基于NCBI数据库的全球鼠伤寒沙门菌的流行和分布特点

Characteristics of epidemiology and distribution of Salmonella Typhimurium worldwide based on NCBI database

目的分析全球鼠伤寒沙门菌的流行和分子特点。方法从NCBI数据库批量下载全球沙门菌基因组和相应血清型及meta信息。使用在线软件ResFinder、PlasmidFinder、Mobile Element Finder和MLST分析抗生素耐药基因(ARGs)、质粒、移动遗传元件(MGEs)在鼠伤寒沙门菌中的分布及其序列分型(STs)。结果323株鼠伤寒沙门菌中共检出101种ARGs,其中最常见的是aac(6′)-Iaa(322/323,99.69%),其次为sul2(155/323,47.99%)、aph(3″)-Ib(128/323,39.63%)、aph(6)-Id(127/323,39.32%)、tet(B)(109/323,33.75%)和blaTEM-1B(106/323,32.82%)。共检出36种质粒,以IncFⅡ(S)(110/323,34.06%)和IncFⅠB(S)(108/323,33.44%)最为常见。另外,鉴定到376个MGEs,包括367种插入序列和9种转座子,以MITEEc1(322/323,99.69%)和ISSen1(308/323,95.36%)最为流行。323株鼠伤寒沙门菌鉴定到32种不同的STs,其中,ST19(157/323,48.61%)和ST34(105/323,32.51%)是最为常见的2种STs,占82%以上。人类来源的115株细菌中鉴定出18种STs,也是以ST19(52/115,45.22%)和ST34(39/115,33.91%)最为常见。结论鼠伤寒沙门菌携带有多种类型的ARGs,并伴有大量插入序列和质粒的流行为耐药的流行播散提供了有利条件,针对该菌应加强感染防控措施。

Objective To analyze the prevalence and molecular characteristics of global Salmonella Typhimurium.Method The genome and the corresponding serovars as well as meta-information of global Salmonella were downloaded in batch from the National Center for Biotechnology Information(NCBI)database using the online softwares,ResFinder,PlasmidFinder,Mobile Element Finder and MLST,to analyze the distribution of antibiotic resistant genes(ARGs),plasmids,mobile genetic elements(MGEs)and the sequence types(STs)among S.Typhimurium strains.Results A total of 101 ARGs were detected in 323 strains of S.Typhimurium,among which the most common was aac(6′)-Iaa(322/323,99.69%),followed by sul2(155/323,47.99%),aph(3″)-Ib(128/323,39.63%),aph(6)-Id(127/323,39.32%),tet(B)(109/323,33.75%),and bla_(TEM-1B)(106/323,32.82%).Totally,36 plasmids were identified,among which IncFⅡ(S)(110/323,34.06%)and IncFⅠB(S)(108/323,33.44%)were the most common.Moreover,376 MGEs were found,including 367 insertion sequences and nine transposons,among which MITEEc1(322/323,99.69%)and ISSen1(308/323,95.36%)were the most popular.Furthermore,323 strains of S.Typhimurium were assigned into 32 different STs,among which,ST19(157/323,48.61%)and ST34(105/323,32.51%)were the most common accounting for over 82%.Among 115 strains of S.Typhimurium from human,18 STs were identified including ST19(52/115,45.22%)and ST34(39/115,33.91%)which were the most common.Conclusion S.Typhimurium carried multiple types of ARGs,in addition to the wide distribution of a large number of insertion sequences and plasmids,whch provide favorable conditions for the spread of drug resistance.Therefore,the measures of prevention and control against the infection from this bacterium should be strengthened.