Emerg Infect Dis. 2017 Oct;23(10):1631-1639. doi: 10.3201/eid2310.161248.
Whole-genome sequencing is rapidly replacing current molecular typing methods for surveillance purposes. Our study evaluates core-genome single-nucleotide polymorphism analysis for outbreak detection and linking of sources of Salmonella enterica serovar Typhimurium and its monophasic variants during a 7-month surveillance period in Denmark. We reanalyzed and defined 8 previously characterized outbreaks from the phylogenetic relatedness of the isolates, epidemiologic data, and food traceback investigations. All outbreaks were identified, and we were able to exclude unrelated and include additional related human cases. We were furthermore able to link possible food and veterinary sources to the outbreaks. Isolates clustered according to sequence types (STs) 19, 34, and 36. Our study shows that core-genome single-nucleotide polymorphism analysis is suitable for surveillance and outbreak investigation for Salmonella Typhimurium (ST19 and ST36), but whole genome-wide analysis may be required for the tight genetic clone of monophasic variants (ST34).
全基因组测序正在迅速取代当前用于监测目的的分子分型方法。我们的研究评估了核心基因组单核苷酸多态性分析在丹麦进行的为期 7 个月的监测期间用于检测沙门氏菌肠炎血清型 Typhimurium 及其单相变体的暴发和溯源的应用。我们重新分析并定义了 8 个以前特征明确的暴发，这些暴发是根据分离株的系统发育关系、流行病学数据和食品溯源调查来确定的。所有暴发均被识别，我们能够排除不相关的病例并纳入更多相关的人类病例。我们还能够将可能的食物和兽医来源与暴发联系起来。分离株根据序列型 (ST) 19、34 和 36 聚类。我们的研究表明，核心基因组单核苷酸多态性分析适合用于沙门氏菌肠炎 Typhimurium（ST19 和 ST36）的监测和暴发调查，但对于单相变体（ST34）的紧密遗传克隆可能需要进行全基因组分析。
