杭州地区临床和食品来源德尔卑沙门菌耐药特征与基因组分析

Antimicrobial resistance and genomic characteristics of Salmonella enterica serovar Derby isolates from clinical patients and food sources in Hangzhou

目的了解杭州地区临床和食品来源德尔卑沙门菌的耐药特征,并进行溯源分析。方法对2015—2020年杭州地区分离的60株德尔卑沙门菌进行药敏分析、脉冲场凝胶电泳(PFGE)分型和全基因组测序,并下载公共数据库基因组进行比较;利用测序数据对菌株进行多位点序列分型(MLST)、核心基因组多位点序列分型(cgMLST)和耐药基因扫描,并构建基于单核苷酸多态性(SNP)位点的系统发育树。结果杭州地区德尔卑沙门菌临床株和食品株对28种药物的耐药率差异均无统计学意义,多重耐药率为76.7%(46/60);所有菌株均检出氨基糖苷乙酰转移酶基因aac(6′)-Iaa和磷霉素耐药基因fosA7;60株德尔卑沙门菌共分为46种PFGE带型、53种cgMLST(HC2)型别,除1株为ST3220型外,其余均为ST40型;基于439株德尔卑沙门菌(包括60株杭州菌株和379株公共数据库菌株)SNP位点构建的系统发育树显示:部分杭州菌株与东南亚菌株进化距离较近,提示可能存在跨境传播,食品株主要来自猪肉和水产类;其他杭州菌株与北京、广州、湖北、重庆等省市的菌株距离较近,提示可能存在跨省传播,食品株主要来自猪肉、牛肉和鸡肉。结论杭州地区德尔卑沙门菌的流行主要由ST40型引起,其多重耐药现象普遍,推测其临床感染与猪牛肉、鸡肉和水产类的消费密切相关,与东南亚地区和境内其他省市可能存在跨地传播。

Objective To analyze the antimicrobial resistance and genomic characteristics of Salmonella enterica serovar Derby strains isolated from human and food sources in Hangzhou.Methods A total of 60 Salmonella enterica serovar Derby strains isolated in Hangzhou during the period from 2015 to 2020 were subjected to antimicrobial susceptibility testing,pulsed field gel electrophoresis(PFGE)typing and whole-genome sequencing.Multilocus sequence typing(MLST),core genome multilocus sequence typing(cgMLST)and the identification of antimicrobial resistance genes were performed using the sequencing data.Phylogenetic tree based on the single nucleotide polymorphism(SNP)sites in the 60 genomes from Hangzhou and 379 genomes from public databases was constructed.Results No significant difference was observed in the drug resistance rates between the clinical strains and food strains in Hangzhou.The multidrug resistance(MDR)rate was 76.7%(46/60).All of the 60 Salmonella Derby strains were positive for the antimicrobial resistance genes aac(6′)-Iaa and fosA7.The 60 strains were subtyped into 46 molecular types by PFGE and 53 molecular types by cgMLST(HC2).Except for one strain belonging to ST3220,the other Salmonella Derby strains were ST40.The phylogenetic analysis showed that some strains isolated in Hangzhou were close to the strains in Southeast Asia,suggesting the possibility of cross-border transmission of ST40 strains,with the main food sources being pork and fish;other strains were close to those circulating in Beijing,Guangzhou,Hubei,Chongqing and other provinces,suggesting the possibility of cross-province transmission of the strains,with the main food sources being pork,beef and chicken.Conclusions The epidemic of Salmonella Derby in Hangzhou was mainly caused by the spread of ST40 strains and MDR was common.Clinical infections might be closely related to the consumption of pork,beef,chicken and fish.There was the possibility of cross-border transmission of Salmonella Derby between Hangzhou and Southeast Asia and cross-province transmission in China.