{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T08:50:46Z","timestamp":1793523046446,"version":"4.5.0"},"reference-count":141,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T00:00:00Z","timestamp":1778544000000},"content-version":"vor","delay-in-days":131,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/V006118\/1"],"award-info":[{"award-number":["MR\/V006118\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003130","name":"Fonds Wetenschappelijk Onderzoek","doi-asserted-by":"publisher","award":["11A0K26N"],"award-info":[{"award-number":["11A0K26N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000050","name":"National Heart, Lung, and Blood Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000050","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100017540","name":"National Heart Lung and Blood Institute Division of Intramural Research","doi-asserted-by":"publisher","award":["R01 HL169265"],"award-info":[{"award-number":["R01 HL169265"]}],"id":[{"id":"10.13039\/100017540","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.fr","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Annals of Intensive Care"],"published-print":{"date-parts":[[2026]]},"DOI":"10.1016\/j.aicoj.2026.100085","type":"journal-article","created":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T09:55:06Z","timestamp":1779357306000},"page":"100085","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":3,"special_numbering":"C","title":["Alveolar dysregulation of host response in pneumonia and ARDS: implications for immune modulation and infection"],"prefix":"10.1016","volume":"16","author":[{"given":"L.S.","family":"Boers","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L.","family":"Maessen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J.","family":"Wauters","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"E.D.","family":"Morrell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A.","family":"Sarma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A.","family":"Conway Morris","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L.D.J.","family":"Bos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"4","key":"10.1016\/j.aicoj.2026.100085_bib0005","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1038\/s41579-022-00821-x","article-title":"The dynamic lung microbiome in health and disease","volume":"21","author":"Natalini","year":"2023","journal-title":"Nat Rev Microbiol."},{"issue":"5","key":"10.1016\/j.aicoj.2026.100085_bib0010","doi-asserted-by":"crossref","first-page":"e61","DOI":"10.1093\/cid\/ciw353","article-title":"Management of adults with hospital-acquired and ventilator-associated Pneumonia: 2016 Clinical Practice Guidelines by the Infectious Diseases Society of America and the American Thoracic Society","volume":"63","author":"Kalil","year":"2016","journal-title":"Clin Infect Dis"},{"key":"10.1016\/j.aicoj.2026.100085_bib0015","article-title":"Severe viral infections requiring intensive care unit admissions- aetiology, co-infections, respiratory interventions and outcomes","author":"Brown","year":"2025","journal-title":"Infection."},{"issue":"2","key":"10.1016\/j.aicoj.2026.100085_bib0020","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1055\/s-0043-1777770","article-title":"Microbiology of severe community-acquired pneumonia and the role of rapid molecular techniques","volume":"45","author":"Pickens","year":"2024","journal-title":"Semin Respir Crit Care Med."},{"issue":"11","key":"10.1016\/j.aicoj.2026.100085_bib0025","doi-asserted-by":"crossref","first-page":"1057","DOI":"10.1136\/thoraxjnl-2013-204282","article-title":"Risk factors for community-acquired pneumonia in adults in Europe: a literature review","volume":"68","author":"Torres","year":"2013","journal-title":"Thorax."},{"issue":"4","key":"10.1016\/j.aicoj.2026.100085_bib0030","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1038\/nrmicro3231","article-title":"The co-pathogenesis of influenza viruses with bacteria in the lung","volume":"12","author":"McCullers","year":"2014","journal-title":"Nat Rev Microbiol."},{"key":"10.1016\/j.aicoj.2026.100085_bib0035","series-title":"Pulmonary inflammation in severe pneumonia is characterised by compartmentalised and mechanistically distinct sub-phenotypes","author":"Jeffrey","year":"2024"},{"issue":"5","key":"10.1016\/j.aicoj.2026.100085_bib0040","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1164\/rccm.201907-1487OC","article-title":"Lung microbiota predict clinical outcomes in critically ill patients","volume":"201","author":"Dickson","year":"2020","journal-title":"Am J Respir Crit Care Med."},{"issue":"11","key":"10.1016\/j.aicoj.2026.100085_bib0045","doi-asserted-by":"crossref","first-page":"2793","DOI":"10.1038\/s41591-023-02617-9","article-title":"Robust airway microbiome signatures in acute respiratory failure and hospital-acquired pneumonia","volume":"29","author":"Montassier","year":"2023","journal-title":"Nat Med."},{"issue":"9","key":"10.1016\/j.aicoj.2026.100085_bib0050","doi-asserted-by":"crossref","first-page":"1491","DOI":"10.1016\/j.cmi.2025.05.026","article-title":"Incidence, microbiology, and mortality of ventilation-associated pneumonia in a large Italian cohort of critically ill patients: results from the PROSAFE project","volume":"31","author":"Colaneri","year":"2025","journal-title":"Clin Microbiol Infect."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0055","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1164\/rccm.200812-1928OC","article-title":"C5a mediates peripheral blood neutrophil dysfunction in critically ill patients","volume":"180","author":"Conway Morris","year":"2009","journal-title":"Am J Respir Crit Care Med."},{"issue":"5","key":"10.1016\/j.aicoj.2026.100085_bib0060","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1007\/s00134-018-5247-0","article-title":"Cell-surface signatures of immune dysfunction risk-stratify critically ill patients: INFECT study","volume":"44","author":"Conway Morris","year":"2018","journal-title":"Intensive Care Med."},{"issue":"6","key":"10.1016\/j.aicoj.2026.100085_bib0065","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1038\/s41590-020-0673-x","article-title":"Alveolar macrophages are epigenetically altered after inflammation, leading to long-term lung immunoparalysis","volume":"21","author":"Roquilly","year":"2020","journal-title":"Nat Immunol."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0070","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-024-53566-x","article-title":"Microbial dynamics and pulmonary immune responses in COVID-19 secondary bacterial pneumonia","volume":"15","author":"Spottiswoode","year":"2024","journal-title":"Nat Commun."},{"issue":"8","key":"10.1016\/j.aicoj.2026.100085_bib0075","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1164\/rccm.202002-0355OC","article-title":"Pulmonary aspergillosis in patients with suspected ventilator-associated pneumonia in UK ICUs","volume":"202","author":"Loughlin","year":"2020","journal-title":"Am J Respir Crit Care Med."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0080","doi-asserted-by":"crossref","DOI":"10.1093\/ofid\/ofx006","article-title":"Hospital-acquired respiratory viral infections: incidence, morbidity, and mortality in pediatric and adult patients","volume":"4","author":"Chow","year":"2017","journal-title":"Open Forum Infect Dis."},{"issue":"2","key":"10.1016\/j.aicoj.2026.100085_bib0085","doi-asserted-by":"crossref","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."},{"issue":"5","key":"10.1016\/j.aicoj.2026.100085_bib0090","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1093\/cid\/cix881","article-title":"Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases","volume":"66","author":"Simner","year":"2018","journal-title":"Clin Infect Dis."},{"issue":"11","key":"10.1016\/j.aicoj.2026.100085_bib0095","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0188251","article-title":"Spectrum of pathogen- and model-specific histopathologies in mouse models of acute pneumonia","volume":"12","author":"Dietert","year":"2017","journal-title":"PLoS One."},{"issue":"3","key":"10.1016\/j.aicoj.2026.100085_bib0100","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1111\/j.1365-2567.2006.02514.x","article-title":"Comparative transcriptional profiling of the lung reveals shared and distinct features of Streptococcus pneumoniae and influenza A virus infection","volume":"120","author":"Rosseau","year":"2007","journal-title":"Immunology."},{"issue":"5","key":"10.1016\/j.aicoj.2026.100085_bib0105","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1016\/j.rmed.2005.06.018","article-title":"Reliability of radiographic findings and the relation to etiologic agents in community-acquired pneumonia","volume":"100","author":"Boersma","year":"2006","journal-title":"Respir Med."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0110","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-021-25040-5","article-title":"Tracheal aspirate RNA sequencing identifies distinct immunological features of COVID-19 ARDS","volume":"12","author":"Sarma","year":"2021","journal-title":"Nat Commun."},{"issue":"11","key":"10.1016\/j.aicoj.2026.100085_bib0115","doi-asserted-by":"crossref","first-page":"1805","DOI":"10.1038\/s41564-022-01237-2","article-title":"Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults","volume":"7","author":"Kalantar","year":"2022","journal-title":"Nat Microbiol."},{"key":"10.1016\/j.aicoj.2026.100085_bib0120","series-title":"Single-cell proteome profiling reveals distinct immunological patterns in the lungs of patients with severe acute respiratory failure","author":"Zhang","year":"2026"},{"key":"10.1016\/j.aicoj.2026.100085_bib0125","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1038\/s41421-020-00225-2","article-title":"The differential immune responses to COVID-19 in peripheral and lung revealed by single-cell RNA sequencing","volume":"6","author":"Xu","year":"2020","journal-title":"Cell Discov."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0130","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-024-49756-2","article-title":"Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19","volume":"15","author":"Neyton","year":"2024","journal-title":"Nat Commun."},{"issue":"3","key":"10.1016\/j.aicoj.2026.100085_bib0135","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1136\/thx.2009.122291","article-title":"Diagnostic importance of pulmonary interleukin-1beta and interleukin-8 in ventilator-associated pneumonia","volume":"65","author":"Conway Morris","year":"2010","journal-title":"Thorax."},{"issue":"6","key":"10.1016\/j.aicoj.2026.100085_bib0140","doi-asserted-by":"crossref","first-page":"1601","DOI":"10.4049\/jimmunol.2000094","article-title":"Influenza infection induces alveolar macrophage dysfunction and thereby enables noninvasive streptococcus pneumoniae to cause deadly pneumonia","volume":"205","author":"Verma","year":"2020","journal-title":"J Immunol."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0145","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1164\/ajrccm\/147.1.38","article-title":"Follow-up protected specimen brushes to assess treatment in nosocomial pneumonia","volume":"147","author":"Montravers","year":"1993","journal-title":"Am Rev Respir Dis."},{"issue":"6","key":"10.1016\/j.aicoj.2026.100085_bib0150","doi-asserted-by":"crossref","first-page":"1371","DOI":"10.1164\/ajrccm.163.6.2007020","article-title":"Resolution of infectious parameters after antimicrobial therapy in patients with ventilator-associated pneumonia","volume":"163","author":"Dennesen","year":"2001","journal-title":"Am J Respir Crit Care Med."},{"issue":"4","key":"10.1016\/j.aicoj.2026.100085_bib0155","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1016\/j.ccm.2018.07.002","article-title":"Inflammation and pneumonia: why are some more susceptible than others?","volume":"39","author":"Mizgerd","year":"2018","journal-title":"Clin Chest Med"},{"issue":"7847","key":"10.1016\/j.aicoj.2026.100085_bib0160","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1038\/s41586-020-03148-w","article-title":"Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia","volume":"590","author":"Grant","year":"2021","journal-title":"Nature."},{"issue":"4","key":"10.1016\/j.aicoj.2026.100085_bib0165","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1164\/rccm.201703-0614LE","article-title":"Peripheral and alveolar cell transcriptional programs are distinct in acute respiratory distress syndrome","volume":"197","author":"Morrell","year":"2018","journal-title":"Am J Respir Crit Care Med."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0170","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/s13054-020-03427-y","article-title":"Alveolar compartmentalization of inflammatory and immune cell biomarkers in pneumonia-related ARDS","volume":"25","author":"Bendib","year":"2021","journal-title":"Crit Care."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0175","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1189\/jlb.0206124","article-title":"cDNA microarray analysis reveals fundamental differences in the expression profiles of primary human monocytes, monocyte-derived macrophages, and alveolar macrophages","volume":"81","author":"Li","year":"2007","journal-title":"J Leukoc Biol."},{"issue":"2","key":"10.1016\/j.aicoj.2026.100085_bib0180","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1093\/infdis\/159.2.189","article-title":"Compartmentalization of intraalveolar and systemic lipopolysaccharide-induced tumor necrosis factor and the pulmonary inflammatory response","volume":"159","author":"Nelson","year":"1989","journal-title":"J Infect Dis."},{"issue":"5","key":"10.1016\/j.aicoj.2026.100085_bib0185","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1165\/rcmb.2024-0201OC","article-title":"PD-L1 and PD-1 are associated with clinical outcomes and alveolar immune cell activation in acute respiratory distress syndrome","volume":"71","author":"Morrell","year":"2024","journal-title":"Am J Respir Cell Mol Biol."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0190","doi-asserted-by":"crossref","first-page":"e13","DOI":"10.1097\/CCM.0000000000005704","article-title":"Alveolar biomarker profiles in subphenotypes of the acute respiratory distress syndrome","volume":"51","author":"Sathe","year":"2023","journal-title":"Crit Care Med."},{"issue":"8","key":"10.1016\/j.aicoj.2026.100085_bib0195","doi-asserted-by":"crossref","first-page":"1486","DOI":"10.1038\/s41418-022-00936-x","article-title":"T cell apoptosis characterizes severe Covid-19 disease","volume":"29","author":"Andre","year":"2022","journal-title":"Cell Death Differ."},{"issue":"9","key":"10.1016\/j.aicoj.2026.100085_bib0200","doi-asserted-by":"crossref","first-page":"912","DOI":"10.1136\/thorax-2023-219989","article-title":"Persistent alveolar inflammatory response in critically ill patients with COVID-19 is associated with mortality","volume":"78","author":"de Brabander","year":"2023","journal-title":"Thorax."},{"issue":"3","key":"10.1016\/j.aicoj.2026.100085_bib0205","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1165\/rcmb.2017-0061OC","article-title":"Cell origin dictates programming of resident versus recruited macrophages during acute lung injury","volume":"57","author":"Mould","year":"2017","journal-title":"Am J Respir Cell Mol Biol."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0210","doi-asserted-by":"crossref","first-page":"L25","DOI":"10.1152\/ajplung.2000.279.1.L25","article-title":"Phenotypic characterization of alveolar monocyte recruitment in acute respiratory distress syndrome","volume":"279","author":"Rosseau","year":"2000","journal-title":"Am J Physiol Lung Cell Mol Physiol."},{"issue":"3","key":"10.1016\/j.aicoj.2026.100085_bib0215","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1164\/rccm.2112012","article-title":"The role of CC chemokine receptor 2 in alveolar monocyte and neutrophil immigration in intact mice","volume":"166","author":"Maus","year":"2002","journal-title":"Am J Respir Crit Care Med."},{"issue":"6","key":"10.1016\/j.aicoj.2026.100085_bib0220","doi-asserted-by":"crossref","first-page":"L1245","DOI":"10.1152\/ajplung.00453.2001","article-title":"Role of resident alveolar macrophages in leukocyte traffic into the alveolar air space of intact mice","volume":"282","author":"Maus","year":"2002","journal-title":"Am J Physiol Lung Cell Mol Physiol."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0225","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1164\/ajrccm.150.1.8025736","article-title":"Evolution of bronchoalveolar cell populations in the adult respiratory distress syndrome","volume":"150","author":"Steinberg","year":"1994","journal-title":"Am J Respir Crit Care Med."},{"issue":"2","key":"10.1016\/j.aicoj.2026.100085_bib0230","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1378\/chest.128.2.525","article-title":"Causes and timing of death in patients with ARDS","volume":"128","author":"Stapleton","year":"2005","journal-title":"Chest."},{"issue":"11","key":"10.1016\/j.aicoj.2026.100085_bib0235","doi-asserted-by":"crossref","first-page":"2450","DOI":"10.1097\/00003246-200211000-00008","article-title":"Incidence, clinical course, and outcome in 217 patients with acute respiratory distress syndrome","volume":"30","author":"Estenssoro","year":"2002","journal-title":"Crit Care Med."},{"issue":"3 Pt 1","key":"10.1016\/j.aicoj.2026.100085_bib0240","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1164\/ajrccm.154.3.8810593","article-title":"Inflammatory cytokines in patients with persistence of the acute respiratory distress syndrome","volume":"154","author":"Goodman","year":"1996","journal-title":"Am J Respir Crit Care Med."},{"issue":"6","key":"10.1016\/j.aicoj.2026.100085_bib0245","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1164\/rccm.201807-1381OC","article-title":"Alveolar macrophage transcriptional programs are associated with outcomes in acute respiratory distress syndrome","volume":"200","author":"Morrell","year":"2019","journal-title":"Am J Respir Crit Care Med."},{"issue":"9354","key":"10.1016\/j.aicoj.2026.100085_bib0250","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1016\/S0140-6736(03)12329-X","article-title":"Ventilator-associated lung injury","volume":"361","author":"Pinhu","year":"2003","journal-title":"Lancet."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0255","doi-asserted-by":"crossref","first-page":"L9","DOI":"10.1152\/ajplung.00443.2022","article-title":"Hyperoxia-induced lung injury in acute respiratory distress syndrome: what is its relative impact?","volume":"325","author":"Lilien","year":"2023","journal-title":"Am J Physiol Lung Cell Mol Physiol."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0260","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1038\/s41598-018-36951-7","article-title":"Hypercapnia alters alveolar epithelial repair by a pH-dependent and adenylate cyclase-mediated mechanism","volume":"9","author":"Cortes-Puentes","year":"2019","journal-title":"Sci Rep."},{"issue":"8","key":"10.1016\/j.aicoj.2026.100085_bib0265","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1164\/rccm.202005-1989OC","article-title":"Airspace macrophages and monocytes exist in transcriptionally distinct subsets in healthy adults","volume":"203","author":"Mould","year":"2021","journal-title":"Am J Respir Crit Care Med."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0270","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-023-43223-0","article-title":"The transcriptional and phenotypic characteristics that define alveolar macrophage subsets in acute hypoxemic respiratory failure","volume":"14","author":"Morrell","year":"2023","journal-title":"Nat Commun."},{"issue":"26","key":"10.1016\/j.aicoj.2026.100085_bib0275","doi-asserted-by":"crossref","first-page":"6243","DOI":"10.1016\/j.cell.2021.11.033","article-title":"SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis","volume":"184","author":"Wendisch","year":"2021","journal-title":"Cell."},{"issue":"10","key":"10.1016\/j.aicoj.2026.100085_bib0280","doi-asserted-by":"crossref","DOI":"10.1172\/jci.insight.99281","article-title":"Cytometry TOF identifies alveolar macrophage subtypes in acute respiratory distress syndrome","volume":"3","author":"Morrell","year":"2018","journal-title":"JCI Insight."},{"issue":"3","key":"10.1016\/j.aicoj.2026.100085_bib0285","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/s41422-020-00455-9","article-title":"Discriminating mild from critical COVID-19 by innate and adaptive immune single-cell profiling of bronchoalveolar lavages","volume":"31","author":"Wauters","year":"2021","journal-title":"Cell Res."},{"issue":"662","key":"10.1016\/j.aicoj.2026.100085_bib0290","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.abn5168","article-title":"A shift in lung macrophage composition is associated with COVID-19 severity and recovery","volume":"14","author":"Chen","year":"2022","journal-title":"Sci Transl Med."},{"issue":"6","key":"10.1016\/j.aicoj.2026.100085_bib0295","doi-asserted-by":"crossref","first-page":"842","DOI":"10.1038\/s41591-020-0901-9","article-title":"Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19","volume":"26","author":"Liao","year":"2020","journal-title":"Nat Med."},{"issue":"4","key":"10.1016\/j.aicoj.2026.100085_bib0300","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1016\/j.immuni.2021.03.005","article-title":"Longitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19","volume":"54","author":"Szabo","year":"2021","journal-title":"Immunity."},{"issue":"23","key":"10.1016\/j.aicoj.2026.100085_bib0305","doi-asserted-by":"crossref","first-page":"2594","DOI":"10.1001\/jama.2011.1829","article-title":"Immunosuppression in patients who die of sepsis and multiple organ failure","volume":"306","author":"Boomer","year":"2011","journal-title":"JAMA."},{"issue":"11","key":"10.1016\/j.aicoj.2026.100085_bib0310","doi-asserted-by":"crossref","first-page":"1859","DOI":"10.1007\/s00134-010-1962-x","article-title":"Low monocyte human leukocyte antigen-DR is independently associated with nosocomial infections after septic shock","volume":"36","author":"Landelle","year":"2010","journal-title":"Intensive Care Med."},{"issue":"6","key":"10.1016\/j.aicoj.2026.100085_bib0315","doi-asserted-by":"crossref","first-page":"678","DOI":"10.1038\/nm0697-678","article-title":"Monocyte deactivation in septic patients: restoration by IFN-gamma treatment","volume":"3","author":"Docke","year":"1997","journal-title":"Nat Med."},{"issue":"3","key":"10.1016\/j.aicoj.2026.100085_bib0320","doi-asserted-by":"crossref","first-page":"R85","DOI":"10.1186\/cc12711","article-title":"Blockade of the negative co-stimulatory molecules PD-1 and CTLA-4 improves survival in primary and secondary fungal sepsis","volume":"17","author":"Chang","year":"2013","journal-title":"Crit Care."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0325","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1097\/SHK.0b013e3182168cce","article-title":"Dose-dependent effect of anti-CTLA-4 on survival in sepsis","volume":"36","author":"Inoue","year":"2011","journal-title":"Shock."},{"issue":"5","key":"10.1016\/j.aicoj.2026.100085_bib0330","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1164\/rccm.201011-1891OC","article-title":"Fas determines differential fates of resident and recruited macrophages during resolution of acute lung injury","volume":"184","author":"Janssen","year":"2011","journal-title":"Am J Respir Crit Care Med."},{"issue":"5","key":"10.1016\/j.aicoj.2026.100085_bib0335","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1016\/j.immuni.2004.09.009","article-title":"Transcriptional suppression of interleukin-12 gene expression following phagocytosis of apoptotic cells","volume":"21","author":"Kim","year":"2004","journal-title":"Immunity."},{"issue":"7","key":"10.1016\/j.aicoj.2026.100085_bib0340","doi-asserted-by":"crossref","first-page":"2619","DOI":"10.1172\/JCI124615","article-title":"The role of macrophages in the resolution of inflammation","volume":"129","author":"Watanabe","year":"2019","journal-title":"J Clin Invest."},{"issue":"5","key":"10.1016\/j.aicoj.2026.100085_bib0345","doi-asserted-by":"crossref","first-page":"1281","DOI":"10.1084\/jem.20161375","article-title":"Phagocytosis imprints heterogeneity in tissue-resident macrophages","volume":"214","author":"AG","year":"2017","journal-title":"J Exp Med."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0350","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1038\/s41590-018-0249-1","article-title":"DEL-1 promotes macrophage efferocytosis and clearance of inflammation","volume":"20","author":"Kourtzelis","year":"2019","journal-title":"Nat Immunol."},{"issue":"10","key":"10.1016\/j.aicoj.2026.100085_bib0355","doi-asserted-by":"crossref","first-page":"1380","DOI":"10.1164\/rccm.201009-1431OC","article-title":"Exudate macrophages attenuate lung injury by the release of IL-1 receptor antagonist in gram-negative pneumonia","volume":"183","author":"Herold","year":"2011","journal-title":"Am J Respir Crit Care Med."},{"issue":"33","key":"10.1016\/j.aicoj.2026.100085_bib0360","doi-asserted-by":"crossref","first-page":"8800","DOI":"10.1073\/pnas.1705365114","article-title":"Mouse macrophages show different requirements for phosphatidylserine receptor Tim4 in efferocytosis","volume":"114","author":"Yanagihashi","year":"2017","journal-title":"Proc Natl Acad Sci USA."},{"issue":"9","key":"10.1016\/j.aicoj.2026.100085_bib0365","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1038\/sj.cdd.4401832","article-title":"Recognition of apoptotic cells by macrophages activates the peroxisome proliferator-activated receptor-gamma and attenuates the oxidative burst","volume":"13","author":"Johann","year":"2006","journal-title":"Cell Death Differ."},{"issue":"9","key":"10.1016\/j.aicoj.2026.100085_bib0370","doi-asserted-by":"crossref","first-page":"6480","DOI":"10.4049\/jimmunol.177.9.6480","article-title":"Decreased alveolar macrophage apoptosis is associated with increased pulmonary inflammation in a murine model of pneumococcal pneumonia","volume":"177","author":"Marriott","year":"2006","journal-title":"J Immunol."},{"issue":"4","key":"10.1016\/j.aicoj.2026.100085_bib0375","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1172\/JCI1112","article-title":"Macrophages that have ingested apoptotic cells in vitro inhibit proinflammatory cytokine production through autocrine\/paracrine mechanisms involving TGF-beta, PGE2, and PAF","volume":"101","author":"Fadok","year":"1998","journal-title":"J Clin Invest."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0380","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1172\/JCI0211638","article-title":"Phosphatidylserine-dependent ingestion of apoptotic cells promotes TGF-beta1 secretion and the resolution of inflammation","volume":"109","author":"Huynh","year":"2002","journal-title":"J Clin Invest."},{"issue":"4","key":"10.1016\/j.aicoj.2026.100085_bib0385","doi-asserted-by":"crossref","first-page":"1968","DOI":"10.4049\/jimmunol.168.4.1968","article-title":"Lipopolysaccharide induces rapid production of IL-10 by monocytes in the presence of apoptotic neutrophils","volume":"168","author":"Byrne","year":"2002","journal-title":"J Immunol."},{"issue":"50","key":"10.1016\/j.aicoj.2026.100085_bib0390","doi-asserted-by":"crossref","first-page":"38376","DOI":"10.1074\/jbc.M605146200","article-title":"Apoptotic cells, through transforming growth factor-beta, coordinately induce anti-inflammatory and suppress pro-inflammatory eicosanoid and NO synthesis in murine macrophages","volume":"281","author":"Freire-de-Lima","year":"2006","journal-title":"J Biol Chem."},{"issue":"2","key":"10.1016\/j.aicoj.2026.100085_bib0395","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1038\/mi.2012.66","article-title":"Aspirin-triggered resolvin D1 reduces mucosal inflammation and promotes resolution in a murine model of acute lung injury","volume":"6","author":"Eickmeier","year":"2013","journal-title":"Mucosal Immunol."},{"issue":"2","key":"10.1016\/j.aicoj.2026.100085_bib0400","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1002\/eji.201040801","article-title":"Saturated-efferocytosis generates pro-resolving CD11b low macrophages: modulation by resolvins and glucocorticoids","volume":"41","author":"Schif-Zuck","year":"2011","journal-title":"Eur J Immunol."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0405","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1186\/1465-9921-13-110","article-title":"Resolvin D1 attenuates inflammation in lipopolysaccharide-induced acute lung injury through a process involving the PPARgamma\/NF-kappaB pathway","volume":"13","author":"Liao","year":"2012","journal-title":"Respir Res."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0410","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/nri.2015.4","article-title":"Specialized pro-resolving mediators: endogenous regulators of infection and inflammation","volume":"16","author":"Basil","year":"2016","journal-title":"Nat Rev Immunol."},{"issue":"5","key":"10.1016\/j.aicoj.2026.100085_bib0415","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1016\/S2213-2600(13)70053-5","article-title":"Chronology of histological lesions in acute respiratory distress syndrome with diffuse alveolar damage: a prospective cohort study of clinical autopsies","volume":"1","author":"Thille","year":"2013","journal-title":"Lancet Respir Med."},{"issue":"10","key":"10.1016\/j.aicoj.2026.100085_bib0420","doi-asserted-by":"crossref","first-page":"2898","DOI":"10.1172\/JCI36498","article-title":"CD4+CD25+Foxp3+ Tregs resolve experimental lung injury in mice and are present in humans with acute lung injury","volume":"119","author":"D\u2019Alessio","year":"2009","journal-title":"J Clin Invest."},{"issue":"6","key":"10.1016\/j.aicoj.2026.100085_bib0425","doi-asserted-by":"crossref","first-page":"1440","DOI":"10.1038\/mi.2014.33","article-title":"Foxp3+ regulatory T cells promote lung epithelial proliferation","volume":"7","author":"Mock","year":"2014","journal-title":"Mucosal Immunol."},{"issue":"4","key":"10.1016\/j.aicoj.2026.100085_bib0430","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1165\/rcmb.2019-0399OC","article-title":"Impact of regulatory T cells on type 2 Alveolar epithelial cell transcriptomes during resolution of acute lung injury and contributions of IFN-gamma","volume":"63","author":"Mock","year":"2020","journal-title":"Am J Respir Cell Mol Biol."},{"issue":"5","key":"10.1016\/j.aicoj.2026.100085_bib0435","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1165\/ajrcmb.24.5.4292","article-title":"Alveolar macrophages that phagocytose apoptotic neutrophils produce hepatocyte growth factor during bacterial pneumonia in mice","volume":"24","author":"Morimoto","year":"2001","journal-title":"Am J Respir Cell Mol Biol."},{"issue":"6","key":"10.1016\/j.aicoj.2026.100085_bib0440","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1164\/rccm.200812-1837OC","article-title":"Macrophage tumor necrosis factor-alpha induces epithelial expression of granulocyte-macrophage colony-stimulating factor: impact on alveolar epithelial repair","volume":"180","author":"Cakarova","year":"2009","journal-title":"Am J Respir Crit Care Med."},{"issue":"2","key":"10.1016\/j.aicoj.2026.100085_bib0445","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1164\/ajrccm.158.2.9711111","article-title":"Hepatocyte growth factor and keratinocyte growth factor in the pulmonary edema fluid of patients with acute lung injury. Biologic and clinical significance","volume":"158","author":"Verghese","year":"1998","journal-title":"Am J Respir Crit Care Med."},{"issue":"8","key":"10.1016\/j.aicoj.2026.100085_bib0450","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1038\/ncb3580","article-title":"Local lung hypoxia determines epithelial fate decisions during alveolar regeneration","volume":"19","author":"Xi","year":"2017","journal-title":"Nat Cell Biol."},{"issue":"6380","key":"10.1016\/j.aicoj.2026.100085_bib0455","doi-asserted-by":"crossref","first-page":"1118","DOI":"10.1126\/science.aam6603","article-title":"Single-cell Wnt signaling niches maintain stemness of alveolar type 2 cells","volume":"359","author":"Nabhan","year":"2018","journal-title":"Science."},{"issue":"22","key":"10.1016\/j.aicoj.2026.100085_bib0460","doi-asserted-by":"crossref","DOI":"10.1172\/JCI165612","article-title":"Regulation of epithelial transitional states in murine and human pulmonary fibrosis","volume":"133","author":"Wang","year":"2023","journal-title":"J Clin Invest."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0465","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1136\/thoraxjnl-2014-205766","article-title":"Diagnostic accuracy of pulmonary host inflammatory mediators in the exclusion of ventilator-acquired pneumonia","volume":"70","author":"Hellyer","year":"2015","journal-title":"Thorax."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0470","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/s40635-015-0062-1","article-title":"Tumor necrosis factor receptor 1 (TNFRI) for ventilator-associated pneumonia diagnosis by cytokine multiplex analysis","volume":"3","author":"Martin-Loeches","year":"2015","journal-title":"Intensive Care Med Exp."},{"issue":"19","key":"10.1016\/j.aicoj.2026.100085_bib0475","doi-asserted-by":"crossref","first-page":"5178","DOI":"10.1182\/blood-2010-08-304667","article-title":"C5a-mediated neutrophil dysfunction is RhoA-dependent and predicts infection in critically ill patients","volume":"117","author":"Morris","year":"2011","journal-title":"Blood."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0480","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1186\/s13054-025-05498-1","article-title":"Longitudinal analysis of lung microbiome, immune response, and metabolism in ventilator-associated pneumonia: a cohort study","volume":"29","author":"Bustos","year":"2025","journal-title":"Crit Care."},{"issue":"5","key":"10.1016\/j.aicoj.2026.100085_bib0485","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1111\/anae.15946","article-title":"Viral infections in critical care: a narrative review","volume":"78","author":"Conway Morris","year":"2023","journal-title":"Anaesthesia."},{"issue":"9","key":"10.1016\/j.aicoj.2026.100085_bib0490","doi-asserted-by":"crossref","first-page":"1204","DOI":"10.1093\/cid\/cix120","article-title":"Epidemiology of multiple herpes viremia in previously immunocompetent patients with septic shock","volume":"64","author":"Ong","year":"2017","journal-title":"Clin Infect Dis."},{"issue":"2","key":"10.1016\/j.aicoj.2026.100085_bib0495","article-title":"Reactivation of multiple viruses in patients with sepsis","volume":"9","author":"Walton","year":"2014","journal-title":"PLoS One."},{"issue":"6","key":"10.1016\/j.aicoj.2026.100085_bib0500","doi-asserted-by":"crossref","first-page":"1850","DOI":"10.1097\/CCM.0b013e31819ffea6","article-title":"Active cytomegalovirus infection is common in mechanically ventilated medical intensive care unit patients","volume":"37","author":"Chiche","year":"2009","journal-title":"Crit Care Med."},{"issue":"3","key":"10.1016\/j.aicoj.2026.100085_bib0505","doi-asserted-by":"crossref","DOI":"10.1002\/rmv.2437","article-title":"Reactivation of herpesviruses during COVID-19: a systematic review and meta-analysis","volume":"33","author":"Shafiee","year":"2023","journal-title":"Rev Med Virol."},{"issue":"3","key":"10.1016\/j.aicoj.2026.100085_bib0510","doi-asserted-by":"crossref","first-page":"R68","DOI":"10.1186\/cc7875","article-title":"Cytomegalovirus infection in critically ill patients: a systematic review","volume":"13","author":"Osawa","year":"2009","journal-title":"Crit Care."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0515","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1186\/s13613-019-0616-6","article-title":"Herpes simplex virus and Cytomegalovirus reactivation among severe ARDS patients under veno-venous ECMO","volume":"9","author":"Hraiech","year":"2019","journal-title":"Ann Intensive Care."},{"issue":"9","key":"10.1016\/j.aicoj.2026.100085_bib0520","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1164\/rccm.200609-1322OC","article-title":"Herpes simplex virus lung infection in patients undergoing prolonged mechanical ventilation","volume":"175","author":"Luyt","year":"2007","journal-title":"Am J Respir Crit Care Med."},{"issue":"8","key":"10.1016\/j.aicoj.2026.100085_bib0525","doi-asserted-by":"crossref","first-page":"1251","DOI":"10.1007\/s00134-024-07529-x","article-title":"Pulmonary herpes simplex virus and cytomegalovirus in patients with acute respiratory distress syndrome related to COVID-19","volume":"50","author":"Boers","year":"2024","journal-title":"Intensive Care Med."},{"issue":"12","key":"10.1016\/j.aicoj.2026.100085_bib0530","doi-asserted-by":"crossref","first-page":"2202","DOI":"10.1007\/s00134-008-1231-4","article-title":"Herpes simplex virus load in bronchoalveolar lavage fluid is related to poor outcome in critically ill patients","volume":"34","author":"Linssen","year":"2008","journal-title":"Intensive Care Med"},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0535","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1186\/s13054-021-03843-8","article-title":"HSV-1 reactivation is associated with an increased risk of mortality and pneumonia in critically ill COVID-19 patients","volume":"25","author":"Meyer","year":"2021","journal-title":"Crit Care."},{"issue":"4","key":"10.1016\/j.aicoj.2026.100085_bib0540","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1111\/j.1469-0691.2009.02704.x","article-title":"Monitoring of herpes simplex virus in the lower respiratory tract of critically ill patients using real-time PCR: a prospective study","volume":"15","author":"De Vos","year":"2009","journal-title":"Clin Microbiol Infect."},{"issue":"3","key":"10.1016\/j.aicoj.2026.100085_bib0545","first-page":"416","article-title":"Herpes simplex virus from the lower respiratory tract in adult respiratory distress syndrome","volume":"126","author":"Tuxen","year":"1982","journal-title":"Am Rev Respir Dis."},{"issue":"3","key":"10.1016\/j.aicoj.2026.100085_bib0550","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1007\/s00134-015-4071-z","article-title":"Cytomegalovirus reactivation and mortality in patients with acute respiratory distress syndrome","volume":"42","author":"Ong","year":"2016","journal-title":"Intensive Care Med."},{"issue":"12","key":"10.1016\/j.aicoj.2026.100085_bib0555","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0051340","article-title":"Cytomegalovirus and herpes simplex virus effect on the prognosis of mechanically ventilated patients suspected to have ventilator-associated pneumonia","volume":"7","author":"Coisel","year":"2012","journal-title":"PLoS One."},{"issue":"8","key":"10.1016\/j.aicoj.2026.100085_bib0560","doi-asserted-by":"crossref","first-page":"1116","DOI":"10.1007\/s00134-005-2706-1","article-title":"Nosocomial viral ventilator-associated pneumonia in the intensive care unit: a prospective cohort study","volume":"31","author":"Daubin","year":"2005","journal-title":"Intensive Care Med."},{"key":"10.1016\/j.aicoj.2026.100085_bib0565","series-title":"Pulmonary CMV and HSV reactivation in critically ill COVID-19 patients with and without aspergillosis: a retrospective observational study","author":"Heylen","year":"2025"},{"issue":"4","key":"10.1016\/j.aicoj.2026.100085_bib0570","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1001\/jama.300.4.413","article-title":"Cytomegalovirus reactivation in critically ill immunocompetent patients","volume":"300","author":"Limaye","year":"2008","journal-title":"JAMA."},{"issue":"8","key":"10.1016\/j.aicoj.2026.100085_bib0575","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1001\/jama.2017.10569","article-title":"Effect of ganciclovir on IL-6 levels among cytomegalovirus-seropositive adults with critical illness: a randomized clinical Trial","volume":"318","author":"Limaye","year":"2017","journal-title":"JAMA."},{"issue":"6","key":"10.1016\/j.aicoj.2026.100085_bib0580","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1016\/j.cmi.2021.12.002","article-title":"Efficacy and safety of antiviral therapy in critically ill patients with mechanical ventilation: a meta-analysis with trial sequential analysis of randomized controlled trials","volume":"28","author":"Gu","year":"2022","journal-title":"Clin Microbiol Infect."},{"issue":"4","key":"10.1016\/j.aicoj.2026.100085_bib0585","doi-asserted-by":"crossref","DOI":"10.1136\/bmjopen-2023-082512","article-title":"Effect of acyclovir therapy on the outcome of mechanically ventilated patients with lower respiratory tract infection and detection of herpes simplex virus in bronchoalveolar lavage: protocol for a multicentre, randomised controlled trial (HerpMV)","volume":"14","author":"Hagel","year":"2024","journal-title":"BMJ Open."},{"issue":"5899","key":"10.1016\/j.aicoj.2026.100085_bib0590","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1126\/science.1164164","article-title":"Noncytotoxic lytic granule-mediated CD8+ T cell inhibition of HSV-1 reactivation from neuronal latency","volume":"322","author":"Knickelbein","year":"2008","journal-title":"Science."},{"issue":"9","key":"10.1016\/j.aicoj.2026.100085_bib0595","doi-asserted-by":"crossref","first-page":"3496","DOI":"10.1073\/pnas.0610847104","article-title":"Selective retention of herpes simplex virus-specific T cells in latently infected human trigeminal ganglia","volume":"104","author":"Verjans","year":"2007","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0600","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1186\/s12873-022-00733-2","article-title":"Role of CD8(+) T cell exhaustion in the progression and prognosis of acute respiratory distress syndrome induced by sepsis: a prospective observational study","volume":"22","author":"Yan","year":"2022","journal-title":"BMC Emerg Med."},{"issue":"4","key":"10.1016\/j.aicoj.2026.100085_bib0605","doi-asserted-by":"crossref","DOI":"10.1002\/jev2.12437","article-title":"Extracellular vesicles derived from M2-like macrophages alleviate acute lung injury in a miR-709-mediated manner","volume":"13","author":"Yang","year":"2024","journal-title":"J Extracell Vesicles."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0610","doi-asserted-by":"crossref","first-page":"2670","DOI":"10.1080\/21505594.2021.1982373","article-title":"Pathogenesis and virulence of herpes simplex virus","volume":"12","author":"Zhu","year":"2021","journal-title":"Virulence."},{"issue":"7","key":"10.1016\/j.aicoj.2026.100085_bib0615","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0254129","article-title":"High rate of HSV-1 reactivation in invasively ventilated COVID-19 patients: immunological findings","volume":"16","author":"Seessle","year":"2021","journal-title":"PLoS One."},{"issue":"12","key":"10.1016\/j.aicoj.2026.100085_bib0620","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1038\/s41579-021-00582-z","article-title":"Pathogenesis of human cytomegalovirus in the immunocompromised host","volume":"19","author":"Griffiths","year":"2021","journal-title":"Nat Rev Microbiol."},{"issue":"6","key":"10.1016\/j.aicoj.2026.100085_bib0625","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1164\/rccm.202310-1815VP","article-title":"Fungal fog in viral storms: necessity for rigor in aspergillosis diagnosis and research","volume":"209","author":"Feys","year":"2024","journal-title":"Am J Respir Crit Care Med."},{"issue":"3","key":"10.1016\/j.aicoj.2026.100085_bib0630","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1016\/j.chest.2023.09.019","article-title":"Prevalence, risk factors, clinical features, and outcome of influenza-associated pulmonary aspergillosis in critically ill patients: a systematic review and meta-analysis","volume":"165","author":"Lu","year":"2024","journal-title":"Chest."},{"issue":"3","key":"10.1016\/j.aicoj.2026.100085_bib0635","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/S2213-2600(23)00408-3","article-title":"Risk factors for COVID-19-associated pulmonary aspergillosis: a systematic review and meta-analysis","volume":"12","author":"Gioia","year":"2024","journal-title":"Lancet Respir Med."},{"issue":"11","key":"10.1016\/j.aicoj.2026.100085_bib0640","doi-asserted-by":"crossref","DOI":"10.1093\/ofid\/ofab478","article-title":"Invasive pulmonary aspergillosis complicating noninfluenza respiratory viral infections in solid organ transplant recipients","volume":"8","author":"Apostolopoulou","year":"2021","journal-title":"Open Forum Infect Dis."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0645","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/s41479-024-00129-9","article-title":"Invasive pulmonary aspergillosis among patients with severe community-acquired pneumonia and influenza in ICUs: a retrospective cohort study","volume":"16","author":"Lee","year":"2024","journal-title":"Pneumonia (Nathan)."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0650","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1186\/s12879-022-07366-7","article-title":"Invasive Aspergillus outbreak in inhalation injury: a case presentation and literature review","volume":"22","author":"Liu","year":"2022","journal-title":"BMC Infect Dis."},{"issue":"1","key":"10.1016\/j.aicoj.2026.100085_bib0655","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-019-48183-4","article-title":"Prevalence and outcome of invasive pulmonary aspergillosis in critically ill patients with liver cirrhosis: an observational study","volume":"9","author":"Lahmer","year":"2019","journal-title":"Sci Rep."},{"issue":"12","key":"10.1016\/j.aicoj.2026.100085_bib0660","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1016\/S2213-2600(22)00259-4","article-title":"Lung epithelial and myeloid innate immunity in influenza-associated or COVID-19-associated pulmonary aspergillosis: an observational study","volume":"10","author":"Feys","year":"2022","journal-title":"Lancet Respir Med."},{"issue":"5","key":"10.1016\/j.aicoj.2026.100085_bib0665","doi-asserted-by":"crossref","first-page":"558","DOI":"10.1038\/nm1765","article-title":"Inhibition of pulmonary antibacterial defense by interferon-gamma during recovery from influenza infection","volume":"14","author":"Sun","year":"2008","journal-title":"Nat Med."},{"issue":"6","key":"10.1016\/j.aicoj.2026.100085_bib0670","doi-asserted-by":"crossref","DOI":"10.1128\/mbio.02854-22","article-title":"Postinfluenza environment reduces aspergillus fumigatus conidium clearance and facilitates invasive aspergillosis in vivo","volume":"13","author":"Liu","year":"2022","journal-title":"mBio."},{"issue":"3","key":"10.1016\/j.aicoj.2026.100085_bib0675","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1164\/rccm.202208-1570OC","article-title":"A pathology-based case series of influenza- and COVID-19-associated pulmonary aspergillosis: the proof is in the tissue","volume":"208","author":"Vanderbeke","year":"2023","journal-title":"Am J Respir Crit Care Med."},{"issue":"3","key":"10.1016\/j.aicoj.2026.100085_bib0680","doi-asserted-by":"crossref","first-page":"e247","DOI":"10.1016\/S2666-5247(23)00368-3","article-title":"Lower respiratory tract single-cell RNA sequencing and neutrophil extracellular trap profiling of COVID-19-associated pulmonary aspergillosis: a single centre, retrospective, observational study","volume":"5","author":"Feys","year":"2024","journal-title":"Lancet Microbe."},{"issue":"Suppl 1","key":"10.1016\/j.aicoj.2026.100085_bib0685","doi-asserted-by":"crossref","first-page":"S271","DOI":"10.1080\/13693780802227159","article-title":"Invasive aspergillosis in glucocorticoid-treated patients","volume":"47","author":"Lewis","year":"2009","journal-title":"Med Mycol"},{"issue":"8","key":"10.1016\/j.aicoj.2026.100085_bib0690","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1513\/AnnalsATS.202505-543ST","article-title":"Research priorities for noninvasive sampling of the lower respiratory tract during acute respiratory failure: an official American thoracic society workshop report","volume":"22","author":"Bain","year":"2025","journal-title":"Ann Am Thorac Soc."},{"issue":"10","key":"10.1016\/j.aicoj.2026.100085_bib0695","doi-asserted-by":"crossref","first-page":"1784","DOI":"10.1007\/s00134-025-08089-4","article-title":"Temporal stability of phenotypes of acute respiratory distress syndrome: clinical implications for early corticosteroid therapy and mortality","volume":"51","author":"Pensier","year":"2025","journal-title":"Intensive Care Med."},{"issue":"11","key":"10.1016\/j.aicoj.2026.100085_bib0700","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1164\/rccm.202105-1302OC","article-title":"Latent class analysis reveals COVID-19-related acute respiratory distress syndrome subgroups with differential responses to corticosteroids","volume":"204","author":"Sinha","year":"2021","journal-title":"Am J Respir Crit Care Med."},{"issue":"11","key":"10.1016\/j.aicoj.2026.100085_bib0705","doi-asserted-by":"crossref","first-page":"1617","DOI":"10.1007\/s00134-022-06871-2","article-title":"Compartmentalisation of immune responses in critical illness: does it matter?","volume":"48","author":"Conway Morris","year":"2022","journal-title":"Intensive Care Med."}],"container-title":["Annals of Intensive Care"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2110582026001202?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2110582026001202?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T09:39:45Z","timestamp":1791970785000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2110582026001202"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"references-count":141,"alternative-id":["S2110582026001202"],"URL":"https:\/\/doi.org\/10.1016\/j.aicoj.2026.100085","relation":{},"ISSN":["2110-5820"],"issn-type":[{"value":"2110-5820","type":"print"}],"subject":[],"published":{"date-parts":[[2026]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Alveolar dysregulation of host response in pneumonia and ARDS: implications for immune modulation and infection","name":"articletitle","label":"Article Title"},{"value":"Annals of Intensive Care","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.aicoj.2026.100085","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier Masson SAS on behalf of Soci\u00e9t\u00e9 de R\u00e9animation de Langue Fran\u00e7aise (French Intensive Care Society).","name":"copyright","label":"Copyright"}],"article-number":"100085"}}