Genotypic Correlates of Pathogen Diversitiy of NTS in Africa and North America

非伤寒沙门氏菌肠道亚种I，血清型鼠伤寒沙门氏菌是一种不断增长和演变的威胁，无论是在撒哈拉以南非洲，它现在是侵入性细菌性感染的主要原因，还是在美国，它已经造成了许多与食物有关的爆发，在那里，它已经将其污染范围扩大到家禽，最近显然能够在花生和西红柿上定居（或至少存活得很好）。在这两种情况下，似乎选择压力正在推动鼠伤寒沙门氏菌的进化，以获得和/或失去利用新传播途径的生物能力。对于鼠伤寒沙门氏菌基因组中的哪些元素被改变以实现这些适应，或者这可能对人类免疫反应产生什么影响，人们知之甚少。我们将使用高通量体外表型来表征撒哈拉以南非洲引起腹泻与非腹泻疾病的菌株。为了更好地理解鼠伤寒沙门氏菌适应背后的遗传特征，我们将使用下一代全基因组来完全表征核心基因组元件的所有等位基因差异，并对缺失基因进行清单分析，并确定在非洲NTS和美国不同食源性来源的许多菌株中存在的新基因。相关的遗传元素将通过等位基因替换在功能上得到验证，在某些情况下通过动物模型毒力试验得到证实。对于功能验证的遗传标记，将开发简化的分析方法（PCR、等位基因特异性PCR或位点特异性DNA测序），然后可以在现场实施，以评估其流行程度和临床意义。

Non-typhoidal Salmonella enterica subspecies I, serovar typhimurium is a growing and evolving threat, both in Sub-Saharan Africa, where it is now a leading cause of invasive, bacteremic infections, and also in the United States, where it has been responsible for numerous food-related outbreaks, where it has expanded its contamination profile historically into poultry, and recently has apparently been able to colonize (or at least survive robustly) on peanuts and tomatoes. In both cases, it appears likely that selection pressures are driving evolution of S. typhimurium to acquire and/or lose biological capabilities to take advantage of new routes of transmission. Less is known about what elements in the genome of S. typhimurium have been altered to enable these adaptations, or what impact that may have on the human immune response. We will use high-throughput in-vitro phenotyping to characterize strains causing diarrheal vs. non-diarrheal disease from Sub-Saharan Africa. To better understand the genetic traits behind adaptation in S. typhimurium we will use next-generation whole genome to fully characterize all allelic differences in core genome elements, and to inventory missing genes, and define the presence of novel genes in many strains from NTS in Africa, and from varying foodborne sources in the USA. Correlated genetic elements will be functionally verified by allelic replacement and in some cases demonstrated by animal model virulence tests. For functionally verified genetic markers, simplified assays will be developed (PCR, Allele-specific PCR or locus-specific DNA sequencing), which can then be implemented in the field to assess their prevalence and clinical significance.