临沂市人源单相鼠伤寒沙门菌耐药基因及分子分型特征分析

Analysis on Monophasic Salmonella Typhimurium drug resistance and molecular typing in Linyi city

目的 了解临沂市人源单相鼠伤寒沙门菌的耐药基因携带情况及分子分型情况,为监测和预防单相鼠伤寒沙门菌感染提供参考。方法 收集2017-2022年27株临沂市人源单相鼠伤寒沙门菌(来自腹泻患者粪便)进行全基因组测序,基于测序数据进行耐药基因预测及分类分析,与公共数据库中的23株单相鼠伤寒沙门菌基因组数据共同进行多位点序列分型(MLST)和核心基因组序列分型(cgMLST)分型分析,以NC_003197基因组为参考序列鉴定所有基因组的单核苷酸多态性(SNP)位点,构建基于SNP位点的系统发育树。结果 27株临沂菌株共预测到9类36种不同的耐药基因,其中携带率较高的耐药基因是aac(6′)-Iaa(27/27)、aph(6)-Id(24/27)、aph(3'')-Ib(23/27)、blaTEM-1B(16/27)、sul2(20/27)、tet(B)(18/27)及qnrS1(10/27),同时携带3类或3类以上耐药基因的菌株占92.59%。多位点序列分型显示27株临沂菌株均为ST34型,分为12个cgMLST型,其中2246331298为优势型别,在23株公共数据库菌株中未发现相同的cgMLST型别。27株临沂菌株与10株ST34型及另外两株ST7832型、ST2379型公共数据库菌株聚集于一个分支内,该分支内26株临沂菌株聚集成簇。结论 临沂市单相鼠伤寒沙门菌耐药严重,菌株呈现明显的遗传多样性,存在潜在暴发的风险。

Objective To investigate the prevalence and molecular typing of drug resistance genes in human Monophasic Salmonella Typhimurium in Linyi city,so as to provide a reference for surveillance and prevention of Monophasic Salmonella Typhimurium infections.Methods Twenty-seven strains of human-origin Monophasic Salmonella Typhimurium(from the faeces of diarrhoea patients)were collected for whole-genome sequencing in Linyi city from 2017 to 2022.MLST and cgMLST genotyping were performed in conjunction with 23 Monophasic Salmonella Typhimurium genomic data from public databases to employ prediction and classification analysis of drug resistance genes based on sequencing data,and single-nucleotide polymorphism(snps)in all genomes were identified using NC_003197genome as reference sequence,aphylogenetic tree based on SNP loci was constructed.Results A total of 36resistance genes of 9 classes were predicted in 27Linyi isolates,the resistant genes were aac(6′)-Iaa(27/27),aph(6)-Id(24/27),aph(3')-Ib(23/27),blaTEM-1B(16/27),sul2(20/27),tet(B)(18/27)and qnrS1(10/27),92.59%of the isolates carried 3or more classes of resistance genes.The multilocus sequence typing showed that all 27Linyi isolates were ST34and were classified into 12 cgMLST types,of which 224631298was the dominant type.No identical cgMLST type was found among the 23strains in the public database.A total of 27strains of Linyi,10strains of ST34and 2strains of ST7832and ST2379were clustered in a branch of public database.Conclusion Based on the whole genome sequencing data,predictive analysis of Linyi shows that Monophasic Salmonella Typhimuriumare highly resistant,the strains have significant genetic diversity,and there is a potential risk of outbreak.