Lower respiratory tract single-cell RNA sequencing and neutrophil extracellular trap profiling of COVID-19-associated pulmonary aspergillosis: a single centre, retrospective, observational study

• Published in: The Lancet. Microbe 2024-03, Vol.5 (3), p.e247-e260
• Main Authors: Feys, Simon, Vanmassenhove, Sam, Kraisin, Sirima, Yu, Karen, Jacobs, Cato, Boeckx, Bram, Cambier, Seppe, Cunha, Cristina, Debaveye, Yves, Gonçalves, Samuel M, Hermans, Greet, Humblet-Baron, Stephanie, Jansen, Sander, Lagrou, Katrien, Meersseman, Philippe, Neyts, Johan, Peetermans, Marijke, Rocha-Pereira, Joana, Schepers, Rogier, Spalart, Valérie, Starick, Marick R, Thevissen, Karin, Van Brussel, Thomas, Van Buyten, Tina, Van Mol, Pierre, Vandenbriele, Christophe, Vanderbeke, Lore, Wauters, Els, Wilmer, Alexander, Van Weyenbergh, Johan, Van De Veerdonk, Frank L, Carvalho, Agostinho, Proost, Paul, Martinod, Kimberly, Lambrechts, Diether, Wauters, Joost
• Format: Article
• Language: English
• Subjects: Adult; Antifungal Agents; COVID-19 - complications; Critical Illness; Extracellular Traps; Female; Humans; Male; Pulmonary Aspergillosis; Respiratory System; Retrospective Studies; Sequence Analysis, RNA
• ISSN: 2666-5247; 2666-5247
• DOI: 10.1016/S2666-5247(23)00368-3

COVID-19-associated pulmonary aspergillosis (CAPA) is a severe superinfection with the fungus Aspergillus affecting patients who are critically ill with COVID-19. The pathophysiology and the role of neutrophil extracellular traps (NETs) in this infection are largely unknown. We aimed to characterise the immune profile, with a focus on neutrophils and NET concentrations, of critically ill patients with COVID-19, with or without CAPA. We conducted a single-centre, retrospective, observational study in two patient cohorts, both recruited at University Hospitals Leuven, Belgium. We included adults aged 18 years or older who were admitted to the intensive care unit because of COVID-19 between March 31, 2020, and May 18, 2021, and who were included in the previous Contagious trial (NCT04327570). We investigated the immune cellular landscape of CAPA versus COVID-19 only by performing single-cell RNA sequencing (scRNA-seq) on bronchoalveolar lavage fluid. Bronchoalveolar lavage immune cell fractions were compared between patients with CAPA and patients with COVID-19 only. Additionally, we determined lower respiratory tract NET concentrations using biochemical assays in patients aged 18 years and older who were admitted to the intensive care unit because of severe COVID-19 between March 15, 2020, and Dec 31, 2021, for whom bronchoalveolar lavage was available in the hospital biobank. Bronchoalveolar lavage NET concentrations were compared between patients with CAPA and patients with COVID-19 only and integrated with existing data on immune mediators in bronchoalveolar lavage and 90-day mortality. We performed scRNA-seq of bronchoalveolar lavage on 43 samples from 39 patients, of whom 36 patients (30 male and six female; 14 with CAPA) were included in downstream analyses. We performed bronchoalveolar lavage NET analyses in 59 patients (46 male and 13 female), of whom 26 had CAPA. By scRNA-seq, patients with CAPA had significantly lower neutrophil fractions than patients with COVID-19 only (16% vs 33%; p=0·0020). The remaining neutrophils in patients with CAPA preferentially followed a hybrid maturation trajectory characterised by expression of genes linked to antigen presentation, with enhanced transcription of antifungal effector pathways. Patients with CAPA also showed depletion of mucosal-associated invariant T cells, reduced T helper 1 and T helper 17 differentiation, and transcriptional defects in specific aspects of antifungal immunity in macrophages and monoc