Nanopore-targeted sequencing improves the diagnosis and treatment of patients with infectious ascites

Ascites, a pathological accumulation of fluid in the peritoneal cavity, often accompanies advanced liver disease or malignancy and can lead to spontaneous bacterial peritonitis (SBP), a life-threatening infection. Rapid pathogen identification is critical for SBP management, yet conventional ascites culture is slow and yields a pathogen in only ~ 20% of cases, leading to frequent broad-spectrum antibiotic use without identification of the causative pathogen. We evaluated a nanopore-targeted sequencing (NTS) assay for rapid, comprehensive pathogen detection in ascitic fluid. Ascites samples from 1,173 patients were analyzed by NTS; conventional culture was performed on 616 of these samples for comparison. NTS simultaneously amplifies and sequences bacterial 16S rRNA, fungal ITS, and Mycobacterium rpoB gene targets. Diagnostic yields and changes in infection markers with therapy were utilized to evaluate the clinical value of NTS in the management of ascites. Here we show that NTS outperforms culture, detecting pathogens in 81.0% of cases (499/616) versus 16.8% (104/616) by culture (p < 0.001). NTS identifies pathogens in 399 culture-negative cases and uncovers polymicrobial infections and difficult-to-culture organisms (anaerobes, fungi, Mycobacterium) that standard methods miss. In SBP patients (n = 56), NTS achieves an 82% pathogen detection rate versus 38% by culture. Patients managed with NTS-guided targeted antibiotics show faster declines in procalcitonin (PCT) than those on empirical therapy. NTS is a rapid, sensitive diagnostic approach for ascitic infections that significantly improves pathogen identification and enables earlier targeted therapy. Its implementation could improve clinical outcomes and antibiotic stewardship in patients with ascites.