{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T14:52:19Z","timestamp":1775832739760,"version":"3.50.1"},"reference-count":26,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T00:00:00Z","timestamp":1764028800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:p>\n                    Metagenomic next-generation sequencing (mNGS) was suggested to potentially replace traditional microbiological methods because of its comprehensiveness. However, the diagnostic utility of mNGS for tissue hasn\u2019t been fully explored, especially for patient with HIV infection. HIV-positive and negative patients with suspected infectious diseases who performed tissue mNGS and conventional microbiological tests (CMTs) were retrospectively enrolled between October, 2020 and May 2024. The microbial spectrum of tissue mNGS and CMTs was analyzed, and the diagnostic accuracy and consistency of mNGS and CMTs for tissue were compared. The related factors of positive rate of mNGS was analyzed. Of 70 patients with suspected infectious diseases, 44 cases were confirmed with the infectious diseases. Among 44 patients with infectious diseases, aerobic bacteria (36.4%) was the most common detected pathogen, followed by mycobacterium tuberculosis (MTB, 18.2%), non-tuberculous mycobacteria (NTM, 13.6%) and fungus (11.4%). The sensitivity of tissue mNGS (72.7%, 95%CI 56.9%-84.5%) was significantly higher than that that in tissue CMTs (29.5%, 95%CI 17.2%-45.4%) (p&amp;lt;0.001), but the specificity was not statistically significant(P = 0.656). mNGS demonstrated higher detection rates than CMTs in the case with single microbial infections (70.0% vs. 30.0%; p&amp;lt;0.01). For the case with multiple microbial infections, the detection rates of mNGS and CMTs was 100.0% and 25.5% (p=1.000), respectively. Both positive mNGS and CMTs were observed in 22.7% patients with infectious diseases, and sole positive mNGS and sole positive CMTs were observed in 50.0% and 6.8% patients, respectively. There were no statistically differences in age, gender, HIV infection, PCT levels, neutrophil counts, CD4\n                    <jats:sup>+<\/jats:sup>\n                    lymphocyte count and antibiotic exposure between mNGS positive and mNGS negative groups (P &amp;gt; 0.05). Tissue mNGS could provide a higher sensitivity, more robust and broader method for pathogen identification by comparison with CMTs. However, CMTs shouldn\u2019t be ignored since the low consistency between CMTs and mNGS.\n                  <\/jats:p>","DOI":"10.3389\/fcimb.2025.1634406","type":"journal-article","created":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T06:24:58Z","timestamp":1764051898000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Diagnostic utility of metagenomic next-generation sequencing for tissue in patients with suspected infectious diseases"],"prefix":"10.3389","volume":"15","author":[{"given":"Yaqing","family":"Liu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuting","family":"Tan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fei","family":"Xia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Songjie","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shi","family":"Zou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qianhui","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jie","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shihui","family":"Song","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qian","family":"Du","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Guo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ke","family":"Liang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2025,11,25]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0262720","article-title":"Prevalence and associated risk factors for tuberculosis among people living with HIV in Nepal","volume":"17","author":"Adhikari","year":"2022","journal-title":"PloS One"},{"key":"B2","doi-asserted-by":"publisher","first-page":"478","DOI":"10.1186\/s12879-023-08417-3","article-title":"Early application of metagenomics next-generation sequencing may significantly reduce unnecessary consumption of antibiotics in patients with fever of unknown origin","volume":"23","author":"Chen","year":"2023","journal-title":"BMC Infect. Dis."},{"key":"B3","doi-asserted-by":"publisher","first-page":"1210","DOI":"10.1186\/s12879-024-10009-8","article-title":"Blood microbiota in HIV-infected and HIV-uninfected patients with suspected sepsis detected by metagenomic next-generation sequencing","volume":"24","author":"Chen","year":"2024","journal-title":"BMC Infect. Dis."},{"key":"B4","doi-asserted-by":"publisher","first-page":"1900250","DOI":"10.1183\/13993003.00250-2019","article-title":"Non-tuberculous mycobacterial pulmonary disease","volume":"54","author":"Cowman","year":"2019","journal-title":"Eur. Respir. J."},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.00535-2020","article-title":"Treatment of nontuberculous mycobacterial pulmonary disease: an official ATS\/ERS\/ESCMID\/IDSA clinical practice guideline","volume":"56","author":"Daley","year":"2020","journal-title":"Eur. Respir. J."},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2022.950531","article-title":"Diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in pediatric pneumonia","volume":"12","author":"Deng","year":"2022","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1007\/s10792-024-03201-x","article-title":"Unveiling challenging corneal infections: a comprehensive etiological diagnosis through metagenomic next-generation sequencing (mNGS) of corneal tissue samples","volume":"44","author":"Dong","year":"2024","journal-title":"Int. Ophthalmol."},{"key":"B8","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1186\/s12879-020-05746-5","article-title":"The diagnostic value of metagenomic next rectanglegeneration sequencing in infectious diseases","volume":"21","author":"Duan","year":"2021","journal-title":"BMC Infect. Dis."},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2023.1271952","article-title":"Clinical utility of metagenomic next-generation sequencing in pathogen detection for lower respiratory tract infections and impact on clinical outcomes in southernmost China","volume":"13","author":"Hao","year":"2023","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.02473-21","article-title":"Improving suspected pulmonary infection diagnosis by bronchoalveolar lavage fluid metagenomic next-generation sequencing: a multicenter retrospective study","volume":"10","author":"Jin","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2024.1382635","article-title":"Application of metagenomic next-generation sequencing for rapid molecular identification in spinal infection diagnosis","volume":"14","author":"Lv","year":"2024","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B12","doi-asserted-by":"publisher","first-page":"116465","DOI":"10.1016\/j.diagmicrobio.2024.116465","article-title":"Metagenomic next-generation sequencing in patients with fever of unknown origin: A comprehensive systematic literature review and meta-analysis","volume":"110","author":"Marra","year":"2024","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"B13","doi-asserted-by":"publisher","first-page":"S231","DOI":"10.1093\/cid\/ciy693","article-title":"Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice","volume":"67","author":"Miao","year":"2018","journal-title":"Clin. Infect. Dis."},{"key":"B14","doi-asserted-by":"publisher","first-page":"831","DOI":"10.1101\/gr.238170.118","article-title":"Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid","volume":"29","author":"Miller","year":"2019","journal-title":"Genome Res."},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2023.1256099","article-title":"Comprehensive evaluation of plasma microbial cell-free DNA sequencing for predicting bloodstream and local infections in clinical practice: a multicenter retrospective study","volume":"13","author":"Pang","year":"2023","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2020.567615","article-title":"Improving pulmonary infection diagnosis with metagenomic next generation sequencing","volume":"10","author":"Qian","year":"2020","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"116402","DOI":"10.1016\/j.diagmicrobio.2024.116402","article-title":"Metagenomic next generation sequencing of bronchoalveolar lavage fluids for the identification of pathogens in patients with pulmonary infection: A retrospective study","volume":"110","author":"Qin","year":"2024","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"B18","doi-asserted-by":"publisher","first-page":"845","DOI":"10.3201\/eid2703.201087","article-title":"Extrapulmonary nontuberculous mycobacteria infections in hospitalized patients, United States, 2009-2014","volume":"27","author":"Ricotta","year":"2021","journal-title":"Emerg. Infect. Dis."},{"key":"B19","doi-asserted-by":"publisher","first-page":"776","DOI":"10.5858\/arpa.2016-0539-RA","article-title":"Validation of metagenomic next-generation sequencing tests for universal pathogen detection","volume":"141","author":"Schlaberg","year":"2017","journal-title":"Arch. Pathol. Lab. Med."},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2022.905132","article-title":"Clinical application and influencing factor analysis of metagenomic next-generation sequencing (mNGS) in ICU patients with sepsis","volume":"12","author":"Sun","year":"2022","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.00005-23","article-title":"Microbiomes detected by bronchoalveolar lavage fluid metagenomic next-generation sequencing among HIV-infected and uninfected patients with pulmonary infection","volume":"11","author":"Tan","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"B22","doi-asserted-by":"publisher","first-page":"414","DOI":"10.1016\/j.ijid.2020.09.007","article-title":"The clinical value of metagenomic next-generation sequencing in the microbiological diagnosis of skin and soft tissue infections","volume":"100","author":"Wang","year":"2020","journal-title":"Int. J. Infect. Dis."},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2022.957073","article-title":"The clinical application of metagenomic next-generation sequencing in infectious diseases at a tertiary hospital in China","volume":"12","author":"Wang","year":"2022","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"106395","DOI":"10.1016\/j.jinf.2024.106395","article-title":"Diagnostic performance of metagenomic next-generation sequencing among hematological Malignancy patients with bloodstream infections after antimicrobial therapy","volume":"90","author":"Xu","year":"2025","journal-title":"J. Infect."},{"key":"B25","doi-asserted-by":"publisher","first-page":"350","DOI":"10.1186\/s12879-024-09236-w","article-title":"Comparison of metagenomic next-generation sequencing and conventional culture for the diagnostic performance in febrile patients with suspected infections","volume":"24","author":"Yang","year":"2024","journal-title":"BMC Infect. Dis."},{"key":"B26","doi-asserted-by":"publisher","first-page":"794","DOI":"10.1111\/hiv.13634","article-title":"Microbiomes detected by cerebrospinal fluid metagenomic next-generation sequencing among patients with and without HIV with suspected central nervous system infection","volume":"25","author":"Zou","year":"2024","journal-title":"HIV Med."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2025.1634406\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T06:24:58Z","timestamp":1764051898000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2025.1634406\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,25]]},"references-count":26,"alternative-id":["10.3389\/fcimb.2025.1634406"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2025.1634406","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,25]]},"article-number":"1634406"}}