HAL ENVT (Ecole Nationale Vétérinaire de Toulouse)
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Optimisation des stratégies de prévention, de surveillance et de lutte de l'influenza aviaire hautement pathogène : apports de la modélisation de la transmission virale
No full textHighly pathogenic avian influenza (HPAI) is a viral disease primarily circulating among birds. Since 2015, France has been one of the most affected countries in Europe. During the 2021–¬2022 crisis, the country recorded up to 1,400 outbreaks in poultry farms, leading to the culling of 19 million birds and losses exceeding one billion euros. The current situation is unprecedented, with a trend towards endemic circulation in European wild bird populations and an increased zoonotic potential. This highlights the urgent need to rethink management strategies to make them more effective and better adapted. In this context, we developed models of viral transmission within poultry farms, with two complementary objectives: to reduce the number and prevalence of outbreaks, and to optimize epidemiological investigations carried out in the event of suspected or confirmed outbreaks. To do this, we first conducted a systematic review of the literature on virus transmission between poultry compartments. Of the four experimental studies using HPAI viruses included in the review, transmission between compartments was reduced by 83% to 100%, on average. Compartmentalization could therefore slow viral spread and limit increases in prevalence. Next, we assessed the impact of preventive vaccination, authorized in Europe since February 2023 and implemented in France since October 2023. The model predicted a tenfold increase in viral extinction in vaccinated duck flocks. In scenarios of viral spread with more than five initially infected ducks, a median of 0.3% of ducks became infectious within 14 days, compared with 99% in unvaccinated flocks. We also compared the effectiveness of different surveillance strategies in vaccinated duck flocks. Enhanced passive surveillance proved to be the most effective: sampling five dead ducks every week detected 85% of simulated outbreaks with a median delay of 9 days after virus introduction. Finally, we showed that the viral loads from a cross-sectional sample of 30 live chickens could be used to estimate the time window of virus introduction in an infected flock. This could guide the timeframe for conducting epidemiological investigations. Overall, this work contributes to strengthening the resilience of the poultry sector, by improving or proposing new tools for prevention, surveillance and control. The models developed could be adapted to support the optimization of HPAI management strategies in other countries.L'influenza aviaire hautement pathogène (IAHP) est une maladie virale qui circule principalement chez les oiseaux. Depuis 2015, la France est l'un des pays européens les plus touchés. Lors de la crise de 2021-2022, le pays a comptabilisé jusqu'à 1 400 foyers en élevages soit 19 millions de volailles abattues et plus d'un milliard d'euros de dépenses. La situation actuelle est inédite, avec une tendance à l'endémisation dans l'avifaune sauvage européenne et une hausse du potentiel zoonotique. Il est urgent de repenser les stratégies de gestion afin qu'elles soient plus efficaces et plus adaptées. Dans ce contexte, nous avons développé des modèles de transmission du virus en élevage, avec deux objectifs complémentaires : réduire le nombre de foyers et leur prévalence, et optimiser les enquêtes épidémiologiques menées en cas de suspicion ou de confirmation de foyer. Pour cela, nous avons tout d'abord mené une revue systématique de la littérature sur la transmission du virus entre des compartiments de volailles. Sur les quatre études expérimentales avec des virus IAHP incluses dans la revue, la transmission entre compartiments était en moyenne réduite de 83 % à 100 %. Ainsi, compartimenter un bâtiment pourrait freiner la transmission virale et ainsi limiter l'augmentation de la prévalence. Ensuite, nous avons estimé l'impact de la vaccination préventive, autorisée en Europe depuis février 2023 et utilisée en France depuis octobre 2023. Le modèle prédisait dix fois plus d'extinction virale dans un élevage de canards vaccinés, et, en cas de propagation avec plus de cinq canards infectés , une médiane de 0,3 % de canards devenaient infectieux dans les 14 jours, contre 99 % sans vaccination. L'efficacité de différentes stratégies de surveillance a également été comparée dans des lots de canards vaccinés. La surveillance évènementielle renforcée s'est révélée être la plus efficace : prélever cinq canards morts toutes les semaines détectait 85 % des foyers simulés avec un délai médian de 9 jours après l'introduction du virus. Enfin, nous avons montré que les charges virales d'un échantillon aléatoire de 30 poulets vivants permettaient d'estimer une fenêtre d'introduction du virus dans un élevage infecté. Ceci pourrait être utilisé pour cibler la fenêtre temporelle sur laquelle mener les enquêtes épidémiologiques. Ces travaux contribuent à renforcer la résilience de la filière avicole en améliorant ou en proposant de nouvelles mesures de prévention, de surveillance et de lutte. Les modèles développés pourraient être adaptés à d'autres pays pour les aider à optimiser leurs stratégies de gestion
Mise en place d’une grille d’évaluation scientifique du bien-être animal chez les lamantins (Trichechus manatus manatus) en parcs zoologiques
No full textAnimal welfare in zoos is a subject of debate, caught between ethical requirements and conservation missions. To address this issue, the French Association of Zoos (AFdPZ) has developed an animal welfare assessment grid (BEA) based on the Five Domains model, with the aim of adapting it to each species in the future. This is the case for the manatee (Trichechus manatus manatus), a vulnerable aquatic mammal that is rarely found in captivity. A specific grid was designed with experts, based on scientific data, and then tested on 14 individuals at the Beauval ZooParc, a leading institution in animal welfare and conservation. In addition, two behavioral indicators, anticipation and willingness to participate (WtP), were evaluated to refine the analysis. The study made it possible to assess the feasibility of the protocol in the field, to propose an initial interpretation of the parameters obtained, and to make adjustments to enhance the sensitivity of the tool.Le bien-être animal en parc zoologique fait débat, entre exigences éthiques et missions de conservation. Pour y répondre, l’Association Française des Parcs Zoologiques (AFdPZ) a élaboré une grille d’évaluation du bien-être animal (BEA) basée sur le modèle des Cinq Domaines, avec pour objectif une adaptation future à chaque espèce. C’est le cas du lamantin (Trichechus manatus manatus), mammifère aquatique vulnérable et peu représenté en captivité. Une grille spécifique a été conçue avec des experts, à partir de données scientifiques, puis testée sur 14 individus du ZooParc de Beauval, établissement de référence en bien-être et conservation. En complément, deux indicateurs comportementaux, l’anticipation et la volonté de participer (WtP), ont été évalués pour affiner l’analyse. L’étude a permis d’évaluer la faisabilité du protocole sur le terrain, de proposer une première interprétation des paramètres obtenus, et des ajustements pour renforcer la sensibilité de l’outil
Avis de l'Anses relatif à « la réévaluation des mesures de gestion IAHP au regard de la stratégie de vaccination actuelle »
No full textAu cours de la dernière décennie, l’Europe a connu plusieurs épizooties majeures d’Influenza aviaire hautement pathogène (IAHP) dont l’épizootie de 2021-2022, d’une ampleur sans précédent en France, avec plus de 1 300 foyers détectés dans les élevages de volailles domestiques. Durant la saison 2023-2024 (du 1er août 2023 au 31 juillet 2024), une moindre circulation de virus de l’IAHP a été observée dans la faune sauvage, chez les oiseaux captifs et les volailles domestiques. En France, un faible nombre de foyers d’IAHP chez des volailles domestiques a ainsi été constaté entre le démarrage de la campagne de vaccination IAHP le 1er octobre 2023 et le mois de juin 2024. Il convient désormais d’évaluer les causes possibles de cette situation.Par ailleurs, la vaccination IAHP a donné un nouvel espoir à la filière volaille, qui avait subi les conséquences néfastes d’une circulation virale exceptionnelle ces dernières saisons. Si la biosécurité est entendue par tous comme étant la pierre angulaire de la prévention de la maladie, les mesures de mise à l’abri restent contraignantes, notamment dans un contexte où le niveau de risque a été abaissé tardivement les saisons passées. En effet, si pour la saison actuelle le contexte épidémiologique favorable a permis d’abaisser le niveau de risque à « négligeable » le 3 mai 2024, celui-ci n’a été atteint qu’au 7 juillet en 2023 et au 3 juin en 2022. Ceci a des conséquences sur le bien-être des animaux liées à l’allongement de la durée du jour, l’augmentation de l’intensité lumineuse et la hausse des températures.Un retour d’expérience sur les six premiers mois de la vaccination IAHP a été réalisé par l’unité EPISABE (Épidémiologie, santé et bien-être) de l’Anses avec l’appui de la DGAL. Ce retour est essentiel pour éclairer les décisions concernant d'éventuels ajustements et l'évolution de la prochaine campagne de vaccination, et les allègements nécessaires pour répondre aux demandes des professionnels. Les résultats complets de ce retour d’expérience ont été mis à disposition des experts du GT dans le cadre de la présente saisine, fin juillet 2024.Dans ce contexte, deux questions sont posées à l’Anses :1. « Quels sont les facteurs ayant contribué à l’amélioration de la situation épizootique vis-à-vis du virus de l’IAHP sur le territoire métropolitain dans un contexte de vaccination contre cette maladie ? Pour répondre à cette question vous pouvez vous appuyer sur le bilan épidémiologique de l’unité EPISABE de l’Anses attendu en juin 2024.2. Réévaluer les mesures de mise à l’abri au regard de la mise en œuvre d’une vaccination IAHP préventive des canards. Cette réévaluation porte sur les mesures appliquées aux canards, ainsi qu’aux autres volailles détenues. » [Saisines liées n°2022-SA-0157 et 2022-SA-0165
Genetic and heat-stress related environmental influences on pig whole-blood gene expression levels
No full textInternational audienceHeat stress causes animal welfare and production issues in pig production systems. Tropical pig breeds, such as the Creole breed (a local breed from the Caribbean) are more adapted to heat stress than cosmopolitan pig breeds selected for production and reproduction traits. Large-white x Creole backcross animals were produced both in a tropical (in Guadeloupe) or a temperate facility (in continental France). Pigs from the temperate facility were also subjected to an experimental heat stress. Here, we focus on the environmental and genetic influences onwhole blood transcriptome of these backcross pigs (n = 359). We identified 2,014 differentially expressed genes (DEGs) between pigs from the tropical and temperate facilities, and 481 DEGs during the experimental heat stress. Through Transcriptome-wide association study, expressions of 156 genes were significantly associated with thermoregulation and production traits. Throughout 18,237 autosome-annotated transcriptomic probes, we detected 9,543 expression quantitative trait loci (eQTLs). Genetic variance was estimated to explain 22.7% of gene expression variance on average, and was higher than 50% for 4.8% of transcripts. Most eQTLs are located in proximal regions (cis-eQTL) while a minority are in distal region (transeQTL) to their assigned genes. We identified 131 trans-eQTL hotspots. We further identified six genes associated with genotype by environment interactions through cis-eQTLs. With the addition of molecular QTLs such as metabolite QTLs (metQTLs) and phenotypic QTLs, colocalizations may reveal genomic regions of high interest for genomic selection of pigs for climate accommodation and heat stress resilience. Altogether, these results provide a better understanding of the impact of climate, heat stress and genetic diversity on the pig whole blood transcriptome
Genetic parameters of slaughter traits measured on Greylag geese after induction of spontaneous liver steatosis
No full textInternational audiencePrevious studies have demonstrated the possibility of inducing hepatic steatosis in geese without resorting to force-feeding, although results were highly variable. The aim of this study was to estimate the genetic parameters of traits of interest for the foie gras industry (liver weight and carcass cut weights) obtained after induction of steatosis without force-feeding. This represents a preliminary step toward designing a breeding program aimed at producing foie gras in a more ethically acceptable way. Two successive experimental flocks, comprising several hundred birds each and derived from a commercial population in 2020 and 2021, were subjected to the induction protocol: feed restriction until 16 weeks of age, followed by ad libitum maize feeding for 10 weeks, during the autumn, in closed facilities with controlled lighting. The populations included nearly equal numbers of males and females, and no significant difference in liver weight was observed between sexes, which is an additional advantage for selection and production. Estimated heritabilities were high (0.56 ± 0.10 for liver weight, 0.45 ± 0.10 for thigh weight, 0.69 ± 0.11 for breast muscle weight), indicating strong potential for improvement of these traits through selection. Moreover, the genetic correlations between liver weight and other traits of interest were either favorable or negligible, particularly with carcass weight (0.62 ± 0.12) and thigh weight (0.69 ± 0.11). Growth traits were also heritable (>0.6 for body weights at 9 and 14 weeks), with body weight gain between these ages moderately heritable (0.33 ± 0.04) and positively correlated with liver weight (0.48 ± 0.14). These results highlight the potential of implementing selection for foie gras production without force-feeding. In addition, an empirical scoring system for liver appearance was also evaluated as a simple alternative to advanced phenotyping tools. This rapid visual classification proved highly heritable (0.67 ± 0.11) and displayed the same favorable correlations with other traits as liver weight itself. This suggests that visual scoring could even replace direct liver weighing in selection programs, at least in the early stages, thus offering breeders a fast and inexpensive method to identify families with a greater predisposition to hepatic steatosis. Overall, these findings open the way to more sustainable and welfare-friendly foie gras production, in line with societal expectations on animal welfare, while offering breeders practical tools to initiate selection in commercial populations
Discrimination entre insuffisance rénale aiguë et crise urémique de maladie rénale chronique au moyen de variables sanguines et échographiques parathyroïdiennes : Étude prospective multicentrique sur 42 chiens
No full textRenal failure, whether chronic or acute, is highly prevalent in veterinary medicine. However, chronic kidney disease often occurs insidiously and is often diagnosed at late stages in practice. Furthermore, differentiation between acute renal failure (ARF) and acute crisis on chronic kidney disease (ACKD) using routine analysis is challenging. The aims of this prospective, multicentric study were to describe phosphocalcic axis variables, such as plasma parathyroid hormone (PTH) and calcitriol (1,25-OH2DVit) and to compare them in ARF and ACKD dogs, in order to identify which are of potential interest to discriminate these affections. Twenty dogs with CKD and twenty-two dogs with AKI were included in this study. Although several variables significantly differed between the two groups, some were particularly interesting, such as the PTH/1,25-OH2DVit ratio and ultrasound parathyroid measures related to the common carotid artery. This work has highlighted which variables would be of interest in differentiating ARF from ACKD. Areas for improvement, such as the measurement of Fibroblast Growth Factor 23, which could be of major diagnostic interest, remains to be studied.L’insuffisance rénale, qu’elle soit chronique ou aiguë, est une affection d’importance majeure en médecine vétérinaire. Or, la maladie rénale chronique survient souvent de façon insidieuse et est souvent diagnostiquée tardivement en pratique. Par ailleurs, la différenciation entre insuffisance rénale aiguë (IRA) et maladie rénale chronique (MRC) en décompensation, ou crise urémique (AMRC), n’est pas toujours possible à l’aide des examens et analyses courantes. Les objectifs de cette étude prospective et multicentrique étaient de décrire des variables liées à l’axe phosphocalcique, comme la parathormonémie ou encore la calcitriolémie, et de les comparer chez des chiens atteints d’IRA et d’AMRC afin d’identifier lesquelles étaient intéressantes pour dichotomiser les patients entre ces affections. Vingt chiens en AMRC et vingt-deux chiens en IRA ont été inclus dans cette étude. Si plusieurs variables étaient significativement différentes entre les deux groupes, certaines se sont montrées particulièrement prometteuses, comme le rapport parathormonémie/calcitriolémie et des variables échographiques rapportées à des mesures de l’artère carotide commune. Ce travail a mis en évidence quelles variables seraient intéressantes pour discriminer l’IRA de l’AMRC. Des pistes d’amélioration demeurent comme le dosage du Fibroblast Growth Factor 23 qui pourrait présenter un intérêt diagnostique majeur
Mutation Rate in Phage lambdaMutation Rate in Phage lambda
No full textInternational audienceNatural acids such as oxalic, formic or lactic acids are used as alternative treatments against Varroa destructor, the parasitic mite of honey bees (Apis mellifera). Lactic acid has recently been shown to impair mites’ grip skills through local action after exposure of adult honey bees. However, little is known about the lethal and sublethal effects of lactic acid on honey bees. In this work, we investigated the effects of chronic oral exposure to lactic acid through a contaminated diet on age-controlled worker bees. We monitored survival under artificial conditions, quantified lactate levels in various worker organs (the digestive tract, the thorax, the fat body, the head and the haemolymph) and analysed the transcriptome of the workers’ heads. Our results indicate that consuming lactic acid at residual concentration (1.5 mg/mL) did not impact the survival. No lactate accumulation was detected in any of the honey bee organs analysed. Furthermore, transcriptomic analysis on the bees’ heads revealed no differences in gene expression. While further research on sublethal effects is still needed, this work provides one of the first reports on the off-target effects of lactic acid on honey bee health
Metabolic Responses of Oxygenic Photogranules to Carbon and Light Fluctuations: Insights from Longitudinal Metabolomics
No full textInternational audienceOxygenic photogranules (OPGs) are biological aggregates primarily composed of cyanobacteria, eukaryotic algae, and heterotrophic bacteria interacting syntrophically [1]. Recognized for their potential in wastewater treatment, OPGs cultivated in sequencing batch reactors (SBR) are subjected to frequent fluctuations in light and carbon availability, potentially impacting their metabolic activity and syntrophic relationships. However, the metabolic responses of OPGs to such environmental changes and their consequences on community function and interactions, remain poorly understood. A major experimental challenge lies in disentangling the metabolic effects induced by environmental fluctuations from those caused by the spatial heterogeneity inherent to the three-dimensional structure of the biomass [2]. To address this challenge, we developed a dedicated experimental system, a co-extraction protocol for metabolome and metatranscriptome analyses, and the integration of longitudinal multi-omics approaches. OPGs were grown in a SBR with synthetic wastewater, and a controlled number of small, homogeneous granules (0.6–1 mm) was selected to reduce internal gradients. Under these conditions, we assumed that all OPGs experienced comparable environmental exposure. A sacrificial sampling strategy was employed, with three carbon availability conditions tested: early addition (at t0), late addition (after 90 minutes), and no carbon addition. Photogranules were exposed to 70 µmol·m⁻²·s⁻¹ of photosynthetically active radiation from 0 to 180 minutes, followed by darkness from 180 to 240 minutes. Eight replicates were collected per condition and time point. Metabolites and RNA were co-extracted according to the protocol described in [3]. NMR-based metabolomic analyses enabled metabolite identification, semi-quantification, and the identification of KEGG metabolic pathways statistically differentiated according to environmental conditions [4,5]. The metatransciptome is currently analyzed.Under carbon-limited conditions, eight KEGG pathways were altered, notably those related to C5-branched dibasic acids, phosphate and phosphinate, taurine and hypotaurine and amino sugar and nucleotide sugar metabolisms. Metabolites such as N-acetylneuraminate, a known precursor of extracellular polymeric substances (EPS) [6], and the amino-acids L-alanine and hypotaurine decreased in the absence of acetate, suggesting mobilization of internal carbon reserves, as previously reported [7]. In contrast, acetate supply sustained both heterotrophic and phototrophic activities. Our results further indicate that the history of carbon availability influenced the metabolic response of OPGs to light changes. When the light was turned off, distinct metabolomic signatures emerged between the early and late carbon addition series, particularly within the “carbon fixation by Calvin cycle” pathway. Differential dynamics of 3-phosphoglycerate and L-alanine suggest that the prior carbon supply modulated the activity of phototrophs. Moreover, other metabolic pathways were affected. Distinct responses of “alanine, aspartate and glutamate metabolism” and especially L-argininosuccinate, a metabolite linked to light response and implicated in biofilm development and cohesion [8], was observed between experimental series. Fatty acid metabolism also varied, with specific changes in polyunsaturated fatty acids, key components of cell membranes and sensitive markers of oxidative stress [9].Overall, these findings highlight how light and carbon availability, shape photogranule metabolism [10]. The integration of ongoing metatranscriptomic and metagenomic analyses will further elucidate the syntrophic relationships between cyanobacteria (notably Leptolyngbya in our system) and heterotrophic bacteria and their contributions to these dynamic processes. Future work will aim to determine whether environmental changes exert lasting effects on OPG functions and activity, particularly in relation to oxidative stress responses, the regulation of EPS and amino acid biosynthesis, and their impact on biofilm formation, structural cohesion, and cell-to-cell communication via quorum sensing
Pathologie infectieuse du pigeon ramier : une espèce au cœur De problèmatiques one health
No full textThe Wood pigeon (Columba palumbus), a widespread species in Europe, is exhibiting changes in migratory behavior, with a trend toward partial sedentarization. This shift has implications for local agriculture and game management. This thesis presents a literature review of infectious diseases affecting the species, focusing on bacterial, viral, parasitic, and fungal infections. Particular attention is given to their zoonotic potential and their impact on both animal and human health within a "One Health" framework. The study also aims to provide diagnostic, therapeutic, and preventive guidelines for wildlife veterinarians, game managers, and pigeon breeders, contributing to a better understanding of the health challenges posed by this species within European ecosystems.Le Pigeon ramier (Columba palumbus), espèce largement répandue en Europe, connaît une évolution de ses flux migratoires marquée par une sédentarisation partielle, avec des répercussions sur l’agriculture locale et la gestion cynégétique. Cette thèse propose une revue bibliographique des maladies infectieuses affectant cette espèce, incluant les principales affections bactériennes, virales, parasitaires et fongiques. L’analyse met en évidence le potentiel zoonotique de ces agents et leurs impacts sur la santé animale et humaine, dans une approche intégrée de type « One Health ». L’étude vise également à fournir des repères diagnostiques, thérapeutiques et préventifs à destination des vétérinaires de la faune sauvage, des gestionnaires cynégétiques et des colombophiles, afin de mieux appréhender les enjeux sanitaires liés à cette espèce au sein des écosystèmes européens
Accurate VLE predictions via COSMO-RS-Guided deep learning models: solubility and selectivity in physical solvent systems for carbon capture
No full textInternational audienceCarbon capture through physical solvents reduces energy consumption and lowers environmental impact compared to conventional chemical absorption methods. Typical properties for solvent screening are solubility and selectivity. However, they require accurate prediction of vapor-liquid equilibrium (VLE) that remains a critical challenge due to the lack of enough available experimental data. This could be supplemented by in silico data prediction provided that current predictions models are improved as this paper intends. When modeling physical solvents, a challenge arises due to the dominant role of non-bonding interactions and molecular geometry. For this purpose, a machine learning pipeline is developed using VLE results obtained from the quantum chemical-based thermodynamic model COnductor like Screening MOdel for Real Solvents (COSMO-RS) and experimental data. A Direct-Message Passing Neural Network (D-MPNN) architecture is employed, leveraging molecular representations, additional features and transfer learning to refine predictions. Two models, solubility and selectivity, are pre-trained over 30000 COSMO-RS simulated data points and fine-tuned with experimental VLE datasets for CO₂ and common gas impurities (H₂S, CH₄, N₂, H₂) respectively. The models’ accuracy is significantly improved over COSMO alone by correcting bias in total pressure predictions. Experimental trends are successfully reproduced in the test data, confirming the physical consistency of the models. Sensitivity analysis confirms that molecular features have the highest impact on estimations, while the scaling effect of additional features is essential for accuracy. These results demonstrate the potential of the proposed methodology to systematically screen and optimize an extensive range of physical solvents on the basis of their chemical structure for carbon capture applications, reducing reliance on costly and time-consuming experimental measurements