Establishing the role of pathogenetic mechanisms in the evolution of epidemic K. pneumoniae lineages.

系统发育学--金黄色葡萄球菌流行谱系分析。利用现有的基因组序列，我们将利用时间和地理数据对不同流行和ST15谱系中的RamR突变进行种群水平的基因组和系统发育分析，以确定(I)额外的突变事件(Ii)具有优势突变的新出现的流行亚谱系，以及(Iii)绘制突变事件的潜在驱动因素图。对ST15和非ST15流行谱系中的RAMA调节子进行比较基因组学研究。利用生物信息学分析得出的数据，我们将鉴定相关菌株，以进行已建立的基于转录和芯片序列的分析，以确定DTP精密医学项目Call 21/22第3页，共4个调控级联和结合RAMA的相互作用。这些数据将对确定RAMA的调控影响至关重要，并有助于对这些变化如何在ST15流行谱系中发生宿主-病原体相互作用的机械性分析。建立ST15(RAMA过表达)和ST15R(RAMA过表达通过基因操作修复)在模拟全身感染的特定小鼠模型中的感染动力学。利用小鼠感染模型，除了评估这些菌株在抗生素存在下的生存能力外，我们还将建立与对抗ST15和ST15R变种感染相关的免疫检查点。这些数据将与David Dockrell教授合作，在现有的Shield联盟筛查中用于建立先天免疫反应，作为诊断或治疗KPN感染的工具。

Phylogenomic-Analyses of Epidemic lineages of KP. Using existing genome sequences, we will undertake a population level genomic and phylogenetic analyses of RamR mutations in different epidemic and ST15 lineages with temporal and geographic data to identify (i) additional mutational events (ii) emerging epidemic sub-lineages with advantageous mutations and (iii) map the potential drivers of mutational events. Undertake comparative genomics of the RamA regulon in ST15 and non-ST15 epidemic lineages. Using data derived from the bioinformatic analyses, we will identify the relevant strains to undertake established transcriptomic and ChIP-seq based analyses, to ascertain the DTP Precision Medicine Project Call 21/22 Page 3 of 4 regulatory cascade and binding interactions of RamA. This data will be critical in defining the regulatory impact of RamA and facilitate mechanistic analyses of how these changes host-pathogen interactions in the ST15 epidemic lineage. Establish the infection dynamics of ST15 (RamA overexpressed) and ST15R (RamA overexpression is repaired using genetic manipulation) in specific murine models which mimic systemic infection. Using the murine model of infection, in addition to assessing the viability of these strains in the presence of antibiotics, we will establish the immune checkpoints which are relevant to counter the infection of ST15 and ST15R variants. These data will be utilized in collaboration with Prof. David Dockrell in existing SHIELD consortium screens to establish innate immune responses as tools for diagnosis or treatment of KPN infection.