Salmonella enterica serovar Typhimurium DT160 was the predominant cause of notified human salmonellosis cases in New Zealand from 2000 to 2010, before it was superseded by another S. Typhimurium strain, DT56 variant (DT56v). Whole genome sequencing and phenotypic testing were used to compare 109 DT160 isolates with eight DT56v isolates from New Zealand animal and human sources. Phylogenetic analysis provided evidence that DT160 and DT56v strains were distantly related with an estimated date of common ancestor between 1769 and 1821. The strains replicated at different rates but had similar antimicrobial susceptibility profiles. Both strains were resistant to the phage expressed from the chromosome of the other strain, which may have contributed to the emergence of DT56v. DT160 contained the pSLT virulence plasmid, and the sseJ and sseK2 genes that may have contributed to the higher reported prevalence compared to DT56v. A linear pBSSB1-family plasmid was also found in one of the DT56v isolates, but there was no evidence that this plasmid affected bacterial replication or antimicrobial susceptibility. One of the DT56v isolates was also sequenced using long-read technology and found to contain an uncommon chromosome arrangement for a Typhimurium isolate. This study demonstrates how comparative genomics and phenotypic testing can help identify strain-specific elements and factors that may have influenced the emergence and supersession of bacterial strains of public health importance.

从 2000 年到 2010 年，在被另一种沙门氏菌取代之前，肠道沙门氏菌鼠伤寒沙门氏菌 DT160 血清型是新西兰通报的人类沙门氏菌病病例的主要原因。鼠伤寒菌株，DT56 变体 (DT56v)。全基因组测序和表型测试用于比较 109 种 DT160 分离株与来自新西兰动物和人类来源的 8 种 DT56v 分离株。系统发育分析提供的证据表明，DT160 和 DT56v 菌株与 1769 年和 1821 年之间的共同祖先的估计日期远相关。这些菌株以不同的速度复制，但具有相似的抗菌敏感性特征。两种菌株都对另一种菌株染色体表达的噬菌体具有抗性，这可能促成了 DT56v 的出现。DT160 含有 pSLT 毒力质粒，sseJ和sseK2与 DT56v 相比，可能导致报告患病率更高的基因。在其中一个 DT56v 分离株中也发现了线性 pBSSB1 家族质粒，但没有证据表明该质粒影响细菌复制或抗菌药物敏感性。其中一个 DT56v 分离株也使用长读长技术进行了测序，发现其含有一种不常见的鼠伤寒分离株染色体排列。这项研究展示了比较基因组学和表型测试如何帮助识别可能影响具有公共卫生重要性的细菌菌株的出现和替代的菌株特异性元素和因素。