Comparative of metagenomic and targeted next-generation sequencing in lower respiratory tract fungal infections
ObjectivesThis study aims to compare the diagnostic efficiency and consistency of metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) in patients with lower respiratory tract fungal infections.MethodsA total of 115 patients with probable pulmonary infection b...
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Frontiers Media S.A.
2025-05-01
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| Series: | Frontiers in Cellular and Infection Microbiology |
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| author | Zhiyang Chen Zhiyang Chen Zhiyang Chen Xin Liu Xin Liu Xin Liu Li Tan Li Tan Li Tan Xing Lyu Xing Lyu Xing Lyu Qichen Long Qichen Long Qichen Long Weimin Wu Weimin Wu Weimin Wu Zhe Guo Zhe Guo Zhe Guo Zhenni Liu Zhenni Liu Zhenni Liu Ziyang Li Ziyang Li Ziyang Li Min Hu Min Hu Min Hu |
| author_facet | Zhiyang Chen Zhiyang Chen Zhiyang Chen Xin Liu Xin Liu Xin Liu Li Tan Li Tan Li Tan Xing Lyu Xing Lyu Xing Lyu Qichen Long Qichen Long Qichen Long Weimin Wu Weimin Wu Weimin Wu Zhe Guo Zhe Guo Zhe Guo Zhenni Liu Zhenni Liu Zhenni Liu Ziyang Li Ziyang Li Ziyang Li Min Hu Min Hu Min Hu |
| author_sort | Zhiyang Chen |
| collection | DOAJ |
| description | ObjectivesThis study aims to compare the diagnostic efficiency and consistency of metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) in patients with lower respiratory tract fungal infections.MethodsA total of 115 patients with probable pulmonary infection between September 2022 and April 2023 were enrolled at the Second Xiangya Hospital, Changsha, China, of which 61 were clinically diagnosed with invasive pulmonary fungal infection (IPFI) and 54 were non-IPFI cases. All patients received bronchoalveolar lavage, with mNGS, tNGS, and cultures being conducted paralleled. Diagnostic effectiveness and consistency in detecting microorganisms were compared.ResultsBoth mNGS and tNGS showed high sensitivity rates of 95.08% each, with specificity of 90.74% and 85.19%, respectively. They also demonstrated positive predictive values (PPVs) of 92.1% and 87.9% and negative predictive values (NPVs) of 94.2% and 93.9%, respectively, in diagnosing IPFI. The sensitivity and NPV of mNGS and tNGS were superior to that of any individual or combined conventional microbiological tests (CMTs) (P < 0.05). The consistency of culture with mNGS and tNGS was 48.70% and 50.43%, respectively. For fungal detection, Pneumocystis jirovecii (26/61, 42.6%; and 28/61, 45.9%), Candida albicans (19/61, 31.1%; and 21/61, 34.4%), and Aspergillus fumigatus (16/61, 26.2%; and 15/61, 24.6%) are most prevalent for mNGS and tNGS in enrolled cases, and the detection rate was greatly higher than that of culture. Furthermore, mNGS and tNGS were capable of diagnosing mixed infections in 65 and 55 out of the 115 cases, whereas only nine cases of bacterial-fungal infection were detected by culture.ConclusionThe diagnostic efficacy of mNGS and tNGS was comparable to that of identified IPFI. NGS-based methodologies present a promising tool for detecting IPFI, which can be a good supplement to CMT. |
| format | Article |
| id | doaj-art-4d1370b5f62a4a67b500e8e9e2acf4c1 |
| institution | Kabale University |
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| language | English |
| publishDate | 2025-05-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Cellular and Infection Microbiology |
| spelling | doaj-art-4d1370b5f62a4a67b500e8e9e2acf4c12025-08-20T03:48:23ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882025-05-011510.3389/fcimb.2025.15345191534519Comparative of metagenomic and targeted next-generation sequencing in lower respiratory tract fungal infectionsZhiyang Chen0Zhiyang Chen1Zhiyang Chen2Xin Liu3Xin Liu4Xin Liu5Li Tan6Li Tan7Li Tan8Xing Lyu9Xing Lyu10Xing Lyu11Qichen Long12Qichen Long13Qichen Long14Weimin Wu15Weimin Wu16Weimin Wu17Zhe Guo18Zhe Guo19Zhe Guo20Zhenni Liu21Zhenni Liu22Zhenni Liu23Ziyang Li24Ziyang Li25Ziyang Li26Min Hu27Min Hu28Min Hu29Department of Clinical Laboratory, The Second Xiangya Hospital of Central South University, Changsha, ChinaMolecular Diagnostic Technology Hunan Engineering Research Center, Changsha, ChinaClinical Medical Research Center for Molecular Diagnosis of Infectious Diseases in Hunan Province, Changsha, ChinaDepartment of Clinical Laboratory, The Second Xiangya Hospital of Central South University, Changsha, ChinaMolecular Diagnostic Technology Hunan Engineering Research Center, Changsha, ChinaClinical Medical Research Center for Molecular Diagnosis of Infectious Diseases in Hunan Province, Changsha, ChinaDepartment of Clinical Laboratory, The Second Xiangya Hospital of Central South University, Changsha, ChinaMolecular Diagnostic Technology Hunan Engineering Research Center, Changsha, ChinaClinical Medical Research Center for Molecular Diagnosis of Infectious Diseases in Hunan Province, Changsha, ChinaDepartment of Clinical Laboratory, The Second Xiangya Hospital of Central South University, Changsha, ChinaMolecular Diagnostic Technology Hunan Engineering Research Center, Changsha, ChinaClinical Medical Research Center for Molecular Diagnosis of Infectious Diseases in Hunan Province, Changsha, ChinaDepartment of Clinical Laboratory, The Second Xiangya Hospital of Central South University, Changsha, ChinaMolecular Diagnostic Technology Hunan Engineering Research Center, Changsha, ChinaClinical Medical Research Center for Molecular Diagnosis of Infectious Diseases in Hunan Province, Changsha, ChinaDepartment of Clinical Laboratory, The Second Xiangya Hospital of Central South University, Changsha, ChinaMolecular Diagnostic Technology Hunan Engineering Research Center, Changsha, ChinaClinical Medical Research Center for Molecular Diagnosis of Infectious Diseases in Hunan Province, Changsha, ChinaDepartment of Clinical Laboratory, The Second Xiangya Hospital of Central South University, Changsha, ChinaMolecular Diagnostic Technology Hunan Engineering Research Center, Changsha, ChinaClinical Medical Research Center for Molecular Diagnosis of Infectious Diseases in Hunan Province, Changsha, ChinaDepartment of Clinical Laboratory, The Second Xiangya Hospital of Central South University, Changsha, ChinaMolecular Diagnostic Technology Hunan Engineering Research Center, Changsha, ChinaClinical Medical Research Center for Molecular Diagnosis of Infectious Diseases in Hunan Province, Changsha, ChinaDepartment of Clinical Laboratory, The Second Xiangya Hospital of Central South University, Changsha, ChinaMolecular Diagnostic Technology Hunan Engineering Research Center, Changsha, ChinaClinical Medical Research Center for Molecular Diagnosis of Infectious Diseases in Hunan Province, Changsha, ChinaDepartment of Clinical Laboratory, The Second Xiangya Hospital of Central South University, Changsha, ChinaMolecular Diagnostic Technology Hunan Engineering Research Center, Changsha, ChinaClinical Medical Research Center for Molecular Diagnosis of Infectious Diseases in Hunan Province, Changsha, ChinaObjectivesThis study aims to compare the diagnostic efficiency and consistency of metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) in patients with lower respiratory tract fungal infections.MethodsA total of 115 patients with probable pulmonary infection between September 2022 and April 2023 were enrolled at the Second Xiangya Hospital, Changsha, China, of which 61 were clinically diagnosed with invasive pulmonary fungal infection (IPFI) and 54 were non-IPFI cases. All patients received bronchoalveolar lavage, with mNGS, tNGS, and cultures being conducted paralleled. Diagnostic effectiveness and consistency in detecting microorganisms were compared.ResultsBoth mNGS and tNGS showed high sensitivity rates of 95.08% each, with specificity of 90.74% and 85.19%, respectively. They also demonstrated positive predictive values (PPVs) of 92.1% and 87.9% and negative predictive values (NPVs) of 94.2% and 93.9%, respectively, in diagnosing IPFI. The sensitivity and NPV of mNGS and tNGS were superior to that of any individual or combined conventional microbiological tests (CMTs) (P < 0.05). The consistency of culture with mNGS and tNGS was 48.70% and 50.43%, respectively. For fungal detection, Pneumocystis jirovecii (26/61, 42.6%; and 28/61, 45.9%), Candida albicans (19/61, 31.1%; and 21/61, 34.4%), and Aspergillus fumigatus (16/61, 26.2%; and 15/61, 24.6%) are most prevalent for mNGS and tNGS in enrolled cases, and the detection rate was greatly higher than that of culture. Furthermore, mNGS and tNGS were capable of diagnosing mixed infections in 65 and 55 out of the 115 cases, whereas only nine cases of bacterial-fungal infection were detected by culture.ConclusionThe diagnostic efficacy of mNGS and tNGS was comparable to that of identified IPFI. NGS-based methodologies present a promising tool for detecting IPFI, which can be a good supplement to CMT.https://www.frontiersin.org/articles/10.3389/fcimb.2025.1534519/fullmNGStNGSdiagnosisinvasive pulmonary fungal infectionfungal |
| spellingShingle | Zhiyang Chen Zhiyang Chen Zhiyang Chen Xin Liu Xin Liu Xin Liu Li Tan Li Tan Li Tan Xing Lyu Xing Lyu Xing Lyu Qichen Long Qichen Long Qichen Long Weimin Wu Weimin Wu Weimin Wu Zhe Guo Zhe Guo Zhe Guo Zhenni Liu Zhenni Liu Zhenni Liu Ziyang Li Ziyang Li Ziyang Li Min Hu Min Hu Min Hu Comparative of metagenomic and targeted next-generation sequencing in lower respiratory tract fungal infections Frontiers in Cellular and Infection Microbiology mNGS tNGS diagnosis invasive pulmonary fungal infection fungal |
| title | Comparative of metagenomic and targeted next-generation sequencing in lower respiratory tract fungal infections |
| title_full | Comparative of metagenomic and targeted next-generation sequencing in lower respiratory tract fungal infections |
| title_fullStr | Comparative of metagenomic and targeted next-generation sequencing in lower respiratory tract fungal infections |
| title_full_unstemmed | Comparative of metagenomic and targeted next-generation sequencing in lower respiratory tract fungal infections |
| title_short | Comparative of metagenomic and targeted next-generation sequencing in lower respiratory tract fungal infections |
| title_sort | comparative of metagenomic and targeted next generation sequencing in lower respiratory tract fungal infections |
| topic | mNGS tNGS diagnosis invasive pulmonary fungal infection fungal |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2025.1534519/full |
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