Short and long read 16s rRNA gene analysis of ascitic fluid infections in critically ill patients using Illumina MiSeq and Nanopore MinION

Infections of the ascitic fluid are serious conditions that require rapid identification and treatment. The risk of mortality increases in intensive care patients as ascites is usually accompanied by other critical pathologies such as gastrointestinal bleeding and bowel perforation, which can lead to sepsis and septic shock. Microbiological diagnostics of ascites samples are hereby important for targeted therapy of abdominal infections. Standard culture techniques have shown their limitations, especially for fastidious organisms such as anaerobic bacteria as well as their time duration until a targeted therapy can be established. Analysis of the 16SrRNA gene is well established for single species identification. New next-generation sequencing methods offer the possibility of multi-pathogen analysis in short time. We aimed to establish a new fast and accurate diagnostic workflow, incorporating short- and long-read sequencing of the 16S rDNA gene for diagnostic analysis of ascitic fluid, to enable a prompt and targeted antibiotic therapy.