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Pediculus Humanus Corporis by Use of Melting Curve Analysis Genotyping

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Pediculus Humanus Corporis by Use of Melting Curve Analysis Genotyping AIX-MARSEILLE UNIVERSITE ÉCOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTÉ FACULTÉ DE MÉDECINE DE MARSEILLE Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR 63, CNRS 7278, IRD 198, Inserm 1095 Thèse présentée pour obtenir le grade universitaire de docteur Discipline : Pathologie Humaine Spécialité : Maladies Infectieuses Rezak DRALI Poux humains : Différenciation, distribution phylogéographique, Host-Switching et contrôle Soutenue le 15 Décembre 2014 devant le jury : Mr le Professeur Pierre MARTY Président du Jury/Rapporteur Mr le Docteur Arezki IZRI Rapporteur Mr le Professeur Philippe BROUQUI Directeur de thèse Mr le Professeur Didier RAOULT Co-directeur de thèse 1 À Tassadit, mon épouse. Merci pour ton soutien indéfectible À ma mère À mes enfants Taous, Mokrane et Ania. 3 Sommaire Avant-propos 7 Résumé 8 Abstract 11 Introduction générale 15 Revue: Taxonomy, lifestyle and current genetic advances of primate’s lice. 23 Chapitre 1: Différenciation pou de tête - pou de corps 59 Article I: Distinguishing Body Lice from Head Lice by Multiplex 63 Real-Time PCR Analysis of the Phum_PHUM540560 Gene. Article II: Bartonella quintana in body lice from scalp hair 75 of homeless persons, France. Article III: Detection of Bartonella quintana in African 81 Body and Head Lice. Chapitre 2: Distribution phylogéographique des poux 91 humains contemporains et anciens. Article IV: A New Clade of African Body and Head Lice Infected 95 by Bartonella quintana and Yersinia pestis – Democratic Republic of the Congo. Article V: Studies of ancient lice reveal unsuspected past 107 migrations of vectors. Article VI: Evidence of sympatry of Clade A and Clade B head lice 119 in a pre-Columbian Chilean mummy from Camarones. Chapitre 3: Host-Switching 127 Article VII: Host switching of human lice to New World monkeys in Amazonia 131 5 Chapitre 4: Détection et monitoring de la résistance moléculaire 161 des poux de corps à la perméthrine Article VIII: Detection of a knockdown resistance mutation 165 associated with permethrin resistance in the body louse Pediculus humanus corporis by use of melting curve analysis genotyping. Article IX: Effect of permethrin-impregnated underwear on 177 body lice in sheltered homeless persons: a randomized controlled trial. Conclusions et perspectives 189 Références 191 Annexes 201 Article X: Matrix-Assisted Laser Desorption Ionization– 203 Time of Flight Mass Spectrometry for Rapid Identification of Tick Vectors. Mini review: Typhus in World War I. 213 Remerciements 219 6 Avant-propos Le format de présentation de cette thèse correspond à une recommandation de la spécialité Maladies Infectieuses et Microbiologie, à l’intérieur du Master des Sciences de la Vie et de la Santé qui dépend de l’Ecole Doctorale des Sciences de la Vie de Marseille. Le candidat est amené à respecter des règles qui lui sont imposées et qui comportent un format de thèse utilisé dans le Nord de l’Europe et qui permet un meilleur rangement que les thèses traditionnelles. Par ailleurs, la partie introduction et bibliographie est remplacée par une revue envoyée dans un journal afin de permettre une évaluation extérieure de la qualité de la revue et de permettre à l’étudiant de commencer le plus tôt possible une bibliographie exhaustive sur le domaine de cette thèse. Par ailleurs, la thèse est présentée sur article publié, accepté ou soumis associé d’un bref commentaire donnant le sens général du travail. Cette forme de présentation a paru plus en adéquation avec les exigences de la compétition internationale et permet de se concentrer sur des travaux qui bénéficieront d’une diffusion internationale. Professeur Didier RAOULT 7 Résumé Les poux hématophages de primates sont des ectoparasites spécifiques de leurs hôtes avec qui ils ont Co évolué depuis environ 25 millions d’années. Ceux infestant l’Homme sont sans doute les mieux étudiés, particulièrement le pou de tête (Pediculus humanus capitis) et le pou de corps (Pediculus humanus humanus). Ce sont deux écotypes indiscernables occupant chacun une niche écologique: les cheveux pour le pou de tête et les vêtements pour le pou de corps. La pédiculose due au pou de tête touche chaque année des centaines de millions d'enfants à travers le monde nonobstant la classe sociale à laquelle ils appartiennent alors que le pou de corps infeste spécialement les populations n’ayant pas un accès facile aux conditions standard d’hygiène, telles les sans-abri, les prisonniers et les réfugiés de guerre. Le pou de corps représente une menace réelle pour l’Homme en raison de son rôle de vecteur dans la transmission de trois maladies graves ayant tué des millions de personnes à travers l’histoire de l’humanité à savoir : le typhus épidémique, la fièvre des tranchées et la fièvre récurrente causées par Rickettsia prowazekii, Bartonella quintana, et Borrelia recurrentis respectivement. Le pou 8 de corps est également soupçonné dans la transmission d'un quatrième agent pathogène fatidique, Yersinia pestis, l'agent de la peste. L'analyse de ADN mitochondrial a permis de classer les poux humains en trois clades A, B et C où seul le clade A distribué mondialement comprend à la fois des poux de tête et des poux de corps. Durant cette thèse, nous avons voulu apporter des réponses à un certain nombre de questions restées posées à travers le traitement de certaines thématiques qui nous semblaient importantes. Ainsi nous avons cherché à (i) trouver un moyen pour différencier entre le pou de tête et le pou de corps, (ii) en savoir d’avantage sur la distribution phylogéographique mondiale des poux humains, (iii) étudier les poux anciens pour nous aider à comprendre la circulation des vecteurs, la circulation des agents pathogènes transmis par ces vecteurs et les flux migratoires des hôtes de ces vecteurs, (iv) étudier le phénomène de Host-Switching à travers P. mjobergi le poux de singe du Nouveau Monde et (v) trouver un moyen efficace de contrôle des poux de corps infestant les sans-abri à Marseille à travers la détection et le monitoring de la résistance des poux aux insecticides. Nous avons obtenu des résultats concrets dans chacune des thématiques abordées, résultats par ailleurs valorisés par des 9 publications scientifiques. En effet, nous avons (i) mis en place un outil moléculaire qui permet de différencier pour la première fois entre le pou de tête et le pou de corps qui a montré efficacité sur le terrain, (ii) mis en évidence l’existence d’un nouveau clade mitochondrial (Clade D) renfermant des poux de tête et des poux de corps susceptible de vectoriser B. quintana et Y. pestis, (iii) retracé les migrations humaines à travers l'analyse de poux anciens provenant de différentes périodes et localisations, (iv) démontré pour la première fois que P. mjobergi est génétiquement proche du pou humain et confirmé l’hypothèse qu’à l’origine P. mjobergi était un pou humain qui a été transféré aux singes du Nouveau Monde par les premiers Hommes à avoir atteint le continent américain il y a des milliers d’années et (v) mis en place un outil de détection et de contrôle de la résistance moléculaire des poux à la perméthrine. Cet outil fut particulièrement utile dans l'étude clinique que nous avons menée pour déterminer si l'utilisation de sous-vêtements imprégnés d'insecticide offrait une protection efficace à long terme contre les poux de corps infestant les personnes sans-abri. Mots clés : pou de tête, pou de corps, différenciation, distribution phylogéographique, poux anciens, Host-Switching, contrôle des poux. 10 Abstract Primate sucking lice are obligate host-specific parasites that have Co evolved with their hosts for over 25 million years. Lice infesting humans are probably the best studied, particularly head louse (Pediculus humanus capitis) and body louse (Pediculus humanus humanus). These are two indistinguishable ecotypes each occupying an ecological niche: hair for head louse and clothing for the body louse. Pediculosis due to head louse affects each year hundreds of millions of children worldwide despite the social class to which they belong while body louse infests especially populations that have not ready access to standard conditions of hygiene, such as the homeless, prisoners and war refugees. Body louse represents a real threat to humans because of its role as vector for the transmission of three deleterious diseases that have killed millions of people, namely epidemic typhus, trench fever and relapsing fever caused by Rickettsia prowazekii, Bartonella quintana, and Borrelia recurrentis respectively. The body louse is also suspected in the transmission of a fourth fateful pathogen, Yersinia pestis, the agent of plague. Mitochondrial DNA allowed the classification of human lice in three 11 clades designed A, B and C where only clade A that is distributed worldwide comprises both head and body lice. During my PhD, some thematic that seemed important have been addressed. Thus we aimed to (i) find a way to differentiate between human head and body lice, (ii) learn more about the worldwide phylogeographic distribution of lice (iii) study of ancient human lice which can help to understand the circulation of vectors, the flow of vector-borne pathogens and the migratory flu hosts of these vectors, (iv) study the host-switching phenomenon through P. mjobergi the lice that parasite New World monkeys and (v) find an efficient way to control body lice infesting homeless people in Marseille. In each of these issues, we obtained concrete results that have led to scientific publications. Indeed, we (i) implemented a molecular tool to differentiate for the first time between head and body louse, (ii) we highlighted the existence of a fourth mitochondrial clade (Clade D) comprising head and body lice that can vectorize B. quintana and Y. pestis, (iii) we traced human migration through the analysis of ancient lice from different periods and different area, (iv) we demonstrated for the first time that P.
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