基于全基因组测序的耐碳青霉烯类抗生素鲍曼不动杆菌耐药基因、毒力因子及同源性分析

摘要：目的 通过应用全基因组测序(whole genome sequencing, WGS)技术分析某三级医疗机构耐碳青霉烯类抗生素鲍曼不动杆菌(carbapenem-resistant Acinetobacter baumannii, CRAB)的耐药基因、毒力因子及同源性。方法 收集该院2020年1月至3月重症监护病房(Intensive care unit, ICU)、神经外科分离的11株医院感染CRAB菌株,通过二代测序平台进行全基因组测序, 应用基因组流行病学中心(Center for genomic epidemiology, CGE)ResFinder 4. 0软件分析其耐药基因型,并应用MORPHEUS在线制作热图,应用毒力因子数据库(virulence factors of pathogenic bacteria, VFDB)VFanalyzer软件筛选毒力因子,应用MLST软件检测菌株的ST型,应用Kaptive软件检测荚膜型,应用CSI Phylogeny 1. 4软件及FigTree v1. 4. 4软件构建最大似然树(maximum likelihoodtree, MLT)以分析其同源性。结果 11株CRAB对亚胺培南、美罗培南、头孢菌素、环丙沙星均呈现耐药,而对阿米卡星、左氧氟沙星耐药的菌株株数较少。11株CRAB共检测出18种耐药基因,11株同时携带碳青霉烯酶耐药基因blaOXA-23和blaOXA-66,β-内酰胺酶耐药基因以blaTEM-1D和blaADC-25为主,大部分菌株携带多种外排泵相关耐药基因及抗菌药物修饰酶耐药基因。11株CRAB均携带多种毒力因子,包括外膜孔蛋白、脂多糖、生物膜、外排泵、磷脂酶和效应蛋白等,如OmpA、Lps、Csu、Pga、Ade、Plc、Bas、Bau、Ent、Hem、Aba、Bfm、Pbp和Kat等。11株CRAB均为ST2-K22型,同源性分析结果显示C组内同源性关系相近,存在院内传播的可能。结论 该院CRAB的耐药性、毒力特征复杂多样,同源性分析显示该院存在1种优势克隆株,该克隆株有医院内传播的风险。

Analysis of resistance genes,virulence factors and homology of carbapenemresistant Acinetobacter baumannii based on whole-genome sequencing

Abstract Objective To analyze the resistance genes, virulence factors and homology of carbapenemresistantAcinetobacter baumannii (CRAB) in a tertiary medical institution by using whole genome sequencing (WGS)technology. Methods Eleven strians of nosocomial infected CRAB isolates from the Intensive Care Unit (ICU)and neurosurgery of the hospital from January 2020 to March 2020 were collected. The next-generation sequencingplatform was used for WGS. ResFinder 4.0 software of Center for Genomic Epidemiology(CGE) was used to analyzethe drug resistance genes. VFanalyzer software of virulence factors database (VFDB) was used to screen the virulencefactors. The MLST software was used to detect the ST type of the strains, and the Kaptive software was used to detectthe capsule types. The heat maps were made by MORPHEUS online, the maximum likelihood tree was constructedby CSI Phylogeny 1. 4 software and FigTree v1. 4. 4 software to analyze the homology of strains. Results Elevenstrians of CRAB were resistant to imipenem, meropenem, cephalosporin and ciprofloxacin, while the number ofstrains resistant to amikacin and levofloxacin was relatively small. Eleven strians of CRAB carried eighteen kindsof drug resistance genes, all of which carried the carbapenemase resistance gene blaOXA-23 and blaOXA-66. The elevenstrians all carried β-lactamase resistance genes, mainly including blaTEM-1D and blaADC-25. Most of the strains carriedmultiple efflux pump-related and antimicrobial drug-modifying enzyme resistance genes. The eleven strians all carriedmany kinds of virulence factors, including outer membrane porin, lipopolysaccharide, biomembrane, efflux pump,phospholipase, effector protein, etc, such as OmpA, Lps, Csu, Pga, Ade, Plc, Bas, Bau, Ent, Hem, Aba, Bfm, Pbp,and Kat. The 11 strains of CRAB were all ST2-K22 type. The homology analysis result showed that the homologyrelationship in group C was similar, and there was the possibility of nosocomial transmission. Conclusion Theresistance and virulence characteristics of CRAB in the hospital were complex and diverse. Homology analysisshowed that there was one dominant clone in the hospital, and this clone has the risk of nosocomial