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. 2025 Aug;44(8):3265-3275.
doi: 10.1007/s10067-025-07525-6. Epub 2025 Jun 20.

Clinical value of metagenomic next-generation sequencing in patients with connective tissue diseases co-infections: a single-center study from southern hospital in China

Yuan-Yuan Xiao  1 , Ai-Ling Lu  1   2 , Han-You Mo  3 , Zhen-Dong He  4 , Jia-Le Wen  4 , Xuan Yin  1
Affiliations

Clinical value of metagenomic next-generation sequencing in patients with connective tissue diseases co-infections: a single-center study from southern hospital in China

Yuan-Yuan Xiao et al. Clin Rheumatol. 2025 Aug.

Abstract

Objectives: This study aimed to assess the clinical value of metagenomic next-generation sequencing (mNGS) in patients with connective tissue diseases (CTDs) co-infections, thereby establishing a foundation for early infection identification and the development of anti-infective regimens.

Methods: This retrospective study analyzed 304 CTD patients with suspected infections at the First Affiliated Hospital of Guangxi Medical University between October 2020 and April 2024. The study compared the diagnostic efficacy between mNGS and conventional microbiological testing (CMT), examined pathogen detection rates across different periods and pathogen types, and evaluated the clinical outcomes of mNGS-guided antimicrobial regimen adjustments.

Results: Among the 180 confirmed infections (Group I), mNGS demonstrated superior diagnostic performance compared to conventional microbiological testing (CMT). mNGS exhibited significantly higher sensitivity (89.6% vs. 57.0%; OR = 6.5, 95% CI: 3.7-11.0, p < 0.001), with a specificity of 81.5%, positive predictive value (PPV) of 97.2%, and negative predictive value (NPV) of 52.4%. mNGS outperformed CMT in detecting bacterial and viral pathogens (p < 0.05). Viral infections were the most common. Compared to prior studies, mNGS exhibited improved pathogen detection rates. mNGS-guided treatment optimization significantly enhanced clinical outcomes, with higher cure rates, lower mortality, and shorter hospital stays.

Conclusion: Current evidence suggests that while mNGS demonstrates superior diagnostic performance over CMT for detecting infections in CTD patients, their combined use provides optimal pathogen identification accuracy and enhanced clinical management. Key Points • This is the larger-scale retrospective study of mNGS application in patients with CTDs co-infections following the Coronavirus Disease 2019 (COVID-19). • We found that the distribution of pathogens and positivity rates have changed in recent years, especially after the COVID-19. • The clinical value of mNGS was further demonstrated through its impact of mNGS results on antibiotic regimens and the analysis of negative samples.

Keywords: Clinical value; Connective tissue diseases; Infections; Metagenomic next-generation sequencing; Pathogens.

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Conflict of interest statement

Declarations. Consent to participate: Patients and/or the public were not involved in the design, conduct, reporting, or dissemination plans of this research. Consent for publication: Not required. Disclosures: None.

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