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Le présent article a pour objectif de discuter de la faisabilité et de l’intérêt que représenterait le suivi d’un indicateur indirect de survenue des avortements élaboré à partir des données d’insémination artificielle, le taux d’avortements précoces, afin d’identifier l’impact d’un évènement abortif, de manière rétrospective ou prospective. Deux études sont présentées pour illustrer le propos, ayant eu pour objet d’estimer, par l’analyse des variations du taux d’avortements précoces, l’impact de l’épizootie de fièvre catarrhale ovine due au sérotype 8 (FCO-8), qui a émergé en France en 2006, puis s’est diffusée dans une large partie du territoire métropolitain en 2007 et 2008. La première étude souligne qu’une analyse des variations temporelles du taux d’avortements précoces à l’échelle du département a permis d’identifier a posteriori l’impact de la FCO-8 sur la survenue d’avortements en élevages de bovins. La seconde étude indique qu’une analyse prospective hebdomadaire des variations temporelles du taux d’avortements précoces aurait permis d’identifier l’impact de la FCO-8 dans un département dans un délai médian de 12 semaines suivant son introduction. Considérant ces résultats, il apparaît pertinent de réfléchir à la mise en place d’une surveillance intégrée des avortements en élevage de bovins, qui reposerait sur deux volets : la déclaration obligatoire des avortements (sous la forme du dispositif actuel en version révisée) et un outil de surveillance syndromique (qui devrait être mis en place à une échelle infra-départementale, en particulier pour améliorer les délais de détection)., This article is aimed at discussing the feasibility and advantages of using artificial insemination data, through a new indicator of mid-term abortions, the mid-term abortion incidence rate, in order to identify the impact of an abortive event retrospectively or prospectively. Two studies are used to illustrate the purpose, based on the analysis of mid-term abortion incidence rate to estimate the impact of the Bluetongue serotype 8 (BT8) epizootic that emerged in France in 2006 and then spread across the country in 2007 and 2008. The first study was a retrospective analysis of the temporal variations of the mid-term abortion incidence rate in each French department enabled to identify a posteriori the impact of BT8 on abortion occurrence. The second study was based on a weekly analysis of the temporal variations of the mid-term abortion incidence rate, and showed that the impact of BT8 would have been identified 12 weeks after the occurrence of the disease in 50% of the departments. These results suggest that there is a need to study the feasibility to implement an integrated surveillance of bovine abortions, based on the mandatory notification of bovine abortions (i.e. the current surveillance system with some improvements) and a syndromic surveillance system (that should be implemented at a lower level than the department, to improve timeliness).

SUMMARYWaterborne disease outbreaks (WBDO) of acute gastrointestinal illness (AGI) are a public health concern in France. Their occurrence is probably underestimated due to the lack of a specific surveillance system. The French health insurance database provides an interesting opportunity to improve the detection of these events. A specific algorithm to identify AGI cases from drug payment reimbursement data in the health insurance database has been previously developed. The purpose of our comparative study was to retrospectively assess the ability of the health insurance data to describe WBDO. Data from the health insurance database was compared with the data from cohort studies conducted in two WBDO in 2010 and 2012. The temporal distribution of cases, the day of the peak and the duration of the epidemic, as measured using the health insurance data, were similar to the data from one of the two cohort studies. However, health insurance data accounted for 54 cases compared to the estimated 252 cases accounted for in the cohort study. The accuracy of using health insurance data to describe WBDO depends on the medical consultation rate in the impacted population. As this is never the case, data analysis underestimates the total number of AGI cases. However this data source can be considered for the development of a detection system of a WBDO in France, given its ability to describe an epidemic signal.

Objectives We aimed to (1) evaluate how frequently the uterus and ovaries of healthy, non-pregnant queens are visible; (2) describe their appearance; (3) take their measurements; and (4) determine intra- and inter-observer variabilities in their measurements. We hypothesised that, using a high-frequency linear probe, the uterus and ovaries could be ultrasonographically visualised during any period of the sexual cycle and with any level of operator expertise. Methods Eight queens were enrolled in the study and the ultrasonographical appearance of their uterus and ovaries assessed with a high-frequency linear probe of 15–19 MHz. The diameter of the uterine horns, body and cervix in transverse and longitudinal sections, and the length of the ovaries were recorded. Three observers of different expertise level participated in the study, and the differences between the separate measurements made per queen were evaluated. Results The ovaries and the entire uterus were visualised in every queen. The ovaries were ovoid structures with submillimetric follicles during anoestrus and additional larger follicles depending on the stage of the cycle. An ovarian pattern suggesting cortex and medulla was observed in half the cases. In the uterus, the serosa was a thin hyperechoic outer rim, and layering was observed in half the cases. The cervix was difficult to identify. The intra- and inter-observer variabilities in the uterine horns and the ovaries were minimal (coefficient of variation [CV] 1.4–4.1%) compared with the differences within the queens (CV 10.9–43.4%). The longitudinal and transverse measurements of the horns and the uterine body were the same. Conclusions and relevance The ovaries and uterine horns in queens are accessible ultrasonographically at any stage of their cycle, and can be measured with low intra- and inter-observer variabilities.

MERCI De NE PAS RAJOUTER DE PDF CAR CE N'EST PAS AUTORISE; International audience; It is necessary to assess surveillance systems for infectious animal diseases to ensure they meet their objectives and provide high-quality health information. Each system is generally dedicated to one disease and often comprises various components. In many animal industries, several surveillance systems are implemented separately even if they are based on similar components. This lack of synergy may prevent optimal surveillance. The purpose of this study was to assess several surveillance systems within the same industry using the semi-quantitative OASIS method and to compare the results of the assessments in order to propose improvements, including future synergies. We have focused on the surveillance of three major equine diseases in France. We have identified the mutual and specific strengths and weaknesses of each surveillance system. Furthermore, the comparative assessment has highlighted many possible synergies that could improve the effectiveness and efficiency of surveillance as a whole, including the implementation of new joint tools or the pooling of existing teams, tools or skills. Our approach is an original application of the OASIS method, which requires minimal financial resources and is not very time-consuming. Such a comparative evaluation could conceivably be applied to other surveillance systems, other industries and other countries. This approach would be especially relevant to enhance the efficiency of surveillance activities when resources are limited.

International audience; Facing the first times of occurence of events of a new type, such as seismic events, arrivals of individuals of a unknown species, occurrences of cases of a new disease..., it is crucial to predict if these events are only ?sporadic?, or if they announce an emerging phenomenon (earthquake, emergence of a population, epidemic). We propose here an exact nonparametric test statistic based on the number of lower records Nn in {?Tk}1 ≤ k ≤ n, ?Tk being the waiting time between two successive events. Under H0 (sporadic events), the {?Tk} are assumed i.i.d., while under H1 (emergent events), the {?Tk} are assumed independent with cdf?s (Cumulative Distributions Functions) {Gk} increasing with k. Under H0, the distribution of Nn is independent of Gk, thus allowing a nonparametric test of H0. To calculate the power of the test under the alternative hypothesis H1, we assume the particular family of cdf?s, , , where G is a continuous cdf on (0, ∞) and a > 1. These distributions represent an exponential occurrence rate of events. We show that the distribution of Nn under H1 depends only on a (and not on G). We estimate a by the Maximum Likelihood Estimator, and give the asymptotic properties of this estimator, as n ? ∞. Finally we illustrate the test on simulations and then on data concerning the atypical BSE (Bovine Spongiform Encephalopathy) in France.

International audience; Studies of the impact of parasites on host performance have mainly focused on body mass, a phenotypic trait that responds relatively slowly to the presence of parasites, and the expectedly faster response of physiological parameters has been mostly overlooked. We filled the gap by measuring the impact of endoparasites on four hematological/biochemical parameters (hematocrit, albumin, creatinine and fructosamine) in two contrasting free-living populations of roe deer. We generally found negative relationships between parasites and physiological parameters. Our findings also indicate little role of host sex on parasite impact and strongest parasite effects on young and senescent hosts. (C) 2014 Elsevier B.V. All rights reserved.

West Nile virus (WNV) infection is a non-contagious disease mainly transmitted by the bites of infected mosquitoes from the genus Culex. The virus is maintained in a mosquito-bird-mosquito cycle, and can accidentally be transmitted to mammalian hosts. Among mammalian hosts, equines and humans are the most sensitive to WNV infection and can develop severe meningoencephalitis. As WNV infections are zoonotic and can be severe in humans and equines, West Nile fever is considered to be a public and animal health concern. After a silent period of almost ten years, WNV re-emerged in France at the periphery of the Camargue area during the summer of 2015, underlining the fact that the Camargue area creates favourable conditions for WNV emergence and amplification in France. The French Network for Epidemiological Surveillance of Equine Diseases (Réseau d'Épidémio-Surveillance en Pathologie Équine [RESPE]) facilitated the early detection of WNV cases in horses. In total, 49 horses were found to be infected; among them, 44 presented clinical signs, 41 with meningoencephalitis and three with hyperthermia only. Six horses among the 41 with nervous symptoms died from the disease or were euthanised (a case fatality rate of 14.6%). The authors describe the characteristics of the 2015 WNV epizootics, the early detection of the first WNV equine cases via the RESPE network and the coordination of WNV surveillance in France.L’infection par le virus de West Nile est une maladie non contagieuse essentiellement transmise lors de piqûres de moustiques infectés appartenant au genre Culex ; le virus se maintient dans la nature au moyen d’un cycle moustique– oiseau–moustique ; la transmission à des hôtes mammifères a lieu de manière accidentelle. Parmi les mammifères hôtes, les plus sensibles à l’infection par le virus de West Nile sont les équidés et l’homme, chez qui l’infection peut se manifester sous forme d’une méningo-encéphalite sévère. Les infections par le virus de West Nile étant des zoonoses potentiellement graves chez l’homme et chez les équidés, la fièvre de West Nile doit être considérée comme une priorité de santé publique et animale. Resté silencieux pendant plus d’une décennie, le virus de West Nile est réapparu en France à l’été 2015 en bordure de la Camargue, confirmant que les conditions de cette région sont favorables à l’émergence et à l’amplification du virus. Le réseau français d’épidémiosurveillance en pathologie équine (RESPE) a contribué à la détection précoce du virus de West Nile chez les chevaux. Au total, 49 chevaux étaient infectés, parmi lesquels 44 présentaient des signes cliniques, correspondant à une méningo-encéphalite pour 41 d’entre eux et à une hyperthermie seule pour les trois autres. Six chevaux parmi les 41 qui présentaient des signes neurologiques ont succombé à la maladie ou ont été euthanasiés (taux de létalité de 14,6 %). Les auteurs de cet article décrivent les principales caractéristiques de l’épizootie de 2015 due au virus de West Nile ainsi que la détection précoce des premiers cas équins grâce au réseau RESPE et la coordination des activités de surveillance du virus en France.La infección por el virus West Nile es una enfermedad no contagiosa que se transmite básicamente por la picadura de mosquitos infectados del género Culex. El virus, que se instala en un ciclo mosquito–ave–mosquito, también puede transmitirse accidentalmente a mamíferos, de entre los cuales los más sensibles a la infección son los equinos y el ser humano, que pueden contraer graves meningoencefalitis. Puesto que las infecciones por este virus son zoonóticas y pueden revestir gravedad en personas y equinos, se considera que la fiebre West Nile es una enfermedad de importancia sanitaria y zoosanitaria. En Francia, tras un periodo silente de más de diez años, el virus reapareció en verano de 2015 en la periferia de la zona de la Camarga, poniendo así de manifiesto que esta zona genera condiciones propicias al surgimiento y la amplificación del virus en el país. La red francesa de vigilancia epidemiológica de patologías equinas (Réseau d’Épidémio-Surveillance en Pathologie Équine: RESPE]) facilitó la rápida detección de caballos infectados por el virus West Nile. Se detectaron en total 49 animales infectados, entre ellos 44 con signos clínicos, de los que 41 sufrían meningoencefalitis y tres solo presentaban hipertermia. Seis de los 41 caballos que mostraban signos neurológicos murieron a causa de la enfermedad o fueron sacrificados con métodos de eutanasia (lo que supone una tasa de letalidad del 14,6%). Los autores describen las principales características de la epizootia causada por el virus West Nile en 2015, la pronta detección de los primeros casos de caballos infectados gracias a la red RESPE y la coordinación de las labores de vigilancia del virus en Francia.

International audience; The obligate intracellular bacterium Coxiella burnetii is the etiological agent of Q fever, a widespread zoonotic disease whose most common animal reservoirs are domestic ruminants. Recently, a variety of Coxiella-like organisms have also been reported from non-mammalian hosts, including pathogenic forms in birds and forms without known effects in ticks, raising questions about the potential importance of non-mammalian hosts as reservoirs of Coxiella in the wild. In the present study, we examined the potential role of globally-distributed seabird ticks as reservoirs of these bacteria. To this aim, we tested for Coxiella infection 11 geographically distinct populations of two tick species frequently found in seabird breeding colonies, the hard tick Ixodes uriae (Ixodidae) and soft ticks of the Ornithodoros (Carios) capensis group (Argasidae). We found Coxiella-like organisms in all O. capensis sensu lato specimens, but only in a few I. uriae specimens of one population. The sequencing of 16S rDNA and GroEL gene sequences further revealed an unexpected Coxiella diversity, with seven genetically distinct Coxiella-like organisms present in seabird tick populations. Phylogenetic analyses show that these Coxiella-like organisms originate from three divergent subclades within the Coxiella genus and that none of the Coxiella strains found in seabird ticks are genetically identical to the forms known to be associated with pathogenicity in vertebrates, including C burnetii. Using this data set, we discuss the potential epidemiological significance of the presence of Coxiella in seabird ticks. Notably, we suggest that these organisms may not be pathogenic forms, but rather behave as endosymbionts engaged in intricate interactions with their tick hosts. (C) 2014 Elsevier GmbH. All rights reserved.

International audience; Bovine cysticercosis is a foodborne disease caused by the cestode Taenia saginata with cattle as the intermediate host and humans as the final host. This disease is responsible for direct financial losses for farmers. It is also economically important because human infestation through raw or undercooked meat consumption can have a negative impact on the confidence the consumer has in the food industry. This study aimed to determine the apparent and true prevalence of bovine cysticercosis in France and describe the locations of identified cysticercosis lesions. The study sample included 4,564,065 cattle slaughtered in 2010 in France, among which 6491 were detected as harbouring cysticercosis lesions using the current EU meat inspection process. The overall apparent prevalence (including both viable and degenerated cysticerci) was estimated at 0.142% [0.142-0.143]. The true overall prevalence defined as the estimation of the prevalence after taking into account the sensitivity of meat inspection (detection fraction) was 1.23% [0.83-1.93]. The true prevalence of cattle with at least one viable cysticercus was 0.113% [0.076-0.189]. Taking into account both our results and those of a previous study on the prevalence of human cysticercosis in France, we estimated that one carcass could infest an average of 8-20 individuals. The spatial distribution of viable cysticerci showed that the highest apparent prevalence was found in eastern France. This study, the largest survey ever conducted on bovine cysticercosis in France, indicated a low but spatially heterogeneous prevalence of the parasite among the cattle population. Considering French eating habits, according to which it is not uncommon to consume undercooked meat, the possibility of humans being infested even though viable cysticerci are not detected during meat inspection is high. Increasing the detection sensitivity of meat inspection through the use of a risk-based meat inspection procedure should improve prevention of human infestation. (C) 2014 Elsevier B.V. All rights reserved.

International audience; The proportion of cattle with offal, partial or whole carcass condemnation could be a useful indicator for animal health syndromic surveillance purposes. It requires first highlighting the factors associated with condemnation in order to include them in a modeling process. This study aims to identify and quantify these factors. It was based on data from ten French cattle slaughterhouses from 2006 to 2010 (n = 1,439,868 cattle). Multivariable multi-nomial logistic regression analyses were performed. Sex, age and slaughterhouse were the main effects for offal, partial and whole carcass condemnation and have to be taken into account when implementing syndromic surveillance systems based on meat inspection data. The presence of an error in cattle identification was identified as a potential indicator for a higher risk of condemnation and should be explored as a potential factor for risk-based meat inspection.

International audience; In Southeast Asia, traditional poultry marketing chains have been threatened by epidemics caused by the highly pathogenic avian influenza H5N1 (HPAI H5N1) virus. In Thailand, the trade of live backyard chickens is based on the activities of traders buying chickens from villages and supplying urban markets with chicken meat. This study aims to quantify the flows of chickens traded during a 1-year period in a province of Thailand. A compartmental stochastic dynamic model was constructed to illustrate trade flows of live chickens from villages to slaughterhouses. Live poultry movements present important temporal variations with increased activities during the 15 days preceding the Chinese New Year and, to a lesser extent, other festivals (Qingming Festival, Thai New Year, Hungry Ghost Festival, and International New Year). The average distance of poultry movements ranges from 4 to 25 km, defining a spatial scale for the risk of avian influenza that spread through traditional poultry marketing chains. Some characteristics of traditional poultry networks in Thailand, such as overlapping chicken supply zones, may facilitate disease diffusion over longer distances through combined expansion and relocation processes. This information may be of use in tailoring avian influenza and other emerging infectious poultry disease surveillance and control programs provided that the cost-effectiveness of such scenarios is also evaluated in further studies.

International audience; The European red squirrel (Sciurus vulgaris) has long been suspected to be a reservoir host of the agents of Lyme borreliosis, in particular B. burgdorferi sensu stricto (s.s.). However, very few data support this hypothesis. Hereafter, we investigated the infections with B. burgdorferi genospecies in road-killed red squirrels collected across France. We also characterized the diversity of hard tick species collected from a subsample of hosts. DNA of B. burgdorferi genospecies were detected and identified from PCR products in ear biopsies using reverse line blot hybridization. Variation in prevalence was investigated according to biogeographic areas (Mediterranean, Atlantic, Continental, and Alpine), season, sex, relative age, and body mass from 273 squirrels collected 2003–2010. Among the 746 identified tick specimens, no adult was observed, 63% were nymphs, and 37% were larvae all belonging to the species Ixodes ricinus except one nymph identified as I. trianguliceps. Overall, no squirrels of Mediterranean origin and no unweaned juveniles were found infested by hard ticks. Only season explained variation in I. ricinus abundance on squirrels, with more ticks present in spring to summer than in autumn to winter. Squirrels of Mediterranean origin (n = 20) were not found infected with B. burgdorferi sensu-lato (s.l.), which is almost certainly related to the low occurrence of I. ricinus in this region. Based on individuals analyzed in the other regions of France, 11.5% (n = 26) unweaned young harboured B. burgdorferi s.l., which indicates that infection occurred already in the nest. In adults (n = 227), the prevalence of infection with B. burgdorferi s.l. was 27.3%, with 18.9% B. burgdorferi s.s., 11.9% B. afzelii, and 3.5% B. garinii. The season and the body mass, sex, and geographic origin of adults had no effect on the frequency of infection. Infection prevalence of S. vulgaris is among the highest found in rodents in Europe, particularly for B. burgdorferi s.s. supporting the hypothesis that sciurids are particularly suitable hosts for this genospecies.

National audience; L’anaplasmose granulocytaire est une zoonose émergente transmise par les tiques, due à la bactérie Anaplasma phagocytophilum. Elle infecte de nombreux mammifères. Les chevreuils, et dans une moindre mesure les rongeurs, sont suspectés d’être des hôtes réservoirs (pouvant être la source d’infection pour les bovins via les tiques), du fait de forte prévalence dans leurs populations. Notre étude vise à caractériser génétiquement les souches d’A. phagocytophilum sur 9 loci chez 120 animaux domestiques malades provenant de toute la France ainsi que des chevreuils, pour mieux comprendre l’implication de chaque espèce hôte dans la circulation des souches. Cette caractérisation génétique nous a permis d’identifier 3 groupes de souches infectant les bovins. Les deux principaux groupes incluent 98 % des souches trouvées chez les bovins et sont génétiquement différentes de celles observées chez les chevreuils. Nos résultats suggèrent que les souches d’A. phagocytophilum infectant les bovins pourraient avoir plusieurs sources, différentes de celle du chevreuil

Livestock and Agroecology: redesigning animal production systems in the 21st century. Regional Symposium on Agroecology for Sustainable Agriculture and Food Systems in Europe and Central Asia

International audience; Canine babesiosis (or piroplasmosis) is an emerging tick-borne disease caused by intraerythrocytic protozoa of the genera Babesia and Theileria. In dogs, infection by these parasites usually induces a haemolytic syndrome that can be fatal when complicated. Canine babesiosis prevalence is high in France, with Babesia canis thought to be the main etiological agent of the disease. This article presents the results of a multiregional prospective longitudinal survey on canine babesiosis conducted in France from October 2006 to December 2007. A total of 836 cases were reported by veterinarians using a multiple choice questionnaire and blood samples from 70 dogs were analyzed using PCR-RFLP to identify species responsible for canine babesiosis cases across the country. The main clinical signs reported were lethargy (98%), anorexia (98%) and hyperthermia≥39°C (80%) followed by pale mucous membranes (54%), modification of urine aspect (45%) and splenomegaly (33%). The dog population at risk was mainly represented by young dogs living in rural areas. Twenty-five out of the 70 blood samples (36%) tested by diagnostic PCR were found to contain Babesia/Theileria genus-specific DNA and all had profiles similar to that of Babesia canis genomic DNA after restriction fragment length polymorphism analyses. The survey results provide a reference for further molecular studies to assess the species and vectors involved in the transmission of the disease in France and across the Mediterranean basin.

International audience; In this study, using capture-mark-recapture (CMR), a common vole population was monitored for one year in an experimental study site dominated by meadows, in which field management followed a gradient of intensiveness. The aim was to estimate the demographic response to agricultural practices of the common vole. During the spring, the numbers captured were highest in the most intensively managed plots. After cereal harvesting, they were higher in meadows with the highest nitrogen input. No difference in survival was found among treatments. However, the pattern of transitions suggested that high mobility explained this result. Also, mechanical interventions like ploughing appeared to have powerful consequences for common vole survival. These results underline the critical role of dispersal and refuge habitats in the maintenance of populations of voles in agroecosystems.

version parue en 2013 puis officielle en 2014; International audience; Leptospirosis is caused by pathogenic species of the Leptospira genus. Animals can have two roles in the epidemiological cycle: they can be an accidental host and suffer of the disease or a reservoir host which does not express any clinical sign and shed bacteria in their urine. Some of the most known reservoirs for leptospirosis are certain rodent species, but the situation is less clear for aquatic rodents, especially for coypu (Myocastor coypus). It has been shown that this species can have kidney carriage for leptospirosis, but the relationship between carriage and individuals or population health has not been investigated yet. We trapped 133 coypus in two wetlands in the East of France during 3 years. For each animal, a complete necropsy, leptospirosis serology, and a specific real-time quantitative PCR (qPCR) for pathogenic leptospires were performed; in addition, for some animals, a specific kidney culture for leptospires and histology on kidney were performed. In spite of a high seroprevalence (respectively 76%and 64 %) and of a significant prevalence of kidney carriage in both areas(respectively 12.1%and 8.0%of positive qPCR on kidney), the trapped animals seemed in good health, and the population did not seem to be affected by the circulation of the bacteria. These findings are concurring arguments to consider coypu as a real reservoir for leptospirosis.

National audience; Different methods are used by the epidemiologist in order to get as close as possible to the causal nature of the relationship between a factor and a disease. However this is just an interpretation since different circumstances may randomly induce non-causal relationships between factors and disease, but also the effect of other interconnected factors. Philosophy identifies three levels of discussion in the use of causality: the distinction between absolute reality and the one perceived by man given his faculties of knowledge; the difficulty of identifying causes from the observation of natural phenomena because a link between phenomena does not necessarily mean causal succession; the problem of induction, in the sense that more conclusive experiments cannot provide definitive evidence, so that the falsificationists propose challenging the hypothesis by trying new tests to reject it. This interdisciplinary approach enhances the contribution of the philosophical perspective to the epidemiological practice, and more largely to research in biology : among others searching for study contexts adapted to challenge the results, establishing a combination of different and complementary arguments to get closer to causality, which draw a link to the ten causality criteria used by epidemiologists to evaluate and discuss the causal nature of a relationship. In conclusion, having a severe critical look at the result is the only way to add credit to the interpretation of a statistically significant relationship in terms of causality.; Différentes pratiques et méthodes, depuis la conception de l’étude jusqu’à l’analyse statistique, permettent à l’épidémiologiste de cerner au mieux la nature causale de la relation entre facteur et maladie, mais celle-ci relève de l’interprétation, car des circonstances non causales peuvent aussi induire une relation, le hasard mais aussi l’effet d’autres facteurs connectés. La philosophie identifie trois niveaux de discussion dans l’usage de la notion de causalité : le problème kantien de la distinction entre réalité absolue et réalité perçue par l’Homme, étant donné ses facultés de connaissance ; le problème positiviste de la difficulté d’identifier des causes à partir de l’observation des phénomènes naturels, liaison entre phénomènes ne signifiant pas nécessairement succession causale ; le problème de l’induction, multiplier les expériences ne pouvant apporter de preuve définitive, les falsificationistes proposant d’étudier la robustesse d’un résultat en le soumettant à de nouveaux tests visant à le réfuter. Il ressort de cette réflexion interdisciplinaire différents apports à la pratique de l’épidémiologie et plus généralement de la recherche en biologie : entre autres rechercher les contextes les plus à même de remettre en question le résultat ; établir une conjonction de résultats différents et complémentaires pour conforter l’hypothèse de causalité, ce qui est en lien avec les dix critères de causalité utilisés par les épidémiologistes pour évaluer et discuter la nature causale d’une relation. En définitive, avoir un regard critique sévère sur les résultats d’étude est la seule façon d’apporter du crédit à l’interprétation quant à la causalité d’une relation statistique significative

International audience; In developing countries, smallholder poultry production contributes to food security and poverty alleviation in rural areas. However, traditional poultry marketing chains have been threatened by the epidemics caused by the Highly Pathogenic Avian Influenza (H5N1) virus. The article presents a value chain analysis conducted on the traditional poultry marketing chain in the rural province of Phitsanulok, Thailand. The analysis is based on quantitative data collected on 470 backyard chicken farms, and on qualitative data collected on 28 poultry collectors, slaughterhouses and market retailers, using semi-structured interviews. The article examines the organization of poultry marketing chains in time and space, and shows how this may contribute to the spread of Highly Pathogenic Avian Influenza H5N1 in the small-scale poultry sector. The article also discusses the practices and strategies developed by value chain actors facing poultry mortality, with their economic and social determinants. More broadly, this study also illustrates how value chain analysis can contribute to a better understanding of the complex mechanisms associated with the spread of epidemics in rural communities.

International audience; The incidence of catheter-associated urinary tract infections in cats catheterised for an obstructive lower urinary tract disease (LUTD) has not previously been evaluated. The objective of this study was to evaluate the frequency of significant bacteriuria in cats with obstructive LUTD managed for 48 h with a closed urine collection system. Eighteen male cats admitted for a non-infectious obstructive LUTD were evaluated. This was a prospective study. A standard protocol was used for aseptic catheter placement and maintenance. Three urine samples were collected from each animal through the catheter immediately after placement, 24 h after placement and just before removal. All samples underwent complete urinalysis, including bacterial culture. Catheter tips were tested by bacterial culture. Six cats (33.3%) developed significant bacteriuria during catheterisation. The causative bacteria were common feline uropathogens (Escherichia coli, Staphylococcus species) in five cases, and Streptococcus bovis in one. One cat developed a fungal infection. The presence of bacteria in urinary sediment was correlated strongly with positive urine culture results. The catheter tips from 10/18 cats (55.5%) were positive for culture. The positive predictive value of a positive culture from the urinary catheter tip was 87.5%. The specificity was 53.8%. The same infectious agents were cultured from both urine and catheter tip in six cases. In summary, one third of cats developed significant bacteriuria during catheterisation. Silent bacteriuria could not be clearly differentiated from true urinary tract infection. The presence of bacteria in the urinary sediment was strongly indicative of bacteriuria. The specificity of urinary catheter tip culture was low.

International audience; Equine encephalosis is a midge-borne viral disease of equines caused by equine encephalosis virus (EEV, Orbivirus, Reoviridae), and closely related to African horse sickness virus (AHSV). EEV and AHSV share com- mon vectors and show similar transmission patterns. Until now EEV has caused outbreaks in Africa and Israel. This study aimed to provide insight in the probability of an EEV outbreak in The Netherlands caused by infected vectors or hosts, the contribution of potential source areas (risk regions) to this probability, and the effectiveness of preventive measures (sanitary regimes). A stochastic risk model constructed for risk assessment of AHSV introduction was adapted to EEV. Source areas were categorized in risk regions (high, low, and very low risk) based on EEV history and the presence of competent vectors. Two possible EEV introduction pathways were considered: importation of infected equines and importation of infected vectors along with their vertebrate hosts. The probability of EEV introduction (PEEV ) was calculated by combining the probability of EEV release by either pathway and the probability of EEV establishment. The median current annual probability of EEV introduction by an infected equine was estimated at 0.012 (90% uncertainty interval 0.002–0.020), and by an infected vector at 4.0 10−5 (90% uncertainty interval 5.3 10−6–2.0 10−4). Equines from high risk regions contributed most to the probability of EEV introduction with 74% on the EEV introduction by equines, whereas low and very low risk regions contributed 18% and 8%, respectively. International movements of horses participating in equestrian events contributed most to the probability of EEV introduction by equines from high risk regions (86%), but also contributed substantially for low and very low risk regions with 47% and 56%. The probability of introducing EEV into The Netherlands is much higher than the probability of intro- ducing AHSV with equines from high risk countries contributing most. The introduction by an infected equine is the most likely pathway. Control measures before exportation of equines showed to have a strong mitigating effect on the probability of EEV introduction. The risk of EEV outbreaks should be taken into account when altering these import regulations.

Several recent public health crises have shown that the surveillance of zoonotic agents in wildlife is important to prevent pandemic risks. High-throughput sequencing (HTS) technologies are potentially useful for this surveillance, but rigorous experimental processes are required for the use of these effective tools in such epidemiological contexts. In particular, HTS introduces biases into the raw data set that might lead to incorrect interpretations. We describe here a procedure for cleaning data before estimating reliable biological parameters, such as positivity, prevalence, and coinfection, using 16S rRNA amplicon sequencing on an Illumina MiSeq platform. This procedure, applied to 711 rodents collected in West Africa, detected several zoonotic bacterial species, including some at high prevalence, despite their never before having been reported for West Africa. In the future, this approach could be adapted for the monitoring of other microbes such as protists, fungi, and even viruses., The human impact on natural habitats is increasing the complexity of human-wildlife interactions and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. We investigated the potential for recent developments in 16S rRNA amplicon sequencing to facilitate the multiplexing of the large numbers of samples needed to improve our understanding of the risk of zoonotic disease transmission posed by urban rodents in West Africa. In addition to listing pathogenic bacteria in wild populations, as in other high-throughput sequencing (HTS) studies, our approach can estimate essential parameters for studies of zoonotic risk, such as prevalence and patterns of coinfection within individual hosts. However, the estimation of these parameters requires cleaning of the raw data to mitigate the biases generated by HTS methods. We present here an extensive review of these biases and of their consequences, and we propose a comprehensive trimming strategy for managing these biases. We demonstrated the application of this strategy using 711 commensal rodents, including 208 Mus musculus domesticus, 189 Rattus rattus, 93 Mastomys natalensis, and 221 Mastomys erythroleucus, collected from 24 villages in Senegal. Seven major genera of pathogenic bacteria were detected in their spleens: Borrelia, Bartonella, Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia. Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia have never before been detected in West African rodents. Bacterial prevalence ranged from 0% to 90% of individuals per site, depending on the bacterial taxon, rodent species, and site considered, and 26% of rodents displayed coinfection. The 16S rRNA amplicon sequencing strategy presented here has the advantage over other molecular surveillance tools of dealing with a large spectrum of bacterial pathogens without requiring assumptions about their presence in the samples. This approach is therefore particularly suitable to continuous pathogen surveillance in the context of disease-monitoring programs. IMPORTANCE Several recent public health crises have shown that the surveillance of zoonotic agents in wildlife is important to prevent pandemic risks. High-throughput sequencing (HTS) technologies are potentially useful for this surveillance, but rigorous experimental processes are required for the use of these effective tools in such epidemiological contexts. In particular, HTS introduces biases into the raw data set that might lead to incorrect interpretations. We describe here a procedure for cleaning data before estimating reliable biological parameters, such as positivity, prevalence, and coinfection, using 16S rRNA amplicon sequencing on an Illumina MiSeq platform. This procedure, applied to 711 rodents collected in West Africa, detected several zoonotic bacterial species, including some at high prevalence, despite their never before having been reported for West Africa. In the future, this approach could be adapted for the monitoring of other microbes such as protists, fungi, and even viruses.

The Highly Pathogenic Avian Influenza H5N1 (HPAI) virus is now considered endemic in several Asian countries. In Cambodia, the virus has been circulating in the poultry population since 2004, with a dramatic effect on farmers’ livelihoods and public health. In Thailand, surveillance and control are still important to prevent any new H5N1 incursion. Risk mapping can contribute effectively to disease surveillance and control systems, but is a very challenging task in the absence of reliable disease data. In this work, we used spatial multicriteria decision analysis (MCDA) to produce risk maps for HPAI H5N1 in poultry. We aimed to i) evaluate the performance of the MCDA approach to predict areas suitable for H5N1 based on a dataset from Thailand, comparing the predictive capacities of two sources of a priori knowledge (literature and experts), and ii) apply the best method to produce a risk map for H5N1 in poultry in Cambodia. Our results showed that the expert-based model had a very high predictive capacity in Thailand (AUC = 0.97). Applied in Cambodia, MCDA mapping made it possible to identify hotspots suitable for HPAI H5N1 in the Tonlé Sap watershed, around the cities of Battambang and Kampong Cham, and along the Vietnamese border.

National audience; L'un des objectifs de la cartographie du risque appliquée en épidémiologie est l'étude et la comparaison de plusieurs modèles pour apporter un soutien aux différentes hypothèses concernant une maladie donnée. Il s'agit notamment du choix des variables explicatives, de leurs interactions, de leur influence sur le risque modélisé ou des hypothèses sur leurs fonctions de répartition. Ayant d'habitude un grand nombre de modèles implémentés pour un problème donné, on a besoin d'une méthode pour comparer leurs performances et sélectionner le meilleur modèle parmi tous ceux considérés. Idéalement, on voudrait identifier celui qui représente le meilleur compromis entre l'ajustement aux données, le lissage des cartes obtenues, la sensibilité du modèle aux perturbations, sagénéralité, sa simplicité et sa facilité d'estimation. On voudrait être capable de comparer des modèles imbriqués aussi que des modèles assez éloignés les uns des autres. A cause de ces divers objectifs, il n'existe pas de procédure de sélection de modèle qui soit universellement valable. Le sujet de notre étude concerne le problème d'identification d'une méthode de sélection de modèle adaptée au cadre spatio-temporel de la cartographie du risque des maladies contagieuses. Notre objectif est d'investiguer la performance du critère le plus utilisé dans la cartographie du risque, le critère DIC, et de proposer des solutions mieux adaptées à notre cadre.

International audience; Les tiques sont des vecteurs majeurs de maladies à la fois animales et humaines (la plupart étant zoonotiques) et dans l'hémisphère nord, elles sont considérées comme les vecteurs les plus importants en santé humaine en raison notamment de la maladie de lyme. Même si l'espèce la plus fréquente en Europe - Ixodes ricinus - est d'abord forestière en raison de l'hygrométrie importante qu'elle exige, on la retrouve cependant dans d'autres biotopes (bordures de prairies, haies, landes...) où elle exploite une grande diversité d'hôtes à la fois dans la faune sauvage (rongeurs, cervidés...) et domestique (bovins, ovins...), qui sont éventuellement des réservoirs d'agents pathogènes. En raison de l'hétérogénéité spatiale de ces différents milieux à l'échelle du paysage, on ne peut pas comprendre la propagation dans l'espace et dans le temps de ces maladies au sein des agro-écosystèmes sans prendre en compte la répartition de ces biotopes ainsi que la distribution et les mouvements des animaux. Le projet OSCAR (Outil de Simulation Cartographique à l'échelle du paysage Agricole du Risque acarologique ; ANR Agrobiosphère, 2012-2016) a pour objectif d'analyser la distribution observée du risque acarologique (défini comme le produit de la densité de tiques par la prévalence des agents pathogènes au sein des tiques), de mieux comprendre la dynamique spatio-temporelle des populations de tiques et d'établir des cartes prédictives du risque acarologique basées sur des scénarios de changement de structure du paysage. Il implique 5 laboratoires (2 du DSA, 1 d'EFPA et 2 du CNRS), qui ont participé aux travaux de collecte d'informations (présence d'animaux domestiques dans les parcelles, localisation de chevreuils équipés de colliers GPS, abondance des micromammifères estimée par piégeage, caractérisation des biotopes étudiés...) et de matériels biologiques (tiques, sangs...) dans 2 zones d'études (les zones Atelier Armorique et Vallons et Côteaux de Gascogne). Des travaux de biologie moléculaire ont permis de caractériser la variabilité génétique au sein des populations de tiques et de rechercher la présence de 3 agents pathogènes dans ces échantillons (Anaplasma phagocytophilum, Borrelia spp. et Babesia spp.). L'analyse des densités de tiques sur la végétation a montré de fortes variations à l'échelle du paysage (avec une absence de tiques en bordure de pâtures lorsque les haies sont trop réduites par exemple). Concernant l'abondance des micromammifères, nous avons observé qu'un réseau de haies et de bosquets plus dense est plus favorable aux mulots sylvestres, tandis que les campagnols roussâtres sont plus abondants dans les habitats boisés isolés. Les importantes fluctuations d'abondance interannuelles de ces rongeurs entraînent de fortes fluctuations des densités du stade nymphal des tiques sur la végétation une saison plus tard. Les prévalences (dans les tiques collectées sur la végétation) des 3 agents pathogènes étudiés se sont avérées faibles (2 à 5 %). Les prévalences d'A. phagocytophilum et de Babesia (B. venatorum et B. capreoli) dans les chevreuils se sont quant à elles révélées importantes (de 65 % à 85 %). L'analyse de la variabilité génétique d'A. phagocytophilum a montré l'existence de plusieurs clades génétiquement distants dont un plus particulièrement associé au chevreuil. Les analyses de génétique des populations des tiques à l'échelle du paysage ont révélé d'importants flux de gènes et une absence de structuration entre populations, suggérant une importante dispersion via les mouvements des hôtes. La dernière année du projet est consacrée à la réalisation d'un modèle spatialisé prenant de compte l'hétérogénéité du paysage afin de prédire les densités de tiques en fonction des différents éléments qui le composent et explorer ainsi par simulation comment la modification de la structure du paysage impactera les densités de tiques

International audience; Hantaviruses are emerging zoonotic viruses that cause human diseases. In this study, sera from 642 mammals from La Réunion and Mayotte islands (Indian Ocean) were screened for the presence of hantaviruses by molecular analysis. None of the mammals from La Réunion island was positive, but hantavirus genomic RNA was discovered in 29/160 (18 %) Rattus rattus from Mayotte island. The nucleoprotein coding region was sequenced from the liver and spleen of all positive individuals allowing epidemiological and intra-strain variability analyses. Phylogenetic analysis based on complete coding genomic sequences showed that this Murinae-associated hantavirus is a new variant of Thailand virus. Further studies are needed to investigate hantaviruses in rodent hosts and in Haemorrhagic Fever with Renal Syndrome (HFRS) human cases.

International audience

International audience

National audience

National audience

Maladie de Lyme et autres infections : rôle des tiques, des bactéries et des animaux. Conférence proposée par l'Association pour le Développement de l'Animation Scientifique et Technique en Auvergne

National audience; Deuxième prix du jury : Antoine VERNAY, qui effectue sa thèse intitulée « Rôle des interactions azote - eau du sol dans les rapports de compétition entre plantes suite à une éclaircie - Application à la régénération de jeunes plants de Chêne en compétition avec la Molinie »

National audience

National audience; L'anaplasmose granulocytaire, est une maladie émergente qui infecte une large gamme de mammifères dont les ruminants et l'homme. Cette maladie est due à une bactérie, Anaplasma phagocytophilum, transmise par les tiques. La description des cycles épidémiologiques de cette bactérie est incomplète, car si on trouve de nombreuses espèces participent au même cycle épidémiologique. Les chevreuils et les rongeurs sont souvent suspectés d'être des hôtes réservoir, du fait des fortes prévalences observées dans leurs populations (jusqu'à 25 % d'individus infectés chez les campagnols roussâtres et 80 % chez les chevreuils). L'objectif de ce travail était de caractériser la diversité génétique d'A. phagocytophilum chez différentes espèces d'hôtes, afin d'identifier les cycles épidémiologiques. Nous avons caractérisé la diversité génétique d'A. phagocytophilum sur 9 loci chez 120 animaux domestiques malades provenant de toute la France (104 bovins, 13 chevaux, 3 chiens) ainsi que 40 chevreuils. L'analyse phologénétique multi-loci nous a permis d'identifier trois groupes de génotypes infectant les bovins. Les deux principaux groupes incluent 98 % des génotypes bactériens trouvés chez les bovins et sont génétiquement distant de ceux observés chez les chevreuils. Un groupe de génotypes implique exclusivement les bovins, alors que le second contient des génotypes partagés par les bovins, les chevaux et les chiens. Le troisième groupe contient tous les génotypes de chevreuils et seulement trois génotypes de bovins. Nous n'avons pas observé de divergence géographique, les trois groupes de génotypes ont été observés simultanément dans le Doubs, le Finistère et les Côtes d'Armor. Bien que les rongeurs soient porteurs de la bactérie, nous n'avons pas réussi à obtenir les séquences, signifiant que les génotypes portés sont sans doute bien différents de ceux trouvés chez les bovins. Ces résultats suggèrent que les chevreuils et les rongeurs ne contribuent pas à la propagation d'A. phagocytophilum chez les animaux domestiques en France. Cette étude montre la complexité des cycles d'A. phagocytophilum, suggère que plusieurs réservoirs sont sans doute impliqués et souligne l'intérêt de l'utilisation des approches moléculaires

Equine viral arteritis (EVA) may have serious economic impact on the equine industry. For this reason, it is monitored in many countries, especially in breeding stock, to avoid its spread during breeding activities. In France, surveillance is mainly based on serological tests, since mares are not vaccinated, but difficulties in interpreting certain series of results may impair the estimation of the number of outbreaks. In this study, we propose specific rules for identifying seroconversion in order to estimate the number of outbreaks that were detected by the breeding stock surveillance component (BSSC) in France between 2006 and 2013. A consensus among multidisciplinary experts was reached to consider seroconversion as a change in antibody titer from negative to at least 32, or as an eight-fold or greater increase in antibody level. Using these rules, 239 cases and 177 outbreaks were identified. Subsequently, we calculated the BSSC's sensitivity as the ratio of the number of detected outbreaks to the total number of outbreaks that occurred in breeding stock (including unreported outbreaks) estimated using a capture-recapture model. The total number of outbreaks was estimated at 215 (95% credible interval 195-249) and the surveillance sensitivity at 82% (CrI95% 71-91). Our results confirm EVA circulation in French breeding stock, show that neutralizing antibodies can persist up to eight years in naturally infected mares and suggest that certain mares have been reinfected. This study shows that the sensitivity of the BSSC is relatively high and supports its relevance to prevent the disease spreading through mating.

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International audience; The vector tick I. ricinus population dynamic is driven by weather conditions, mainly temperature and relative humidity. Both variables are of major concern in the context of climate warming. Providing relevant predictions for present and future tick activity time patterns requires integrating the joint effect of temperature and relative humidity on the life cycle biological processes in population dynamic models (PDM). A PDM of I. ricinus was established in which the biological processes varied with temperature and relative humidity time series. The PDM focused on host-questing and survival. Both were a priori modelled from expert knowledge and literature data respectively. The parameters associated with each process were then posteriori estimated based on observed field and laboratory data, using a Bayesian inference method. The posteriori parameters can be integrated in a PDM for simulations so as to assess their ability to fit to observed field time series

International audience; Since the first description of Anaplasma platys Infection (ApI), the disease has been sporadically reportedworldwide. Whereas it is considered a subclinical disease in the United States or in Australia, severe casesare reported in Europe. Thus far, little information is available regarding the clinical and laboratory find-ings associated with the disease and the implication of co-infections with other vector-borne pathogens(VBPs) in Southern Europe. The purpose of the study was to describe clinical and laboratory findings inPCR-confirmed naturally infected dogs in the Mediterranean Basin, and to assess the potential impact ofco-infections with other VBPs. This is a retrospective analysis of medical records from 32 client-owneddogs diagnosed with ApI using PCR-based assays. Anorexia (62.5%) and weight loss (43.8%) were the majorchanges, whereas lethargy was less frequent (34.4%). Lymphadenomegaly (43.8%), hyperthermia (40.6%)and hemorrhage (37.5%) were frequent clinical abnormalities, whereas cutaneous signs (31.3%), muscu-loskeletal disorders (21.9%), splenomegaly (15.6%), dehydration and ocular inflammation (12.5%) wereless common. Hematological abnormalities included thrombocytopenia (81.0%), anemia (81.0%), leukocy-tosis (33.3%) and leucopenia (23.8%). Seven dogs (33.3%) were severely thrombocytopenic. Among the 28dogs with complete testing, 15 and 13 were mono- and co-infected, respectively. Co-infections includedEhrlichia canis (3 dogs), Leishmania infantum (4), Babesia vogeli (2) and Hepatozoon canis (5). One dog wasinfected concurrently with Anaplasma platys, Ehrlichia canis and Babesia vogeli. The 1-month mortalityrate was 23.9% and only 38.1% improved. In the univariate analysis the 15 mono- and the 13 co-infecteddogs did not differ regarding the relative frequencies of clinical and laboratory findings. Sequencing andphylogenetic analyses suggested the existence of 2 different groups of strains: one of them might havehigher pathogenicity. In all, ApI was associated with a wide variety of non-specific clinical findings. Themost common laboratory findings were thrombocytopenia and anemia. Co-infections were frequent butappeared of limited clinical impact. The absence of improvement despite appropriate treatment, highfrequency of hemorrhagic disorders, and case fatalities, suggested the existence of pathogenic Europeanstrains supported by subsequent molecular analyses.

National audience; Deuxième prix du jury : Antoine VERNAY, qui effectue sa thèse intitulée « Rôle des interactions azote - eau du sol dans les rapports de compétition entre plantes suite à une éclaircie - Application à la régénération de jeunes plants de Chêne en compétition avec la Molinie »

International audience

National audience

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.

Une base de données bibliométrique établie à partir du Web of Science Core collection® a recensé les articles scientifiques publiés entre 2006 et 2013 dans le domaine des maladies infectieuses et zoonotiques des animaux d’élevage, incluant poissons et abeilles ; seules les revues internationales et les articles rédigés en anglais ont été considérés. La production scientifique française de ce domaine, de 400 publications par an environ, représente 4,3% de la production scientifique mondiale. L’auteur principal de ces articles est d’une équipe française dans 60% des cas, et le nombre de publications augmente de 3% par an, à comparer à 5% au niveau mondial. Quarante-quatre pourcents des articles portent sur les ruminants, 20% sur les volailles, 11% les poissons, 10% le porc, 5% le lapin, 4% le cheval, 1% les abeilles, le reste concernant différentes espèces. Le nombre d’articles est en diminution pour le lapin et le cheval, en augmentation pour les volailles, les poissons, le porc et les abeilles ; 44% des articles portent sur des virus, 31% sur des bactéries, 22% sur des parasites, 5% sur les prions. Cette distribution et les familles d’agents pathogènes étudiés sont très semblables à ce qui est produit au niveau mondial, avec des nuances. Une collaboration internationale est présente dans 62% des cas, et cette proportion augmente progressivement. Les principaux pays partenaires sont les pays européens limitrophes de la France, ainsi que les Etats Unis et dans une moindre mesure le Canada, la Chine et l’Afrique du sud., A bibliometric database based on the Web of Science Core collection® includes scientific papers published between 2006 and 2013 on infectious and zoonotic diseases affecting livestock animals, including fish and bees ; only international journals and papers written in English were considered. The French scentific production reached around 400 papers per year and represented 4.3% of the international scientific production. The main author was from a French research team for 60% of the papers and the number of publications shows a 3% annual increase rate, to be compared to the international rate of 5%. Forty-four percent of the papers dealt with ruminants, 20% poultry, 11% fish, 10% pigs, 5% rabbits, 4% horses, 1% bees and the others were multipecies. The number of papers decreased progressively for rabbits and horses, whereas it increased for poultry, fish, pigs and bees; 44% of the papers concerned viruses, 31% bacteria, 22% parasites, 5% prions. These distributions as well as the families of pathogens studied were quite similar to what is observed worldwide, with small differences. An international collaboration was observed for 62% of the papers, and this percentage increased progressively. The main partner countries were the neighbourhood countries of France as well as the United States and to a lesser extent Canada, China and South Africa.

International audience; Background: Various methods are currently used for the early detection of West Nile virus (WNV) but their outputs are not quantitative and/or do not take into account all available information. Our study aimed to test a multivariate syndromic surveillance system to evaluate if the sensitivity and the specificity of detection of WNV could be improved. Methods: Weekly time series data on nervous syndromes in horses and mortality in both horses and wild birds were used. Baselines were fitted to the three time series and used to simulate 100 years of surveillance data. WNV outbreaks were simulated and inserted into the baselines based on historical data and expert opinion. Univariate and multivariate syndromic surveillance systems were tested to gauge how well they detected the outbreaks; detection was based on an empirical Bayesian approach. The systems' performances were compared using measures of sensitivity, specificity, and area under receiver operating characteristic curve (AUC). Results: When data sources were considered separately (i.e., univariate systems), the best detection performance was obtained using the data set of nervous symptoms in horses compared to those of bird and horse mortality (AUCs equal to 0.80, 0.75, and 0.50, respectively). A multivariate outbreak detection system that used nervous symptoms in horses and bird mortality generated the best performance (AUC = 0.87). Conclusions: The proposed approach is suitable for performing multivariate syndromic surveillance of WNV outbreaks. This is particularly relevant, given that a multivariate surveillance system performed better than a univariate approach. Such a surveillance system could be especially useful in serving as an alert for the possibility of human viral infections. This approach can be also used for other diseases for which multiple sources of evidence are available.

Human leptospirosis is a zoonotic and potentially fatal disease that has increasingly been reported in both developing and developed countries, including France. However, our understanding of the basic aspects of the epidemiology of this disease, including the source of Leptospira serogroup Australis infections in humans and domestic animals, remains incomplete. We investigated the genetic diversity of Leptospira in 28 species of wildlife other than rats using variable number tandem repeat (VNTR) and multispacer sequence typing (MST). The DNA of pathogenic Leptospira was detected in the kidney tissues of 201 individuals out of 3,738 tested individuals. A wide diversity, including 50 VNTR profiles and 8 MST profiles, was observed. Hedgehogs and mustelid species had the highest risk of being infected (logistic regression, OR = 66.8, CI95% = 30.9–144 and OR = 16.7, CI95% = 8.7–31.8, respectively). Almost all genetic profiles obtained from the hedgehogs were related to Leptospira interrogans Australis, suggesting the latter as a host-adapted bacterium, whereas mustelid species were infected by various genotypes, suggesting their interaction with Leptospira was different. By providing an inventory of the circulating strains of Leptospira and by pointing to hedgehogs as a potential reservoir of L. interrogans Australis, our study advances current knowledge on Leptospira animal carriers, and this information could serve to enhance epidemiological investigations in the future.

In the early twentieth century, only a few count distributions (binomial and Poisson distributions) werecommonly used in modeling. These distributions fail to model bimodal or overdispersed data, especially data related to phenomena for which the occurrence of a given event increases the chance of additional events occurring. New count distributions have since been introduced to address such phenomena; they are named "contagious" distributions. This group of distributions, which includes the negative binomial, Neyman, Thomas and Pólya-Aeppli distributions, can be expressed as mixture distributions or as stopped-sum distributions. They take into account bimodality and overdispersion, and show a greater flexibility with regards to value distributions. The aim of this literature review is to 1) explain the introduction of these distributions, 2) describe each of these overdispersed distributions, focusing in particular on their definitions, their basic properties, and their practical utility, and 3) compare their strengths and weaknesses by modeling overdispersed real count data (bovine tuberculosis cases)., Au début du vingtième siècle, seules quelques lois de comptage (loi binomiale, loi de Poisson) sontcouramment utilisées en modélisation. Elles trouvent leur limite dans la modélisation de données bimodales ousurdispersées, notamment celles associées à un phénomène dont la survenue engendre d’autres occurrences. Pour les modéliser, de nouvelles lois sont élaborées, dites "lois contagieuses". Ces distributions, telles que la loi binomiale négative, la loi de Neyman, la loi de Thomas ou encore la loi de Pólya-Aeppli, peuvent s’exprimer sous forme de mélange de lois usuelles ou encore de somme de variables aléatoires dont l’indice est borné par une variable aléatoire.Elles permettent d’ajuster des répartitions bimodales, surdispersées et très irrégulières. L’objectif de notre revue de la littérature est de décrire l’apparition de ces lois surdispersées, d’effectuer un descriptif de chacune de ces distributions, en s’intéressant en particulier à leurs différentes caractérisations, à leurs propriétés élémentaires et à leur utilisation potentielle, et enfin de les comparer en les appliquant à des données réelles surdispersées (cas de tuberculose bovine).

National audience