一起甲型副伤寒暴发菌株的基因组遗传和耐药特征  

Genetic and drug resistance characterization of the Salmonella Paratyphi Acausing an outbreak

作　　者：张宏宾[1] 顾敏华[1] 高海英[1] 李玲[1] 刘晓骏[1] 葛以跃[2] 赵康辰[2] 陈银[2] 崔伦标[2] 吴斌[2] ZHANG Hong-bin;GU Min-hua;GAO Hai-ying;LI Ling;LIU Xiao-jun;GE Yi-yue;ZHAO Kang-chen;CHEN Yin;CUI Lun-biao;WU Bin(Jiangyin Municipal Center for Disease Control and Prevention,Jiangsu Wuxi 214400,China;不详)

机构地区：[1]江阴市疾病预防控制中心,江苏无锡214400 [2]江苏省疾病预防控制中心国家卫生健康委员会肠道病微生物重点实验室

出　　处：《江苏预防医学》2020年第4期371-374,共4页Jiangsu Journal of Preventive Medicine

基　　金：国家自然科学基金青年科学基金项目(No.31700035);无锡市卫生计生委科研项目(No.Q201737);江苏省疾病预防控制中心科教强业工程青年人才(JKRC2016004)。

摘　　要：目的了解2016年江阴市一起甲型副伤寒暴发菌株的基因组遗传和耐药特征。方法采用二代测序技术(NGS),对分离到的9株菌株进行全基因组测序。经数据过滤和de novo组装后,获得基因组序列。将其与公共数据库下载国内流行株和国际参比菌株比较,获取单拷贝核心基因序列SNP,构建系统发生树。同时通过比对MLST数据库,获取MLST分型情况;通过比对ResFinder数据库和ARDB数据库获取耐药基因携带情况。采用Kirby-Bauer纸片扩散法进行15种临床常用抗生素敏感性测试。结果组装后9株甲型副伤寒菌株均为4.5M左右,且均为ST85型;系统发生树分析显示这9株菌株聚在一起,且同云南元江甲型副伤寒暴发菌株的亲缘关系最近。9株菌株均对四环素、氯霉素、复方新诺明、萘啶酸、红霉素和阿奇霉素耐药,均携带了介导氨基糖苷类耐药的aac(6′)-Iaa基因,以及介导喹诺酮类耐药的gyrA p、S83F和parC p.T57S突变,同时还携带ABC、RND和MF家族外排泵相关的耐药基因。结论本暴发疫情是由共同来源的、具有多重耐药性ST85型甲型副伤寒沙门菌引起。应用基因组数据可更精细分析菌株遗传进化特征、亲缘关系及耐药基因携带情况,对临床用药有一定指导作用。Objective To understand the genetic and drug resistance characteristics of SalmonellaParatyphiA strains causing an outbreak in Jiangyin city in 2016.Methods Whole genome sequencing of 9 strains isolated from the outbreak was carried out by next-generation sequencing technology(NGS).The genomic sequences were obtained after data filtration and de novo assembly,followed by comparison with the reference strains and the domestic strains isolated from different regions and years in the public database.Single copy SNP of core gene sequence was obtained and phylogenetic tree was constructed.The MLST typing of strains was obtained from the MLST database alignment analysis;the drug resistance genes were obtained by analyzing the ResFinder database and the ARDB database.The Kirby-Bauer method was used to test the sensitivity of isolated strains to 15 clinically commonly used antibiotics.Results After the assembly,the genome sizes of the 9 strains were all about 4.5 M,and all were ST85 type.The phylogenetic tree analysis showed that 9 strains formed 1 cluster,with the closest genetic relationship to the Yunnan Yuanjiang outbreak strains.All the 9 strains were resistant to tetracycline,chloramphenicol,cotrimoxazole,nalidixic acid,erythromycin and azithromycin;All carried the amino acid glycoside-resistant aac(6′)-Iaa gene,the quinolone-resistant gyrA p.S83 Fand parC p.T57S mutations,as well as the ABC,RND and MF family of efflux pump-related resistance genes.Conclusion This outbreak was caused by a common source of multi-drug resistant ST85 type Salmonella paratyphi A.Genomic data can be used to analyze the genetic evolutional characteristics,genetic relationship and drug resistance gene carrying status of strains,which can guide clinical medication.

关 键 词：甲型副伤寒沙门菌 二代测序 耐药基因 

分 类 号：R516.3[医药卫生—内科学]