目的：了解不同时期分离鼠伤寒沙门氏菌的基因组多态性。方法：采用solexa高通量测序技术对 12株分离于1954-1980年与2018-2020年的鼠伤寒沙门氏菌标准菌株进行全基因组测序，以此进行菌株的多位点序列分型(MLST)分析；应用生物信息分析软件对测序菌株基因组的基因功能注释，并对预测的毒力基因、耐药基因、插入元件(IS)、前噬菌体和CRISPR序列进行比较分析。通过比较基因学分析拟合泛基因组和核心基因组积累曲线，与来源于其他国家已发表的代表性菌株构建系统发育分子进化树。结果：不同时期分离的12株鼠伤寒沙门氏菌的染色体全基因组序列大小无明显差异，约为4.8 Mbp。 共发现5种不同MLST型别，以ST19为主(66.6%)。注释结果显示每株鼠伤寒沙门氏菌基因组含有大量 (＞20个)耐药基因；同时也发现不同菌株基因组之间毒力基因、IS、前噬菌体和CRISPR序列数量不尽相同；比较基因学分析证实鼠伤寒沙门氏菌核心基因组相对稳定，而泛基因组所含基因持续增加、高度可变。系统发育进化树显示，来源不同时期和国家的15株分离菌株形成3个不同进化分支，分子进化聚类与菌株的分离年代和地域无明显相关性。结论：解析了12株不同时期分离的鼠伤寒沙门氏菌标准菌株的全基因组序列，发现不同时期分离的菌株基因组数据和分子进化无明显相关性，这些结果不仅为后续探究鼠伤寒沙门氏菌耐药机制与遗传进化规律等研究奠定基础，同时也对标准菌株监管提供科学数据支持。
Objective: To understand the genomic polymorphisms of Salmonella typhimurium isolated in different periods. Methods: Solexa high-throughput sequencing technology was used to sequence the whole genome of 12 strains of S. typhimurium isolated in 1954-1980 and 2018-2020. Based on the genomic sequences of these strains, the multi-locus sequence typing (MLST) analysis was conducted. The gene function of the genomes of the sequenced strains were annotated using bioinformatics software, and those predicted virulence genes, resistance genes, insertion elements (IS), prophage and CRISPR sequences were analyzed comparatively. Based on comparative genomic analysis, the pan-genome and core genome accumulation curves were fitted. The phylogenetic evolutionary tree was constructed with published representative strains from other countries. Results: There was no signifi cant diff erence in the whole genome sequence of the chromosomes of 12 strains of S. typhimurium isolated in diff erent periods, which was about 4.8 Mbp. A total of fi ve distinct MLST types were found, among which ST19 was the predominant (66.6%). The annotation results shows that each strain contained a large number of (＞20) drug resistance genes. It was also found that the number of virulence genes, IS, prophages and CRISPR sequences varied among the genomes of different strains. Comparative genomic analysis confi rmed that the core genome of S. typhimurium was relatively stable, while the pan-genome contains continuously increasing and highly variable genes. The phylogenetic tree revealed that 15 isolated strains from diff erent periods and countries formed three diff erent evolutionary branches, and the molecular evolution clustering had no obvious correlation with isolation time and region of these strains. Conclusion: The complete genome sequences of 12 strains of S. typhimurium isolated in different periods were analyzed, and there were no obvious correlation between the genomic data and molecular evolution of these strains isolated in diff erent periods. These results not only laid a foundation for the subsequent studies on the drug resistance mechanism and genetic evolution of S. typhimurium, but also provided scientifi c data support for the regulation of standard strains.
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