{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T05:07:20Z","timestamp":1779944840617,"version":"3.53.1"},"reference-count":24,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T00:00:00Z","timestamp":1779926400000},"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. Immunol."],"abstract":"<jats:sec>\n                    <jats:title>Objective<\/jats:title>\n                    <jats:p>To analyze the pathogenic etiology of pulmonary infection after solid organ transplantation and construct a prognostic prediction model based on metagenomic next-generation sequencing (mNGS) technology, systematically identifying key predictors to provide evidence for clinical risk stratification and individualized interventions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Clinical data were retrospectively collected from patients who developed pulmonary infection after liver or kidney transplantation at a single hospital between January 2020 and December 2023. All patients underwent mNGS detection of bronchoalveolar lavage fluid or sputum for pathogen identification. Collected data included demographic characteristics, transplant-related parameters, underlying diseases, laboratory test results, mNGS pathogen detection outcomes, and prognostic indicators. The dataset was randomly divided into a training set (n=262) and a test set (n=66). Within an AutoML framework, model hyperparameters were optimized using the Improved Dharma Optimization Algorithm (IDRA). Feature importance was validated bidimensionally via LASSO regression and SHAP interpretable models, with an interactive MATLAB-based decision support system developed.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      The overall positive detection rate of pathogens by mNGS significantly exceeded that of conventional methods (84.76% vs. 61.89%, P&amp;lt;0.001). No statistically significant differences existed in baseline characteristics or laboratory indicators between the training and test sets (all P&amp;gt;0.05), confirming randomized stratified sampling validity. Both cohorts showed highly consistent proportions of poor prognosis events (training set: 27.48% vs. test set: 28.79%, \u03c7\n                      <jats:sup>2<\/jats:sup>\n                      =0.045, P\u00a0=\u00a00.832). The prediction model achieved a ROC-AUC of 0.9694 and PR-AUC of 0.9690 in the training set, and ROC-AUC of 0.9206 (95% CI: 0.854-0.987) with PR-AUC of 0.9273 (95% CI: 0.867-0.988) in the test set, outperforming comparative models. Fourteen key variables were ultimately selected: mNGS bacterial detection, mNGS fungal detection, procalcitonin (PCT), C-reactive protein (CRP), mNGS viral detection, white blood cell count, creatinine, post-transplantation time, neutrophil percentage, diabetes, age, total bilirubin, alanine aminotransferase (ALT), and lymphocyte percentage. The feature overlap rate with AutoML-screened variables was 78.6% (11\/14). SHAP analysis revealed descending importance ranking: mNGS bacterial detection, mNGS fungal detection, PCT, etc.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Integrating multidimensional clinical data with explainable machine learning techniques, this study confirms the central role of pathogenic etiology characteristics in prognostic prediction for post-transplant pulmonary infection and demonstrates the potential for real-time risk assessment to inform clinical decisions. However, prospective validation across diverse care settings is required to establish its efficacy as an interventional guide. This work offers innovative tools and methodological frameworks to advance precision diagnosis and management, subject to ongoing refinement through multicenter collaboration.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fimmu.2026.1734832","type":"journal-article","created":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T04:56:14Z","timestamp":1779944174000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Etiological study of pulmonary infections following solid organ transplantation using metagenomic next-generation sequencing and development of a risk prediction model: a retrospective cohort study"],"prefix":"10.3389","volume":"17","author":[{"given":"Hanshui","family":"Jiang","sequence":"first","affiliation":[{"name":"Department of Pulmonary and Critical Care Medicine, Shulan (Hangzhou) Hospital, Shulan International Medical College, Zhejiang Shuren University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erdan","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Pulmonary and Critical Care Medicine, Shulan (Hangzhou) Hospital, Shulan International Medical College, Zhejiang Shuren University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingqing","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Pulmonary and Critical Care Medicine, Shulan (Hangzhou) Hospital, Shulan International Medical College, Zhejiang Shuren University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zongyu","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Pulmonary and Critical Care Medicine, Shulan (Hangzhou) Hospital, Shulan International Medical College, Zhejiang Shuren University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Pulmonary and Critical Care Medicine, Shulan (Hangzhou) Hospital, Shulan International Medical College, Zhejiang Shuren University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,5,28]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1159\/000508262","article-title":"Solid organ transplantation in amyloidosis","volume":"143","author":"Theodorakakou","year":"2020","journal-title":"Acta Haematol"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.3390\/v13102019","article-title":"Viral enteritis in solid-organ transplantation","volume":"13","author":"Abbas","year":"2021","journal-title":"Viruses"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1097\/MOT.0000000000001075","article-title":"Overview of pregnancy in solid-organ transplantation","volume":"28","author":"Yenebere","year":"2023","journal-title":"Curr Opin Organ Transplant"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1016\/j.transproceed.2023.06.008","article-title":"Non-lung solid organ transplantation from sars-cov-2-positive donors to uninfected recipients","volume":"55","author":"Wade","year":"2023","journal-title":"Transplant Proc"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1210\/endrev\/bnaa030","article-title":"Metabolic consequences of solid organ transplantation","volume":"42","author":"Bhat","year":"2021","journal-title":"Endocr Rev"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.3390\/ijms23073677","article-title":"Necroptosis in solid organ transplantation: a literature overview","volume":"23","author":"Lukenaite","year":"2022","journal-title":"Int J Mol Sci"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1097\/CM9.0000000000002120","article-title":"Metagenomic next-generation sequencing for the diagnosis of Pneumocystis jirovecii pneumonia in solid organ transplant recipients","volume":"135","author":"Lu","year":"2022","journal-title":"Chin Med J (Engl)"},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2022.751617","article-title":"Invasive pulmonary aspergillosis diagnosis via peripheral blood metagenomic next-generation sequencing","volume":"9","author":"Ma","year":"2022","journal-title":"Front Med (Lausanne)"},{"key":"B9","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1016\/j.idc.2023.04.002","article-title":"Updates in molecular diagnostics in solid organ transplantation recipients","volume":"37","author":"Everhart","year":"2023","journal-title":"Infect Dis Clin North Am"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2023.1103626","article-title":"The application of metagenomic next-generation sequencing in patients with infection or colonization caused by Lichtheimia species","volume":"13","author":"Chen","year":"2023","journal-title":"Front Cell Infect Microbiol"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1097\/QCO.0000000000000722","article-title":"Central nervous system infections after solid organ transplantation","volume":"34","author":"Kunnathu Puthanveedu","year":"2021","journal-title":"Curr Opin Infect Dis"},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiae343","article-title":"Clinical impact of plasma metagenomic next-generation sequencing on infection diagnosis and antimicrobial therapy in immunocompromised patients","volume":"231","author":"Yin","year":"2025","journal-title":"J Infect Dis"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2022.872813","article-title":"Diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in pneumocystis jirovecii pneumonia in non-hiv immunosuppressed patients","volume":"12","author":"Sun","year":"2022","journal-title":"Front Cell Infect Microbiol"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1097\/QCO.0000000000001002","article-title":"Pneumocystis jirovecii in solid organ transplant recipients: updates in epidemiology, diagnosis, treatment, and prevention","volume":"37","author":"Saadatzadeh","year":"2024","journal-title":"Curr Opin Infect Dis"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.3760\/cma.j.cn121430-20211008-01439","article-title":"Diagnostic value of detection of pathogens in bronchoalveolar lavage fluid by metagenomics next-generation sequencing in organ transplant patients with pulmonary infection","volume":"33","author":"Meng","year":"2021","journal-title":"Zhonghua Wei Zhong Bing Ji Jiu Yi Xue"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1177\/20499361241308643","article-title":"Clinical utility of plasma microbial cell-free dna sequencing in determining microbiologic etiology of infectious syndromes in solid organ transplant recipients","volume":"11","author":"Shah","year":"2024","journal-title":"Ther Adv Infect Dis"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.2147\/IDR.S257587","article-title":"Metagenomic next-generation sequencing in diagnosis of a case of pneumocystis jirovecii pneumonia in a kidney transplant recipient and literature review","volume":"13","author":"Chen","year":"2020","journal-title":"Infect Drug Resist"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2022.812698","article-title":"Characteristics and prognostic factors of non-hiv immunocompromised patients with pneumocystis pneumonia diagnosed by metagenomics next-generation sequencing","volume":"9","author":"Duan","year":"2022","journal-title":"Front Med (Lausanne)"},{"key":"B19","doi-asserted-by":"publisher","first-page":"25","DOI":"10.2147\/IDR.S485083","article-title":"A rare q-fever infection diagnosed using metagenomic next-generation sequencing in liver transplantation patient: a case report and literature review","volume":"18","author":"Niu","year":"2025","journal-title":"Infect Drug Resist"},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.1016\/S2666-5247(23)00170-2","article-title":"Transmission of yellow fever vaccine virus through blood transfusion and organ transplantation in the usa in 2021: report of an investigation","volume":"4","author":"Gould","year":"2023","journal-title":"Lancet Microbe"},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.1016\/j.jiph.2025.102742","article-title":"Diagnosis of donor-derived malassezia restricta & aspergillus species invasive fungal infection in renal transplant recipient using next generation sequencing - a report of 2 cases and literature review","volume":"18","author":"Alameer","year":"2025","journal-title":"J Infect Public Health"},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.26298","article-title":"Viral metagenomics analysis of kidney donors and recipients: Torque teno virus genotyping and prevalence","volume":"92","author":"Kulifaj","year":"2020","journal-title":"J Med Virol"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1159\/000546660","article-title":"Infection of enterocytozoon bieneusi in a patient with long-term immunosuppression after liver transplantation: a case report and literature review","volume":"19","author":"Hong","year":"202","journal-title":"Case Rep Gastroenterol"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2022.863399","article-title":"Whole genome profiling of lung microbiome in solid organ transplant recipients reveals virus involved microecology may worsen prognosis","volume":"12","author":"Pan","year":"2022","journal-title":"Front Cell Infect Microbiol"}],"container-title":["Frontiers in Immunology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2026.1734832\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T04:56:31Z","timestamp":1779944191000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2026.1734832\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,28]]},"references-count":24,"alternative-id":["10.3389\/fimmu.2026.1734832"],"URL":"https:\/\/doi.org\/10.3389\/fimmu.2026.1734832","relation":{},"ISSN":["1664-3224"],"issn-type":[{"value":"1664-3224","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,28]]},"article-number":"1734832"}}