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Next generation sequencing and Respiratory Infections management: What needs are met , what needs are not ?

par Michel, Charlotte
Président du jury Langer, Ingrid
Promoteur Vandenberg, Olivier
Co-Promoteur Hallin, Marie
Publication Non publié, 2025-12-09

Thèse de doctorat

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Résumé :

High-throughput or next-generation sequencing (NGS) methods were developed 25 years ago and have gradually been implemented across all areas of life sciences. Clinical microbiology laboratories (CMLs) initially shared the excitement surrounding the promising innovations in this field. Indeed, these techniques theoretically can blindly detect, in a single test, the presence of any microorganism in a sample. They also allow for an easier study of a microbial genomes than previously possible. However, NGS applied to the diagnosis of infectious diseases has proven to be most complex and is still not routinely available. The objective of this work was to assess the usefulness of NGS in a CML by testing its application in various contexts of respiratory infection management. First, it was retrospectively tested in a fatal case of pneumonia in an immunocompromised patient. This event led us to conduct an opinion survey among clinicians involved in the treatment of infectious diseases about the possible integration of NGS into routine clinical practice. Respiratory infections were one of the most pressing concerns expressed by responding clinicians, which led us to explore the applicability and added value of NGS in three key areas: the clinical diagnosis of severe pneumonia, the prevention and control of nosocomial respiratory infections, and the epidemiological surveillance of genetic mechanisms involved in antimicrobial resistance among respiratory pathogens.Whole-genome sequencing enabled us to highlight interspecies recombination events that led to multidrug resistance in Haemophilus influenzae but failed to resolve a possible case of Legionella pneumophila transmission from a hospital environment to a patient. Metagenomics, on the other hand, allowed us to detect fungi and fastidious pathogens in immunocompromised patients with severe pneumonia, but did not demonstrate added value for bacterial pneumonia in immunocompetent patients.These various applications taught us, through experience, that implementing NGS in the routine activities of a CML remains difficult and that many pitfalls and obstacles are inevitably linked to this technology: sequencing errors and contamination, issues with data processing, translation and storage, but above all, challenges in establishing a clinically efficient workflow. As a fully turnkey solution is still far from being available, the application of NGS in clinical microbiology remains a process that requires careful consideration. Moreover, appropriate reporting and proper clinical interpretation of the results require a multidisciplinary approach involving bioinformaticians, microbiologists, and clinicians.