Integrating metagenomic next-generation sequencing into a multimodal diagnostic framework for spinal infection: enhancing etiological identification and clinical prediction.

BACKGROUND

Spinal infection (SI) remains diagnostically challenging because of heterogeneous etiologies, nonspecific clinical manifestations, and the limited sensitivity of conventional microbiological approaches, particularly following empirical antimicrobial exposure. Although metagenomic next-generation sequencing (mNGS) enables unbiased pathogen detection, its incremental clinical value beyond pathogen identification and its role within integrated diagnostic strategies remain incompletely established.

METHODS

We retrospectively analyzed 208 consecutive patients with suspected SI between August 2022 and August 2025. Final diagnoses were established using a multidisciplinary-adjudicated composite reference standard incorporating clinical, radiological, microbiological, and histopathological evidence. The diagnostic performance of mNGS was compared with conventional culture and histopathology. Furthermore, multimodal predictive models integrating clinical variables and microbiological information were developed using L1-regularized logistic regression.

RESULTS

In the comparative cohort, mNGS achieved a significantly higher diagnostic yield than culture (66.5% vs. 27.41%, P < 0.001). Among confirmed SI cases, mNGS demonstrated higher sensitivity than conventional culture (91.67% vs. 40.15%, P < 0.001). mNGS identified a substantially broader pathogen spectrum, ranging from fastidious organisms such as Mycobacterium tuberculosis and Brucella to rare pathogens including Talaromyces marneffei and Coxiella burnetii, and maintained robust sensitivity (98.2%) despite prior antibiotic exposure. While an integrated clinical model achieved an AUC of 0.916, mNGS as a standalone modality provided superior discriminative power (AUC = 0.889) compared to histopathology (AUC = 0.836), the Conventional Biomarker Model (AUC = 0.742), and culture (AUC = 0.693).

CONCLUSIONS

mNGS is a high-yield diagnostic tool for spinal infection, particularly in culture-negative and antibiotic-pretreated scenarios. Integrating mNGS into a multimodal clinical framework facilitates etiological clarity and precision antimicrobial therapy.