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Foot and mouth disease (FMD) is a highly contagious viral disease that affects all Artiodactyla. Seven immunologically distinct serotypes of FMD virus (FMDV) exist. In Chad, although FMD is included in the list of diseases monitored by the Chadian Animal Disease Surveillance Network (REPIMAT), the epidemiological situation remains unclear. A serological survey was conducted in the cattle population in eight of the nine administrative regions of the country (those regions with the highest cattle densities), to evaluate the prevalence and serotypes of circulating FMDV.A total of 796 sera from randomly selected cattle were analysed at the World Organisation for Animal Health/Food and Agriculture Organization of the United Nations FMD Reference Laboratory at the Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna(IZSLER), in Brescia (Italy). An enzyme-linked immunosorbent assay (ELISA), called 3ABC ELISA, was used to detect antibodies against non-structural proteins (NSPs), as well as a series of six competitive ELISAs to detect and serotype antibodies against the structural proteins of FMDV serotypes O, A, SAT 1, SAT 2, Asia 1 and C. Based on the detection of anti-NSP antibodies, the animal-level seroprevalence was 35.6%(95% confidence interval [CI]: 32.2-38.9) and the herd-level seroprevalence was 62.3% (95%CI: 53.0-71.5). FMD was present in all livestock administrative divisions surveyed, with a higher prevalence in southern regions, which are characterised by higher rainfall and humidity and more important transboundary animal movements. Cattle aged more than four years had a higher seroprevalence, which may be due to repeated exposure. Semi-sedentary farming and transhumance were also risk factors. Antibodies against serotypes A, O, SAT 1 and SAT 2 were detected.

International audience; Unravelling the ecological structure of emerging plant pathogens persisting in multi-host systems is challenging. In such systems, observations are often heterogeneous with respect to time, space and host species, and may lead to biases of perception. The biased perception of pathogen ecology may be exacerbated by hidden fractions of the whole host population, which may act as infection reservoirs. We designed a mechanistic-statistical approach to help understand the ecology of emerging pathogens by filtering out some biases of perception. This approach, based on SIR (Susceptible-Infected-Removed) models and a Bayesian framework, disentangles epidemiological and observational processes underlying temporal counting data. We applied our approach to French surveillance data on Xylella fastidiosa, a multi-host pathogenic bacterium recently discovered in Corsica, France. A model selection led to two diverging scenarios: one scenario without a hidden compartment and an introduction around 2001, and the other with a hidden compartment and an introduction around 1985. Thus, Xylella fastidiosa was probably introduced into Corsica much earlier than its discovery, and its control could be arduous under the hidden compartment scenario. From a methodological perspective, our approach provides insights into the dynamics of emerging plant pathogens and, in particular, the potential existence of infection reservoirs.

International audience; AbstractThe first pan-European harmonized active epidemiological surveillance program on honeybee colony mortality (EPILOBEE) was set up across 17 European Member States to estimate honeybee colony mortality over winter and during the beekeeping season. In nine Member States, overwinter losses were higher and statistically different from the empirical level of 10 % under which the level of overwinter mortality was considered as acceptable with usual beekeeping conditions. In four other countries, these losses were lower. Using multivariable Poisson regression models, it was showed that the size of the operation and apiary and the clinically detected varroosis, American foulbrood (AFB), and nosemosis before winter significantly affected 2012–2013 overwinter losses. Clinically detected diseases, the size of the operation and apiary, and the non-participation to a common veterinary treatment significantly affected 2013 summer losses. EPILOBEE was a prerequisite to implement future projects studying risk factors affecting colony health such as multiple and co-exposure to pesticides.

International audience; Mycobacterium bovis infection was first described in free-ranging wildlife in France in 2001, with subsequent detection in hunter-harvested ungulates and badgers in areas where outbreaks of bovine tuberculosis (TB) were also detected in cattle. Increasing concerns regarding TB in wildlife led the French General Directorate for Food (DGAL) and the main institutions involved in animal health and wildlife management, to establish a national surveillance system for TB in free-ranging wildlife. This surveillance system is known as “Sylvatub.” The system coordinates the activities of various national and local partners. The main goal of Sylvatub is to detect and monitor M. bovis infection in wildlife through a combination of passive and active surveillance protocols adapted to the estimated risk level in each area of the country. Event-base surveillance relies on M. bovis identification (molecular detection) (i) in gross lesions detected in hunter-harvested ungulates, (ii) in ungulates that are found dead or dying, and (iii) in road-killed badgers. Additional targeted surveillance in badgers, wild boars and red deer is implemented on samples from trapped or hunted animals in at-risk areas. With the exception of one unexplained case in a wild boar, M. bovis infection in free-living wildlife has always been detected in the vicinity of cattle TB outbreaks with the same genotype of the infectious M. bovis strains. Since 2012, M. bovis was actively monitored in these infected areas and detected mainly in badgers and wild boars with apparent infection rates of 4.57–5.14% and 2.37–3.04%, respectively depending of the diagnostic test used (culture or PCR), the period and according to areas. Sporadic infection has also been detected in red deer and roe deer. This surveillance has demonstrated that M. bovis infection, in different areas of France, involves a multi-host system including cattle and wildlife. However, infection rates are lower than those observed in badgers in the United Kingdom or in wild boars in Spain.

Background From 2006 to 2010, France experienced two bluetongue epidemics caused by serotype 1 (BTV-1) and 8 (BTV-8) which were controlled by mass vaccination campaigns. After five years without any detected cases, a sick ram was confirmed in August 2015 to be infected by a BTV-8 strain almost identical to that circulating during the previous outbreak. By then, part of the French cattle population was expected to be still protected, since bluetongue antibodies are known to last for many years after natural infection or vaccination. The objective of this study was to estimate the proportion of cattle in France still immune to BTV-8 at the time of its re-emergence in 2015. Results We used BTV group-specific cELISA results from 8525 cattle born before the vaccination ban in 2013 and 15,799 cattle born after the ban. Samples were collected from January to April 2016 to estimate seroprevalence per birth cohort. The overall seroprevalence in cattle at national and local levels was extrapolated from seroprevalence results per birth cohort and their respective proportion at each level. To indirectly assess pre-immune status of birth cohorts, we computed prevalence per birth cohort on infected farms in autumn 2015 using 1377 RT-PCR results. These revealed limited BTV circulation in 2015. Seroprevalence per birth cohort was likely to be connected to past exposure to natural infection and/or vaccination with higher seroprevalence levels in older animals. A seroprevalence of 95% was observed for animals born before 2008, of which > 90% were exposed to two compulsory vaccination campaigns in 2008-2010. None of the animals born before 2008 were found to be infected, unlike 19% of the young cattle which had never been vaccinated. This suggests that most ELISA-positive animals were pre-immune to BTV-8. We estimated that 18% (from 12% to 32% per département) of the French cattle population was probably pre-immune in 2015. Conclusions These results strongly suggest a persistence of antibodies for at least 5-6 years after natural infection or vaccination. The herd immunity of the French cattle population probably limited BTV circulation up to 2015, by which time more than 80% of cattle were naive. Electronic supplementary material The online version of this article (10.1186/s12917-018-1388-1) contains supplementary material, which is available to authorized users.

BGPI: équipe 6Paper based on work presented at the Joint EFSA-EPPO Workshop: Modelling in Plant Health – how can models support risk assessment of plant pests and decision-making? 12th–14th December 2016, Parma, Italy; International audience; The optimization of management strategies for plant diseases is a difficult task because of the complexity and variability of epidemic dynamics. Thanks to their ability to numerically simulate many scenarios, models can be used to estimate epidemiological parameters, assess the effectiveness of different management strategies and optimize them. This article presents the PESO (parameter estimation–simulation–optimization) modelling framework to help improve plant disease management strategies. This framework is based on (i) the characterization of the epidemic dynamics to estimate key epidemiological parameters, (ii) the use of spatially explicit models to simulate epidemic dynamics and disease management, and (iii) the use of numerical optimization methods to identify better management strategies. This approach is generic and can be applied to many diseases. The work presented here focuses on sharka (caused by Plum pox virus), which has a worldwide impact on the Prunus industry, and is associated with huge disease management costs in many countries, especially in France.

International audience; Bovine tuberculosis (bTB) is a common disease in cattle and wildlife, with an impact on animal and human health, and economic implications. Infected wild animals have been detected in some European countries, and bTB reservoirs in wildlife have been identified, potentially hindering the eradication of bTB from cattle populations. However, the surveillance of bTB in wildlife involves several practical difficulties and is not currently covered by EU legislation. We report here the first assessment of the sensitivity of the bTB surveillance system for free-ranging wildlife launched in France in 2011 (the Sylvatub system), based on scenario tree modelling. Three surveillance system components were identified: (i) passive scanning surveillance for hunted wild boar, red deer and roe deer, based on carcass examination, (ii) passive surveillance on animals found dead, moribund or with abnormal behaviour, for wild boar, red deer, roe deer and badger and (iii) active surveillance for wild boar and badger. The application of these three surveillance system components depends on the geographic risk of bTB infection in wildlife, which in turn depends on the prevalence of bTB in cattle. We estimated the effectiveness of the three components of the Sylvatub surveillance system quantitatively, for each species separately. Active surveillance and passive scanning surveillance by carcass examination were the approaches most likely to detect at least one infected animal in a population with a given design prevalence, regardless of the local risk level and species considered. The awareness of hunters, which depends on their training and the geographic risk, was found to affect surveillance sensitivity. The results obtained are relevant for hunters and veterinary authorities wishing to determine the actual efficacy of wildlife bTB surveillance as a function of geographic area and species, and could provide support for decision-making processes concerning the enhancement of surveillance strategies.

The Schmallenberg virus (SBV) emerged in Europe in 2011 and caused a widespread epidemic in ruminants. In France, SBV emergence was monitored through a national multi-stakeholder surveillance and investigation system. Based on the monitoring data collected from January 2012 to August 2013, we describe the spread of SBV in France during two seasons of dissemination (vector seasons 2011 and 2012) and we provide a large-scale assessment of the impact of this new disease in ruminants. SBV impact in infected herds was primarily due to the birth of stillborns or deformed foetuses and neonates. Congenital SBV morbidity level was on average moderate, although higher in sheep than in other ruminant species. On average, 8% of lambs, 3% of calves and 2% of kids born in SBV-infected herds showed typical congenital SBV deformities. In addition, in infected herds, farmers reported retrospectively a lower prolificacy during the vector season, suggesting a potential impact of acute SBV infection during mating and early stages of gestation. Due to the lack of available control and prevention measures, SBV spread quickly in the naive ruminant population. France continues to monitor for SBV, and updated information is made available online on a regular basis [ http://www.plateforme-esa.fr/ ]. Outbreaks of congenital SBV are expected to occur sporadically from now on, but further epidemics may also occur if immunity at population level declines.

Background African horse sickness (AHS) is a major, Culicoides-borne viral disease in equines whose introduction into Europe could have dramatic consequences. The disease is considered to be endemic in sub-Saharan Africa. Recent introductions of other Culicoides-borne viruses (bluetongue and Schmallenberg) into northern Europe have highlighted the risk that AHS may arrive in Europe as well. The aim of our study was to provide a spatiotemporal quantitative risk model of AHS introduction into France. The study focused on two pathways of introduction: the arrival of an infectious host (PW-host) and the arrival of an infectious Culicoides midge via the livestock trade (PW-vector). The risk of introduction was calculated by determining the probability of an infectious animal or vector entering the country and the probability of the virus then becoming established: i.e., the virus’s arrival in France resulting in at least one local equine host being infected by one local vector. This risk was assessed using data from three consecutive years (2010 to 2012) for 22 regions in France. Results The results of the model indicate that the annual risk of AHS being introduced to France is very low but that major spatiotemporal differences exist. For both introduction pathways, risk is higher from July to October and peaks in July. In general, regions with warmer climates are more at risk, as are colder regions with larger equine populations; however, regional variation in animal importation patterns (number and species) also play a major role in determining risk. Despite the low probability that AHSV is present in the EU, intra-EU trade of equines contributes most to the risk of AHSV introduction to France because it involves a large number of horse movements. Conclusion It is important to address spatiotemporal differences when assessing the risk of ASH introduction and thus also when implementing efficient surveillance efforts. The methods and results of this study may help develop surveillance techniques and other risk reduction measures that will prevent the introduction of AHS or minimize AHS’ potential impact once introduced, both in France and the rest of Europe. Electronic supplementary material The online version of this article (doi:10.1186/s12917-015-0435-4) contains supplementary material, which is available to authorized users.

International audience; After the unexpected emergence of Bluetongue virus serotype 8 (BTV-8) in northern Europe in 2006, another arbovirus, Schmallenberg virus (SBV), emerged in Europe in 2011 causing a new economically important disease in ruminants. The virus, belonging to the Orthobunyavirus genus in the Bunyaviridae family, was first detected in Germany, in The Netherlands and in Belgium in 2011 and soon after in the United Kingdom, France, Italy, Luxembourg, Spain, Denmark and Switzerland. This review describes the current knowledge on the emergence, epidemiology, clinical signs, molecular virology and diagnosis of SBV infection.

La mortalité bovine est un problème important, tant au plan économique que du point de vue du bien-être animal. Nous avons analysé les données enregistrées dans la base de données nationale d'identification de 2003 à 2009, décrivant la carrière d'environ 75 millions de bovins, afin de fournir des statistiques fiables de la mortalité bovine en France. Les résultats de cette étude constituent un référentiel pouvant être utilisé pour évaluer des situations observées en élevage. En moyenne sur cette période, le risque de mortalité périnatale des mâles et des femelles atteignait respectivement 7,9% et 6,0% dans le cheptel laitier, et 4,7% et 3,2% dans le cheptel allaitant. Le risque de mortalité annuel moyen des animaux de plus de deux ans était de 3,5% chez les laitiers et de 2,0% chez les allaitants. La mortalité des bovins laitiers était significativement plus élevée que celle des allaitants pour les dix classes d'âge étudiées, sauf celle de un à deux ans. La modélisation des données hebdomadaires a permis de décrire la saisonnalité des taux de mortalité, qui était différente selon le sous-groupe populationnel considéré. Les taux de mortalité des veaux de moins de sept jours présentaient notamment deux pics d'ampleur équivalente (en décembre et juillet), tandis que les autres classes d'âge présentaient un pic principal en hiver, visiblement associé chez les adultes au pic de vêlage. Les résultats de cette modélisation ont par ailleurs révélé une augmentation significative des taux de mortalité de 2003 à 2009, probablement en partie due à l'épizootie de fièvre catarrhale ovine qui s'est propagée en France en 2007-2008. L'augmentation des taux de mortalité bovine a déjà été constatée dans de nombreux pays, suggérant la nécessité de mettre en place des mesures correctrices., Cattle mortality represents both an economical and an animal welfare issue. We analyzed the data recorded in the National Cattle Register from 2003 to 2009, gathering data about 75 million cattle, to provide reliable statistics of cattle mortality in France. On average over this period, the perinatal mortality risk in males and females reached respectively 7.9% and 6.0% in dairy cattle, and 4.7% and 3.2% in beef cattle. The average annual mortality risk of animals over two years was 3.5% for dairy and 2.0% for beef cattle. Mortality of dairy cattle was significantly higher than that of beef cattle for the ten age groups studied, except for those of one to two years. Weekly data were modeled to describe the seasonality of mortality, which was different among the different sub-population groups. The mortality rate of calves less than seven days old showed two peaks of equal magnitude (in December and July), while other age groups showed a major peak in the winter, apparently associated in adults to the peak of calving. The modeling results of the model also revealed a significant increase in death rates from 2003 to 2009, probably partly due to the blue tongue epizootic that spread in France from 2007 to 2008. Rising rates of cattle mortality have already been observed in many countries, suggesting the need to implement corrective measures.

The Caribbean region is considered to be at risk for avian influenza (AI) due to a large backyard poultry system, an important commercial poultry production system, the presence of migratory birds, and disparities in the surveillance systems. The Caribbean Animal Health Network (CaribVET) has developed tools to implement AI surveillance in the region with the goals to have 1) a regionally harmonized surveillance protocol and specific web pages for AI surveillance on www.caribvet.net, and 2) an active and passive surveillance for AI in domestic and wild birds. A diagnostic network for the Caribbean, including technology transfer and AI virus molecular diagnostic capability in Guadeloupe (real-time reverse transcription-polymerase chain reaction for the AI virus matrix gene), was developed. Between 2006 and 2009, 627 samples from four Caribbean countries were tested for three circumstances: importation purposes, following a clinical suspicion of AI, or through an active survey of wild birds (mainly waders) during the southward and northward migration periods in Guadeloupe. None of the samples tested were positive, suggesting a limited role of these species in the AI virus ecology in the Caribbean. Following low pathogenic H5N2 outbreaks in the Dominican Republic in 2007, a questionnaire was developed to collect data for a risk analysis of AI spread in the region through fighting cocks. The infection pathway of the Martinique commercial poultry sector by AI, through introduction of infected cocks, was designed, and recommendations were provided to the Caribbean Veterinary Services to improve cock movement control and biosecurity measures. The CaribVET and its organization allowed interaction between diagnostic and surveillance tools on the one hand and epidemiologic studies on the other, both of them developed in congruence with regional strategies. Together, these CaribVET activities contribute to strengthening surveillance of avian influenza virus (AIV) in the Caribbean region and may allow the development of research studies on both AI risk analysis and on AIV ecology.

Contagious bovine pleuropneumonia is a bacterial disease caused by Mycoplasma mycoides subsp. mycoides SC (MmmSC), and included in list A of the Office International des Epizooties. It is one of the major constraints to cattle raising in sub-Saharan and south-westem Africa and also a threat to all countries currently free of the disease. MmmSC strains were considered very homogeneous until 1995, when various techniques such as enzymatic restriction of whole DNA or Southern blotting showed that this was not the case. These techniques are unfortunately difficult to standardize and require the extraction of DNA from an MmrnSC culture. We therefore decided to investigate the possibility of constructing a molecular epidemiology tool based on multilocus sequence analysis (MLSA) with PCR amplification of various loci followed by sequencing. Six loci were found suitable for this purpose and an additional PCR was designed to detect the presence of an 8.8 kb deletion described by others in some strains. Fifteen different MLSA profiles were evidenced in our study. They allowed a clear distinction between European, south-western African and sub-Saharan strains. In addition, the results obtained on strain PO 1967 confirmed its European origin, even though it does not exhibit the 8.8 kb deletion. This new tool for contagious bovine pleuropneumonia may prove particularly useful for identifying MmmSC strains in countries at risk from contamination. It can also easily be refined by adding more strains or other loci of interest.

Contagious caprine pleuropneumonia (CCPP) is a major threat to goat farming in developing countries. Its exact distribution is not well known, despite the fact that new diagnostic tools such as PCR and competitive ELISA are now available. The authors developed a study of the molecular epidemiology of the disease, based on the amplification of a 2400 bp long fragment containing two duplicated gene coding for a putative membrane protein. The sequence of this fragment, obtained on 19 Mycoplasma capricolum subsp. capripneumoniae (Mccp) strains from various geographical locations, gave 11 polymorphic positions. The three mutations found on gene H2prim were silent and did not appear to induce any amino acid modifications in the putative translated protein. The second gene may be a pseudogene not translated in vivo, as it bore a deletion of the ATG codon found in the other members of the "Mycoplasma mycoides cluster" and as the six mutations evidenced in the Mccp strains would induce modifications in the translated amino acids. In addition, an Mccp strain isolated in the United Arab Emirates showed a deletion of the whole pseudogene, a further indication that this gene is not compulsory for mycoplasma growth. Four lineages were defined, based on the nucleotide sequence. These correlated relatively well with the geographical origin of the strains: North, Central or East Africa. The strain of Turkish origin had a sequence similar to that found in North African strains, while strains isolated in Oman had sequences similar to those of North or East African strains. The latter is possibly due to the regular import of goats of various origins. Similar molecular epidemiology tools have been developed by sequencing the two operons of the 16S rRNA gene or by AFLP. All these various techniques give complementary results. One (16S rRNA) offers the likelihood of a finer identification of strains circulating in a region, another (H2) of determining the geographical origin of the strains. These tools can make a very useful contribution to understanding the epidemiology of CCPP.

In France, a national surveillance plan to monitor congenital Schmallenberg virus (SBV) outbreaks was set up in January 2012, and has shown that SBV had become widespread throughout the country since mid-2011. However, the number of SBV-infected farms cannot accurately be estimated through congenital SBV reporting alone. Therefore, GDS France (National Animal Health Farmers' Organization) conducted serological investigations in cattle and sheep holdings in several departments in spring 2012 to assess SBV exposure in 2011. A serological study was also conducted in the department of Saône-et-Loire (southern Burgundy) to establish an accurate local overview of circulation of virus in 2011 among cattle. The study was conducted following guidelines elaborated by the French Platform for animal health surveillance. Results indicated differences in within-herd seroprevalence between cattle herds and sheep herds in departments where outbreaks of congenital SBV were reported in early 2012 and a great heterogeneity in seroprevalence between areas (even between areas geographically close to each other). In departments which had been severely affected in early 2012, the overall impact of SBV infection in cattle herds during the 2012-2013 calving season will probably be low. On the other hand, given the low proportion of immunised ewes in sheep SBV outbreaks, sheep flocks which were already affected in early 2012 may once again face congenital cases of SBV.

The mandatory bovine abortion notification system in France aims to detect as soon as possible any resurgence of bovine brucellosis. However, under-reporting seems to be a major limitation of this system. We used a unilist capture-recapture approach to assess the sensitivity, i.e. the proportion of farmers who reported at least one abortion among those who detected such events, and representativeness of the system during 2006-2011. We implemented a zero-inflated Poisson model to estimate the proportion of farmers who detected at least one abortion, and among them, the proportion of farmers not reporting. We also applied a hurdle model to evaluate the effect of factors influencing the notification process. We found that the overall surveillance sensitivity was about 34%, and was higher in beef than dairy cattle farms. The observed increase in the proportion of notifying farmers from 2007 to 2009 resulted from an increase in the surveillance sensitivity in 2007/2008 and an increase in the proportion of farmers who detected at least one abortion in 2008/2009. These patterns suggest a raise in farmers' awareness in 2007/2008 when the Bluetongue Virus (BTV) was detected in France, followed by an increase in the number of abortions in 2008/2009 as BTV spread across the country. Our study indicated a lack of sensitivity of the mandatory bovine abortion notification system, raising concerns about the ability to detect brucellosis outbreaks early. With the increasing need to survey the zoonotic Rift Valley Fever and Q fever diseases that may also cause bovine abortions, our approach is of primary interest for animal health stakeholders to develop information programs to increase abortion notifications. Our framework combining hurdle and ZIP models may also be applied to estimate the completeness of other clinical surveillance systems.

Schmallenberg virus (SBV) infection is an emerging livestock disease caused by a novel Orthobunyavirus which was first identified in Germany in November 2011. Non-specific clinical signs such as fever, decreased milk production and diarrhoea are associated with the acute infection in cattle, while late abortions and birth defects in newborns can be associated with the infection of pregnant cows, ewes and goats (Hoffmann and others 2012, Van den Brom and others 2012). As of March 30, 2012, since the first identification of congenital forms of SBV virus infection in The Netherlands in December 2011, about 3000 confirmed outbreaks have been reported in eight European countries (Belgium, France, Germany, Italy, Luxembourg, The Netherlands, Spain, UK) (French National Surveillance Platform for Animal Health 2012). However, little is known about SBV virus infection, especially with regard to its clinical impact in the affected herds. SBV emergence is closely monitored in France. Farmers are urged to contact their veterinarian when encountering cases of ruminant neonates or fetuses stillborn, malformed or showing nervous disorders. A brain sample is collected on any newborn suspected of congenital SBV until a first confirmation of the infection is obtained for the herd. An SBV diagnostic test is performed in state diagnostic laboratories, using real-time quantitative reverse transcription PCR (RT-qPCR). The first cases of SBV virus infection were …