Thèse Développement d'Un Modèle In Vitro Imitant l'Environnement Pulmonaire pour Étudier les Interactions Bactériennes Afin de Mieux Prédire la Pneumopathie Acquise Sous Ventilation Mécanique H/F

Doctorat.Gouv.Fr

Établissement : Université de Limoges
École doctorale : Biologie, Chimie, Santé
Laboratoire de recherche : Anti-Infectieux : supports moléculaires des résistances et innovations thérapeutiques
Direction de la thèse : Olivier BARRAUD ORCID 0000000320159206
Début de la thèse : 2026-10-01
Date limite de candidature : 2026-05-18T23:59:59

La pneumonie acquise sous ventilation mécanique (PAVM) demeure l'infection nosocomiale la plus fréquente et la première cause de prescription d'antibiotiques en réanimation. La colonisation des voies respiratoires est un facteur de risque reconnu, mais elle n'est pas systématiquement associée à la survenue d'une PAVM. Staphylococcus aureus est un pathogène majeur, responsable de près d'un quart des cas de PAVM en Europe occidentale. Cependant, de nombreux patients colonisés par S. aureus ne développent jamais de PAVM, ce qui suggère un rôle protecteur potentiel du microbiote respiratoire.
L'objectif principal de cette thèse est de démontrer l'effet protecteur ou délétère de certains taxons du microbiote respiratoire sur le développement précoce de la PAVM à S. aureus et de développer un outil de PCR quantitative ciblant ces bactéries afin de mieux identifier les patients à haut et à faible risque de développer une PAVM.

Ventilator-associated pneumonia (VAP) remains the most common healthcare-associated infection and the first cause of antibiotic prescription in intensive care units (ICU) [1]. It affects 10 to 25% of patients who require mechanical ventilation (MV) for more than 48 hours [2]. Colonization of the respiratory tract is a recognized risk factor [3], but it is not systematically associated with the onset of VAP. Staphylococcus aureus is a major pathogen, accounting for nearly a quarter of VAP cases in Western Europe [4]. However, many patients colonized with S. aureus never develop VAP, suggesting a potential protective role of the respiratory microbiota.
Several studies exploring respiratory microbiota have detected a decreased proportion in some taxa (such as Corynebacterium, Rothia or Bifidobacterium) during MV [5]. These taxa appear to play a protective role in other lung diseases against the adhesion of pathogens to lung cells [6] and towards inflammation [7], however their role in VAP has not yet been explored. In addition, in cohorts of MV patients who did not receive antibiotics and who developed early S. aureus VAP, our unit showed an increase in the proportion of certain anaerobic bacteria (mainly Prevotella) a few days before VAP onset [8]. Several hypotheses point to an important role for these anaerobic bacteria in the metabolism of respiratory mucus. Anaerobic bacteria of the phylum Bacteroidetes (which includes Prevotella) possess an enzymatic arsenal that enables them to break down mucus, which is the sole source of nutrients for bacteria in the respiratory tract [9].

The overall objective of the thesis is to show a protective or deleterious effect of some taxa of the respiratory tract microbiota on the development of early S. aureus VAP and to develop a quantitative PCR-based tool targeting those bacteria to better identify patients at high and low risk of VAP development.

The first part of the thesis will aim to develop a coculture model to evaluate the role of specific species of the respiratory microbiota on S. aureus growth. Ex vivo coculture in liquid sputum medium and in a lung-on-chip model will be developed. Using this organoid model, analyses of the lung microbiota evolution and metabolic pathways that either facilitate or block S. aureus growth (having therefore a deleterious or protective effect on the development of VAP) will also be investigated through the complementary assessment of bacterial transcriptomic, human mucus and metabolite composition over time.
Ultimately, specific PCR targeting the bacteria of interest will be developed using digital droplet PCR (ddPCR). We will evaluate the diagnostic performance of the ddPCR in a collection of endotracheal aspirates of MV patients and determine its sensitivity/specificity to detect patients at high and low risk of VAP.