengthened.