Modélisation statistique des associations et des interactions entre des parasites transmis par des vecteurs, à partir de données issues d'études transversales

Multiparasitism and specifically statistical associations among parasites, have a strong influence on the ecology of parasites. This influence reinforced when parasites interact and thus modify their effect on hosts. However, the identification of associations and interactions between parasites is complex at the population level. Our aim was to model multi-parasite associations and interactions, in particular for parasites of medical, veterinary or agricultural importance. We first present a review of the literature on the different causes and consequences of multiparasitism and the methods and tools available to better understand the phenomena that generate them. In a second step we worked on the detection of multi-parasite associations. We developed a new approach « association screening » to statistically test the presence of multi-parasite associations on a global scale. We used this method to identify associations and to reveal precisely associated parasites in different host populations. Then, we focused on the study of interactions between parasites. We developed a model to identify the interactions between two vector-borne and persistent parasites in a host, using data from cross-sectional studies. One way to increase our capacity to detect parasite interactions in populations is the taking into account common risk factors. Taking into account interactions increases diagnosis, treatments and prevention of infectious diseases.Le multiparasitisme et surtout les associations qui en découlent, ont une grande influence sur l’écologie des parasites concernés. Elle est d’autant plus grande que les parasites peuvent interagir et ainsi modifier leurs effets sur les hôtes. Cependant, l’identification des associations et interactions de parasites est complexe au niveau populationnel. Notre objectif était de modéliser les associations et les interactions multiparasitaires, notamment dans le cadre des parasites d’importance médicale, vétérinaire ou agronomique. Nous avons tout d’abord réalisé une revue bibliographique sur les différentes causes et conséquences du multiparasitisme ainsi que sur les méthodes et outils disponibles pour comprendre les phénomènes qui le génèrent. Dans un second temps, nous nous sommes intéressés tout particulièrement à la détection des associations multiparasitaires. Nous avons développé une nouvelle méthode « de screening des associations » pour tester statistiquement la présence d’associations de parasites à une échelle globale. Nous avons utilisé cette méthode pour identifier les associations et pour révéler précisément les parasites associés au sein de diverses populations d’hôtes. Puis, nous avons étudié les interactions entre les parasites. Nous avons développé un modèle pour identifier les interactions entre deux parasites vectorisés et persistants chez un hôte, à partir de données issues d’études transversales. L’une des voies de progression de la connaissance sur les interactions est la prise en compte des facteurs de risque communs. La prise en compte des interactions contribue à améliorer le diagnostic, les traitements et la prévention des maladies infectieuses

Specific Read Only Data Management for Memory Hierarchy Optimization

International audienceThe multiplication of the number of cores inside embedded systems has raised the pressure on the memory hierarchy. The cost of coherence protocol and the scalability problem of the memory hierarchy is nowadays a major issue. In this paper, a specific data management for read-only data is in-vestigated because these data can be duplicated in several memories without being tracked. Based on analysis of stan-dard benchmarks for embedded systems, we show that read-only data represent 62% of all the data used by applications and 18% of all the memory accesses. A specific data path for read-only data is then evaluated by using simulations. On the first level of the memory hierarchy, removing read-only data of the L1 cache and placing them in another read-only cache improve the data locality of the read-write data by 30% and decrease the total energy consumption of the first level memory by 5%

Variation and correlations between sexual, asexual and natural enemy resistance life-history traits in a natural plant pathogen population

BackgroundUnderstanding the mechanisms by which diversity is maintained in pathogen populations is critical for epidemiological predictions. Life-history trade-offs have been proposed as a hypothesis for explaining long-term maintenance of variation in pathogen populations, yet the empirical evidence supporting trade-offs has remained mixed. This is in part due to the challenges of documenting successive pathogen life-history stages in many pathosystems. Moreover, little is understood of the role of natural enemies of pathogens on their life-history evolution.ResultsWe characterize life-history-trait variation and possible trade-offs in fungal pathogen Podosphaera plantaginis infecting the host plant Plantago lanceolata. We measured the timing of both asexual and sexual stages, as well as resistance to a hyperparasite of seven pathogen strains that vary in their prevalence in nature. We find significant variation among the strains in their life-history traits that constitute the infection cycle, but no evidence for trade-offs among pathogen development stages, apart from fast pathogen growth coninciding with fast hyperparasite growth. Also, the seemingly least fit pathogen strain was the most prevalent in the nature.ConclusionsWe conclude that in the nature environmental variation, and interactions with the antagonists of pathogens themselves may maintain variation in pathogen populations.Peer reviewe

Tick-borne pathogens of zoonotic and veterinary importance in Nigerian cattle

Additional file 1: Multiple infections by tick-borne pathogens according to age classes and overall number of animals. (PDF 19 kb)BACKGROUND : Ticks and tick-borne diseases undermine cattle fitness and productivity in the whole of sub-Saharan Africa, including Nigeria. In this West African country, cattle are challenged by numerous tick species, especially during the wet season. Consequently, several TBDs are known to be endemic in Nigerian cattle, including anaplasmosis, babesiosis, cowdriosis and theilerioris (by Theileria mutans and Theileria velifera). To date, all investigations on cattle TBDs in Nigeria have been based on cytological examinations and/or on serological methods. This study aimed to ascertain the occurrence of tick-borne pathogens of veterinary and zoonotic importance in cattle in Nigeria using molecular approaches. METHODS : In October 2008, 704 whole blood samples were collected from indigenous cattle in the Plateau State, Nigeria. Analysis for tick-borne pathogens was conducted by means of PCR-based reverse line blotting (RLB) and sequencing targeting a panel of five genera of microorganisms (i.e. Babesia, Theileria, Anaplasma, Ehrlichia and Rickettsia spp.). RESULTS : In total, 561/704 (82.6 %) animals were found infected, with 465 (69.6 %) of them being infected by two or more microorganisms, with up to 77 possible combinations of pathogens detected. Theileria mutans was the most prevalent microorganism (66.3 %), followed by Theileria velifera (52.4 %), Theileria taurotragi (39.5 %), Anaplasma marginale (39.1 %), Anaplasma sp. (Omatjenne) (34.7 %), Babesia bigemina (7.9 %), Anaplasma centrale (6.3 %), Anaplasma platys (3.9 %), Rickettsia massiliae (3.5 %), Babesia bovis (2.0 %) and Ehrlichia ruminantium (1.1 %). Calves were found significantly less infected than juvenile and adult cattle. CONCLUSIONS : This study provides updated, molecular-based information on cattle TBDs in Nigeria. The molecular approach employed allowed the diagnosis of numerous positive cases including carrier statuses, multiple infections and novel pathogen detections within the indigenous cattle population. Moreover, the RLB method here described enabled the detection of veterinary agents not only pertaining to bovine health, including also those of zoonotic importance. The high prevalence recorded for T. mutans, T. velifera, A. marginale, T. taurotragi and Anaplasma sp. (Omatjenne), suggests they may be endemically established in Nigeria, whereas the lower prevalence recorded for other microorganisms (i.e. A. centrale and B. bovis) highlights a less stable epidemiological scenario, requiring further investigations.The UK’s Biotechnology and Biological Sciences Research Council (BBSRC) under the ‘Combating Infectious Diseases in Livestock for International Development’ (CIDLID) scheme, and the European Union’s Seventh Framework Program (FP7/2007–2013) under grant agreement n° 221948, Integrated Control of Neglected Zoonoses (ICONZ).http://www.parasitesandvectors.comam2016Veterinary Tropical Disease

Tick-borne diseases and co-infection: Current considerations

Over recent years, a multitude of pathogens have been reported to be tick-borne. Given this, it is unsurprising that these might co-exist within the same tick, however our understanding of the interactions of these agents both within the tick and vertebrate host remains poorly defined. Despite the rich diversity of ticks, relatively few regularly feed on humans, 12 belonging to argasid and 20 ixodid species, and literature on co-infection is only available for a few of these species. The interplay of various pathogen combinations upon the vertebrate host and tick vector represents a current knowledge gap. The impact of co-infection in humans further extends into diagnostic challenges arising when multiple pathogens are encountered and we have little current data upon which to make therapeutic recommendations for those with multiple infections. Despite these short-comings, there is now increasing recognition of co-infections and current research efforts are providing valuable insights into dynamics of pathogen interactions whether they facilitate or antagonise each other. Much of this existing data is focussed upon simultaneous infection, however the consequences of sequential infection also need to be addressed. To this end, it is timely to review current understanding and highlight those areas still to address

Association of Fasciola gigantica co-infection with bovine tuberculosis infection and diagnosis in a naturally infected cattle population in Africa

Bovine tuberculosis (bTB), caused by Mycobacterium bovis, remains a major livestock and public health problem in both high and low-income countries. With the current absence of an effective vaccine, control in cattle populations is reliant on regular testing and removal of positive animals. However, surveillance and control are hampered by imperfect diagnostic tests that have poorly described properties in naturally infected populations. Recent research in cattle co-infected with the temperate liver fluke, Fasciola hepatica, has raised concerns about the performance of the intradermal skin test in high fluke incidence areas. Further, recent studies of parasitic co-infections have demonstrated their impact on Th1 and Th2 responses, concurrent disease pathology and susceptibility to mycobacterial infections. Here we report for the first time the association of co-infection with the tropical liver fluke, Fasciola gigantica, with the presence of bTB-like lesions and the IFN-γ response in naturally infected African cattle. After adjusting for age and sex we observed a complex interaction between fluke status and breed. Fulani cattle had a higher risk of having bTB-like lesions than the mixed breed group. The risk of bTB-like lesions increased in the mixed breed group if they had concurrent evidence of fluke pathology but was less clear in the coinfected Fulani breed. Further, we observed a slight decline in the IFN-γ levels in fluke infected animals. Finally we explored factors associated with IFN-γ false negative results compared to the presence of bTB-like lesions. Fulani cattle had a higher risk of having a false negative result compared to the mixed breed group. Further, the mixed breed cattle had an increased risk of being false negative if also co-infected with fluke. Interesting, as with the risk of bTB-like lesions, this association was less clear in the Fulani cattle with weak evidence of a slight decrease in risk of having a false negative test result when fluke pathology positive. This interesting interaction where different breeds appear to have different responses to co-infections is intriguing but further work is needed to confirm and understand more clearly the possible confounding effects of different other co-infections not measured here, breed, management or exposure risks

Co-infections and environmental conditions drive the distributions of blood parasites in wild birds

Experimental work increasingly suggests that non-random pathogen associations can affect the spread or severity of disease. Yet due to difficulties distinguishing and interpreting co-infections, evidence for the presence and directionality of pathogen co-occurrences in wildlife is rudimentary. We provide empirical evidence for pathogen co-occurrences by analysing infection matrices for avian malaria (Haemoproteus and Plasmodium spp.) and parasitic filarial nematodes (microfilariae) in wild birds (New Caledonian Zosterops spp.). Using visual and genus-specific molecular parasite screening, we identified high levels of co-infections that would have been missed using PCR alone. Avian malaria lineages were assigned to species level using morphological descriptions. We estimated parasite co-occurrence probabilities, while accounting for environmental predictors, in a hierarchical multivariate logistic regression. Co-infections occurred in 36% of infected birds. We identified both positively and negatively correlated parasite co-occurrence probabilities when accounting for host, habitat and island effects. Two of three pairwise avian malaria co-occurrences were strongly negative, despite each malaria parasite occurring across all islands and habitats. Birds with microfilariae had elevated heterophil to lymphocyte ratios and were all co-infected with avian malaria, consistent with evidence that host immune modulation by parasitic nematodes facilitates malaria co-infections. Importantly, co-occurrence patterns with microfilariae varied in direction among avian malaria species; two malaria parasites correlated positively but a third correlated negatively with microfilariae. We show that wildlife co-infections are frequent, possibly affecting infection rates through competition or facilitation. We argue that combining multiple diagnostic screening methods with multivariate logistic regression offers a platform to disentangle impacts of environmental factors and parasite co-occurrences on wildlife disease

Read Only Data Specific Management for an Energy Efficient Memory System

Les problématiques de consommation dans la hiérarchie mémoire sont très présentes dans les architectures actuelles que ce soit pour les systèmes embarqués limités par leurs batteries ou pour les supercalculateurs limités par leurs enveloppes thermiques. Introduire une information de classification dans le système mémoire permet une gestion hétérogène, adaptée à chaque type particulier de données. Nous nous sommes intéressé dans cette thèse plus précisément aux données en lecture seule et étudions les possibilités d’une gestion spécifique dans la hiérarchie mémoire à travers un codesign compilation/architecture. Cela permet d’ouvrir de nouveaux potentiels en terme de localité des données, passage à l’échelle des architectures ou design des mémoires. Evaluée par simulation sur une architecture multi-coeurs, la solution mise en oeuvre permet des gains significatifs en terme de réduction de la consommation d’énergie à performance constante.The energy consumption of the memory system in modern architectures is a major issue for embedded system limited by their battery or supercalculators limited by their Thermal Design Power. Using a classification information in the memory system allows a heterogeneous management of data, more specific to each kind of data. During this thesis, we focused on the specific management of read-only data into the memory system through a compilation/architecture codesign. It allows to explore new potentials in terms of data locality, scalability of the system or cache designs. Evaluated by simulation with multi-core architecture, the proposed solution others significant energy consumption reduction while keeping the performance stable

Gestion hétérogène des données dans les hiérarchies mémoires pour l’optimisation énergétique des architectures multi-coeurs

The energy consumption of the memory system in modern architectures is a major issue for embedded system limited by their battery or supercalculators limited by their Thermal Design Power. Using a classification information in the memory system allows a heterogeneous management of data, more specific to each kind of data. During this thesis, we focused on the specific management of read-only data into the memory system through a compilation/architecture codesign. It allows to explore new potentials in terms of data locality, scalability of the system or cache designs. Evaluated by simulation with multi-core architecture, the proposed solution others significant energy consumption reduction while keeping the performance stable.Les problématiques de consommation dans la hiérarchie mémoire sont très présentes dans les architectures actuelles que ce soit pour les systèmes embarqués limités par leurs batteries ou pour les supercalculateurs limités par leurs enveloppes thermiques. Introduire une information de classification dans le système mémoire permet une gestion hétérogène, adaptée à chaque type particulier de données. Nous nous sommes intéressé dans cette thèse plus précisément aux données en lecture seule et étudions les possibilités d’une gestion spécifique dans la hiérarchie mémoire à travers un codesign compilation/architecture. Cela permet d’ouvrir de nouveaux potentiels en terme de localité des données, passage à l’échelle des architectures ou design des mémoires. Evaluée par simulation sur une architecture multi-coeurs, la solution mise en oeuvre permet des gains significatifs en terme de réduction de la consommation d’énergie à performance constante