2022—2023年临沂市人源肠炎沙门菌耐药及分子分型特征分析

Analysis of Drug Resistance and Molecular Typing of Humanized Salmonella Enteritidis in Linyi from 2022 to 2023

目的:了解2022—2023年临沂市腹泻病例监测中肠炎沙门菌耐药情况及分子分型特征,为监测和预防沙门菌感染提供参考依据。方法:对31株临沂市人源肠炎沙门菌进行药敏试验和全基因组测序,并分析分离株的多位点序列分型(MLST)、耐药基因和抗生素耐药表型。以NZ_CP018657为参考基因组,采用CSI Phylogeny1.4鉴定44株肠炎沙门菌基因组(含13株公共数据库基因组)的单核苷酸多态性(Single Nucleotide Polymorphism,SNP)位点,通过构建基于单核苷酸多态性的系统发育树,来进行菌株间系统发育关系的分析。结果:29株肠炎沙门菌鉴定为ST11型,另外2株未在数据库中查到对应的ST型。31株肠炎沙门菌临沂分离株均为多重耐药菌,对各种抗生素耐药率介于3.23%~100.00%,其中氨苄西林、氨苄西林-舒巴坦的耐药率最高(100.00%),未发现对美罗培南、厄他培南及阿米卡星耐药菌株。25株分离株对14种抗菌药物中的3~5种耐药,分为14种耐药谱;基于全基因组测序数据共预测到8类15种耐药基因,以氨基糖苷类耐药基因为(54.11%)最多,其中aac(6’)-Iaa携带率达到100.00%。44株肠炎沙门菌共鉴定得到23821个SNP位点,据此构建系统发育树显示31株临沂分离株分为3个分支,其中25株分离株聚集形成一个分支,亲缘关系较近。结论:2022—2023年临沂市肠炎沙门菌多重耐药严重,分子分型结果提示临沂市存在明显的肠炎沙门菌优势株,建议相关部门应根据本地区肠炎沙门菌耐药和分子分型特征加强监测,为该血清型来源、传播和感染等环节提供有效预警。

Objective:To understand the drug resistance and molecular typing characteristics of Salmonella enteritis in diarrhea cases monitored in Linyi city from 2022 to 2023,and provide reference for monitoring and preventing Salmonella infection.Method:Whole genome sequencing and drug sensitivity testing were performed on 31 strains of Salmonella enteritidis from Linyi city,to analyze the multi site sequence typing(MLST),resistance genes,and antibiotic resistance phenotype of the isolated strains.Using NZ-CP018657 as the reference genome,CSI Phylogeny 1.4 was used to identify single nucleotide polymorphism(SNP)sites in the genomes of 44 Salmonella enteritis strains(including 13 common database genomes),and a phylogenetic tree based on SNP was constructed to analyze the phylogenetic relationships between strains.Result:29 strains of Salmonella enteritis were identified as ST11 type,and the corresponding ST types were not found in the database for the other 2 strains.31 strains of Salmonella enteritis isolated in Linyi are all antibiotic multidrug-resistant bacteria,with resistance rates to various antibiotics ranging from 3.23%to 100.00%.Among them,ampicillin and Ampicillin sulbactam have the highest resistance rates(100.00%),and no strains resistant to meropenem,ertapenem or amikacin were found.25 isolated strains are resistant to 3~5 out of 14 antibiotics,divided into 14 drug resistance spectrums.Based on whole genome sequencing data,a total of 8 categories and 15 resistance genes were predicted,with aminoglycoside resistance genes(54.11%)being the most common,and the aac(6’)-Iaa carrying rate was 100%.A phylogenetic tree was constructed based on 23821 SNP sites identified from 44 strains of Salmonella enteritis.The results showed that 31 Linyi isolates were divided into 3 branches,of which 25 isolates clustered to one branch with close genetic relationships.Conclusion:From 2022 to 2023,multiple drug resistance of Salmonella enteritidis was severe in Linyi city.Molecular typing results indicate there are obvious dominant strains of Salmonella enteritidis in our city.It is recommended that relevant departments strengthen monitoring based on local Salmonella enteritidis resistance and molecular typing characteristics,and provide effective warnings for the source,transmission,and infection of this serotype.