E. coli Variome

描述（由申请人提供）：我们建议在全基因组和全人群范围内确定所有主要肠道和肠外大肠杆菌的遗传变异。大肠杆菌致病型，与多个菌株共享的基因的正选择足迹的分析。分析的主要重点将是详细描述在正选择下发生在E.大肠杆菌，并适应致病菌株。我们的计划是收集E.大肠杆菌，将包括从超过20，000株大肠杆菌中选出的约2，500株分离株。来自地球仪的大肠杆菌菌株。将确定这些菌株的克隆多样性，并使用454技术对克隆多样性分离株进行高通量测序。250-300株E.将通过检测热点突变-影响相同氨基酸位置的重复（遗传学上不连锁的）突变，分析大肠杆菌菌株（从头获得或在公共数据库中可获得）的阳性选择足迹。热点突变是趋同进化的标志--这是这种变化在特定环境中适应意义的最强有力的标志之一。我们预计有几百个核心基因受到正选择热点突变的影响。特定热点突变与不同致病型的遗传关联将在整个人群水平上得到验证。此外，我们将测试新的基因分型标记的克隆分辨率的E。在临床和环境诊断中的潜在应用。最后，积极选择的变异的功能影响将被调查的基因参与调控大肠杆菌。大肠杆菌毒力因子 公共卫生相关性：大肠杆菌变异组项目将汇编主要大肠杆菌和肠外大肠杆菌病原体的所有遗传变异，分析多个菌株共享的基因中的正选择足迹。 核心基因中特定热点突变与新型基因分型标记的遗传关联将在人群水平上进行验证。 最后，致病性适应性变异的功能影响将被调查的基因参与调控大肠杆菌毒力因子。

DESCRIPTION (provided by applicant): We propose to determine on a genome-wide and population-wide scale genetic variations across all major diarrheal and extra-intestinal E. coli pathotypes, with the analysis of positive selection footprints in genes shared by multiple strains. The main focus of the analysis will be to characterize in detail small nucleotide variations (point substitutions and indels) that occur under positive selection in the core genes of E. coli and are adaptive to pathogenic strains. Our plan is to assemble pathotype-representative collection of E. coli that will encompass approximately 2,500 isolates selected from over 20,000 E. coli strains from around the globe. Clonal diversity of these strains will be determined and clonally diverse isolates will be subjected to high-throughput sequencing using 454 technology. Genomes of 250-300 E. coli strains (obtained de novo or available in public databases) will be analyzed for footprints of positive selection by detecting hot-spot mutations - repeated (phylogenetically-unlinked) mutations affecting the same amino acid position. Hot-spot mutations are indicative of convergent evolution - one of the strongest indications of the adaptive significance of such changes in specific environments. We expect that there are several hundred core genes affected by positively-selected hot-spot mutations. Genetic association of specific hot-spot mutations with different pathotypes will then be validated on a population-wide level. Also, we will test the clonal resolution of novel genotyping markers of E. coli for potential application in clinical and environmental diagnostics. Finally, functional effects of positively-selected variations will be investigated for genes involved in the regulation of E. coli virulence factors. PUBLIC HEALTH RELEVANCE: The E.coli Variome Project will compile all genetic variations across major diarrheal and extra-intestinal E.coli pathogens, with the analysis of positive selection footprints in genes shared by multiple strains. Genetics association of specific hot-spot mutations in core genes and novel genotyping markers will be validated on a population-wide level. Finally, function effects of pathogenicity-adaptive variations will be investigated for genes involved in the regulation of E.coli virulence factors.