Metagenomic next-generation sequencing provides a rapid and accurate diagnosis of pathogens in patients undergoing immunosuppressive therapy

Abstract

Background: Patients receiving immunosuppressive regimens are at increased risk of life-threatening infections from microorganisms. The comprehensive analysis of the types and composition of pathogenic microorganisms in clinical specimens from immunosuppressed patients is of great importance for prognosis and diagnosis.

Methods: Three hundred and sixty clinical samples from 199 patients were enrolled in this study. The results of metagenomics next-generation sequencing (mNGS) detection were analysed, and diagnostic performance was compared with that of conventional methods (CMs). Differences in microbiological detection were analysed between immunosuppressant monotherapy and combination therapy. The differences in microflora between blood samples and non-blood samples were also examined.

Results: The positive rate of the mNGS results was higher than that of the CMs results in all types of samples, and the number of pathogens detected by mNGS was also greater than that of CMs. The percentage of co-infection detected by mNGS was 45.56% which was higher than that of CMs (6.67%, 24 out of 360). In the immunosuppressant single-drug group, 58.1% of the samples were mixed infections, while in the two-drug combination group, single infections accounted for 56% of the samples. Multiple pathogen infection (63.8%) was the most common type of infection in non-blood samples, of which 28.4% were viral and bacterial co-infections. A single pathogen accounted for 53.8% of the infections detected in blood samples, of which 35.9% were individual viruses. Non-blood samples have a higher negative predictive value (88.9% vs. 77.5%) and accuracy (100% vs. 92%) than blood samples.

Conclusions: mNGS is superior to CMs for the diagnosis of infections in patients treated with immunosuppressants. The immunosuppressive medication regimen needs to be adjusted when the patients have serious infections. Blood samples could be used for rapid diagnosis of suspected viral infection, and samples from infectious sites have significant advantages in detecting bacterial and viral co-infection.

Keywords

clinical / diagnosis / immunosuppressant / metagenomics next-generation sequencing (mNGS) / pathogenic microorganisms

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2025 The Author(s). Clinical and Translational Discovery published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.