Department of Food Science, Cornell University, Ithaca, New York, USA.
mBio. 2024 Oct 16;15(10):e0191324. doi: 10.1128/mbio.01913-24. Epub 2024 Sep 17.
Most foodborne salmonellosis outbreaks are linked to agricultural animal products with a few serovars accounting for most isolated from specific animal products, suggesting an adaptation to the corresponding animal hosts and their respective environments. Here, we utilized whole-genome sequence (WGS) data to analyze the evolution and population genetics of seven serovars frequently isolated from ground beef (Montevideo, Cerro, and Dublin), chicken (Kentucky, Infantis, and Enteritidis), and turkey (Reading) in the United States. In addition, publicly available metadata were used to characterize major clades within each serovar with regard to public health significance. Except for Dublin, all serovars were polyphyletic, comprising 2-6 phylogenetic groups. Further partitioning of the phylogenies identified 25 major clades, including 12 associated with animal or environmental niches. These 12 clades differed in evolutionary parameters (e.g., substitution rates) as well as public health relevant characteristics (e.g., association with human illness, antimicrobial resistance). Overall, our results highlight several critical trends: (i) the generation time appears to be more dependent on source than serovar and (ii) all serovars contain clades and sub-clades that are estimated to have emerged after the year 1940 and that are enriched for isolates associated with humans, agricultural animals, antimicrobial resistance (AMR), and/or specific geographical regions. These findings suggest that serotyping alone does not provide enough resolution to differentiate isolates that may have evolved independently, present distinct geographic distribution and host association, and possibly have distinct public health significance.
Non-typhoidal are major foodborne bacterial pathogens estimated to cause more than one million illnesses, thousands of hospitalizations, and hundreds of deaths annually in the United States. More than 70% of outbreaks in the United States have been associated with agricultural animals. Certain serovars include persistent strains that have repeatedly contaminated beef, chicken, and turkey, causing outbreaks and sporadic cases over many years. These persistent strains represent a particular challenge to public health, as they are genetically clonal and widespread, making it difficult to differentiate distinct outbreak and contamination events using whole-genome sequence (WGS)-based subtyping methods (e.g., core genome allelic typing). Our results indicate that a phylogenetic approach is needed to investigate persistent strains and suggest that the association between a serovar and an agricultural animal is driven by the expansion of clonal subtypes that likely became adapted to specific animals and associated environments.
大多数食源性沙门氏菌病暴发与食用动物产品有关，少数血清型占从特定动物产品中分离出的大多数，这表明它们适应了相应的动物宿主及其各自的环境。在这里，我们利用全基因组序列（WGS）数据来分析七种经常从美国的碎牛肉（蒙得维的亚、塞罗和都柏林）、鸡肉（肯塔基、因凡蒂尼斯和肠炎）和火鸡（雷丁）中分离出来的血清型的进化和种群遗传学。此外，还利用公开的元数据来描述每个血清型内与公共卫生意义重大的主要进化枝。除了都柏林血清型外，所有血清型都是多系的，包括 2-6 个系统发育群。进一步的系统发育分割确定了 25 个主要进化枝，包括 12 个与动物或环境小生境有关的进化枝。这 12 个进化枝在进化参数（例如，替代率）以及与公共卫生相关的特征（例如，与人类疾病的关联、抗微生物药物耐药性）方面存在差异。总的来说，我们的结果突出了几个关键趋势：（i）产生时间似乎更多地取决于来源而不是血清型，（ii）所有血清型都包含估计在 1940 年后出现的进化枝和亚进化枝，并且富含与人类、农业动物、抗微生物药物耐药性（AMR）和/或特定地理区域相关的分离株。这些发现表明，仅进行血清分型不足以区分可能独立进化、具有不同地理分布和宿主关联且可能具有不同公共卫生意义的分离株。
非伤寒性 是美国每年估计导致超过 100 万人患病、数千人住院和数百人死亡的主要食源性细菌性病原体。美国 70%以上的 暴发与食用动物有关。某些血清型包括反复污染牛肉、鸡肉和火鸡的持续性菌株，导致多年来暴发和散发性病例。这些持续性菌株对公共卫生构成了特别的挑战，因为它们在遗传上是克隆的和广泛存在的，因此使用基于全基因组序列（WGS）的分型方法（例如核心基因组等位基因分型）很难区分不同的暴发和污染事件。我们的结果表明，需要采用系统发育方法来研究持续性菌株，并表明 血清型与食用动物之间的关联是由可能适应特定动物及其相关环境的克隆亚型的扩展驱动的。
