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International audience; The coffee berry borer (CBB) Hypothenemus hampei (Coleoptera: Scolytidae) is the most important insect pest affecting coffee production worldwide and generating huge economic losses. As most of its life cycle occurs inside the coffee berry, its control is extremely difficult. To tackle this issue, we solve an optimal control problem based on a berry age-structured dynamical model that describes the infestation dynamics of coffee berries by CBB during a cropping season. This problem consists in applying a bio-insecticide at discrete times in order to maximise the economic profit of healthy coffee berries while minimising the CBB population for the next cropping season. We derive analytically the first-order necessary optimality conditions of the control problem. Numerical simulations are provided to illustrate the effectiveness of the optimal control strategy.

PRRSv is responsible for significant worldwide production losses and its control is a major challenge for the swine industry. Vaccination, the main control measure, does not allow to eradicate the infection and only confers a partial protection to the host. This lack of efficiency is mainly due to the strong variability in PRRSv strain virulence, which induces highly variable within-host dynamics. Consequently, there is a real need to better understand the interactions between the virus and the immune response in order to improve PRRSv control. To tackle this issue, a dynamic and deterministic modelling approach was chosen. We developed an original immunological model consisting in an integrative representation of the within-host dynamics. It describes the immune mechanisms at the between-cell scale, including the innate response, the activation and orientation of the adaptive response and their complex regulations by the major cytokines. By the definition of parameter sets based on published experimental and modelling studies, this approach allowed us to explore various scenarios in terms of host susceptibility, strain virulence, as well as dose and duration of viral exposure. Our first results show that similar infection durations associated with contrasted immune dynamics can be explained by the consideration of the immune mechanisms affected by the strain virulence. They provide new insights to explain apparent inconsistencies between experimental data. We then showed that the exposure, whose effect is often neglected, has an impact on the within-host dynamics, which varies depending on the virulence level. Finally, the within-host dynamics induced by the infection of a vaccinated pig is currently under exploration, opening up promising leads to improve vaccine efficiency. All these results provide new insights to guide further experimental and modelling approaches and they offer promising prospects to improve PRRSv control at the herd level by an immuno-epidemiological modelling approach.

National audience

International audience; Porcine Respiratory and Reproductive Syndrome Virus (PRRSV) infection is a major concern for swine industry. Our partial understanding of the interactions between the virus and the immune system is the major reason for the lack of efficient control measures. The PRRS virus replicates mainly in the pulmonary macrophages which: (1) are responsible for inflammation and viral destruction by phagocytosis; and (2) participate in the induction and orientation of the adaptive immune response. Consequently, macrophage infection hampers the whole immune response. The interactions between macrophages and virus during the first steps of infection have not been thoroughly investigated and their influence on the infection resolution is unknown. Here, we propose an original model simulating immune and infection dynamics to explore these complex mechanisms and test biological hypotheses. We highly detail the immune functions and infectious statuses of macrophages and take into account interactions between innate and adaptive responses and cytokines regulations. We use the model to study the relative influence of macrophage – virus interactions on the infection resolution comparatively to adaptive mechanisms.

International audience

International audience

International audience; Classical scrapie is a transmissible spongiform encephalopathy that affects small ruminants. Due to potential health risks, it is submitted to eradication measures. It is characterised in sheep by a genetic factor based on the PrP major susceptibility gene. Therefore, control strategies partly rely on selective breeding. Scrapie transmission mechanisms are still incompletely understood. The long infectious and undetectable incubation period makes direct data analyses difficult, hence the interest of a modelling approach. Our aim was to study the impact of control strategies, based on selective breeding, on the disease spread within a flock. To achieve this goal, an epidemiological dynamic model was coupled to the optimal outputs of a genetic model, through the breeding function. \\ The realistic SI-based epidemiological model takes into account demographic and epidemiological processes, including seasonality in breeding and transmission, genetic and age-dependent susceptibilities, long and variable incubation periods, etc. The genetic deterministic dynamic model represents breeding programs including overlapping generations, different selection steps and strategies for males and females, and non-random mating. It maximises scrapie resistance, while simultaneously minimising the loss of genetic progress in milk production. The resulting model was applied to French dairy flocks exhibiting contrasting PrP genotype frequencies. The epidemiological model was calibrated using French outbreak data. The robustness of the results was tested by a sensitivity analysis. \\ Several breeding strategies, corresponding to various levels of genetic loss, were compared. They had a strong impact on the disease outbreak and are therefore an efficient tool to control scrapie. However, their efficacy in terms of disease eradication strongly depended on the scrapie introduction scenarios (e.g. one initial infected ewe vs. one per year). These results hence emphasise the contribution of our original approach, which combines genetic and epidemiological models in a realistic framework.}

La maîtrise du portage de Salmonella est une des préoccupations majeures de la filière porcine notamment depuis l’adoption de la directive européenne sur les zoonoses. L’objectif de cette étude est de simuler de manière exploratoire, la mise en œuvre de mesures de maîtrise sur le portage de salmonelles chez le porc charcutier au départ pour l’abattoir et d’évaluer l’effet de ces mesures à partir de plusieurs critères. Nous avons développé un modèle mathématique pour simuler à la fois, la dynamique des populations de truies et de porcs dans un élevage naisseur-engraisseur, la gestion de la conduite en bandes par l’éleveur et la propagation des salmonelles. Dans cette étude, le modèle épidémiologique est utilisé pour tester trois niveaux de réduction de la valeur de la probabilité d’infection traduisant l’application d’une mesure. Une mesure dont l’action sur les animaux est tem- poraire et une autre dont l’action est durable ont été testées sur différentes catégories d’animaux. Trois critères d’évaluation ont été utilisés afin de comparer l’effet de l’application de mesures. Pour ces trois critères, l’application de mesures dont l’action est durable entraîne une diminution plus élevée de la séroprévalence dans les lots de porcs charcutiers qu’une mesure dont l’ac- tion n’est que temporaire. L’effet de la mise en œuvre d’une mesure (quelle que soit la durée de son action) diffère si la mesure est appliquée sur les truies ou sur les porcs. Dans une perspective de maîtrise, la détermination d’un critère approprié dépend des objectifs à atteindre dans un contexte donné., Since the new European regulation dealing with zoonosis, control of Salmonella carriage is one of major public concern in pork food chain. The objective of this study was to simulate in an exploratory way, the implementation of control measures of Salmonella carriage in groups of slaughter pigs and to assess the effect of these measures from several criteria. We developed a stochastic mathematical model to represent the pig and sow populations within a farrow-to-finish herd, the herd management and the Salmonella spread. In this study, the epidemiological was used to test three reduction levels of the infection probability representing the control measure implementation. One measure with action on animals was long-lasting and one with a tem- porary action was tested on several animal populations. Three assessment criteria were used to compare the effect of control measure implementation. For the three criteria tested, the implementation of control measure with a long-lasting action led to a higher decrease of the seroprevalence in groups of slaughter pigs than a measure with a temporary action. The implementa- tion of a measure (whatever its action duration) differed if it was implemented on sows or on pigs. In a control perspective, the identification of an appropriate criterion depends on objectives to reach in terms of prevalence improvement.

International audience

International audience; Pork products contribute to human cases of salmonellosis. The Salmonella contamination level of pigs at slaughter age is a critical point in the contamination of the human food chain. The aim of this study was to estimate the number of shedder and carrier pigs at slaughter age under three biosecurity strategies. A stochastic mathematical model was hence developed to simulate the pig population dynamics and the pathogen tr ansmission within a farrow -to-finish herd in which the batch farrowing system was set. We considered, both, the biological variability and the producers’ management that can alter the contact structure and thus, the transmission of Salmonella. The proportion of pigs at slaughter age either carrying or shedding Salmonella was almost twice higher when batch mixing occurred. Our modelling approach allowed us to investigate the magnitude of the effects of biosecurity strategies

National audience

National audience

Après avoir brossé un tableau des connaissances actuelles sur les sources de contamination et les voies de transmission des Encéphalopathies Spongiformes Transmissibles (EST), l’article présente l’éventail des travaux réalisés à l’INRA sur la résistance de l’agent pathogène dans le milieu extérieur, les sources d’infection, les voies de transmission et la dynamique de la maladie dans les populations animales, en matière de tremblante et d’Encéphalopathie Spongiforme Bovine (ESB). Ces travaux sont menés en collaboration avec de nombreuses équipes nationales et internationales, à travers des projets scientifiques nationaux et européens. Trois approches complémentaires sont poursuivies. Des travaux expérimentaux portent sur la rémanence et la dispersion de la protéine prion dans le sol, ainsi que sur le rôle possible des nématodes parasites dans la contamination des animaux. Des études épidémiologiques de terrain sont conduites pour analyser les facteurs de transmission de la tremblante, relatifs aux rongeurs, acariens du foin, parasites, pratiques d’élevage au sens large et voisinage, et de l’ESB, focalisées sur le rôle de l’alimentation. Enfin, divers modèles mathématiques basés sur les données de terrain permettent de simuler le devenir à long terme des épidémies de tremblante et d’ESB selon différents scénarii, ou de tester certaines hypothèses biologiques quant aux sources de contamination. Les encadrés apportent des éclairages et des résultats sur plusieurs de ces études., After providing an up-to-date overview on our knowledge concerning the infection sources and the transmission routes of Transmissible Spongiform Encephalopathies (TSE), this paper presents a variety of studies carried out at INRA on the resistance of the agent, the infection sources, the transmission routes and the disease dynamic, both for scrapie and Bovine Spongiform Encephalopathy (BSE). These studies involve various national and international collaborations, within French and European projects. Three different approaches were followed. Experimental studies were done on the persistence and dispersion of the prion protein in the soil, as well as on the effect of nematode worms as a possible way of transmission between animals. Epidemiological studies were carried out on the transmission routes of scrapie, concerning rodents, hay mites, worms, husbandry aspects, and the transmission of BSE, focused on feeding. Finally, different mathematical models based on field data simulate the long-term dynamics of scrapie and BSE depending on various scenarios, and allow testing some hypotheses on infection sources. The insets provide more details on these studies.

The aim of this thesis is to propose, on the one hand, a framework for mathematical analysis and simulation of the burrowing nematode Radopholus similis dynamic interaction with banana or plantain roots, and the other hand to identify the best control mean in order to optimize the economical yield of banana and plantain crops.In the first step, we study the infestation dynamics of banana or plantain plants by R. similis. Two control strategies are analyzed: pesticides, which are widely used, and fallow deployment, which is more environmentally friendly. To represent the host-parasite dynamics, two semi-discrete models are proposed. In these models, during each cropping season, free nematodes enter the plant roots, on which they feed and reproduce. At the end of the cropping season, fruits are harvested. In the firstmodel, the parent plant is cut down to be replaced by one of its suckers and pesticides are applied. In the second model, the parent plant is uprooted and a fallow period is introduced, inducing the decay of the free pest populations; at the beginning of the next cropping season, a pest-free vitro-plant is planted. For both models, we find a condition of global stability of the pest-free equilibrium. Then, the effective reproduction number of the pest is computed, assuming that the infestation dynamics is fast compared to the other processes, which leads to the model order reduction. Conditions on the pesticide load or the fallow duration are then derived to ensure the stability of the pest-free equilibrium. Finally, numerical simulations illustrated these theoretical results.In a second step, we propose an eco-friendly optimization of banana or plantain yield by the control of the burrowing nematode. This control relies on fallow deployment. The optimization is based on the multi-seasonal model in which fallow periods follow cropping seasons. The aim is to find the best way, in terms of profit, to allocate the durations of fallow periods between the cropping seasons, over a fixed time horizon spanning several seasons. The existence of an optimal allocation is proven and an adaptive random search algorithm is proposed to solve the optimization problem. For a relatively long time horizon, deploying one season less than the maximum possible number of cropping seasons allows us to increase the fallow period durations and result in a better multi-seasonal profit. For regular fallow durations, the profit is lower than the optimal solution, but the final soil infestation is also lower.In the last step, we propose a strategy of mixed control where cropping seasons can succeed each other by vegetative growth of the plant or by planting a healthy vitro-plant, after eventually a fallow. We derive an optimization problem in order to know when to implement one or the other reproductive strategy and to know how long to make the fallow period last in case of fallow deployment. We obtain initial results and present perspectives., Le but de cette thèse est de proposer d’une part un cadre d’analyse mathématique de l’interaction dynamique du nématodes endoparasite Radopholus similis avec les racines de bananier ou de plantain. D’autre part, nous avons pour objectif d’identifier le meilleur moyen d’optimiser le rendement des cultures de bananiers et plantains via le contrôle du nématode.Dans un premier temps, nous étudions la dynamique d’infestation des bananiers/plantains par R. similis. Deux stratégies de lutte sont ainsi analysées : la lutte chimique, qui est encore largement utilisées, et le déploiement de jachère, qui est plus écologique. Pour représenter la dynamique hôte-parasite, nous proposons deux modèles semi-discrets. Dans ces modèles, au cours de chaque saison de culture, les nématodes libres pénètrent dans les racines des plantes dont ils se nourrissent et se reproduisent. À la fin de la saison de culture, le régime de fruit est récolté. Dans le premier modèle, la plante mère est coupée pour être remplacée par l’un de ses rejets et des pesticides sont appliqués. Dans le deuxième modèle, la plante mère est déracinée et une période de jachère est introduite, induisant la décroissance de la population de nématodes libres dans le sol. Au début de la saison de culture suivante, un rejet sain est planté. Pour les deux modèles, nous trouvons une condition de stabilité globale de l’équilibre sans ravageur. Ensuite, nous calculons le taux de reproduction effectif du ravageur en supposant que la dynamique d’infestation est rapide par rapport aux autres processus, ce qui conduit à la réduction des modèles. Nous trouvons ensuite des conditions sur la charge de pesticides ou la durée de la jachère qui entrainent la stabilité locale de l’équilibre sans ravageurs. Des simulations numériques illustrent ces résultats théoriques.Dans un deuxième temps, nous proposons une optimisation écologique du rendement de banane/plantain en contrôlant le nématode via le déploiement en jachère. L’optimisation est basée sur le modèle multi-saisonnier avec jachère précédent. L’objectif est de trouver la meilleure distribution des durées de jachère entre les saisons de culture, sur un horizon temporel fixe s’étalant sur plusieurs saisons. Nous prouvons l’existence d’une distribution optimale et proposons un algorithme de recherche aléatoire adaptative pour résoudre le problème d’optimisation. Pour un horizon de temps relativement long, le déploiement d’une saison de moins que le nombre maximum de saisons de culture pouvant être déployé nous permet d’augmenter les durées de jachère et de générer ainsi un meilleur rendement multi-saisonnier. Nous obtenons, après des régularations des durées de jachère, un rendement inférieur à la solution optimale non régulée, mais l’infestation finale est meilleure dans ces cas.Pour finir, nous proposons une stratégie de lutte mixte où les saisons de culture peuvent se succéder par croissance végétative de la plante ou en plantant un rejet sain, après éventuellement une jachère. Nous obtenons ainsi un problème d’optimisation dont le but est de savoir quand mettre en œuvre l’une ou l’autre des deux stratégies de reproduction, et de savoir combien de temps durera la période de jachère en cas de déploiement vide jachère. Nous obtenons les premiers résultats et présentons les perspectives.