Portail des publications scientifiques de VetAgro Sup
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Laboratory network surveillance of equine diseases
No full textInternational audienceBackground: The French Network for Surveillance of Equine Diseases (RESPE) is an online veterinary reporting and information system created in 1999 for early detection of equine syndromes and nonnotifiable diseases in France. It aims to provide an early warning to all the equine industry stakeholders to implement immediate and collective management measures when necessary. To increase its surveillance coverage, the RESPE is developing a laboratory-based surveillance component, that centralises laboratory analysis results from a network of sentinel laboratories. Diagnostic laboratory results from different laboratories must be comparable and reliable to ensure effective epidemiological indicators for surveillance use. However, equine influenza, strangles, and equine herpesvirus-1 and -4 (EHV-1 and EHV-4) infections which pose significant risks to the equine industry, are non-notifiable diseases. Thus, diagnostic laboratory methods are not standardised, and each laboratory can develop its own test.Objectives: To compare the PCR diagnostic laboratory results for equine influenza, strangles, EHV-1 and EHV-4 infections obtained bydifferent laboratories.Study design: In vitro studies.Methods: Interlaboratory comparisons (ILC) were performed to assess the capacity of participating laboratories in diagnosing the targeted diseases using their PCR methods. ILCs were organised in 2022 and 2023. These consisted of sending panels of samples of known status, i.e. containing or not containing targeted pathogen DNA or RNA. The results obtained by the laboratories using their own method on the blinded samples were compared with the results obtained by LABEO, RESPE's support laboratory.Results: Six laboratories participated in the ILCs. The percentage of participating laboratories that correctly identified the samples was 80% for equine influenza and EHV-1, and 100% for strangles and EHV-4.Main limitations: Samples were artificially contaminated and none were at the detection limit.Conclusions: These results highlighted the importance of ensuring the reliability and comparability of the laboratory diagnostic methods for effective surveillance of equine infectious diseases.Ethical animal research: Not required: quality improvement activity.Informed consent: Not applicable.Competing interests: None declared.Funding: French Institute of horse and riding (IFCE), Conseil Départemental du Calvados, Fonds EPERON, French Ministry in charge of Agriculture, Conseil Départemental de la Manche, National Horseracing Federation (FNCH)
Unravelling the main genomic features of Mycoplasma equirhinis
No full text2/3International audienceBackground: Mycoplasma spp. are wall-less bacteria with small genomes (usually 0.5-1.5 Mb). Many Mycoplasma (M.) species are known to colonize the respiratory tract of both humans and livestock animals, where they act as primary pathogens or opportunists. M. equirhinis was described for the first time in 1975 in horses but has been poorly studied since, despite regular reports of around 14% prevalence in equine respiratory disorders. We recently showed that M. equirhinis is not a primary pathogen but could play a role in co-infections of the respiratory tract. This study was a set up to propose the first genomic characterization to better our understanding of the M. equirhinis species.Results: Four circularized genomes, two of which were generated here, were compared in terms of synteny, gene content, and specific features associated with virulence or genome plasticity. An additional 20 scaffold-level genomes were used to analyse intra-species diversity through a pangenome phylogenetic approach. The M. equirhinis species showed consistent genomic homogeneity, pointing to potential clonality of isolates despite their varied geographical origins (UK, Japan and various places in France). Three different classes of mobile genetic elements have been detected: insertion sequences related to the IS1634 family, a putative prophage related to M. arthritidis and integrative conjugative elements related to M. arginini. The core genome harbours the typical putative virulence-associated genes of mycoplasmas mainly involved in cytoadherence and immune escape.Conclusion: M. equirhinis is a highly syntenic, homogeneous species with a limited repertoire of mobile genetic elements and putative virulence genes
Maintien de la multifonctionnalité des prairies permanentes et adaptation des systèmes fourragers au changement climatique dans le Massif central
No full textPermanent grasslands are multifunctional and provide many ecosystem services. They are, however, threatened by both climate change and the intensification of agricultural practices, which leads to degradation (i.e. to biodiversity losses and less ecosystem services). Conversion to arable land is another threat on biodiversity. Two issues therefore need to be reconciled: i) maintaining the diversity of services that permanent grasslands provide to society, and ii) adapting forage systems to climate change. The livestock production systems framework, which combines a production system and decision-making system, is used here to analyse the direct and indirect effects of climate change on permanent grasslands. The direct effects are changes in grassland under the effects of climate variation, and the indirect effects are changes in grassland in response to adaptations by farmers.In order to understand the direct effects of climate change on permanent grasslands, we used the botanical surveys previously carried out to establish a functional typology of grasslands in the Massif Central. Their distribution along gradients of altitude and latitude, independently of management factors, enabled us to study the effect of climate change on the multifunctionality of permanent grasslands according to fertilisation and their species richness. Using a structural equation model, we identified species richness as the pivotal variable in the effects of mineral and organic fertilisation, and climate on grassland multifunctionality. A rise in the average annual temperature is associated with a decline in grassland biodiversity and multifunctionality.We then interviewed 15 dairy farmers in the Massif Central about their perceptions of climate change and permanent grasslands, and analysed how these perceptions influenced their strategies for adapting to climate change. We observed a marked effect of the climatic context, with a contrast between the southern Massif Central lowlands, where farmers already experienced pronounced droughts and high summer temperatures, and the other areas. In the latter areas, the perception of permanent grassland remains positive, and its diversity within and between plots is the basis of the adaptation strategies implemented by farmers. In the south of the Massif Central, farmers place more emphasis on the dis-services associated with the use of permanent grassland, and base their adaptation strategy on a crop rotation in which they have integrated temporary grassland, fodder crops and trees.Finally, using our structural equation model, we simulated the effect of a 1.5°C rise in mean temperature on changes in the multifunctionality of permanent grassland that farmers considered to be representative of their system. We also distinguished between farms according to the proportion of permanent grassland in their agricultural area. This analysis shows that the degradation and conversion of permanent grassland to crops does not affect all farms in the same way. On some farms, the conversion of certain grasslands to crop rotations preserves permanent grassland that receive little fertilisation on other plots of the farm.This thesis highlights the importance of combining ecological and socio-cognitive approaches in order to understand the different ways in which climate change influences the management of grassland-based farms. The results of our work on grazing farmers' perceptions of permanent grassland and on the barriers and lock-ins to adaptation could be used by farm advisors, to help farmers make the transitions needed to adapt to current climatic and ecological challenges.Les prairies permanentes sont multifonctionnelles et rendent ainsi de nombreux services écosystémiques à la société. Elles sont menacées par le changement climatique et par l'intensification des pratiques agricoles qui les menacent de dégradation (i.e. baisse de biodiversité et de leur capacité à fournir des services). Elles reculent sous l'effet de la conversion de leurs surfaces au profit des cultures. Deux enjeux sont alors à concilier: i) maintenir la diversité de services que les prairies permanentes rendent à la société et ii) adapter les systèmes fourragers au changement climatique. La cadre des systèmes d'élevage qui combine un système biotechnique et un système décisionnel est ici utilisé pour analyser les effets directs et indirects du changement climatique sur les prairies permanentes. Les effets directs sont les évolutions des prairies sous l'effet de variations du climat, et les effets indirects sont les évolutions des prairies en réponse aux adaptations des éleveurs au changement climatique.Afin de comprendre les effets directs du changement climatique sur les prairies permanentes, nous avons utilisé les relevés botaniques précédemment réalisés pour établir une typologie fonctionnelle des prairies du Massif central. Leur distribution le long de gradients d'altitude et de latitude, indépendamment des facteurs de gestion, nous a permis d'étudier l'effet du changement climatique sur la multifonctionnalité des prairies permanentes selon les modes de fertilisation et leur richesse spécifique. Grâce à un modèle d'équation structurelle, nous avons identifié la richesse spécifique comme variable pivot des effets de la fertilisation et du climat. L'élévation de la température annuelle moyenne conditionne la baisse de leur biodiversité et de leur multifonctionnalité.Par la suite, nous avons interrogé 15 éleveurs bovins laitiers du Massif central sur leurs perceptions du changement climatique, de leurs prairies permanentes et analysé comment ces perceptions influencent leurs stratégies d'adaptation au changement climatique. Nous avons observé un effet marqué du contexte climatique avec un fort contraste entre les zones collinéennes du sud du Massif central, où les éleveurs font déjà face à des sécheresses prononcées et à des températures estivales élevées, et les autres zones. Dans ces dernières, la perception des prairies permanentes reste positive et leur diversité inter- et intra-parcelle est à la base des stratégies d'adaptation mises en œuvre par les éleveurs. Au sud du Massif central, les éleveurs insistent plus sur les dis-services liés à l'utilisation des prairies permanentes, et fondent leur stratégie d'adaptation sur un assolement dans lequel ils ont intégré des prairies temporaires, des cultures fourragères et des arbres.Enfin, grâce à notre modèle d'équation structurale, nous avons simulé l'effet d'une élévation de la température moyenne de 1,5°C sur l'évolution de la multifonctionnalité de prairies permanentes que les éleveurs jugeaient représentatives de leur système. Nous avons également distingué les exploitations selon la part de prairies permanentes dans la surface agricole. Cette analyse révèle que les phénomènes de dégradation et de conversion des prairies permanentes au profit des cultures ne touchent pas toutes les exploitations de la même manière. Dans certaines, la conversion de certaines parcelles préserve des prairies permanentes peu fertilisées sur une autre partie du parcellaire.Cette thèse met en évidence l'importance de combiner des approches écologiques et socio-cognitives pour comprendre les voies par lesquelles le changement climatique influence la gestion des écosystèmes prairiaux. Les apports de notre travail sur la perception qu'ont les éleveurs herbagers des prairies permanentes, et sur les freins à l'adaptation pourront être mobilisés par le conseil aux éleveurs, afin de les accompagner dans les transitions permettant de faire face aux défis climatiques et écologiques
Treatment approaches to horses with acute diarrhea admitted to referral institutions: A multicenter retrospective study
No full text3International audienceBackground This study aimed to describe and compare therapeutic approaches for horses with acute diarrhea in different geographic regions worldwide. Methods Clinical information was retrospectively collected from diarrheic horses presented to participating institutions between 2016 and 2020, including fluid therapy on admission, antimicrobial drugs, probiotics, anti-endotoxic medications, anti-inflammatory drugs, gastroprotectants, digital cryotherapy, and toxin-binding agents. Seasonal and geographic differences were investigated. Results 1438 horses from 26 participating hospitals from 5 continents were included. On admission, 65% (926/1419) of horses were administered a fluid bolus. Antimicrobial drugs were administered to 55% (792/1419) within the first 24 hours of admission, with penicillin and gentamicin being the most used combination (25%, 198/792). Horses with leukopenia (OR: 2.264, 95%CI: 1.754 to 2.921; P<0.001) or meeting systemic inflammatory response syndrome criteria (OR: 2.542, 95%CI: 1.919 to 3.368; P<0.001) had higher odds of being administered antimicrobial drugs. Other treatments administered included probiotics (15%, 215/1438), polymyxin B (13%; 187/1438), pentoxifylline (8%; 118/1438), gastroprotectants (44%; 626/1419), digital cryotherapy (34%; 489/1435), plasma transfusion (13%; 182/1410) and toxin-binding agents (36%; 515/1438). Limitations Due to the retrospective nature of the study, the rationale for treatment decisions was unavailable, and associations with survival could not be evaluated. Conclusions Treatments varied between hospitals from different geographic regions. Prospective clinical trials are required to evaluate the effects of various treatments on survival
Association between cytokines, nitric oxide, hemodynamic and microcirculation in a porcine model of sepsis
No full text3International audienceSystemic inflammation and hemodynamic or microvascular alterations are a hallmark of sepsis and play a role in organs hypoperfusion and dysfunction. Pimobendan, an inodilator agent, could be an interesting option for inotropic support and microcirculation preservation during shock. The objectives of this study were to evaluate effect of pimobendan on cytokine and nitric oxide (NO) release and investigate whether changes of macro and microcirculation parameters are associated with the release of cytokines and NO in pigs sepsis model. After circulatory failure, induced by intravenous inoculation of live Pseudomonas aeruginosa, eight animals were treated with pimobendan and eight with placebo. Pimobendan did not affect cytokines secretion (TNF-α, IL-6 and IL-10), but decreased time-dependently NO release. Data of macro and microcirculation parameters, NO and TNF- α recorded at the time of circulatory failure (Thypotension) and the time maximum of production cytokines was used for analyses. A positive correlation was observed between TNF-α and cardiac index (r = 0.55, p = 0.03) and a negative with systemic vascular resistance (r = -0.52, p = 0.04). Positive correlations were seen both between IL-10, 30 min after resuscitation (T30min), and systolic arterial pressure (r = 0.57, p = 0.03) and cardiac index (r = 0.67, p = 0.01), and also between IL-6, taken 2 h after resuscitation and systolic arterial pressure (r = 0.53, p = 0.04). Negative correlations were found between IL-10 and lactate, measured resuscitation time (r = -0.58, p = 0.03). Regarding microcirculation parameters, we observed a positive correlation between IL-6 and IL-10 with the microvascular flow index (r = 0.52, p = 0.05; r = 0.84, p = 0.0003) and a negative correlation with the heterogeneity index with TNF-α and IL-10 (r = -0.51, p = 0.05; r = -0.74, p = 0.003) respectively. NO derivatives showed a positive correlation with temperature gradient (r = 0.54, p = 0.04). Pimobendan did not show anti-inflammatory effects in cytokines release. Our results also, suggest changes of macro- and microcirculation are associated mainly with low levels of IL-10 in sepsis
Impacts of Artificial Light At Night on immunity in the common toad.
No full textInternational audienc
Hotspot of recombination in Metamycoplasma equirhinis: evidence of multiple horizontal gene transfer events originating from bacteria sharing the same ecological niche
No full textInternational audienceMycoplasma genomes were long thought to be shaped exclusively by successive gene losses. In-depth analyses of their genomes have clearly demonstrated the contribution of horizontal gene transfer (HGT) to the evolution and plasticity of many mycoplasma species. Therefore, HGT may be used by mycoplasmas as a mean to adapt to new environmental stresses or ecological niches. A recent effort to sequence and analyze the genomes of 24 Metamycoplasma (M.) equirhinis, a species associated with the equine respiratory disease complex in horses, revealed that all these genomes are overall syntenic except for a few regions, one of which is adjacent to the CRISPR/Cas locus (Martineau et al., IOM submission number 80). This locus turned out to be highly variable between the 24 genomes with eight different genetic patterns resulting from rearrangements affecting i) the presence and/orgeneral genetic organization of the CRISPR/Cas locus, but also ii) the genomic region downstream of the CRISPR/Cas locus, which was defined as a hot spot of genetic diversity.Remarkably, all the genes downstream of the CRISPR/Cas system were horizontally acquired and appeared to originate from bacteria belonging to the Bacillota and Fusobacteriota phyla, many of them being commonly found in the respiratory tract of horses. In silico analyses further revealed that some of the coding sequences present in these regions shared high homologies with previously described defense mechanisms such as restriction-modification or toxin-antitoxin (TA) systems. In particular, the presence of at least one candidate TA system was identified in half of the genomes and shared high amino acid homology with one of the TA systems functionally characterized in Mycoplasma mycoides subsp. capri (1). The functional characterization of these systems is currently ongoing using different heterologous expression systems. These results suggest that M. equirhinis can acquire and potentially exchange genetic material with other phylogenetically distant bacteria that share the same ecological niche, i.e. the equine respiratory tract. The coding sequences located in this hotspot of recombination have putative functions linked to bacterial defense systems.1. Hill V, Akarsu H, Barbarroja RS, Cippa VL, Kuhnert P, Heller M, et al. Minimalistic mycoplasmas harbor different functional toxin-antitoxin systems.PLoS Genet.2021. https://doi.org/10.1371/journal.pgen.100936
Contribution à l'évaluation de la mesure de gratuité des transports en commun le week-end à Clermont Auvergne Métropole: Rapport final du projet EGRET
No full textThe EGRET project, funded by SMTC-AC, was designed to contribute to the evaluation of the effects of the free public transport scheme introduced at weekends on Clermont-Ferrand public transport network from 4 December 2021. EGRET was structured around three different tasks. Task T0 aimed, on the one hand, to clarify the objectives, as well as the expected positive and negative effects of the fare-free transport measure and, on the other hand, to grasp the key elements (context and stakes, place of the measure in the transport and mobility policy...) to be taken into account for carrying out a statistical analysis of the effectiveness of the measure. The aim of task T1 was to evaluate the specific effect of the measure on public transport ridership. The analyses were based on econometric models comparing public transport ridership levels before and after the introduction of free travel, while controlling for certain factors (e.g. petrol prices, weather, etc.) which could have an impact on patronage. The results show that free public transport led to a 47% increase in ridership on weekends, and that this increase was significantly higher for tramways (+54%) than for bus lines (+45%). However, the analyses show that the effect of the measure on weekday ridership is not statistically significant. EGRET project task T2 aimed to understand the mechanisms underlying the increase in weekend public transport ridership and the determinants of changes in mobility behaviour induced by free public transport (individual and household characteristics, residential location). Statistical and econometric analyses carried out in this task were based on the 2022 CEREMA Certified Mobility Survey (EMC²). Descriptive statistics relating to the web section of the EMC² survey show that almost 53% of public transport users living within the SMTC-AC's territorial jurisdiction declare that they use more public transport due to the free travel measure, whether at weekends and/or during the week. They also show that this increase in the use of public transport is mainly linked to shopping and leisure trips. Econometric analyses show that the age, income level, family structure and residential location significantly affect the probability that people use more public transport because of the free transport measure. The report is divided into four main parts. The first part presents the work carried out in task T0 of the project. The second part reviews the scientific literature, aiming mainly to summarise the effects and mechanisms identified in empirical studies, in order to compare them with the results obtained as part of the EGRET project. The third and fourth parts present the methods and results of the analyses carried out respectively in task T1 and task T2 of the EGRET project.Le projet EGRET, commandité par le SMTC-AC, visait à apporter des éléments sur l’évaluation des effets de la mesure de gratuité des transports en commun mise en place le week-end sur le réseau de transport en commun clermontois à compter du 4 décembre 2021. Le projet EGRET s’articulait autour de trois tâches différentes. La tâche T0 visait, d’une part, à clarifier les objectifs, ainsi que les effets positifs et négatifs attendus de la mesure de gratuité et, d’autre part, à appréhender les éléments incontournables (contexte et enjeux, place de la mesure dans la politique des transports et des mobilités …) à prendre en compte pour l’analyse statistique de l’efficacité de la mesure. La tâche T1 avait pour objectif d’évaluer l’effet propre de la mesure sur la fréquentation des transports en commun. Les travaux réalisés dans cette tâche s’appuient sur des analyses économétriques comparant les niveaux de fréquentation des transports en commun avant et après la gratuité, tout en contrôlant certains facteurs (ex : prix de l’essence, météo…) qui pourraient impacter la fréquentation. Les résultats montrent que la gratuité a entrainé une hausse de la fréquentation des transports en commun le week-end de +47 % et que cette hausse est significativement plus élevée pour le tramway (+54%) que pour les lignes de bus (+45%). Par contre, les analyses montrent que l’effet de la gratuité le week-end sur la fréquentation en semaine est statistiquement non significatif. La tâche T2 du projet EGRET avait pour objectifs d’appréhender les mécanismes sous-jacents à la hausse de fréquentation des transports en commun le week-end et les déterminants des changements de comportement de mobilité induits par la gratuité (caractéristiques des individus et des ménages, localisation résidentielle). Les analyses statistiques et économétriques développées dans cette tâche se sont appuyées sur l’Enquête Mobilité Certifiée CEREMA (EMC²) de 2022. Les statistiques descriptives portant sur le volet web de l’enquête EMC² montrent que près de 53% des usagers des transports en commun résidant au sein du ressort territorial du SMTC-AC utilisent davantage les transports en commun suite à la mesure de gratuité, que ce soit le week-end et/ou la semaine. Elles montrent également que cette hausse de l’usage des transports en commun est principalement liée à des déplacements réalisés pour les motifs achats et loisirs. Les résultats des analyses économétriques montrent que l’âge des individus, le niveau de revenu et la structure familiale du ménage auquel ils appartiennent, ou encore leur localisation résidentielle conditionnent de manière significative la probabilité de prendre davantage les transports en commun du fait de la gratuité. Ce rapport comprend quatre grandes parties. La première partie présente les travaux menés dans le cadre de la tâche T0 du projet. La deuxième partie présente une revue de la littérature scientifique, qui vise principalement à faire la synthèse des effets et mécanismes identifiés dans les études empiriques, pour les mettre ensuite en regard des résultats obtenus dans le cadre du projet EGRET. Les troisième et quatrième parties présentent la méthodologie et les résultats des analyses réalisées respectivement dans le cadre de la tâche T1 et de la tâche T2 du projet EGRET