{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T17:36:58Z","timestamp":1785346618189,"version":"3.55.0"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T00:00:00Z","timestamp":1761609600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Rapid and accurate identification of pathogens is essential for managing lung infections in patients following kidney transplantation. This study aimed to compare the diagnostic performance and clinical utility of conventional detection methods and metagenomic next-generation sequencing (NGS) in kidney transplant recipients with respiratory infections.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We conducted a retrospective analysis of metagenomic NGS and conventional detection method results in 71 patients, examining the spectrum of pathogen detection characteristics between the 2 methods.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>The overall positivity rate of conventional detection methods was statistically significantly lower than that of metagenomic NGS (61.97% vs 84.51%, P\u2005=\u2005.004). Among the 38 participants who tested positive by both methods, metagenomic NGS identified a greater number of pathogens than conventional detection methods. Following metagenomic NGS results, antibiotic therapy was modified in 71.83% of participants, leading to improved prognoses in 33.33% of patients. In additionally, metagenomic NGS demonstrated a shorter turnaround time than conventional detection methods. The most prevalent bacteria identified in pulmonary infections among kidney transplant recipients were Klebsiella pneumoniae, while cytomegalovirus was the most common virus and Pneumocystis jirovecii was the predominant fungus.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>This study offers preliminary insights into the spectrum of pathogens responsible for pulmonary infections following kidney transplantation, laying the foundation for better understanding their clinical characteristics. In patients with post-transplant pulmonary infections, metagenomic NGS outperforms conventional detection methods in terms of pathogen detection, speed, positivity rate, sensitivity, and ability to diagnose mixed infections.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/labmed\/lmaf035","type":"journal-article","created":{"date-parts":[[2025,6,6]],"date-time":"2025-06-06T07:50:26Z","timestamp":1749196226000},"source":"Crossref","is-referenced-by-count":2,"title":["The clinical value of metagenomic next-generation sequencing for diagnosing pulmonary infections in kidney transplant recipients"],"prefix":"10.1093","volume":"57","author":[{"given":"Xiaohong","family":"Qin","sequence":"first","affiliation":[{"name":"Department of Clinical Laboratory, the 923th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army , Nanning ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Panyan","family":"Liu","sequence":"additional","affiliation":[{"name":"Infection Diagnosis Center, Guangxi KingMed Diagnostics , Nanning ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"DaQing","family":"Lu","sequence":"additional","affiliation":[{"name":"The Third People\u2019s Hospital of Nanning , Nanning ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tingting","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, the 923th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army , Nanning ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunhong","family":"Li","sequence":"additional","affiliation":[{"name":"Infection Diagnosis Center, Guangxi KingMed Diagnostics , Nanning ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenfeng","family":"Deng","sequence":"additional","affiliation":[{"name":"Infection Diagnosis Center, Guangxi KingMed Diagnostics , Nanning ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiang","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, the 923th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army , Nanning ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,10,28]]},"reference":[{"key":"2026012111365285400_CIT0001","doi-asserted-by":"publisher","first-page":"S19","DOI":"10.1016\/j.ajt.2024.01.012","article-title":"OPTN\/SRTR 2022 annual data report: kidney [J]","volume":"24","author":"Lentine","year":"2024","journal-title":"Am J Transplant."},{"key":"2026012111365285400_CIT0002","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1016\/j.idc.2010.01.005","article-title":"Infection in organ transplantation: risk factors and evolving patterns of infection [J]","volume":"24","author":"Fishman","year":"2010","journal-title":"Infect Dis Clin North Am."},{"key":"2026012111365285400_CIT0003","doi-asserted-by":"publisher","first-page":"456","DOI":"10.1111\/nep.13401","article-title":"Infection is the chief cause of mortality and non-death censored graft loss in the first year after renal transplantation in a resource limited population: a single centre study [J]","volume":"24","author":"Gopalakrishnan","year":"2019","journal-title":"Nephrology (Carlton)."},{"key":"2026012111365285400_CIT0004","doi-asserted-by":"publisher","first-page":"1685","DOI":"10.1111\/ajt.16408","article-title":"Respiratory viral infections in solid organ transplant recipients: new insights from multicenter data [J]","volume":"21","author":"Gartner","year":"2021","journal-title":"Am J Transplant."},{"key":"2026012111365285400_CIT0005","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 [J]","volume":"141","author":"Schlaberg","year":"2017","journal-title":"Arch Pathol Lab Med."},{"key":"2026012111365285400_CIT0006","doi-asserted-by":"publisher","first-page":"1356","DOI":"10.1016\/j.chest.2020.11.008","article-title":"Added diagnostic utility of clinical metagenomics for the diagnosis of pneumonia in immunocompromised adults [J]","volume":"159","author":"Azar","year":"2021","journal-title":"Chest."},{"key":"2026012111365285400_CIT0007","doi-asserted-by":"publisher","first-page":"10265","DOI":"10.3389\/ti.2022.10265","article-title":"Metagenomic next-generation sequencing for diagnosing infections in lung transplant recipients: a retrospective study [J]","volume":"35","author":"Ju","year":"2022","journal-title":"Transpl Int."},{"key":"2026012111365285400_CIT0008","doi-asserted-by":"publisher","first-page":"885877","DOI":"10.3389\/fbioe.2023.885877","article-title":"Clinical application value of metagenomic next-generation sequencing in the diagnosis of central nervous system infections [J]","volume":"11","author":"Liu","year":"2023","journal-title":"Front Bioeng Biotechnol."},{"key":"2026012111365285400_CIT0009","doi-asserted-by":"publisher","first-page":"4921","DOI":"10.1038\/s41598-023-31974-1","article-title":"Metagenomic next-generation sequencing versus traditional laboratory methods for the diagnosis of central nervous system opportunistic infections in HIV-infected Chinese adults [J]","volume":"13","author":"Deng","year":"2023","journal-title":"Sci Rep."},{"key":"2026012111365285400_CIT0010","doi-asserted-by":"publisher","first-page":"901549","DOI":"10.3389\/fpubh.2022.901549","article-title":"Application of metagenomic next-generation sequencing in the diagnosis and treatment of recurrent urinary tract infection in kidney transplant recipients [J]","volume":"10","author":"Duan","year":"2022","journal-title":"Front Public Health."},{"key":"2026012111365285400_CIT0011","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1186\/s12879-021-06205-5","article-title":"A case of chlamydia psittaci caused severe pneumonia and meningitis diagnosed by metagenome next-generation sequencing and clinical analysis: a case report and literature review [J]","volume":"21","author":"Shi","year":"2021","journal-title":"BMC Infect Dis."},{"key":"2026012111365285400_CIT0012","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 [J]","volume":"67","author":"Miao","year":"2018","journal-title":"Clin Infect Dis."},{"key":"2026012111365285400_CIT0013","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform [J]","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics."},{"key":"2026012111365285400_CIT0014","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 [J]","volume":"29","author":"Miller","year":"2019","journal-title":"Genome Res."},{"key":"2026012111365285400_CIT0015","doi-asserted-by":"publisher","first-page":"1180","DOI":"10.1101\/gr.171934.113","article-title":"A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples [J]","volume":"24","author":"Naccache","year":"2014","journal-title":"Genome Res."},{"key":"2026012111365285400_CIT0016","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1111\/ajt.14557","article-title":"OPTN\/SRTR 2016 annual data report: kidney [J]","volume":"18","author":"Hart","year":"2018","journal-title":"Am J Transplant."},{"key":"2026012111365285400_CIT0017","doi-asserted-by":"publisher","first-page":"1136588","DOI":"10.3389\/fcimb.2023.1136588","article-title":"Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia [J]","volume":"13","author":"Lin","year":"2023","journal-title":"Front Cell Infect Microbiol."},{"key":"2026012111365285400_CIT0018","doi-asserted-by":"publisher","first-page":"1566","DOI":"10.3390\/genes13091566","article-title":"Next generation and other sequencing technologies in diagnostic microbiology and infectious diseases [J]","volume":"13","author":"Hilt","year":"2022","journal-title":"Genes (Basel)."},{"key":"2026012111365285400_CIT0019","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1093\/jambio\/lxad102","article-title":"Application of metagenomic next-generation sequencing in the diagnosis and resistome analysis of community-acquired pneumonia pathogens from bronchoalveolar lavage samples [J]","volume":"134","author":"Chen","year":"2023","journal-title":"J Appl Microbiol."},{"key":"2026012111365285400_CIT0020","doi-asserted-by":"publisher","first-page":"ofad631","DOI":"10.1093\/ofid\/ofad631","article-title":"Applicability of bronchoalveolar lavage fluid and plasma metagenomic next-generation sequencing assays in the diagnosis of pneumonia [J]","volume":"11","author":"Han","year":"2024","journal-title":"Open Forum Infect Dis."},{"key":"2026012111365285400_CIT0021","doi-asserted-by":"publisher","first-page":"991011","DOI":"10.3389\/fcimb.2023.991011","article-title":"Application of metagenomic next-generation sequencing in the diagnosis of urinary tract infection in patients undergoing cutaneous ureterostomy [J]","volume":"13","author":"Huang","year":"2023","journal-title":"Front Cell Infect Microbiol."},{"key":"2026012111365285400_CIT0022","doi-asserted-by":"publisher","first-page":"1413434","DOI":"10.3389\/fmicb.2024.1413434","article-title":"Direct prediction of antimicrobial resistance in Pseudomonas aeruginosa by metagenomic next-generation sequencing [J]","volume":"15","author":"Cao","year":"2024","journal-title":"Front Microbiol."},{"key":"2026012111365285400_CIT0023","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 [J]","volume":"110","author":"Qin","year":"2024","journal-title":"Diagn Microbiol Infect Dis."},{"key":"2026012111365285400_CIT0024","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1164\/rccm.201706-1097LE","article-title":"Metagenomic sequencing detects respiratory pathogens in hematopoietic cellular transplant patients [J]","volume":"197","author":"Langelier","year":"2018","journal-title":"Am J Respir Crit Care Med."},{"key":"2026012111365285400_CIT0025","doi-asserted-by":"publisher","first-page":"205","DOI":"10.3389\/fcimb.2018.00205","article-title":"Detection of pulmonary infectious pathogens from lung biopsy tissues by metagenomic next-generation sequencing [J]","volume":"8","author":"Li","year":"2018","journal-title":"Front Cell Infect Microbiol."},{"key":"2026012111365285400_CIT0026","doi-asserted-by":"publisher","first-page":"7","DOI":"10.7754\/Clin.Lab.2024.240149","article-title":"Systemic lupus erythematosus complicated with mycobacterium leprae infection: a rare case report [J]","volume":"70","author":"Zhou","year":"2024","journal-title":"Clin Lab."},{"key":"2026012111365285400_CIT0027","doi-asserted-by":"publisher","first-page":"1417","DOI":"10.1007\/s00256-023-04450-0","article-title":"Isolated neural arch tuberculosis with tuberculomas: case report [J]","volume":"53","author":"Xiao","year":"2024","journal-title":"Skeletal Radiol."},{"key":"2026012111365285400_CIT0028","doi-asserted-by":"publisher","first-page":"e32647","DOI":"10.1016\/j.heliyon.2024.e32647","article-title":"Case report: multiple organ failure caused by Japanese spotted fever [J]","volume":"10","author":"Zhou","year":"2024","journal-title":"Heliyon."},{"key":"2026012111365285400_CIT0029","doi-asserted-by":"publisher","first-page":"894678","DOI":"10.3389\/fcimb.2022.894678","article-title":"Metagenomic next-generation sequencing provides prognostic warning by identifying mixed infections in nocardiosis [J]","volume":"12","author":"Jiao","year":"2022","journal-title":"Front Cell Infect Microbiol."},{"key":"2026012111365285400_CIT0030","doi-asserted-by":"publisher","first-page":"1253020","DOI":"10.3389\/fcimb.2023.1253020","article-title":"Metagenomic next-generation sequencing assistance in identifying non-tuberculous mycobacterial infections [J]","volume":"13","author":"Wang","year":"2023","journal-title":"Front Cell Infect Microbiol."},{"key":"2026012111365285400_CIT0031","doi-asserted-by":"publisher","first-page":"12065","DOI":"10.3389\/ti.2024.12065","article-title":"Beyond the first year: epidemiology and management of late-onset opportunistic infections after kidney transplantation [J]","volume":"37","author":"Esnault","year":"2024","journal-title":"Transpl Int."}],"container-title":["Laboratory Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/labmed\/article-pdf\/57\/1\/lmaf035\/65003476\/lmaf035.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/labmed\/article-pdf\/57\/1\/lmaf035\/65003476\/lmaf035.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T16:36:58Z","timestamp":1769013418000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/labmed\/article\/doi\/10.1093\/labmed\/lmaf035\/8305045"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,28]]},"references-count":31,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1,7]]}},"URL":"https:\/\/doi.org\/10.1093\/labmed\/lmaf035","relation":{},"ISSN":["0007-5027","1943-7730"],"issn-type":[{"value":"0007-5027","type":"print"},{"value":"1943-7730","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026]]},"published":{"date-parts":[[2025,10,28]]},"article-number":"lmaf035"}}