Clinical efficacy of metagenomic next-generation sequencing for the detection of pathogens in peritoneal dialysis-related peritonitis: a prospective cohort study

Metagenomic next-generation sequencing (mNGS) has been reported to improve pathogen identification in infectious diseases. This prospective cohort study aimed to explore the etiological diagnostic value of mNGS in peritoneal dialysis (PD)-related peritonitis. Patients with PD-related peritonitis were consecutively recruited at the Nephrology Department of Nanjing Drum Tower Hospital. PD effluent samples for mNGS and culture were collected simultaneously. The positive rate, detection time, and consistency of mNGS and culture were compared. From August 1, 2021 to August 31, 2022, 38 patients with 41 episodes of PD-related peritonitis were enrolled. The positive rate of mNGS was higher than that of culture, although not statistically significant (92.7% vs 78.0%, P = 0.109). The average reporting time of mNGS was significantly shorter than that of culture (30.4 ± 10.5 vs 86.9 ± 22.2 h, P < 0.001). mNGS identified more co-pathogens and unusual pathogens than culture, with multiple pathogens being detected in nearly half of the samples. Among the 30 samples that tested positive by both methods, 27 (90%) showed completely (13 cases) or partly (14 cases) matched results between mNGS and culture. Fourteen patients (with 14 episodes of peritonitis) had used antibiotics within 2 weeks before specimen collection. Antibiotic usage led to a significant decrease in the culture-positive rate (57.1% vs 88.9%, P = 0.042), while the mNGS-positive rate remained unaffected (92.9% vs 92.6%, P = 1.000). This study revealed that mNGS exhibited higher sensitivity and shorter reporting time compared to culture in detecting pathogens in PD-related peritonitis. For samples that yielded positive results by both methods, the consistency between mNGS and culture was substantial. mNGS may offer a novel approach for the etiological diagnosis of PD-associated peritonitis, particularly in cases involving prior antibiotic use and unusual pathogens.