Metagenomic next-generation sequencing in suspected septic arthritis: A critical appraisal of clinical utility in 82 cases

OBJECTIVES: To evaluate the diagnostic utility of metagenomic next-generation sequencing (mNGS) compared to conventional culture in patients with suspected septic arthritis, stratified by synovial fluid white blood cell (SF-WBC) count. METHODS: A retrospective observational study was conducted on 82 consecutive patients with clinically suspected septic arthritis. Patients were categorized based on actual clinical testing pathways: complete triple testing (routine analysis, culture, and mNGS; n = 54), culture and mNGS only (n = 27), or mNGS only (n = 1). Detection rates, turnaround times, and clinical impact were analyzed across WBC strata. RESULTS: mNGS demonstrated a significantly higher overall detection rate than culture (65.9% vs 33.3%, P < 0.001). This diagnostic advantage was most pronounced in the diagnostically challenging subgroup of patients with SF-WBC count <25,000/µL, where mNGS had a significantly higher pathogen detection rate than culture (50.0% [19/38] vs 23.7% [9/38]; P < 0.05). Among the 27 patients positive by both methods, mNGS revealed discrepant or additional findings in 9 cases (33.3%), including viruses, fungi, and fastidious bacteria, which required clinical adjudication. The median reporting time was shorter for mNGS than culture (67 vs 86 hours, P < 0.001). Clinical management was guided solely by mNGS in 23 patients (28.0%), including 21 culture-negative cases and 2 where mNGS results preceded culture. CONCLUSION: mNGS provides significant diagnostic value in suspected septic arthritis, particularly in culture-negative cases and those with low SF-WBC counts. It should be used selectively as an adjunct to culture, which remains essential for antimicrobial susceptibility testing.