Métagénomique du microbiote intestinal du poulet : outils, applications, perspectives

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Genome Sequences of Two Bovine Mastitis-Causing [i]Escherichia coli[/i] Strains

Escherichia coli is one of the main pathogenic agents causing inflammatory infections in the bovine udder. Here, we report the draft genome sequences of two strains isolated from different cases of clinical mastitis

Wahlund effects and sex-biased dispersal in Ixodes ricinus, the European vector of Lyme borreliosis : new tools for old data

Population genetics can help us better understand species microevolution and population biology, but inferences made from the genetic polymorphisms of field-collected organisms critically rely on sampling design. The population structure of the tick Ixodes ricinus L. (Acari, Ixodidae), a commonly encountered ectoparasite and the principal vector of human Lyme disease in Europe, has been the focus of some study, but many ecological aspects of this species remain poorly understood. Here, we apply a Bayesian clustering approach to observed and simulated data to examine within-population structure in I. ricinus, and to re-analyse patterns of sex-biased dispersal based on this substructure. We found between 18 and 27 distinct clusters within each of the 12 subsamples examined with a significant drop of heterozygote deficits. Parallel analyses on a comparable species, the seabird tick Ixodes uriae, indicated that these clusters can reflect important ecological features of the species (i.e., local host-associations). Analyses that considered the within-population clustering pattern of I. ricinus showed reversed patterns of sex-biased dispersal as compared to raw data (i.e., female-biased instead of male-biased dispersal). Simulated data supported the hypothesis that these scale-dependant patterns could be due to a combination of sex-specific dispersal and mortality. These different results raise new questions on the dispersal and host use strategies of I. ricinus and the potential importance of these ecological features for disease transmission. Furthermore, this work underlines the importance of taking into account patterns of genetic substructure when investigating sex-biased dispersal in natural populations

Training and education provided by Microbial Culture Collections in Europe (I): Panorama on tools, and contents produced and used within the MIRRI consortium

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Structure génétique et évolution de la spécialisation chez deux ectoparasites hématophages, les tiques Ixodes uriae et I. ricinus, vecteurs de la borréliose de Lyme

De nombreuses études ont été consacrées à expliquer la diversité du vivant. Chez les parasites, la spécialisation pour différents types d'hôtes peut être un processus clé dans l'émergence et le maintien de cette diversité. Les traits d'histoire de vie du parasite et de ses hôtes conditionnent la structuration de la variation génétique dans le temps et l'espace, et de là, la possibilité des divergences liées à l'hôte. Dans cette thèse, nous nous sommes intéressés à l'évolution de la spécialisation dans deux systèmes hôtes/parasites impliquant des vecteurs de la borréliose de Lyme: les tiques Ixodes uriae, qui exploite les oiseaux marins coloniaux des régions polaires, et Ixodes ricinus, que l'on rencontre sur un large spectre d'hôtes terrestres en Europe. Ces deux congénériques ont en commun de nombreux traits, mais diffèrent notablement dans les types d'hôtes qu'ils exploitent et leur stratégie de rencontre. D'après les éléments de la biologie de base de ces espèces, nous avons formulé plusieurs hypothèses sur la répartition de l'information génétique de ces parasites en populations naturelles, et plus particulièrement entre leurs hôtes à l'échelle locale. De larges échantillonnages ont été réalisés, et les tiques ont été caractérisées à l'aide marqueurs microsatellites et mitochondriaux. Ces données ont été analysées à l'aide de différents outils statistiques fréquemment utilisés en phylogéographie et en génétique des populations, incluant des méthodes récemment développées. Dans leur ensemble, les résultats ont permis d'établir un scénario d'évolution récente et récurrente de la spécialisation chez I. uriae, qui varie en fonction des traits des hôtes et leurs interaction locale avec la tique. Nos résultats suggèrent également l'existence chez I. ricinus de races spécialisées sur différents types d'hôtes (oiseaux, petit mammifères, etc.), et de mécanisme d'appariement assorti des partenaires sexuels au sein de ces races. Cette étude souligne l'importance des traits des parasites dans leur diversification (dispersion, stratégie de rencontre des hôtes et d'appariement). En particulier, la formation des races d'hôtes dans les populations de tiques va fortement affecter la circulation des pathogènes qu'ils transportent, et remet ainsi en cause nos connaissances actuelles sur l'épidémiologie des maladies à tiques comme la borréliose de LymeMany studies have been devoted to understanding the origin of life's vast diversity. In parasitic organisms, host specialization may be a key process in the emergence and maintenance of this diversity. Host and parasite life history traits can shape the spatial and temporal patterns of genetic variation, and thus, the possibility of host-associated divergence. In this thesis, we examine the evolution of host specialization in two host/parasite systems involving tick vectors of Lyme borreliosis: Ixodes uriae, a tick that exploits colonial seabirds in polar regions and, Ixodes ricinus, a tick with a large spectrum of terrestrial hosts in Europe. These congeneric species share many traits, but differ noticeably by the characteristics of the hosts they exploit and the strategies they use to encounter these hosts. Based on the basic biology of these ticks, we have formulated several hypotheses concerning the distribution of their genetic variation in natural populations and particularly among their local hosts. Ticks were sampled across a large spatial scale and were characterized using microsatellite and mitochondrial markers. We analyzed this data using different statistical tools frequently employed in phylogeography and population genetics, including some recently developed methods. Taken as a whole, our results support a scenario of recent and recurrent evolution of host races in I. uriae, where the local outcome of the interaction varies in space and among host species. Our results also suggest the existence of races specialized on different host types within I. ricinus populations (birds, rodents, lizards, etc), and a potential mechanism for assortative mating in these races. Overall, the work presented in this thesis highlights the importance of parasitic traits for the diversification process (dispersal, host encounter strategies, mate pair formation). More specifically, the frequent evolution of specific host races within tick populations will have importance consequences for the circulation of the pathogens they carry and, as such, calls into question our current understanding of the epidemiology of tick-borne diseases such as Lyme borreliosis.MONTPELLIER-BU Sciences (341722106) / SudocSudocFranceF

Data from: Tracing the colonization and diversification of the worldwide seabird ectoparasite Ixodes uriae

Historical patterns of dispersal and population isolation are key components shaping contemporary genetic diversity across landscapes and require explicit consideration when examining the relative role of different factors in driving the evolution of host specificity in parasitic organisms. In this study, we investigate the worldwide colonisation history of a common ectoparasite of seabirds, the tick Ixodes uriae. This tick has a circumpolar distribution across both hemispheres, but has repeatedly formed host-specific races within different regions. By combining mitochondrial and nuclear data, we infer how this species spread to its present-day distribution and how the colonisation process has affected the geographic and host-associated structure of this tick within regions. We demonstrate that I. uriae is highly structured and isolates into four genetic groups that correspond to well-defined geographical regions. Molecular dating suggests that the diversification of I. uriae began in the early Miocene (22 Myr) and that this tick colonised most of the Southern hemisphere before moving into northern latitudes via two independent routes. However, no relationship between the degree of host race divergence and colonisation history was evident, supporting previous hypotheses that host specialization evolves relatively rapidly in this parasite, but does not typically lead to speciation. We discuss the possible historical and contemporary mechanisms of large scale dispersal for this ectoparasite and how its biological characteristics may condition current patterns of genetic diversity. More generally, our results illustrate how combining broad-scale sampling and modern molecular tools can help disentangle complex patterns of diversification in widespread parasites

Tracing the colonization and diversification of the worldwide seabird ectoparasite[i] Ixodes uriae[/i]

Historical patterns of dispersal and population isolation are key components shaping contemporary genetic diversity across landscapes and require explicit consideration when examining the relative role of different factors in driving the evolution of host specificity in parasitic organisms. In this study, we investigate the worldwide colonization history of a common ectoparasite of seabirds, the tick Ixodes uriae. This tick has a circumpolar distribution across both hemispheres but has repeatedly formed host-specific races within different regions. By combining mitochondrial and nuclear data, we infer how this species spread to its present-day distribution and how the colonization process may have affected the geographic and host-associated structure of this tick within regions. We demonstrate that I. uriae is highly structured at a global scale and isolates into four genetic groups that correspond to well-defined geographical regions. Molecular dating suggests that the diversification of I. uriae began in the early Miocene (22 Myr) and that this tick colonized most of the southern hemisphere before moving into northern latitudes via two independent routes. However, no relationship between the degree of host race divergence and colonization history was evident, supporting previous hypotheses that host specialization evolves relatively rapidly in this parasite, but does not typically lead to speciation. We discuss the possible historical and contemporary mechanisms of large-scale dispersal for this ectoparasite and how its biological characteristics may condition current patterns of genetic diversity. More generally, our results illustrate how combining broad-scale sampling and modern molecular tools can help disentangle complex patterns of diversification in widespread parasites

Genome sequences of 17 Pasteurella multocida strains involved in cases of rabbit Pasteurellosis

International audienceThis article reports draft genome sequences of 17 Pasteurella multocida strains isolated from naturally infected rabbits. The total lengths of the assembled contigs ranged between 2.21 and 2.48 Mb, and the total number of genes detected on the contigs ranged between 2,088 and 2,416

Super Shedding in Enteric Pathogens: A Review

International audienceSuper shedding occurs when a small number of individuals from a given host population shed high levels of a pathogen. Beyond this general definition, various interpretations of the shedding patterns have been proposed to identify super shedders, leading to the description of the super shedding phenomenon in a wide range of pathogens, in particular enteric pathogens, which are of considerable interest. Several underlying mechanisms may explain this observation, including factors related to the environment, the gut microbiota, the pathogen itself (i.e., genetic polymorphism), and the host (including immune factors). Moreover, data suggest that the interplay of these parameters, in particular at the host-pathogen-gut microbiota interface, is of crucial importance for the determination of the super shedding phenotype in enteric pathogens. As a phenomenon playing an important role in the epidemics of enteric diseases, the evidence of super shedding has highlighted the need to develop various control strategies