Diagnostic performance of nanopore-targeted sequencing for pulmonary infections in a tuberculosis-endemic setting: A...

Pulmonary infections in tuberculosis (TB)-endemic settings are heterogeneous and commonly polymicrobial. Nanopore-targeted sequencing (NTS) enables detection of mycobacteria, bacteria, and fungi in a single targeted assay. However, performance across pathogen classes in TB-endemic cohorts remains limited.

We conducted a prospective study at a specialized TB hospital, enrolling adults with suspected pulmonary infections across five predefined diagnostic categories: pulmonary TB, nontuberculous mycobacterial pulmonary disease, bacterial, fungal, and polymicrobial infection. Respiratory specimens (n = 312) from 305 patients were tested in parallel by conventional microbiological testing (CMT) and NTS. Blinded clinical diagnoses served as the reference standard.

Among 283 paired cases, NTS identified the adjudicated pathogens in 263 cases, whereas culture identified them in 185 cases. NTS showed a sensitivity/specificity of 83.0%/99.4% for Mycobacterium tuberculosis, 89.8%/98.2% for nontuberculous mycobacteria, 92.9%/91.1% for fungi, and 97.4%/57.8% for bacteria. In 72 polymicrobial infections, NTS detected all adjudicated pathogens in 77.8% vs 62.5% for CMT, a nonsignificant difference (P = 0.06). Overall, NTS provided a 12.2% incremental diagnostic yield.

NTS offers sensitive, single-assay detection of diverse pulmonary pathogens in TB-endemic settings. By streamlining workflows and improving detection of fastidious or co-infecting organisms, it may complement conventional methods. However, bacterial NTS findings in nonsterile respiratory specimens require clinical correlation.