Analysis of microorganisms and drug-resistance mutations detected by probe-capture metagenomics among HIV-infected patients with pneumonia
BackgroundProbe-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...
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Frontiers Media S.A.
2025-07-01
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| author | Qianhui Chen Qianhui Chen Pingzheng Mo Pingzheng Mo Rongrong Yang Rongrong Yang Huan Xu Huifang Liu Zhongwei Zhang Zhongwei Zhang Qian Du Qian Du Qunqun Jiang Qunqun Jiang Qinglian Guo Liangjun Chen Yongxi Zhang Yongxi Zhang Yong Xiong Yong Xiong Liping Deng Liping Deng |
| author_facet | Qianhui Chen Qianhui Chen Pingzheng Mo Pingzheng Mo Rongrong Yang Rongrong Yang Huan Xu Huifang Liu Zhongwei Zhang Zhongwei Zhang Qian Du Qian Du Qunqun Jiang Qunqun Jiang Qinglian Guo Liangjun Chen Yongxi Zhang Yongxi Zhang Yong Xiong Yong Xiong Liping Deng Liping Deng |
| author_sort | Qianhui Chen |
| collection | DOAJ |
| description | BackgroundProbe-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.MethodsWe 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.ResultsA 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, Pneumocystis jirovecii, Mycobacterium tuberculosis complex, HHV-7, Candida albicans and Aspergillus. For specific organisms, the detection rate of CMV and Candida albicans by Probe-Capture Metagenomics was significantly higher than that of conventional microbiological tests (p < 0.0001). Moreover, the detection rates of CMV (p = 0.0167) and Pneumocystis jirovecii (p = 0.04) in patients with CD4+T count ≥ 200 cells/μL were higher than that with CD4+T count < 200 cells/μL. Importantly, Probe-Capture Metagenomics can uncover potentially clinically relevant drug-resistance mutations linked to HIV and bacteria.ConclusionProbe-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. |
| format | Article |
| id | doaj-art-9a5dd5d0af284c2bb229c5abb72c109e |
| institution | Kabale University |
| issn | 1664-302X |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Microbiology |
| spelling | doaj-art-9a5dd5d0af284c2bb229c5abb72c109e2025-08-20T03:58:45ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-07-011610.3389/fmicb.2025.16169371616937Analysis of microorganisms and drug-resistance mutations detected by probe-capture metagenomics among HIV-infected patients with pneumoniaQianhui Chen0Qianhui Chen1Pingzheng Mo2Pingzheng Mo3Rongrong Yang4Rongrong Yang5Huan Xu6Huifang Liu7Zhongwei Zhang8Zhongwei Zhang9Qian Du10Qian Du11Qunqun Jiang12Qunqun Jiang13Qinglian Guo14Liangjun Chen15Yongxi Zhang16Yongxi Zhang17Yong Xiong18Yong Xiong19Liping Deng20Liping Deng21Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, ChinaAIDS Research Center, Wuhan University, Wuhan, ChinaDepartment of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, ChinaAIDS Research Center, Wuhan University, Wuhan, ChinaDepartment of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, ChinaAIDS Research Center, Wuhan University, Wuhan, ChinaVision Medicals Co. Ltd., Guangzhou, ChinaVision Medicals Co. Ltd., Guangzhou, ChinaDepartment of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, ChinaAIDS Research Center, Wuhan University, Wuhan, ChinaDepartment of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, ChinaAIDS Research Center, Wuhan University, Wuhan, ChinaDepartment of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, ChinaAIDS Research Center, Wuhan University, Wuhan, ChinaDepartment of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, ChinaDepartment of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, ChinaDepartment of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, ChinaAIDS Research Center, Wuhan University, Wuhan, ChinaDepartment of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, ChinaAIDS Research Center, Wuhan University, Wuhan, ChinaDepartment of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, ChinaAIDS Research Center, Wuhan University, Wuhan, ChinaBackgroundProbe-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.MethodsWe 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.ResultsA 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, Pneumocystis jirovecii, Mycobacterium tuberculosis complex, HHV-7, Candida albicans and Aspergillus. For specific organisms, the detection rate of CMV and Candida albicans by Probe-Capture Metagenomics was significantly higher than that of conventional microbiological tests (p < 0.0001). Moreover, the detection rates of CMV (p = 0.0167) and Pneumocystis jirovecii (p = 0.04) in patients with CD4+T count ≥ 200 cells/μL were higher than that with CD4+T count < 200 cells/μL. Importantly, Probe-Capture Metagenomics can uncover potentially clinically relevant drug-resistance mutations linked to HIV and bacteria.ConclusionProbe-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.https://www.frontiersin.org/articles/10.3389/fmicb.2025.1616937/fullmicroorganismsprobe-capture metagenomicsHIVpneumoniadrug resistance |
| spellingShingle | Qianhui Chen Qianhui Chen Pingzheng Mo Pingzheng Mo Rongrong Yang Rongrong Yang Huan Xu Huifang Liu Zhongwei Zhang Zhongwei Zhang Qian Du Qian Du Qunqun Jiang Qunqun Jiang Qinglian Guo Liangjun Chen Yongxi Zhang Yongxi Zhang Yong Xiong Yong Xiong Liping Deng Liping Deng Analysis of microorganisms and drug-resistance mutations detected by probe-capture metagenomics among HIV-infected patients with pneumonia Frontiers in Microbiology microorganisms probe-capture metagenomics HIV pneumonia drug resistance |
| title | Analysis of microorganisms and drug-resistance mutations detected by probe-capture metagenomics among HIV-infected patients with pneumonia |
| title_full | Analysis of microorganisms and drug-resistance mutations detected by probe-capture metagenomics among HIV-infected patients with pneumonia |
| title_fullStr | Analysis of microorganisms and drug-resistance mutations detected by probe-capture metagenomics among HIV-infected patients with pneumonia |
| title_full_unstemmed | Analysis of microorganisms and drug-resistance mutations detected by probe-capture metagenomics among HIV-infected patients with pneumonia |
| title_short | Analysis of microorganisms and drug-resistance mutations detected by probe-capture metagenomics among HIV-infected patients with pneumonia |
| title_sort | analysis of microorganisms and drug resistance mutations detected by probe capture metagenomics among hiv infected patients with pneumonia |
| topic | microorganisms probe-capture metagenomics HIV pneumonia drug resistance |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1616937/full |
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