Evaluation of targeted sequencing for pathogen identification in bone and joint infections: a cohort study from China.

Purpose: Bone and joint tuberculosis (BJTB) is a distinct variant of tuberculosis in which clinical diagnosis often leads to relative misdiagnosis and missed diagnoses. This study aimed to evaluate the diagnostic accuracy of the targeted nanopore sequencing (TNPseq) assay for BJTB patients in China.

Method: The study enrolled a cohort of 163 patients with suspected BJTB. Diagnostic testing was performed using the TNPseq assay on samples including punctured tissue, pus, and blood. The diagnostic accuracy of the TNPseq assay was then compared with that of the T-SPOT and Xpert MTB/RIF assays.

Result: TNPseq exhibited superior performance in terms of accuracy, demonstrating a sensitivity of 76.3% (95% CI: 71.0-81.6%) and a specificity of 98.8% (95% CI: 93.5-100%) in clinical diagnosis. When evaluated against a composite reference standard, TNPseq demonstrated a sensitivity of 74.4% (95% CI: 69.3-79.5%) and a specificity of 98.8% (95% CI: 93.7-100%). These results exceed the performance of both the T-SPOT and Xpert MTB/RIF tests. Notably, TNPseq demonstrated high specificity and accuracy in puncture specimens, with a sensitivity of 75.0% (95% CI: 70.2-79.8%) and a specificity of 98.3% (95% CI: 92.7-100%), as well as in pus samples, with a sensitivity of 83.3% (95% CI: 78.6-88.1%) and a specificity of 100% (95% CI: 100-100%). Additionally, TNPseq facilitated the detection of mixed infection scenarios, identifying 20 cases of bacterial-fungal co-infection, 17 cases of bacterial-viral co-infection, and two cases of simultaneous bacterial-fungal-viral co-infection.

Conclusion: TNPseq demonstrated great potential in the diagnosis of BJTB due to its high sensitivity and specificity. The ability of TNPseq to diagnose pathogens and detect drug resistance genes can also guide subsequent treatment. Expanding the application scenarios and scope of TNPseq will enable it to benefit more clinical treatments.