We are extremely grateful to patients and their families for their willingness to participate in this study. Authors also warmly acknowledge Y. Rombouts, L. Boyer, T. Henry, M. Tiraby, and all lab members for their outstanding advice and support on this project.

This project was supported by the ATIP-Avenir program (to E. Meunier), Fondation pour la Recherche Médicale “Amorçage Jeunes Equipes” (AJE20151034460 to E. Meunier), the Agence Nationale de la Recherche (ANR Psicopak to E. Meunier), the Agence nationale de recherche sur le sida et les hépatites- Maladies infectieuses émergentes (to E. Meunier), the European Research Council (StG INFLAME 804249 to E. Meunier), the European Society of Clinical Microbiology and Infectious Diseases (to R. Planès), Invivogen-Conventions industrielles de formation par la recherche PhD grant (to M. Pinilla), Vaincre La Mucoviscidose, and Region Occitanie (Groupement de Recherche pour des Applications INnovantes avec les Entreprises) grants to C. Cougoule. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Author contribution: M. Pinilla: Conceptualization, Methodology, Investigation, Resources, Writing—original draft/review and editing, Visualization, Supervision; R. Mazars: Investigation, Methodology, Resources; R. Vergé: Investigation, Methodology, Resources; L. Gorse: Investigation, Methodology, Resources; M. Paradis: Investigation, Methodology, Resources; B. Suire: Investigation, Methodology, Resources; K. Santoni: Investigation, Methodology, Resources; K.S. Robinson: Methodology, Resources; G.A. Toh: Methodology, Resources; L. Prouvensier: Methodology, Resources; S.A. Leon-Icaza: Methodology, Resources; A. Hessel: Methodology, Resources; D. Pericat: Methodology, Resources; M. Murris: Methodology, Resources; H. Guet-Revillet: Methodology, Resources; A. Henras: Investigation, Methodology, Resources; J. Buyck: Methodology, Resources; E. Ravet: Methodology, Resources, Supervision; F.L. Zhong: Methodology, Resources, Supervision; C. Cougoule: Methodology, Formal analysis, Funding acquisition, Writing—original draft/review and editing, Visualization; R. Planès: Conceptualization, Methodology, Formal analysis, Funding acquisition, Writing—original draft/review and editing, Visualization, Supervision; and E. Meunier: Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Supervision, Writing—original draft/review and editing.