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Bronchopneumonies Infectieuses Des Jeunes Bovins: De La Complexité Du Microbiome Aux Particularités Évolutives Et Cliniques De Virus Respiratoires Encore Méconnus

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Bronchopneumonies Infectieuses Des Jeunes Bovins: De La Complexité Du Microbiome Aux Particularités Évolutives Et Cliniques De Virus Respiratoires Encore Méconnus En vue de l'obtention du DOCTORAT DE L'UNIVERSITÉ DE TOULOUSE Délivré par : Institut National Polytechnique de Toulouse (Toulouse INP) Discipline ou spécialité : Pathologie, Toxicologie, Génétique et Nutrition Présentée et soutenue par : M. ELIAS SALEM le mercredi 24 octobre 2018 Titre : Bronchopneumonies infectieuses des jeunes bovins: de la complexité du microbiome aux particularités évolutives et cliniques de virus respiratoires encore méconnus. Ecole doctorale : Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingénieries (SEVAB) Unité de recherche : Interactions Hôtes - Agents Pathogènes (IHAP) Directeur(s) de Thèse : M. GILLES MEYER MME MARIETTE DUCATEZ Rapporteurs : M. ETIENNE THIRY, UNIVERSITE DE LIEGE Mme CAROLINE LEROUX, INRA LYON Membre(s) du jury : Mme CAROLINE LEROUX, UNIVERSITE LYON 1, Président M. GILLES MEYER, ECOLE NATIONALE VETERINAIRE DE TOULOUSE, Membre Mme CECILE MALNOU, UNIVERSITE TOULOUSE 3, Membre Mme GAELLE SIMON, ANSES, Membre Mme MARIETTE DUCATEZ, ECOLE NATIONALE VETERINAIRE DE TOULOUSE, Membre TABLE DES MATIERES Table des matières .......................................................................................... i Liste des figures ............................................................................................. iv Liste des tableaux .......................................................................................... iv Liste des abréviations ..................................................................................... v ETUDE BIBLIOGRAPHIQUE ......................................................................... 1 I. importanceLes bronchopneumonies infectieuses chez les bovins : définition et 2 1. Définition .............................................................................................. 2 2. Importance des BPI ............................................................................. 4 II. Les agents pathogènes respiratoires bovins ....................................... 8 1. Fréquence des agents infectieux ......................................................... 8 2. Pouvoir pathogène des principales bactéries .................................... 13 3. Pouvoir pathogène des principaux virus ............................................ 17 4. Interactions entre agents pathogènes respiratoires ........................... 23 III. Identification de nouveaux agents pathogènes respiratoires ............. 29 1. Notions sur les maladies émergentes chez l’homme ......................... 29 2. Les nouvelles méthodes pour identifier de « nouveaux » agents pathogènes 33 IV. Les « nouveaux » virus respiratoires bovins : cas de l’influenzavirus de type D 38 1. Historique des infections à virus influenza A (IAV) chez les bovins ... 38 2. Découverte d’un nouveau virus influenza de type D chez les bovins 41 3. Propriétés générales des virus Influenza D ....................................... 42 4. Réservoir, spectre d’hôte et pouvoir pathogène ................................ 46 V. Environnement microbien et pathologie respiratoire .......................... 52 1. La notion de microbiote ..................................................................... 52 2. Le microbiote respiratoire de l’homme ............................................... 57 3. Interactions microbiome et agents pathogènes : le pathobiome ........ 64 4. Microbiome et pathobiome respiratoire bovin .................................... 66 DESCRIPTION DES TRAVAUX DE RECHERCHE ..................................... 77 Chapitre I : Identification des virus respiratoires bovins ............................... 78 I. Introduction et connaissances actuelles ............................................ 78 II. Détection des virus respiratoires par approche NGS chez des veaux affectés par la bronchopneumonie infectieuse ...................................................... 81 1. Matériel et Méthodes ......................................................................... 81 2. Résultats ............................................................................................ 86 III. Caractérisation génétique des coronavirus bovins : évolution et épidémiologie moléculaire ..................................................................................... 96 Article : « Global transmission, spatial segregation and recombination determine the long-term evolution and epidemiology of Bovine Coronaviruses » . 97 Chapitre 2 : Identification et caractérisation du bactériote respiratoire bovin ............................................................................................................................... 132 I. Introduction ...................................................................................... 132 II. Article : « Microbial ecology of the upper and lower respiratory tract in calves: interactions and dysbiosis during acute bronchopneumonia » ................ 136 Chapitre 3 : l’influenzavirus de type D : répartition géographique et pouvoir pathogène ............................................................................................................... 176 I. Introduction ...................................................................................... 176 II. Article : « Serologic evidence for influenza C and D virus among ruminants and Camelids, Africa, 1991-2015 » ..................................................... 178 III. Article : « Pathogenesis, host innate immune response and aerosol transmission of influenza D virus in cattle » ......................................................... 184 DISCUSSION GENERALE ET PERSPECTIVES ...................................... 229 BIBLIOGRAPHIE ....................................................................................... 243 ANNEXES .................................................................................................. 293 I. Résultats détaillés du virome respiratoire ........................................ 293 LISTE DES FIGURES Figure 1 : Arbre de décision sur l'émergence des maladies et agents pathogènes. .............................................................................................................. 32 Figure 2 : Représentation schématique d’un virus de type influenza D ....... 43 Figure 3 : Virus influenza D (C/OK) en microscopie électronique ................ 43 Figure 4 : Le génome du virus influenza D .................................................. 44 Figure 5 : Chronologie des études sur les communautés microbiennes ...... 58 Figure 6 : Evolution du nombre d’études sur le microbiome respiratoire ..... 59 Figure 7 : Résistance de colonisation .......................................................... 66 Figure 8 : Représentation du processus de préparation des échantillons pour le séquençage NGS métagénomique du virome respiratoire. .................................. 85 LISTE DES TABLEAUX Tableau 1 : Pouvoir pathogène des différents agents respiratoires bovins démontré lors d’infections expérimentales. ............................................................... 13 Tableau 2 : Abondances relatives trouvées dans les poumons et les nœuds lymphatiques (NL) .................................................................................................... 71 Tableau 3 : Résultats de détection des 7 agents pathogènes respiratoires dans les prélèvements respiratoires avec le LSI vetmax screening kit. .................... 88 Tableau 4 : Détection des principaux virus par NGS .................................. 89 Tableau 5 : Correspondance entre la détection par RT-qPCR et le séquençage NGS. .................................................................................................... 89 Tableau 6: Résultats détaillés du virome respiratoire ................................ 293 LISTE DES ABREVIATIONS ADN : acide désoxyribonucléique ADNc : acide désoxyribonucléique complémentaire ARN : acide ribonucléique ARNr : acide ribonucléique ribosomique ATT : aspiration trans-trachéale BAAV : bovine associated adenovirus BAD3 : bovine adenovirus type 3 BAT2 : bovine alveolar type 2 epithelial cells BAV : bovine astrovirus BRV : bovine rhinitis virus BCOV : bovine coronavirus BLAST : Basic Local Alignment Search Tool BOHV1: bovine herpesvirus type 1 BoNV : bovine nidovirus BPI : bronchopneumonie infectieuse BPI3 : bovine parainfluenza virus type 3 BPV : bovine parvovirus BRAV : bovine rhinitis virus type A BRBV : bovine rhinitis virus type B BRSV : bovine respiratory synctial virus BVDV : bovine viral diarrhea virus BWA : burrows-wheeler aligner CAR : Cilia-associated respiratory bacterium CFU : colony forming unit CMH : complexe majeur d’histocompatibilité cp : cytopathogène Cq : cycle de quantification ECP : effet cytopathique ENP : écouvillon nasal profond FISH : fluorescence in situ hybridization GAAS : genome relative abundance and average size Gb : gigabase H. s : Histphilus somni HCoV : human coronavirus HEF : hemagglutinine ésterase fusion HRT 18G : human rectal tumor IAV : influenza A virus IbpA : immunoglobulin binding protein type A IBR : infectious bovine rhinotracheatis IBV : influenza B virus ICV : influenza C virus IDV : influenza D virus IFHI1 : interferon induced with helicase C domain 1 IFNγ : interferon gamma IGV : integrative genomics viewer IHA : l’inhibition de l’hémagglutination IL-10 : interleukine 10 IL-12 : interleukine 12 IL-1β : interleukine 1 beta IL-4 : interleukine 4 ISG15 : Interferon-stimulated gene 15 LEfSe : Linear Discriminant Analysis using effect size LBA : lavage broncho-alvéolaire LDA : laboratoire départemental d’analyse LPS : lipopolysaccharide
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