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Streptococcus Pneumoniae Interactions phage-hôte chez Streptococcus pneumoniae Thèse SIHAM OUENNANE Doctorat en microbiologie Philosophiae doctor (Ph. D.) Québec, Canada ©Siham Ouennane, 2017 Interactions phage-hôte chez Streptococcus pneumoniae Thèse SIHAM OUENNANE Sous la direction de : Sylvain Moineau, directeur de recherche ii RÉSUMÉ Streptococcus pneumoniae est une bactérie à la fois commensale et pathogène opportuniste chez l’humain. Elle est responsable de nombreuses infections telles que la pneumonie, la méningite, l’otite moyenne et la sinusite. En maladie infectieuse, S. pneumoniae occupe une place importante en tant que l’une des principales causes de morbidité et de mortalité dans le monde. Elle est dotée de plusieurs capacités fascinantes, comme la compétence naturelle pour l’aider à résister aux antibiotiques et la grande diversité des sérotypes capsulaires pour contourner la vaccination. Puisque la résistance aux antibiotiques ne cesse de menacer l’efficacité des thérapies standards, la thérapie par phage est maintenant reconsidérée comme une des alternatives thérapeutiques. La réévaluation des phages fait renaitre l’espoir thérapeutique, mais sans élucider leur mécanisme d’interaction et décortiquer leur mystère cet espoir restera modeste. Ce projet de doctorat consiste à mieux comprendre les phages infectant S. pneumoniae et les interactions phage-hôte. Dans un premier temps, le potentiel des pneumophages à infecter Streptococcus mitis, une espèce phylogénétiquement proche de S. pneumoniae, a été mis en évidence. Deux pneumophages se sont avérés les premiers phages virulents capables d’infecter S. mitis, bactérie pathogène responsable d’endocardite. Les deux phages pouvaient non seulement se répliquer dans S. mitis mais également produisent des plages de lyses plus visibles. Ensuite, la comparaison du génome des phages a confirmé que le changement de l’hôte n’induit aucune variation aux génomes des phages testés. Cependant, plusieurs mutations ont été observées dans la séquence génomique du podophage sauvage et il a fait ensuite l’objet d’une nouvelle annotation. Dans un deuxième temps, l’étude des interactions phage-hôte chez S. pneumoniae a été approfondie. Pour ce faire, l’implication de plusieurs facteurs de l’hôte dans la réplication des pneumophages a été étudiée. Plusieurs gènes pneumococciques se sont avérés nécessaires ou impliqués pour assurer l'efficacité de la réplication des phages seuls ou en cocktail. D’un autre côté, en étudiant ces facteurs de l’hôte, des gènes/ protéines potentiellement essentiels à la viabilité de S. pneumoniae ont été identifiés. iii Cette étude a aussi permis d’identifier de nouvelles cibles thérapeutiques et donne un nouvel aperçu du réseau complexe des interactions phage-hôte. iv ABSTRACT Streptococcus pneumoniae is a commensal and opportunistic pathogen bacterium, exclusively found in humans. It is the main agent of many infections such as pneumonia, meningitis, otitis media and sinusitis. S. pneumoniae infections are a major cause of morbidity and mortality worldwide. S. pneumoniae has several fascinating abilities, such as natural competence to facilitate the acquisition of antibiotic resistance genes and diversity of capsular serotypes to circumvent the vaccination. The rise of antibiotic resistant bacteria continues to threaten the effectiveness of standard therapies and as such phage therapy is now reconsidered as a therapeutic alternative. The reevaluation of phages as therapeutic agents must go through a better understanding of phage-bacterium interactions. This PhD thesis aims to better understand S. pneumoniae virulent phages and phage- host interactions. First, the ability of pneumophages to infect Streptococcus mitis, a species phylogenetically related to S. pneumoniae, was demonstrated. The pneumophages are the first two virulent phages able to infect this pathogenic bacterium, the common cause of bacterial endocarditis. Both pneumophages could not only replicate in S. mitis but also produced more visible plaques on this host. The comparison of the genomes of each phage grown on both hosts produced identical nucleotide sequences, confirming that S. mitis as a host does not induce any nucleotide variation. However, the genomic sequence of wild-type podophage was different than the previously reported sequence and it was the subject of a new annotation. In addition, S. pneumoniae phage-host interactions were investigated. The involvement of several host factors in replication of both pneumophages was observed. Indeed, several pneumococcal genes were found to be necessary or involved to ensure efficient phage replication. Moreover, the study of these host factors has led to the identification of new genes that appear to be essential for viability and normal growth of S. pneumoniae. This project led to identify new potential therapeutic targets and provided new insight into the complex network of phage-host interactions. v vi Table des matières RÉSUMÉ ..................................................................................................................................... iii ABSTRACT ................................................................................................................................. v Table des matières ...................................................................................................................... vii Liste des tableaux ........................................................................................................................ xi Liste des figures .......................................................................................................................... xii Liste des abréviations ................................................................................................................ xiii Remerciements ........................................................................................................................... xv Chapitre I. Introduction ................................................................................................................ 1 Avant-propos ................................................................................................................................ 1 Streptococcus pneumoniae ........................................................................................................... 1 Présentation .............................................................................................................................. 1 Mécanisme de la transformation naturelle ............................................................................ 3 Croissance et division cellulaire ........................................................................................... 6 Physiopathologie des infections à S. pneumoniae .................................................................. 12 Données épidémiologiques ................................................................................................. 12 Mécanismes de la colonisation de l’hôte ............................................................................ 14 Processus d’infection et infections associées ...................................................................... 18 Facteurs de virulence .............................................................................................................. 19 Capsule polysaccharidique ................................................................................................. 20 Pneumolysine ...................................................................................................................... 22 Protéines de surface ............................................................................................................ 22 Traitements antipneumococciques ......................................................................................... 25 Traitements préventifs ........................................................................................................ 25 Traitement et résistance aux antibiotiques .......................................................................... 27 Bactériophages ........................................................................................................................... 30 Rappel historique .................................................................................................................... 30 Classification des bactériophages ........................................................................................... 32 Réplication des bactériophages .............................................................................................. 34 Phages infectant Streptococcus pneumoniae .......................................................................... 36 Problématique, hypothèses et objectifs du projet ....................................................................... 41 vii Chapitre 2. Diverse virulent pneumophages infect Streptococcus mitis .................................... 43 Résumé ................................................................................................................................... 43 Avant-propos .......................................................................................................................... 43 Contributions des auteurs.................................................................................................... 43 Publication .........................................................................................................................
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