Clinical utility of nanopore amplicon sequencing in various culture-negative infectious diseases: a case series report

Identifying the causative pathogen is essential for selecting optimal antimicrobial therapy, and nanopore amplicon sequencing is an emerging approach for rapid nucleic acid based pathogen detection. This study reports clinical cases in which nanopore sequencing was used alongside conventional culture of clinical specimens obtained from infection sites, aiding clinical decision-making. From July 2024 to October 2025, eight patients with various infectious diseases were enrolled. All patients had at least one underlying disease, and their clinical diagnoses varied, including brain abscess, osteoarticular infection, pneumonia, and skin infection. Specimens, including abscess, ligament, intervertebral disc, joint fluid, sputum, and skin, were collected from infection sites for both routine culture and nanopore sequencing. Conventional cultures yielded no organisms in any of the clinical specimens. Nanopore sequencing was performed using the MinION device, and generated reads were analyzed through the EPI2ME platform. Nanopore amplicon sequencing identified pathogens in culture-negative infections, revealing fungi in three patients and bacteria in five. Targeted antimicrobial therapy based on sequencing led to clinical improvement in all cases. This case series demonstrates the potential utility of nanopore sequencing for detecting pathogens in culture-negative infections. Nanopore sequencing may inform treatment decisions when cultures are negative or are confounded by antibiotics.