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.
Key words
Salmonella typhimurium； whole genome sequences； virulence genes； drug resistance genes
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References
[1] Patra SD,Mohakud NK,Panda RK,et al.Prevalence andMultidrug Resistance in Salmonella Enterica Typhimurium:an Overview in South East Asia[J].World MicrobiolBiotechnol，2021，37（11）：185.
[2] Rincón-gamboa SM,Poutou-pi?ales RA,Carrascalcamacho AK.Antimicrobial Resistance of NonTyphoid Salmonella in Meat and Meat Products[J].Foods，2021，10（8）：1731.
[3] Havelaar AH,Kirk MD,Torgerson PR,et al.World HealthOrganization Global Estimates and Regional Comparisonsof the Burden of Foodborne Disease in 2010[J].PLoSMed，2015，12（12）：e1001923.
[4] Schultz BM,Melo-gonzalez F,Salazar GA,et al.NewInsights on the Early Interaction Between Typhoid andNon-typhoid Salmonella Serovars and the Host Cells[J].Front Microbiol，2021，12：647044.
[5] Scallan E,Hoekstra RM,Angulo FJ,et al.Foodborne IllnessAcquired in the United States-Major Pathogens [J].EmergInfect Dis，2011，17（1）：7-15.
[6] Ford L,Wang Q,Stafford R,et al.Seven SalmonellaTyphimurium Outbreaks in Australia Linked by TraceBack and Whole Genome Sequencing[J].Foodborne PathogDis.2018，15（5）：285-292.
[7] 王珊珊，石继春，杜宗利，等.乳酶生生产用菌种的全基因组序列分析研究[J].中国医药生物技术，2020，15（6）：577-583.
[8] Xu Y,Zhu Y,Wang Y,et al.Whole Genome SequencingRevealed Host Adaptation-focused Genomic Plasticity ofPathogenic Leptospira[J].Sci Rep，2016，6：20020.
[9] Zhang K,Ge H,He J,et al.Salmonella Typhimurium ST34Isolate Was More Resistant than the ST19 Isolate in China,2007-2019[J].Foodborne Pathog Dis，2022，19（1）：62-69.
[10] Gómez-baltazar A,Vázquez-garcidue?as MS,Larsen J,et al.Comparative Stress Response to Food PreservationConditions of ST19 and ST213 Genotypes of SalmonellaEnterica Serotype Typhimurium[J].Food Microbiol，2019，82：303-315.
[11] 程招敏，蓝锴，柏彩英，等.鼠伤寒沙门菌分子分型及耐药性特点[J].国际检验医学杂志，2016，37（12）：1601-1603.
[12] Gómez-baltazar A,Vázquez-garcidue?as MS,Larsen J,et al.Comparative Stress Response to Food PreservationConditions of ST19 and ST213 Genotypes of SalmonellaEnterica Serotype Typhimurium[J].Food Microbiol，2019，82：303-315.
[13] Tran-dien A,Le Hello S,Bouchier C,et al.EarlyTransmissible Ampicillin Resistance in ZoonoticSalmonella Enterica Serotype Typhimurium in the Late1950s:a Retrospective,Whole-genome SequencingStudy[J].Lancet Infect Dis，2018，18（2）：207-214.
[14] Herrero-fresno A,Olsen JE.Salmonella TyphimuriumMetabolism Affects Virulence in the Host-A Minireview[J].Food Microbiol，2018，71：98-110.
[15] Lucas RL,Lee CA.Unravelling the Mysteries of VirulenceGene Regulation in Salmonella Typhimurium[J].MolMicrobiol，2000，36（5）：1024-33.
[16] Vyas P,Harish.Anti-CRISPR Proteins as a TherapeuticAgent against Drug-resistant Bacteria[J].Microbiol Res，2022，257：126963.
[17] Watson BNJ,Steens JA,Staals RHJ,et al.Coevolutionbetween Bacterial CRISPR-Cas Systems and theirBacteriophages[J].Cell Host Microbe，2021，29（5）：715-725.
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