Evolving microbiology of spondylodiscitis: a 1380-patient study on diagnostic performance

Spondylodiscitis has become a global challenge due to complex aetiology, insidious onset, and rising incidence, yet large-scale epidemiological trend data are lacking and no standardised diagnostic workflow exists internationally, resulting in widespread empirical therapy and delayed targeted treatment. This study aimed to analyse annual changes and epidemiological trends in the pathogen spectrum of spondylodiscitis over three years and to evaluate the diagnostic performance and accuracy of different microbiological detection methods, including conventional culture, metagenomic next-generation sequencing(mNGS), and targeted serological assays. In this single-centre study from April 2022 to June 2025, 1380 consecutive adult patients with spondylodiscitis had lesion specimens submitted for conventional culture, of whom 482 also underwent mNGS. The three-year period was divided into three 12-month intervals to analyse temporal trends in pathogen distribution at species and genus levels by both culture and mNGS, together with targeted serological tests (T-SPOT.TB, standard agglutination test for brucellosis, and fungal biomarkers when indicated). Clinical outcomes following the diagnostic workflow were also assessed. A total of 1380 patients were included (mean age 59.2 ± 14.3 years, 59.5% male), mNGS was performed in 482 patients with a positivity rate of 88.2% (425/482), significantly higher than conventional culture performed in 1380 patients (43.4%, 599/1380; p < 0.001). mNGS findings: in 2022–2023 ( n = 185), Escherichia coli was the most common pathogen (23.8%), followed by Mycobacterium tuberculosis (11.4%) and Brucella (10.3%). In 2023–2024 ( n = 68), Staphylococcus aureus predominated (20.6%). In 2024–2025 ( n = 229), M. tuberculosis complex rebounded to 16.6%. At genus level, Staphylococcus spp. increased from 22.2% to 24.9%, An increase in the Mycobacterium spp. level was observed, from 12.4% to 17.9%, and Enterobacteriaceae decreased from 28.6% to 11.4%. Conventional culture findings: among 599 culture-positive cases, M. tuberculosis was the leading pathogen in 2022–2023 (26.2%) and decreased progressively to 8.8% in 2024–2025. Staphylococcus aureus showed a numerical increase from 7.6% to 8.6% over the same period, though not statistically significant. At genus level, Mycobacterium spp. declined from 28.0% to 10.5%, Staphylococcus spp. from 9.2% to 15.8%, and Enterobacteriaceae has slightly increased. T-SPOT.TB positivity was 25.9% (496/1919) with 180 confirmed cases, standard agglutination test (SAT) 12.0% (222/1855) all confirmed, (1,3)-β-D-glucan test (G-test) 5.0% (79/1597) with 9 confirmed, galactomannan test (GM-test) 4.0% (64/1598) with 7 confirmed, and blood culture 19.7% (345/1750) with 340 confirmed. Multidrug-resistant organisms increased from 6 cases to 47. Favourable outcomes were achieved in the majority of patients. 1074 (77.8%) recovered, 197 (14.3%) improved, and 109 (7.9%) experienced treatment failure. Over the three-year period, tuberculous infections gradually decreased while pyogenic bacteria, particularly Staphylococcus aureus , increased, along with a rise in multidrug-resistant organisms. Among specific diagnostic tests, SAT showed the highest diagnostic yield, while other serological assays had limited value. Both mNGS and lesion culture effectively identified pathogens, with mNGS offering a higher positivity rate. Favorable clinical outcomes were achieved through a diagnostic workflow that confirmed the pathogen and guided antibiotic selection. None.