Characterization of pyelonephritis and cystitis E. coli isolates – Comparison of bacterial traits involved in colonization of the lower or upper urinary tract

尿路致病性大肠埃希菌(UPEC)是引起下、上尿路感染最常见的病原菌。肾脏和尿囊在解剖学和免疫反应等方面有很大的不同。我们假设UPEC适应肾脏和膀胱之间截然不同的环境，例如，在紧张性和营养可获得性方面。也有流行病学证据表明肾盂肾炎和膀胱炎分离株不同。我们假设UPEC在上尿路感染和下尿路感染中采用不同的适应策略。我们将对肾盂肾炎和膀胱炎分离株进行比较基因组学研究，以确定分别决定肾脏和膀胱致病性的细菌因素。以选定的毒力因子和小分子调控RNA为例，我们将在基因调控和功能水平上研究细菌在肾脏中的适应。我们将在小鼠感染模型中使用双重RNA-SEQ分析感染肾脏中细菌和宿主基因的全局表达。此外，我们将使用报告基因模块、组织透明、光片显微镜以及双光子显微镜来跟踪这些因子在感染器官中或感染过程中的表达。进一步的功能鉴定将包括体外研究UPEC分离株或定义的突变体与不同生长和感染条件下分离的收集管之间的相互作用。

Uropathogenic Escherichia coli (UPEC) are the most common pathogens of lower and upper urinary tract infections (UTIs). Kidneys and urinary bladders differ significantly, among other things, anatomically and in terms of an immune response. We assume that UPEC adapt to the respective environment which profoundly differs between kidney and bladder, e.g., in terms of tonicity and nutrient availability. There is also epidemiological evidence that pyelonephritis and cystitis isolates differ. We hypothesize that UPEC employ different adaptation strategies during upper and lower UTI. We will perform comparative genomics on pyelonephritis and cystitis isolates to identify bacterial factors that determine pathogenicity in the kidneys and bladder, respectively. Using selected virulence factors and small regulatory RNAs as examples, we will investigate bacterial adaptation in the kidney at the gene regulatory and functional levels. We will analyze global bacterial and host gene expression in the infected kidney using dual RNA-seq in a murine infection model. Furthermore, we will use reporter gene modules, tissue clearing, and lightsheet microscopy as well as two-photon microscopy to follow the expression of these factors in the infected organ or during the course of infection. Further functional characterization will include in vitro studies of the interaction between UPEC isolates or defined mutants and isolated collecting ducts under different growth and infection conditions.