Analysis of microorganisms and drug-resistance mutations detected by probe-capture metagenomics among HIV-infected patients with pneumonia.
Qianhui Chen, Pingzheng Mo, Rongrong Yang, Huan Xu, Huifang Liu, Zhongwei Zhang, Qian Du, Qunqun Jiang, et al. (13 authors)
Frontiers in microbiology · 2025-01
Abstract
BACKGROUND: Probe-Capture Metagenomics is a newly developed method for detecting infectious pathogens. However, its application in HIV-infected patients with pulmonary infection remains limited. This study utilized Probe-Capture Metagenomics to analyze lung microbiomes and Drug Resistance Mutations of HIV and bacteria in people living with HIV (PLWH) with pneumonia.
METHODS: We retrospectively investigated lung microorganisms in PLWH hospitalized at Zhongnan Hospital of Wuhan University. A combination of bronchoalveolar lavage fluid Probe-Capture Metagenomics and conventional microbiological tests were performed in all patients.
RESULTS: A total of 91 patients were included in the study. Excluding the EB and Torque teno virus, at least two organisms were identified in 85 patients using Probe-Capture Metagenomics combined with conventional microbiological tests. The top six detected organisms were CMV,,, HHV-7,. For specific organisms, the detection rate of CMV andby Probe-Capture Metagenomics was significantly higher than that of conventional microbiological tests ( < 0.0001). Moreover, the detection rates of CMV ( = 0.0167) and( = 0.04) in patients with CD4T count ≥ 200 cells/μL were higher than that with CD4T count < 200 cells/μL. Importantly, Probe-Capture Metagenomics can uncover potentially clinically relevant drug-resistance mutations linked to HIV and bacteria.
CONCLUSION: Probe-Capture Metagenomics provides a promising method of detecting suspected opportunistic infections in PLWH with pneumonia, especially for mixed infections and rare microorganisms. In addition, Probe-Capture Metagenomics was a potential valuable tool for genotyping resistance testing of HIV and bacteria.