Diagnostic Value of Metagenomic Next-Generation Sequencing for Multi-Pathogenic Pneumonia in HIV-Infected Patients

Abstract

Background

To evaluate the value and challenges of real-world clinical application of metagenomic next-generation sequencing (mNGS) for bronchoalveolar lavage fluid (BALF) in HIV-infected patients with suspected multi-pathogenic pneumonia.

Methods

Fifty-seven HIV-infected patients with suspected mixed pneumonia who were agreed to undergo the bronchoscopy were recruited and retrospectively reviewed the results of mNGS and conventional microbiological tests (CMTs) of BALF from July 2020 to June 2022.

Results

54 patients were diagnosed with pneumonia including 49 patients with definite pathogens and five patients with probable pathogens. mNGS exhibited a higher diagnostic accuracy for fungal detection than CMTs in HIV-infected patients with suspected pulmonary infection. The sensitivity of mNGS in diagnosis of pneumonia in HIV-infected patients was much higher than that of CMTs (79.6% vs 61.1%; P < 0.05). Patients with mixed infection had lower CD4 T-cell count and higher symptom duration before admitting to the hospital than those with single infection. The detection rate of mNGS for mixed infection was significantly higher than that of CMTs and more co-pathogens could be identified by mNGS. The most common pattern of mixed infection observed was fungi-virus (11/29, 37.9%), followed by fungi-virus-bacteria (6/29, 20.7%) coinfection in HIV-infected patients with multi-pathogenic pneumonia.

Conclusion

mNGS improved the pathogens detection rate and exhibited advantages in identifying multi-pathogenic pneumonia in HIV-infected patients. Early performance of bronchoscopy and mNGS are recommended in HIV-infected patients with low CD4 T cell counts and long duration of symptoms. The most common pattern of mixed infection observed was fungi-virus, followed by fungi-virus-bacteria coinfection in HIV infected patients with multi-pathogenic pneumonia.

Keywords:

• HIV
• multi-pathogenic pneumonia
• metagenomic next-generation sequencing
• conventional microbiological tests
• bronchoalveolar lavage fluid

Ethics Approval and Informed Consent

This study conforms to the ethical norms of the 1975 Helsinki Declaration. Due to the retrospective nature of the study, written informed consent from the patients was not required. The research protocol was approved by the Institutional Review Committee of the First Affiliated Hospital of Zhejiang University. All the data used for analysis were anonymized.

Acknowledgments

We thank all the participants in this study.

Disclosure

The authors declare no conflicts of interest.

Additional information

Funding

This study was funded by the Natural Science Foundation of China (Young Scientist Fund, 81500491) and the National Key Research and Development Program of China (2022YFC2304500). These funding agencies have no role in the design, data collection, analysis, interpretation of the research, or in the writing of the manuscript.