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

作为非伤寒沙门氏菌I亚种，鼠伤寒沙门氏菌是一种日益增长和不断演变的威胁，在撒哈拉以南非洲，它现在是侵袭性细菌性感染的主要原因，在美国，它也是造成多次与食品有关的疫情的罪魁祸首，历史上它在美国将污染范围扩大到家禽，最近似乎能够在花生和西红柿上定居(或至少顽强生存)。在这两种情况下，很可能是选择压力正在推动鼠伤寒沙门氏菌的进化，以获得和/或失去利用新的传播途径的生物学能力。关于鼠伤寒沙门氏菌基因组中的哪些成分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。我们将使用高通量的体外表型来鉴定撒哈拉以南非洲地区引起腹泻性和非腹泻性疾病的菌株。为了更好地了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充分表征核心基因组元素中的所有等位基因差异，并对缺失的基因进行清点，并确定非洲NTS和美国不同食源性来源的许多菌株中是否存在新基因。相关的遗传因素将通过等位基因替换在功能上进行验证，在某些情况下还将通过动物模型毒力测试进行验证。对于功能验证的遗传标记，将开发简化的分析方法(聚合酶链式反应、等位基因特异性聚合酶链式反应或基因位点特异性DNA测序)，然后可以在现场实施，以评估其患病率和临床意义。

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.