Evaluation of High-Throughput Gene Chip Array for Enhanced Diagnosis of Bone and Joint Infections: A Comparative Analysis with mNGS and Conventional Culture Methods.

Background: While conventional culture-based diagnosis of bone and joint infections (BJI) requires prolonged incubation periods and metagenomic next-generation sequencing (mNGS) remains cost-prohibitive for routine clinical use, there is an urgent need for diagnostic strategies that balance timeliness with economic feasibility. This study investigates the clinical utility of a high-throughput (HT) gene chip array as a novel solution, offering significantly shorter turnaround time while maintaining cost-effectiveness than mNGS expenses.

Methods: Thirty-six patients of the BJI group (28 positives and 8 negatives diagnosed by clinician) and 20 patients of respiratory tract infection (RTI) group (14 positives and 6 negatives diagnosed by clinician) were included in this study. Synovial fluid and ultrasound fluid samples of BJI group and alveolar lavage fluid samples of RTI group were collected and subjected to microbiological analysis performed by HT gene chip array, metagenomic next-generation sequencing (mNGS) and conventional culture. Sensitivity, specificity, accuracy, positive predictive value (PPV) and negative predictive value (NPV) were calculated. Positive and negative percent agreement and Cohen`s kappa coefficient were calculated.

Results: The sensitivity and accuracy of HT gene chip assay for BJI detection was 71.43% and 77.78%, respectively (p value <0.05). HT gene chip assay exhibited the 100% of specificity and PPV, which is significantly higher than those of mNGS (62.5%, 89.29%) and conventional culture (78.57% and 88.89%). Our results position HT gene chip assay as a clinically actionable solution for accurate and timely bone and joint infection management.

Conclusion: HT gene chip assay demonstrates superior diagnostic specificity and cost-effectiveness with rapid turnaround, significantly reducing unnecessary invasive procedures while maintaining high concordance with mNGS, and exhibited higher clinical value of BJI diagnosis compared with mNGS and conventional culture.