Case Report: NGS-guided rapid diagnosis of tuberculous otitis media—a rare case of dual-site Mycobacterium tuberculosis infection

Background Tuberculous otitis media (TOM) is an exceptionally rare form of extrapulmonary tuberculosis that was usually diagnosed only after long-standing ear discharge or profound hearing loss. This case reported a young man in whom deafness was the sentinel event leading to the discovery of pulmonary tuberculosis and molecular confirmation of concurrent TOM. Case presentation A 23-year-old male presented with bilateral, progressive hearing loss that had been labeled “chronic suppurative otitis media” by local clinics. Persistent constitutional symptoms prompted chest imaging that revealed bilateral cavitary infiltrates. Broncho-alveolar lavage metagenomic next-generation sequencing identified Mycobacterium tuberculosis complex (MTBC). After transfer to our tuberculosis center, targeted NGS of serous middle-ear fluid detected MTBC; the isolate carried an rpsL K43R mutation conferring streptomycin resistance, identical to the pulmonary strain. Standard four-drug anti-tuberculosis therapy was initiated; within 4 weeks, cough and fever resolved, inflammatory markers normalized, and the pulmonary cavity showed reduction in size compared to baseline. Conclusion This case highlights that unexplained hearing loss may serve as an early indicator of disseminated tuberculosis. High-throughput sequencing of aural discharge enables rapid diagnosis of TOM, facilitates resistance-guided treatment, and helps trace the pathways of pathogen transmission.