{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T06:01:54Z","timestamp":1785132114480,"version":"3.55.0"},"reference-count":46,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T00:00:00Z","timestamp":1785110400000},"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:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Patients treated with systemic anti-tumor therapies are more likely to develop pulmonary infections due to weakened immune systems. This study aims to evaluate the clinical application of radial endobronchial ultrasound (R-EBUS) combined with metagenomic next-generation sequencing (mNGS) in the diagnosis and treatment of pulmonary infections among patients undergoing systemic anti-tumor therapy.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>This study is a single-center retrospective analysis that includes 84 patients with pulmonary infections following systemic anti-tumor therapy. Patients were stratified into sepsis (SOFA score \u22652, n=32) and non-sepsis (SOFA score &amp;lt;2, n=52) groups based on Sepsis-3.0 criteria. BALF samples were subjected to both mNGS and conventional microbiological tests (CMT). Pathogen profiles, diagnostic performance, clinical impact on antimicrobial therapy, and microbiome diversity were analyzed.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      mNGS demonstrated a significantly higher positive detection rate than CMT (95.24% vs. 30.95%,\n                      <jats:italic>P<\/jats:italic>\n                      &amp;lt;\u00a00.001). mNGS identified a broader spectrum of pathogens, including bacteria, fungi, and viruses, and detected mixed infections more frequently than CMT. The clinical impact of mNGS was positive in 84.52% of cases, primarily by initiating targeted therapy or confirming empirical treatment. Microbiome analysis revealed significantly lower alpha diversity (Shannon, ACE, Chao1 indices) in the severe group compared to the non-severe group.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>EBUS-guided mNGS of BALF was associated with improved pathogen detection in malignancy patients with pulmonary infections, leading to a high rate of beneficial antimicrobial adjustments. Distinct microbial signatures are associated with infection severity, suggesting potential diagnostic and therapeutic implications.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fcimb.2026.1799148","type":"journal-article","created":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T05:41:20Z","timestamp":1785130880000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Clinical value of radial endobronchial ultrasound combined with metagenomic next-generation sequencing in the malignant tumors patients with pulmonary infection"],"prefix":"10.3389","volume":"16","author":[{"given":"Yongchun","family":"Song","sequence":"first","affiliation":[{"name":"Department of Radiation Oncology, Tianjin\u2019s Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer","place":["Tianjin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaojing","family":"Zhang","sequence":"additional","affiliation":[{"name":"WillingMed Technology (Beijing) Co., Ltd","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongjing","family":"Wang","sequence":"additional","affiliation":[{"name":"Tianjin University of Traditional Chinese Medicine","place":["Tianjin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yufei","family":"Wang","sequence":"additional","affiliation":[{"name":"Tianjin University of Traditional Chinese Medicine","place":["Tianjin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Tianjin University of Traditional Chinese Medicine","place":["Tianjin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yifan","family":"Li","sequence":"additional","affiliation":[{"name":"Tianjin University of Traditional Chinese Medicine","place":["Tianjin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinrui","family":"Cui","sequence":"additional","affiliation":[{"name":"Tianjin University of Traditional Chinese Medicine","place":["Tianjin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaodan","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Respiratory Medicine, Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine","place":["Tianjin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuqian","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Respiratory Medicine, Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine","place":["Tianjin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Respiratory Medicine, Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine","place":["Tianjin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingshen","family":"Su","sequence":"additional","affiliation":[{"name":"Department of Respiratory Medicine, Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine","place":["Tianjin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yafeng","family":"Zheng","sequence":"additional","affiliation":[{"name":"WillingMed Technology (Beijing) Co., Ltd","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Gai","sequence":"additional","affiliation":[{"name":"WillingMed Technology (Beijing) Co., Ltd","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Respiratory Medicine, Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine","place":["Tianjin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,7,27]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"2565","DOI":"10.3390\/diagnostics13152565","article-title":"Clinical applications of endobronchial ultrasound (Ebus) scope: Challenges and opportunities","volume":"13","author":"Biondini","year":"2023","journal-title":"Diagn. (Basel)"},{"key":"B2","doi-asserted-by":"publisher","first-page":"663","DOI":"10.1038\/s41564-018-0349-6","article-title":"Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease","volume":"4","author":"Blauwkamp","year":"2019","journal-title":"Nat. Microbiol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1016\/j.jare.2023.02.018","article-title":"Clinical evaluation of cell-free and cellular metagenomic next-generation sequencing of infected body fluids","volume":"55","author":"Chen","year":"2023","journal-title":"J. Adv. Res."},{"key":"B4","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1016\/j.ijid.2022.07.054","article-title":"Diagnostic performance of metagenomic next-generation sequencing for the detection of pathogens in bronchoalveolar lavage fluid in patients with pulmonary infections: Systematic review and meta-analysis","volume":"122","author":"Chen","year":"2022","journal-title":"Int. J. Infect. Dis."},{"key":"B5","doi-asserted-by":"publisher","first-page":"2080","DOI":"10.21037\/apm-20-2578","article-title":"Metagenomic next-generation sequencing of radial ultrasound bronchoscopy-guided \"cocktail\" specimens as an efficient method for the diagnosis of focal pulmonary infections: A randomised study","volume":"10","author":"Chen","year":"2021","journal-title":"Ann. Palliat Med."},{"key":"B6","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1007\/s43657-023-00135-9","article-title":"Bronchoalveolar lavage fluid microbiota is associated with the diagnosis and prognosis evaluation of lung cancer","volume":"4","author":"Cheng","year":"2024","journal-title":"Phenomics"},{"key":"B7","doi-asserted-by":"publisher","first-page":"1191","DOI":"10.1016\/s1473-3099(18)30310-4","article-title":"Estimates of the global, regional, and national morbidity, mortality, and aetiologies of lower respiratory infections in 195 countries, 1990-2016: A systematic analysis for the Global Burden of Disease Study 2016","volume":"18","year":"2018","journal-title":"Lancet Infect. Dis."},{"key":"B8","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1186\/s12890-018-0713-6","article-title":"Clinical updates of approaches for biopsy of pulmonary lesions based on systematic review","volume":"18","author":"Deng","year":"2018","journal-title":"BMC Pulm. Med."},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.3390\/diagnostics15161991","article-title":"Metagenomic next-generation sequencing in infectious diseases: Clinical applications, translational challenges, and future directions","volume":"15","author":"Elbehiry","year":"2025","journal-title":"Diagnostics"},{"key":"B10","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1016\/j.cmi.2023.05.034","article-title":"Clinical metagenomic sequencing of plasma microbial cell-free DNA for febrile neutropenia in patients with acute leukaemia","volume":"30","author":"Feng","year":"2024","journal-title":"Clin. Microbiol. Infect."},{"key":"B11","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1186\/s12931-024-02887-y","article-title":"A single-center, retrospective study of hospitalized patients with lower respiratory tract infections: Clinical assessment of metagenomic next-generation sequencing and identification of risk factors in patients","volume":"25","author":"Gao","year":"2024","journal-title":"Respir. Res."},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2025.1724935","article-title":"Effect of Balf-based Mngs on clinical outcomes of immunocompromised subjects with opportunistic pulmonary infections: A multicenter propensity score-matched study","volume":"15","author":"Guo","year":"2026","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1080\/08998280.2015.11929263","article-title":"Uses, limitations, and complications of endobronchial ultrasound","volume":"28","author":"Jalil","year":"2015","journal-title":"Proc. (Bayl Univ. Med. Cent)"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2026.1730022","article-title":"Metagenomic next-generation sequencing for diagnosis of immune checkpoint inhibitor-associated pneumonitis: A retrospective comparative clinical performance study","volume":"16","author":"Jiang","year":"2026","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B15","doi-asserted-by":"publisher","first-page":"1232","DOI":"10.1186\/s12879-024-10108-6","article-title":"High utility of bronchoalveolar lavage fluid metagenomic next-generation sequencing approach for etiological diagnosis of pneumonia","volume":"24","author":"Jiang","year":"2024","journal-title":"BMC Infect. Dis."},{"key":"B16","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":"B17","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.00404-21","article-title":"Host-microbe metagenomics: A lens to refocus our perspective on infectious and inflammatory diseases","volume":"6","author":"Kalantar","year":"2021","journal-title":"mSystems"},{"key":"B18","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1016\/s1470-2045(09)70069-5","article-title":"Nosocomial infections in patients with cancer","volume":"10","author":"Kamboj","year":"2009","journal-title":"Lancet Oncol."},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1038\/d41586-024-01123-3","article-title":"Exploring the lung microbiome's role in disease","author":"King","year":"2024","journal-title":"Nature"},{"key":"B20","doi-asserted-by":"publisher","first-page":"E12353","DOI":"10.1073\/pnas.1809700115","article-title":"Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults","volume":"115","author":"Langelier","year":"2018","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B21","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.816631","article-title":"Metagenomic next-generation sequencing for the microbiological diagnosis of abdominal sepsis patients","volume":"13","author":"Li","year":"2022","journal-title":"Front. Microbiol."},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1155\/2020\/2367505","article-title":"The value of combined radial endobronchial ultrasound-guided transbronchial lung biopsy and metagenomic next-generation sequencing for peripheral pulmonary infectious lesions","volume":"2020","author":"Li","year":"2020","journal-title":"Can. Respir. J."},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2026.1812778","article-title":"Diagnostic performance and clinical utility of metagenomic next-generation sequencing in suspected pulmonary infections: A comparative study stratified by immune status","volume":"16","author":"Li","year":"2026","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B25","doi-asserted-by":"publisher","first-page":"1393","DOI":"10.1186\/s12879-024-10292-5","article-title":"Clinical application value of simultaneous plasma and bronchoalveolar lavage fluid metagenomic next generation sequencing in patients with pneumonia-derived sepsis","volume":"24","author":"Li","year":"2024","journal-title":"BMC Infect. Dis."},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2025.1646194","article-title":"Optimization of decision thresholds for Mycobacterium tuberculosis can effectively improve the performance of Mngs in tuberculosis diagnosis","volume":"15","author":"Li","year":"2025","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"416","DOI":"10.1186\/s12879-022-07381-8","article-title":"Diagnostic value of metagenomic next-generation sequencing of bronchoalveolar lavage fluid for the diagnosis of suspected pneumonia in immunocompromised patients","volume":"22","author":"Lin","year":"2022","journal-title":"BMC Infect. Dis."},{"key":"B28","doi-asserted-by":"publisher","first-page":"4878","DOI":"10.1177\/0300060519866953","article-title":"Metagenomic next-generation sequencing diagnosis of peripheral pulmonary infectious lesions through virtual navigation, radial Ebus, ultrathin bronchoscopy, and Rose","volume":"47","author":"Liu","year":"2019","journal-title":"J. Int. Med. Res."},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2024.1439472","article-title":"Application of metagenomic next-generation sequencing and targeted metagenomic next-generation sequencing in diagnosing pulmonary infections in immunocompetent and immunocompromised patients","volume":"14","author":"Liu","year":"2024","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B30","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1007\/s15010-024-02185-1","article-title":"Utilizing metagenomic next-generation sequencing for pathogen detection and diagnosis in lower respiratory tract infections in real-world clinical practice","volume":"52","author":"Lv","year":"2024","journal-title":"Infection"},{"key":"B31","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1186\/s12931-022-02230-3","article-title":"Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing","volume":"23","author":"Miao","year":"2022","journal-title":"Respir. Res."},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1002\/mbo3.70104","article-title":"Next-generation sequencing in infectious-disease diagnostics: Economic, regulatory, and clinical pathways to adoption","volume":"14","author":"Osei Sekyere","year":"2025","journal-title":"Microbiol. Open"},{"key":"B33","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1016\/j.ccc.2020.09.001","article-title":"Infectious disease complications in patients with cancer","volume":"37","author":"Seo","year":"2021","journal-title":"Crit. Care Clin."},{"key":"B34","doi-asserted-by":"publisher","first-page":"3427","DOI":"10.1007\/s00262-023-03524-1","article-title":"Cancer management during the Covid-19 world pandemic","volume":"72","author":"Sobhani","year":"2023","journal-title":"Cancer Immunol. Immunother."},{"key":"B35","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1186\/s12890-023-02681-4","article-title":"Pathogen distribution in pulmonary infection in Chinese patients with lung cancer: A systematic review and meta-analysis","volume":"23","author":"Wang","year":"2023","journal-title":"BMC Pulm. Med."},{"key":"B36","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1186\/s12931-023-02654-5","article-title":"Clinical application of bronchoalveolar lavage fluid metagenomics next-generation sequencing in cancer patients with severe pneumonia","volume":"25","author":"Wang","year":"2024","journal-title":"Respir. Res."},{"key":"B37","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"B38","doi-asserted-by":"publisher","first-page":"362","DOI":"10.1016\/j.chest.2024.07.144","article-title":"Effect of metagenomic next-generation sequencing on clinical outcomes of patients with severe community-acquired pneumonia in the Icu: A multicenter, randomized controlled trial","volume":"167","author":"Wu","year":"2025","journal-title":"Chest"},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2022.977591","article-title":"Metagenomic next-generation sequencing indicates more precise pathogens in patients with pulmonary infection: A retrospective study","volume":"12","author":"Wu","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B40","doi-asserted-by":"publisher","first-page":"1279","DOI":"10.1038\/s41590-019-0451-9","article-title":"The influence of the microbiome on respiratory health","volume":"20","author":"Wypych","year":"2019","journal-title":"Nat. Immunol."},{"key":"B41","doi-asserted-by":"publisher","first-page":"1815","DOI":"10.2147\/idr.S401707","article-title":"Clinical efficacy and diagnostic value of metagenomic next-generation sequencing for pathogen detection in patients with suspected infectious diseases: A retrospective study from a large tertiary hospital","volume":"16","author":"Xiao","year":"2023","journal-title":"Infect. Drug Resist."},{"key":"B42","doi-asserted-by":"publisher","first-page":"761","DOI":"10.1080\/22221751.2020.1747363","article-title":"Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in Covid-19 patients","volume":"9","author":"Xiong","year":"2020","journal-title":"Emerg. Microbes Infect."},{"key":"B43","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1016\/j.jinf.2022.11.020","article-title":"Utility of plasma cell-free DNA next-generation sequencing for diagnosis of infectious diseases in patients with hematological disorders","volume":"86","author":"Xu","year":"2023","journal-title":"J. Infect."},{"key":"B44","doi-asserted-by":"publisher","first-page":"3579","DOI":"10.2147\/idr.S472129","article-title":"Utility of metagenomic next-generation sequencing for diagnosis of infectious diseases in critically ill immunocompromised pediatric patients","volume":"17","author":"Xu","year":"2024","journal-title":"Infect. Drug Resistance"},{"key":"B45","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2024.1435823","article-title":"Severe pneumonia with empyema due to multiple anaerobic infections: Case report and literature review","volume":"11","author":"Yu","year":"2024","journal-title":"Front. Med."},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.1016\/j.heliyon.2024.e35287","article-title":"Clinical impact of metagenomic next-generation sequencing of bronchoalveolar lavage fluids for the diagnosis of pulmonary infections in respiratory intensive care unit","volume":"10","author":"Zhang","year":"2024","journal-title":"Heliyon"}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2026.1799148\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T05:41:21Z","timestamp":1785130881000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2026.1799148\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,27]]},"references-count":46,"alternative-id":["10.3389\/fcimb.2026.1799148"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2026.1799148","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,27]]},"article-number":"1799148"}}