Agriculture In France Research Articles

Harnessing uncertainty: A deep mechanistic approach for cautious diagnostic and forecast of Bovine Respiratory Disease

Bovine Respiratory Disease (BRD) is a prevalent infectious disease of respiratory tract in cattle, presenting challenges in accurate diagnosis and forecasting due to the complex interactions of multiple risk factors. Common methods, including mathematical epidemiological models and data-driven approaches such as machine learning models, face limitations such as difficult parameter estimation or the need for data across all potential outcomes, which is challenging given the scarcity and noise in observing BRD processes. In response to these challenges, we introduce a novel approach known as the Bayesian Deep Mechanistic method. This method couples a data-driven model with a mathematical epidemiological model while accounting for uncertainties within the processes. By utilising 265 lung ultrasound videos as sensor data from 163 animals across 9 farms in France, we trained a Bayesian deep learning model to predict the infection status (infected or non-infected) of an entire batch of 12 animals, also providing associated confidence levels. These predictions, coupled with their confidence levels, were used to filter out highly uncertain diagnoses and diffuse uncertainties into the parameterisation of a mathematical epidemiological model to forecast the progression of infected animals. Our findings highlight that considering the confidence levels (or uncertainties) of predictions enhances both the diagnosis and forecasting of BRD. Uncertainty-aware diagnosis reduced errors to 32 %, outperforming traditional automatic diagnosis. Forecast relying on veterinarian diagnoses, considered the most confident, had a 23 % error, whilst forecast taking into account diagnosis uncertainties had a close 27.2 % error. Building upon uncertainty-awareness, our future research could explore integrating multiple types of sensor data, such as video surveillance, audio recordings, and environmental parameters, to provide a comprehensive evaluation of animal health, employing multi-modal methods for processing this diverse data.

Tillage and land use management effects on soil organic matter and soil microbial biomass in a field network of practical farms in France, Romania, and Sweden

A reduction in tillage intensity, organic farming, and introduction of ley-grass periods into the crop rotation are means to improve the sustainable use of arable soils. The current study uses an on-farm approach to investigate soils from different practical farms in Northern France, Central Sweden, and Romania in comparison with previously published results from randomized field-experiments nearby. No-tillage generally increased the mean SOC and total N contents of arable fields in comparison with ploughing. However, this increase was only significant for the 70 % increase at 0–10 cm depth in France. No-tillage had no general effects on MBC or MBN and increased the ergosterol content at 0–10 cm depth in France and Sweden but not in Romania. Averaging depths and tillage systems, median MBC significantly increased in the order France (220 μg g−1 soil), Romania (324 μg g−1 soil), and Sweden (384 μg g−1 soil), whereas the median MB-C/N ratios followed the order France (5.6), Sweden (8.3), and Romania (10.4). The study region-specific changes in soil pH significantly affected covariate MBC and MBN in the regression equations for equal slopes ANCOVA models. In Northern France, organic farming and ley-grass implementation into the crop rotation increased SOC and total N contents to the level of the no-tillage fields. On-farm research gives similar results to long-term field experiments in France, Romania, and Sweden. For this reason, on-farm research on practical fields is an important, less expensive alternative to randomized field experiments, with a high potential for investigating actual and relevant research objectives. This will intensify exchange in knowledge between scientists and farmers.

Spatialization at a fine geographical level of environmental exposure to multiple pesticides used in agriculture in France (1979-2005)

Spatialization at a fine geographical level of environmental exposure to multiple pesticides used in agriculture in France (1979-2005)

Characterization of Influenza D Virus Reassortant Strain in Swine from Mixed Pig and Beef Farm, France.

Influenza D virus was isolated from pigs on a mixed pig and beef farm in France. Investigation suggested bull-to-pig transmission and spread among pigs. The swine influenza D virus recovered was a reassortant of D/660 and D/OK lineages. Reported mutations in the receptor binding site might be related to swine host adaptation.

Lack of Efficacy of Albendazole against Dicrocoelium dendriticum Infection in a Sheep Farm in France.

Dicrocoeliosis is a common parasitic disease in European sheep farming. The prevalence of infection by this parasite can reach almost 70% in areas where the environment is favorable to intermediate hosts. In France, only one drug is currently available for the treatment of dicrocoeliosis: albendazole at a dose of 15 mg/kg in a single administration. However, a control coproscopy following a routine treatment led us to suspect that the efficacy of albendazole against Dicrocoelium dendriticum had diminished. Therefore, we carried out an efficacy test on 15 animals by treating them with albendazole at a dose of 15 mg/kg and performing a coproscopy on D0 and a control coproscopy 14 days later. We obtained a 39% reduction in the excretion of D. dendriticum eggs. This shows a reduction in the expected efficacy of albendazole, which is normally more than 90% in other studies involving this molecule at a dosage of 15 mg/kg. These results are of major concern as albendazole is currently the only drug available in France to treat dicrocoeliosis.

74. Biosecurity compliance in poultry farms in France: What does the current situation look like and what are the expectations of farmers?

74. Biosecurity compliance in poultry farms in France: What does the current situation look like and what are the expectations of farmers?

Pathogenicity and escape to pre-existing immunity of a new genotype of swine influenza H1N2 virus that emerged in France in 2020

In 2020, a new genotype of swine H1N2 influenza virus (H1avN2–HA 1C.2.4) was identified in France. It rapidly spread within the pig population and supplanted the previously predominant H1avN1-HA 1C.2.1 virus. To characterize this new genotype which is genetically and antigenically distant from the other H1avNx viruses detected in France, an experimental study was conducted to compare the outcomes of H1avN2 and H1avN1 infections in pigs and evaluate the protection conferred by the only inactivated vaccine currently licensed in Europe containing an HA 1C (clade 1C.2.2) antigen. Infection with H1avN2 induced stronger clinical signs and earlier shedding than H1avN1. The neutralizing antibodies produced following H1avN2 infection were unable to neutralize H1avN1, and vice versa, whereas the cellular-mediated immunity cross-reacted. Vaccination slightly altered the impact of H1avN2 infection at the clinical level, but did not prevent shedding of infectious virus particles. It induced a cellular-mediated immune response towards H1avN2, but did not produce neutralizing antibodies against this virus. As in vaccinated animals, animals previously infected by H1avN1 developed a cross-reacting cellular immune response but no neutralizing antibodies against H1avN2. However, H1avN1 pre-infection induced a better protection against the H1avN2 infection than vaccination, probably due to higher levels of non-neutralizing antibodies and a mucosal immunity. Altogether, these results showed that the new H1avN2 genotype induced a severe respiratory infection and that the actual vaccine was less effective against this H1avN2-HA 1C.2.4 than against H1avN1-HA 1C.2.1, which may have contributed to the H1avN2 epizootic and dissemination in pig farms in France.

First Isolation of the Heteropathotype Shiga Toxin-Producing and Extra-Intestinal Pathogenic (STEC-ExPEC) E. coli O80:H2 in French Healthy Cattle: Genomic Characterization and Phylogenetic Position.

The emerging heteropathotype shigatoxigenic (STEC) and extra-intestinal pathogenic Escherichia coli (ExPEC) O80:H2 has been the second leading cause of pediatric HUS in France since the mid-2010s. In contrast with other highly pathogenic STEC serotypes, for which ruminants have clearly been identified as the main human infection source, this heteropathotype's reservoir remains unknown. In this context, we describe for the first time the isolation of seven STEC O80:H2 strains from healthy cattle on a single cattle farm in France. This study aimed at (i) characterizing the genome and (ii) investigating the phylogenetic positions of these O80:H2 STEC strains. The virulomes, resistomes, and phylogenetic positions of the seven bovine isolates were investigated using in silico typing tools, antimicrobial susceptibility testing and cgMLST analysis after short-read whole genome sequencing (WGS). One representative isolate (A13P112V1) was also subjected to long-read sequencing. The seven isolates possessed ExPEC-related virulence genes on a pR444_A-like mosaic plasmid, previously described in strain RDEx444 and known to confer multi-drug resistance. All isolates were clonally related and clustered with human clinical strains from France and Switzerland with a range of locus differences of only one to five. In conclusion, our findings suggest that healthy cattle in France could potentially act as a reservoir of the STEC-ExPEC O80:H2 pathotype.

Bayesian estimation of the sensitivity and specificity of coprological and serological diagnostic tests for the detection of Ascaris suum infection on pig farms

Coprological and serological diagnostic tests were compared to define the status of a pig farm with regard to Ascaris suum. On each of the 100 farms in France visited for the study, 10 blood samples were taken from pigs at the end of fattening (at least 22 weeks old) and 20 to 30 faecal samples were taken, depending on the category of animals present on the farm (10 sows, 10 piglets aged 10 to 12 weeks and 10 pigs at the end of fattening, aged at least 22 weeks). A SERASCA® ELISA test (Laboratory of Parasitology, Ghent University) was performed on each blood sample (cut-off 0.5) and a coprological analysis on each faecal sample. A Bayesian approach was used to estimate the sensitivity and specificity of the coprological and serological tests. A farm was considered positive if at least one A. suum egg was observed in the faecal samples. With regard to the serological test, various hypotheses were tested in order to define the number of seropositive animals required to consider a farm positive for A. suum. The coprological test has very good specificity in the search for A. suum, whether 20 or 30 samples are taken per farm. However, even with an increase in the number of samples, the sensitivity of this diagnostic approach is very low (less than 30%). On the other hand, the serological diagnostic method, which consists of taking blood samples from 10 animals at the end of fattening, has good sensitivity and seems better suited to defining the status of a farm with regard to A. suum, provided that a farm is considered seropositive only if two out of 10 samples are positive.

Assessing the environmental impacts of conventional and organic scenarios of rainbow trout farming in France

In France, rainbow trout farming in conventional flow-through systems raises environmental concerns. To address this, there is a growing interest in organic aquaculture. In this study, we employed an attributional life cycle assessment (LCA) to analyze the environmental impacts of rainbow trout production, comparing conventional and organic practices in a model fish farm. Our life cycle impact assessment revealed that organic farming significantly reduced environmental impacts per tonne of trout in seven of the nine selected impact categories. Notably, freshwater ecotoxicity exhibited the most significant difference, with organic systems showing a 35% decrease. The only exceptions were freshwater eutrophication and water dependence, where organic production led to higher impacts per tonne of trout. In conventional farming, emissions amounted to 14 kg of P eq./tonne, whereas in organic farming, the emissions were slightly higher (15 kg of P eq./tonne). For water dependence, one tonne of trout production in the conventional system mobilized 128 103 m3 vs. 185 103 m3 in the organic system. The environmental benefits of organic production were even more marked when using a surface-based functional unit (m2y). We demonstrated the benefits of organic trout production from an environmental perspective. However, our findings highlight the caution needed when interpreting LCA comparisons of such production systems that can be highly influenced by methodological choices such as the functional unit used.

Potential impacts of the Common Agricultural Policy's Income Stabilisation Tool on farmers' incomes and crop diversity: A French case study

AbstractThis paper analyses the potential impacts of a hypothetical implementation of the Income Stabilisation Tool (IST) in France for the field crops sector. The IST is a risk management tool available within the 2014–2020 Common Agricultural Policy (CAP) to support farmers facing a severe drop in their incomes. This analysis was conducted using a farm‐level model relying on expected utility theory and based on positive mathematical programming with risk. The model was applied to a sample of 1375 field crop farms in France derived from Farm Accountancy Data Network (FADN) data. Simulation results show that the uptake rate of the tool is relatively low, less than 37% in all scenarios. It is strongly dependent on CAP public support and on how much premium farmers have to pay. Highest uptake rates are observed in farms specialising in Other Field Crops, such as potatoes, pulses and sugar beet, and farms located in regions highly exposed to climatic risks. Previous experience with insurance favours the acceptance of the IST. Model results also show that the IST improves adopters' income and reduces income inequality. However, its impacts on crop diversity, measured by the Shannon index, are negative.

Wind Speed Ramp Rate Predictions Using Wind Farm SCADA Data Assimilation and a WRF Ensemble

This study presents a novel method for improving wind power ramp events forecasts up to six hours ahead by utilizing data assimilation of SCADA measurements with an ensemble of Weather Research and Forecasting (WRF) models estimates. Leveraging data from nine wind farms in France and Belgium, the approach aims to improve WRF model predictions for wind speed and ramp event timing. The methodology employs grid and observational nudging techniques, enhancing model accuracy by incorporating real-time observational data. Key findings demonstrate that nudging significantly reduces Mean Absolute Error (MAE), decreases the Time Distortion Index (TDI), and increases the Probability of Detection (POD) of ramp events. Nudged ensemble members outperform non-nudged counterparts, exhibiting better accuracy in identifying true ramp events and reducing false alarms. MAE, TDI and POD improvements are as high as 3.7%, 8.5% and 37%, respectively. The study also explores the benefits of an ensemble approach, highlighting improved accuracy in predicting ramp rate magnitudes and providing valuable insights for grid stability management. This research contributes to wind power forecasting, showcasing the importance of integrating SCADA data into predictive models.

Is Chorioptes texanus to Displace Chorioptes bovis? Notes on the Mites Causing Bovine Chorioptic Mange in Central Europe

Chorioptic mange is the most common type of bovine mange in central Europe, affecting mainly housed dairy cattle. Until 1976, when Chorioptes texanus were described for the first time from mangy cattle in Brazil, bovine chorioptic mange was thought to be caused only by C. bovis mites. In Europe, C. texanus parasitism in cattle was for the first time reported in Germany in 1998. Following the repeated diagnosis of C. texanus mites in skin scrapings from local cattle in recent years, scrapings from cattle that were clinically suspicious for chorioptic mange were requested and provided during the years from 2019 to 2022 from Austria, France, Germany, and Switzerland (from 6, 17, 28, and 7 farms, respectively) and from dairy cows of 1 farm in Canada. Mites were isolated from the scrapings, cleared, and microscopically identified based on their morphology. Examination of scrapings revealed the presence of C. texanus in the cattle from 2 farms in Austria, 13 farms in France, 7 farms in Germany, 1 farm in Switzerland, and in the specimens from Canada. Chorioptes bovis mites were recovered only in scrapings from 5 farms in Germany and Psoroptes ovis mites in scrapings of cattle from 2 farms in France. The scrapings did not reveal co-infestations of C. bovis and C. texanus or of Chorioptes species and P. ovis. The records of C. texanus from Austria, France, Switzerland, and Canada constitute the first descriptions of this mite species in these countries. Although this investigation was based on an opportunistic collection of the material and was of small extent, the results suggest a widespread occurrence of C. texanus in central Europe and may emphasize the need for studies to closely investigate the nature of the causative agents of chorioptic mange in cattle and other hosts.

Changes in the European Union definition for endocrine disruptors: how many molecules remain a cause for concern? The example of crop protection products used in agriculture in France in the six last decades.

The endocrine-disrupting effects of phytopharmaceutical active substances (PAS) on human health are a public health concern. The CIPATOX-PE database, created in 2018, listed the PAS authorized in France between 1961 and 2014 presenting endocrine-disrupting effects for humans according to data from official international organizations. Since the creation of CIPATOX-PE, European regulations have changed, and new initiatives identifying substances with endocrine-disrupting effects have been implemented and new PAS have been licensed. The study aimed to update the CIPATOX-PE database by considering new 2018 European endocrine-disrupting effect identification criteria as well as the new PAS authorized on the market in France since 2015. The endocrine-disrupting effect assessment of PAS from five international governmental and non-governmental initiatives was reviewed, and levels of evidence were retained by these initiatives for eighteen endocrine target organs. The synthesis of the identified endocrine-disrupting effects allowed to assign an endocrine-disrupting effect level of concern for 241 PAS among 980 authorized in France between 1961 and 2021. Thus, according to the updated CIPATOX-PE data, 44 PAS (18.3%) had an endocrine-disrupting effect classified as "high concern," 133 PAS (55.2%) "concern," and 64 PAS (26.6%) "unknown effect" in the current state of knowledge. In the study, 42 PAS with an endocrine-disrupting effect of "high concern" are similarly classified in CIPATOX-PE-2018 and 2021, and 2 new PAS were identified as having an endocrine-disrupting effect of "high concern" in the update, and both were previously classified with an endocrine-disrupting effect of "concern" in CIPATOX-PE-2018. Finally, a PAS was identified as having an endocrine-disrupting effect of "high concern" in CIPATOX-PE-2018 but is now classified as a PAS not investigated for endocrine-disrupting effects in CIPATOX-PE-2021. The endocrine target organs associated with the largest number of PAS with an endocrine-disrupting effect of "high concern" is the reproductive system with 31 PAS. This is followed by the thyroid with 25 PAS and the hypothalamic-pituitary axis (excluding the gonadotropic axis) with 5 PAS. The proposed endocrine-disrupting effect indicator, which is not a regulatory classification, can be used as an epidemiological tool for occupational risks and surveillance.

First detection and characterisation of Eimeria zaria in European chickens

The global poultry industry has experienced dramatic growth in recent decades, increasing the significance of pathogens of chickens. Protozoan parasites of the genus Eimeria can cause the disease coccidiosis, compromising animal health and welfare, and incurring significant annual costs. Seven Eimeria species have long been recognised to infect chickens, supplemented by three new candidate species first reported from Australia in 2007/8. Named Eimeria lata, Eimeria nagambie and Eimeria zaria, one or more of these new species have been reported in Australia, several countries in sub-Saharan Africa, India, Venezuela, and most recently the United States of America, but none have been detected in Europe. Here, a panel of 56 unvaccinated broiler chicken farms were sampled in the final week of production from France, Greece, Italy, the Netherlands, the Republic of Ireland, and the United Kingdom to assess the occurrence of all ten Eimeria species using specific polymerase chain reaction (PCR). Overall, 39 of 56 (69.6%) farms were found to host at least one species. Eimeria acervulina, E. tenella, and E. maxima were most common, with E. mitis and E. praecox also widespread. Eimeria necatrix was detected on one farm in France, while E. brunetti was not detected. Eimeria zaria was detected for the first time in Europe, appearing in Greece and Italy (one occurrence each). New primers were designed to confirm detection of E. zaria and provide template for phylogenetic comparison with the reference isolate from Australia. Detection of E. zaria in Europe reinforces the importance of integrated control for coccidiosis given the lack of protection induced by current anticoccidial vaccines.

Nearly complete genome sequence of a Perhabdovirus isolated on European perch (Perca fluviatilis).

We report a nearly full-length genome of a Perhabdovirus isolated in 2022 on perch on a French farm. This virus is genetically related to virus 20/43, which was associated with an outbreak of perch on a farm in France in 2019. Both viruses represent a specific lineage of perch rhabdovirus.

1. Evolution, diversity and typology of pig farms in France: Lessons from the 2020 agricultural census and comparison with the 2010 and 2000 censuses

1. Evolution, diversity and typology of pig farms in France: Lessons from the 2020 agricultural census and comparison with the 2010 and 2000 censuses

Influence of gender on the development of sustainable agriculture in France

Having long been confined to the role of family farm helper, women now make up more than a quarter of farm managers in France. Alongside that, the agricultural world needs to transition towards more sustainable practices and models. Inadequate or incomplete research can be found on how gender influences farmers’ practices and even fewer studies that focus on the situation in France. In this paper, the relationship between the specific topic of French women farmers and their role in sustainable agriculture is explored through qualitative research. An initial conclusion is reached on the existence of a gender effect in the practice of sustainable agriculture. Four explanations to this correlation are discussed to explain the dynamics between gender and sustainable agriculture: the importance of care and differentiated socialisation in choices that women make, the role of access to the profession and working conditions, the specific profile of women involved in sustainable systems and the potentially more welcoming dimension of the agroecological space. Although analysed separately, it is likely a combination of these explanations that allows us to understand the greater sensitivity of women to engage in sustainable agricultural practices.

Combining crop-exposure matrices and land use data to estimate indices of environmental and occupational exposure to pesticides.

Exposure assessment represents a major challenge for studies on the relation between pesticides and health. We developed a method combining information from crop-exposure matrices (CEMs) and land use data, in order to compute indices of environmental and occupational pesticide exposure. We illustrate our approach using French data (1979-2010). We used CEMs for five crops (straw cereals, grain corn, corn fodder, potatoes, vineyards) that describe use (annual probability, frequency, intensity) of pesticide subgroups, chemical families, and active substances by region and time since 1960. We combined these data with land use data from agricultural censuses (1979, 1988, 2000, 2010) to compute indices of environmental and occupational pesticide exposure in cantons (small French administrative units). Indices of environmental exposure were calculated based on the area of each crop in the cantons, while indices of occupational exposure depended on combinations of crops in each farm from the cantons. To illustrate our approach, we selected a pesticide group (herbicides), chemical family of herbicides (phenoxyacetic acids), and active substance from the phenoxyacetic acids chemical family (2,4-D). The estimated proportion of the area of crops with CEMs and of farms sprayed with herbicides was close to 100% between 1979-2010, but the estimated average annual number of applications increased. There were decreasing time-trends for phenoxyacetic acids and 2,4-D over the same period for all indices of exposure. There was a high use of herbicides throughout France in 2010, except in the South coast. For phenoxyacetic acids and 2,4-D, the spatial distribution was heterogeneous for all indices of exposure, with the highest values in the Centre and North regions. Assessment of pesticide exposure is a key issue for epidemiological studies on their association with health outcomes. However, it presents some unique challenges, particularly for retrospective exposure and the investigation of chronic diseases. We present a method to compute indices of exposure by combining information from crop-exposure matrices for five crops and land use data. Specificities of environmental and occupational exposure are addressed using different methods. These methods are applied to pesticides used in agriculture in France for five crops (3 groups, 91 chemical families,197 activesubstances) to produce indices at a small geographic scale from 1979 to 2010 for the whole metropolitan France. Besides using these indices in French epidemiological studies, our approach could be relevant for other countries.

Ultra-Short-Term Wind Power Forecasting Based on CGAN-CNN-LSTM Model Supported by Lidar.

Accurate prediction of wind power is of great significance to the stable operation of the power system and the vigorous development of the wind power industry. In order to further improve the accuracy of ultra-short-term wind power forecasting, an ultra-short-term wind power forecasting method based on the CGAN-CNN-LSTM algorithm is proposed. Firstly, the conditional generative adversarial network (CGAN) is used to fill in the missing segments of the data set. Then, the convolutional neural network (CNN) is used to extract the eigenvalues of the data, combined with the long short-term memory network (LSTM) to jointly construct a feature extraction module, and add an attention mechanism after the LSTM to assign weights to features, accelerate model convergence, and construct an ultra-short-term wind power forecasting model combined with the CGAN-CNN-LSTM. Finally, the position and function of each sensor in the Sole du Moulin Vieux wind farm in France is introduced. Then, using the sensor observation data of the wind farm as a test set, the CGAN-CNN-LSTM model was compared with the CNN-LSTM, LSTM, and SVM to verify the feasibility. At the same time, in order to prove the universality of this model and the ability of the CGAN, the model of the CNN-LSTM combined with the linear interpolation method is used for a controlled experiment with a data set of a wind farm in China. The final test results prove that the CGAN-CNN-LSTM model is not only more accurate in prediction results, but also applicable to a wide range of regions and has good value for the development of wind power.