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Enhanced pathogen detection and gut microbiome alterations in pyogenic liver abscess: insights from next-generation sequencing

Year: 2026

Type: article

Abstract: OBJECTIVES: Pyogenic liver abscess (PLA) is a life-threatening infection with high mortality in Asia. Although Klebsiella pneumoniae is commonly implicated, emerging data suggest a more diverse microbial spectrum. This study investigated pathogen detection using conventional culture and next-generation sequencing (NGS) and characterized gut microbiome alterations in PLA patients compared to healthy controls. METHOD: This was a prospective, multicenter cohort study conducted across eight tertiary hospitals. We enrolled 100 PLA patients who underwent percutaneous aspiration. Abscess aspirates underwent both conventional culture and 16 S rRNA-based NGS. Stool samples from PLA patients and 100 healthy controls were analyzed for gut microbiome composition using NGS. RESULTS: Culture positivity was 82%, with abscess cultures positive in 77 cases and blood cultures in 32. K. pneumoniae was the most frequently isolated pathogen (67%), and polymicrobial infections were identified in only 3% of cases by culture. NGS of abscess aspirates was available in 92% of patients, including 15 culture-negative cases. NGS identified polymicrobial infections in 16.3% of patients-more than fivefold higher than culture. Among 77 patients who underwent both culture and NGS, 13 (16.9%) showed discordance, mostly due to polymicrobial or anaerobic organisms identified by NGS. Stool NGS analysis revealed significantly reduced alpha diversity in PLA patients compared to healthy controls (Shannon index 2.9 vs. 3.5, p < 0.001), increased abundance of Enterococcus species (27.1% vs. 8.6%, p < 0.001), and depletion of SCFA-producing genera including Faecalibacterium, Roseburia, and Lachnospira species. Despite K. pneumoniae dominance in abscesses, its stool abundance did not significantly differ between PLA patients and controls. CONCLUSION: NGS improves the detection of anaerobes and mixed infections in PLA. The gut microbiota of PLA patients shows marked dysbiosis, suggesting a potential role in disease pathogenesis and future therapeutic targets.

Source: Gut Pathogens

DOI: 10.1186/s13099-026-00799-4