Ascites bactericidal capacity in patients with decompensated cirrhosis

Patients with decompensated cirrhosis are at high risk of developing bacterial infections. The most common infection is spontaneous bacterial peritonitis (SBP) in ascites fluid, caused by gut bacterial translocation. Here we investigated the bactericidal activity of cell-free ascites fluid (AF) and ascites macrophages. Extra-intestinal pathogenic Escherichia coli (ExPEC) and Klebsiella pneumoniae strains, representative of the most common causes of SBP, were resistant to killing in cell-free ascites fluid. To identify the genetic basis of this survival advantage, we performed a transposon-based genome-wide screen and identified a requirement for genes involved in O-antigen biosynthesis for survival of both organisms in cell-free ascites fluid.To generate the data presented in this SRA submission, we conducted transposon insertion-site directed sequencing (TraDIS) experiments using miniTn5 libraries of E. coli strain EC958 and K. pneumoniae strain Kp52.145. The experimental design involved exposing approximately 1 million mutants from each library to cell-free ascites fluid from a single donor for 90 minutes to allow survival of resistant mutants while eliminating susceptible ones. We then enriched surviving mutants through 4-hour growth in LB broth and extracted genomic DNA. In parallel, mutant libraries were exposed to heat-inactivated ascites fluid as a negative control, since this treatment abolishes bactericidal activity. DNA from both test and control samples underwent standard processing and sequencing.