Detection Blind Spots in Microbial Culture, tNGS, and mNGS: Anaerobic Bacterial Infections in the Lung-A...

Aspiration pneumonia is often associated with specific obligate anaerobic bacteria, particularly oral commensals, as causative agents; however, these infections are frequently misdiagnosed in clinical settings. This retrospective analysis of two patients presenting with fever and cough demonstrates that, in the setting of inconclusive routine microbiological testing and tNGS results, along with ineffective empirical antimicrobial therapy, comprehensive mNGS analysis of BALF microbiota-combined with the presence of high-risk oral factors (such as dental caries and severe periodontitis)-facilitated the diagnosis of anaerobic pneumonia. In both cases, tNGS was unable to detect anaerobic pathogens due to the limited scope of anaerobic bacterial targets in commercial panels. In contrast, comprehensive mNGS, when correctly interpreted in conjunction with clinical context, can detect anaerobic sequences. The key difference lies in that mNGS offers a broader detection capability, but it requires careful correlation with clinical circumstances to distinguish between true pathogens and colonizing bacteria. Specifically, Case 1 revealed the presence of Bacteroides timidum and Fusobacterium nucleatum. Case 2 identified Prevotella oralis, Streptococcus australis, and Actinomyces caries. The administration of targeted anti-anaerobic therapy (metronidazole, ornidazole) subsequently resulted in significant improvement in clinical symptoms and radiographic findings. These cases underscore the diagnostic value of integrating metagenomic next-generation sequencing (mNGS) with clinical risk factor assessment when conventional diagnostics produce negative results.