2018-2021年乌鲁木齐市鼠伤寒沙门菌基因组特征分析  

Genome characteristics of Salmonella typhimurium isolated in Urumqi from 2018 to 2021

作　　者：杨毅[1] 胡海 胡锦瑞 杨艳梅[1] 尚月梅[1] 高鹏芳 杜小莉[2] 刘金悦 崔志刚[2] 周海健[2] 卢耀勤[1] YANG Yi;HU Hai;HU Jin-rui;YANG Yan-mei;SHANG Yue-mei;GAO Peng-fang;DU Xiao-li;LIU Jin-yue;CUI Zhi-gang;ZHOU Hai-jian;LU Yao-qin(Urumqi Center for Disease Control and Prevention,Urumqi 830000,China;National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases/Institute for Communicable Disease Prevention and Control,Beijing 102206,China;North China University of Science and Technology,Tangshan 063000,China)

机构地区：[1]乌鲁木齐市疾病预防控制中心,乌鲁木齐830000 [2]国家致病菌识别网中心实验室,中国疾病预防控制中心传染病预防控制所,北京102206 [3]华北理工大学附属医院,唐山063000

出　　处：《中国人兽共患病学报》2024年第11期1042-1048,共7页Chinese Journal of Zoonoses

基　　金：新疆维吾尔自治区科技创新团队(No.2022TSYCTD0015);“西部之光”访问学者项目。

摘　　要：目的分析2018-2021年乌鲁木齐市鼠伤寒沙门菌(S.1,4,[5],12:i:1,2)的基因组特征,为该菌的流行监测及引起的疫情处置提供依据。方法收集26株乌鲁木齐市肠道门诊监测腹泻样本分离的鼠伤寒沙门菌,利用全基因组测序(WGS)结合生物信息学分析MLST类型、核心基因组多位点序列(cgMLST)型别、质粒、耐药基因和毒力基因特征,通过全基因组单核苷酸多态性(wgSNPs)构建进化树,分析菌株间的同源性及国内不同来源流行克隆株之间的种群进化关系。结果26株鼠伤寒沙门菌基因组序列共注释到10类47种耐药基因,其中编码氨基糖苷类耐药基因aac(6′)-Iaa(100%)、β-内酰胺类耐药基因blaTEM-1B(30.8%)、四环素类耐药基因tetA(42.3%)、喹诺酮类qnrS1耐药基因(30.8%)和磺胺类耐药基因sul3(23.1%)的携带率较高;喹诺酮耐药决定区(QRDR)存在gyrA位点突变。此外,还检测到12种不同的质粒,以IncFIB(S)和IncFII(S)(34.6%)为主;不同时期分离菌株间所含有毒力基因差异不大。cgMLST显示分离的鼠伤寒沙门菌优势型别为cgST36414,包含10株菌。wgSNPs分析表明,本地区鼠伤寒沙门菌与国内15个省市流行趋势相一致,同时也存在本地区独有的进化特征。结论本地区鼠伤寒沙门菌普遍携带多种耐药基因和质粒复制子,对耐药性的传播和进化起关键作用。多样化的克隆群与食物链上不同来源菌群之间可能存在密切传播联系,给公共卫生监测和预防带来严峻挑战。建议加强基于互联网信息系统的实验室监测网络建设,以提高监测系统的时效性并限制多耐药克隆株的传播扩散。This study was aimed at analyzing the genomic characteristics of Salmonella typhimurium(1,4,[5],12:i:1,2)in Urumqi from 2018 to 2021,to provide evidence for the monitoring of this serotype and handling of public health emergencies.A total of 26 Salmonella typhimurium isolates were obtained from the feces of people with diarrhea in Urumqi.Whole-genome sequencing(WGS)combined with bioinformatic analy sis was used to predict serovars,MLST types,plasmid replicons,antimicrobial resistance genes,and virulence genes;in addition phylogenomic analysis based on genome-wide single nucleotide polymorphisms(wgSNPs)was conducted to determine the epidemiological relatedness among isolates.A total of 47 resistance genes representing ten categories were detected with a high prevalence,including aac(6′)-Iaa(100%),blaTEM-1B(30.8%),tet(A)(42.3%),qnrS1(30.8%),and sul3(23.1%),encoding resistance to aminoglycosides,β-lactams,tetracyclines,quinolones,and sulfa,in addition to chromosomic mutations affecting the gyrA gene.Moreover,12 plasmids were detected,among which IncFIB(S)and IncFII(S)(34.6%)were dominant.The differences in virulence genes among strains isolated in different periods were reflected primarily in the typical virulence genes associated with Salmonella virulence mechanisms.In addition,cgMLST indicated that the dominant type of Salmonella typhimurium was cgST36414,containing 10 strains.Moreover,wgSNP analysis indicated that Salmonella typhimurium isolates in Urumqi were consistent with the epidemic trends in 15 provinces and cities in China and also showed local evolution.Salmonella typhimurium isolates in Urumqi frequently carried a variety of resistance genes and plasmid replicons,which are key in the dissemination and evolution of drug resistance.Close communication links may exist with various sources of flora in the food chain,thus posing severe challenges in public health monitoring and prevention.Therefore,the construction of the laboratory routine monitoring network based on internet information systems should b

关 键 词：鼠伤寒沙门菌 流行病学分析 全基因组测序 耐药基因 种群结构 

分 类 号：R378.2[医药卫生—病原生物学]