Animal board invited review: Improving animal health and welfare in the transition of livestock farming systems: Towards social acceptability and sustainability.

The need to integrate more clearly societal expectations on livestock farming has led the authors of this article to consider that livestock farming systems must be redesigned to position health and welfare at the heart of their objectives. This article proposes a vision of the advances in knowledge required at different scales to contribute to this transformation. After defining health and welfare of animals, the article emphasises the need to consider health in a broader perspective, to deepen the question of positive emotional experiences regarding welfare, and raises the question of how to assess these two elements on farms. The positive interactions between health and welfare are presented. Some possible tensions between them are also discussed, in particular when improving welfare by providing a more stimulating and richer environment such as access to outdoor increases the risk of infectious diseases. Jointly improving health and welfare of animals poses a number of questions at various scales, from the animal level to the production chain. At the animal level, the authors highlight the need to explore: the long-term links between better welfare and physiological balance, the role of microbiota, the psycho-neuro-endocrine mechanisms linking positive mental state and health, and the trade-off between the physiological functions of production, reproduction and immunity. At the farm level, in addition to studying the relationships at the group level between welfare, health and production, the paper supports the idea of co-constructing innovative systems with livestock farmers, as well as analysing the cost, acceptability and impact of improved systems on their working conditions and well-being. At the production chain or territory levels, various questions are raised. These include studying the best strategies to improve animal health and welfare while preserving economic viability, the labelling of products and the consumers' willingness to pay, the consequences of heterogeneity in animal traits on the processing of animal products, and the spatial distribution of livestock farming and the organisation of the production and value chain. At the level of the citizen and consumer, one of the challenges is to better inter-relate sanitary and health perspectives on the one hand, and welfare concerns on the other hand. There is also a need to improve citizens' knowledge on livestock farming, and to develop more intense and constructive exchanges between livestock farmers, the livestock industry and citizens. These difficult issues plead for interdisciplinary and transdisciplinary research involving various scientific disciplines and the different stakeholders, including public policy makers through participatory research.

Insights on the carbon footprint of radiotherapy in France.

The French healthcare system is responsible for 8% of the national footprint. Achieving a net zero emissions scenario will require a 4-5 fold decrease of carbon emissions in the coming years. The carbon footprint of radiation therapy has not been specifically studied to date. In this review we summarize the content of the carbon footprint dedicated session at the annual meeting of the French society of radiation oncology (SFRO). We discuss the French healthcare system carbon footprint and its major drivers and our work on the estimation of the carbon footprint of external beam radiation therapy in the French setting. We developed a dedicated methodology to estimate the carbon footprint related to radiation therapies, and describe the main drivers of emissions based on a single centre as an example, namely patient's rides, accelerators acquisition and maintenance and data storage. Based on the carbon footprint calculated in our centres, we propose mitigation strategies and an estimation of their respective potential. Our results may be extrapolated to other occidental settings by adapting emission factors (kilograms of carbon per item or euro) to other national settings. External beam radiation therapy has a major carbon footprint that may be mitigated in many ways that may impact how radiation therapy treatments are delivered, as well as the national organization of the radiotherapy sector. This needs to be taken into account when thinking about the future of radiotherapy.

Global formal live poultry and hatching egg trade network (2004-2016): description and association with poultry disease reporting and presence.

As international trade constitutes one of the main spread pathways of diseases, a better understanding of the trade behaviors of countries will help identify strengths and areas for improvement in the approach of national authorities to controlling poultry diseases globally. Using data reported to the United Nations Comtrade and the World Organisation for Animal Health (OIE) between 2004 and 2016 by 193 countries, we used a network analysis on trade data of poultry hatching eggs, live poultry of less than 185 g and live poultry of 185 g or more to determine that: 1) quantities traded between countries are substantial, and tend to increase (average increase of 800,000 poultry heads and 21,000 tons of hatching eggs each year equivalent to an increase by 2-fold in 17 yr); 2) the stability of the networks was low (a quarter to half of trade relationships maintained between 2 consecutive years) and the subnetworks favorable to the spread of diseases were in general consistent with regional clustering, trade exchanges being equally at intracontinental and intercontinental levels; 3) countries with highest number of partners were located in the same world regions for the 3 poultry networks - Americas and Europe for export (up to 107 partners) and Africa, Asia and Europe for import (up to 36 partners); 4) for live poultry, biggest exporting countries shared more poultry disease surveillance data, and reported more disease presence than others, which did not stop them from trading. Biggest importers reported less poultry disease surveillance data and reported more disease presence than others; and 5) the main structural and trend characteristics of the international trade networks were in general similar for the 3 networks. The information derived from this work underlines the importance of applying the preventive measures advocated by the OIE and will support countries to reduce the risk of introduction of pathogens causing poultry diseases.

Waterborne disease outbreak detection: an integrated approach using health administrative databases.

Hundreds of waterborne disease outbreaks (WBDO) of acute gastroenteritis (AGI) due to contaminated tap water are reported in developed countries each year. Such outbreaks are probably under-detected. The aim of our study was to develop an integrated approach to detect and study clusters of AGI in geographical areas with homogeneous exposure to drinking water. Data for the number of AGI cases are available at the municipality level while exposure to tap water depends on drinking water networks (DWN). These two geographical units do not systematically overlap. This study proposed to develop an algorithm which would match the most relevant grouping of municipalities with a specific DWN, in order that tap water exposure can be taken into account when investigating future disease outbreaks. A space-time detection method was applied to the grouping of municipalities. Seven hundred and fourteen new geographical areas (groupings of municipalities) were obtained compared with the 1,310 municipalities and the 1,706 DWN. Eleven potential WBDO were identified in these groupings of municipalities. For ten of them, additional environmental investigations identified at least one event that could have caused microbiological contamination of DWN in the days previous to the occurrence of a reported WBDO.

Description of two waterborne disease outbreaks in France: a comparative study with data from cohort studies and from health administrative databases.

Waterborne 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.

Pilot simulation study using meat inspection data for syndromic surveillance: use of whole carcass condemnation of adult cattle to assess the performance of several algorithms for outbreak detection.

The objective of this study was to assess the performance of several algorithms for outbreak detection based on weekly proportions of whole carcass condemnations. Data from one French slaughterhouse over the 2005-2009 period were used (177 098 slaughtered cattle, 0.97% of whole carcass condemnations). The method involved three steps: (i) preparation of an outbreak-free historical baseline over 5 years, (ii) simulation of over 100 years of baseline time series with injection of artificial outbreak signals with several shapes, durations and magnitudes, and (iii) assessment of the performance (sensitivity, specificity, outbreak detection precocity) of several algorithms to detect these artificial outbreak signals. The algorithms tested included the Shewart p chart, confidence interval of the negative binomial model, the exponentially weighted moving average (EWMA); and cumulative sum (CUSUM). The highest sensitivity was obtained using a negative binomial algorithm and the highest specificity with CUSUM or EWMA. EWMA sensitivity was too low to select this algorithm for efficient outbreak detection. CUSUM's performance was complementary to the negative binomial algorithm. The use of both algorithms on real data for a prospective investigation of the whole carcass condemnation rate as a syndromic surveillance indicator could be relevant. Shewart could also be a good option considering its high sensitivity and simplicity of implementation.

Forty research issues for the redesign of animal production systems in the 21st century.

Agroecology offers a scientific and operational framework for redesigning animal production systems (APS) so that they better cope with the coming challenges. Grounded in the stimulation and valorization of natural processes to reduce inputs and pollutions in agroecosystems, it opens a challenging research agenda for the animal science community. In this paper, we identify key research issues that define this agenda. We first stress the need to assess animal robustness by measurable traits, to analyze trade-offs between production and adaptation traits at within-breed and between-breed level, and to better understand how group selection, epigenetics and animal learning shape performance. Second, we propose research on the nutritive value of alternative feed resources, including the environmental impacts of producing these resources and their associated non-provisioning services. Third, we look at how the design of APS based on agroecological principles valorizes interactions between system components and promotes biological diversity at multiple scales to increase system resilience. Addressing such challenges requires a collection of theories and models (concept-knowledge theory, viability theory, companion modeling, etc.). Acknowledging the ecology of contexts and analyzing the rationales behind traditional small-scale systems will increase our understanding of mechanisms contributing to the success or failure of agroecological practices and systems. Fourth, the large-scale development of agroecological products will require analysis of resistance to change among farmers and other actors in the food chain. Certifications and market-based incentives could be an important lever for the expansion of agroecological alternatives in APS. Finally, we question the suitability of current agriculture extension services and public funding mechanisms for scaling-up agroecological practices and systems.

Estimating spatial and temporal variations of the reproduction number for highly pathogenic avian influenza H5N1 epidemic in Thailand.

Since 2003, highly pathogenic avian influenza (HPAI) H5N1 virus has spread, causing a pandemic with serious economic consequences and public health implications. Quantitative estimates of the spread of HPAI H5N1 are needed to adapt control measures. This study aimed to estimate the variations of the reproduction number R in space and time for the HPAI H5N1 epidemic in Thailand. Transmission between sub-districts was analyzed using three different and complementary methods. Transmission of HPAI H5N1 was intense (R(t)>1) before October 2004, at which point the epidemic started to progressively fade out (R(t)<1). The spread was mainly local, with 75% of the putative distances of transmission less than 32km. The map of the mean standardized ratio of transmitting the infection (sr) showed sub-districts with a high risk of transmitting infection. Findings from this study can contribute to discussions regarding the efficacy of control measures and help target surveillance programs.

Epidemiological survey of trichinellosis in wild boar (Sus scrofa) and fox (Vulpes vulpes) in a French insular region, Corsica.

The Mediterranean island of Corsica was considered Trichinella-free until 2004, when T. britovi larvae were discovered in domestic pigs at meat inspection. One red fox was also found infected the same year and in the same area than the infected pigs. This last finding highlighted the presence of trichinellosis in Corsican wildlife. A Trichinella survey was thus performed in wild boar (Sus scrofa) and fox (Vulpes vulpes), the two large wild species present on the island, to determine prevalence of muscle larvae and antibodies. Diaphragm muscles of 1881 wild boars and 74 forelegs of foxes were tested by artificial digestion. No Trichinella larva was identified. The highly sensitive ELISA was used to test muscle fluid samples of 1492 wild boars. The apparent serological prevalence of Trichinella infections in wild boar was 2.01% (95% CI: 1.36-2.86). The present results suggest that wildlife is currently exposed to Trichinella in Corsica. In this context, adequate cooking and veterinary controls of meat offer the only complete sanitary warranties to consumers.

Seroprevalence and factors associated with Toxoplasma gondii infection in wild boar ( Sus scrofa) in a Mediterranean island.

Knowledge of the factors affecting the presence of Toxoplasma gondii in wildlife is limited. Here we analyse which local landscape characteristics are associated with the presence of toxoplasmosis in wild boar, Sus scrofa, on the island of Corsica, France. Meat juice samples from 1399 wild boars collected during two hunting seasons were tested for T. gondii antibodies using the modified agglutination test (titre 1:4). The overall seroprevalence was 0.55 (95% CI 0.50-0.59) for the first year and 0.33 (95% CI 0.29-0.35) for the second year. Seroprevalence varied according to age and county. At the county level, seropositivity in adults was related to farm density during year 1, and to habitat fragmentation, farm density and altitude during year 2. The exposure of wild boar to T. gondii is thus variable according to landscape characteristics and probably results in a variable risk of transmission of toxoplasmosis to humans.

Genetic characterization of Toxoplasma gondii from wild boar (Sus scrofa) in France.

Toxoplasma gondii strains isolated from domestic animals and humans have been classified into three clonal lineages types I-III, with differences in terms of pathogenicity to mice. Much less is known on T. gondii genotypes in wild animals. In this report, genotypes of T. gondii isolated from wild boar (Sus scrofa) in France are described. During the hunting seasons 2002-2008, sera and tissues of individuals from two French regions, one continental and one insular, were tested for Toxoplasma infection. Antibodies to T. gondii were found in 26 (17.6%) of 148 wild boars using the modified agglutination test (MAT, positivity threshold: 1:24). Seroprevalence was 45.9% when considering a threshold of 1:6. Hearts of individuals with a positive agglutination (starting dilution 1:6) (n=60) were bioassayed in mice for isolation of viable T. gondii. In total, 21 isolates of T. gondii were obtained. Genotyping of the isolates using 3 PCR-restriction fragment length polymorphism markers (SAG1, SAG2 and GRA7) and 6 microsatellite loci analysis (TUB2, TgM-A, W35, B17, B18 and M33) revealed that all belonged to type II lineage. These results underline that wild boar may serve as an important reservoir for transmission of T. gondii, and that strains present in wildlife may not be different from strains from the domestic environment.

Complementary approach of data analysis and modeling to estimate the pattern of the BSE epidemic: the example of France.

Clinical surveillance was the only way to detect bovine spongiform encephalopathy (BSE) until July 2000 in France. From the 103 cases identified as such between 1991 and June 2000, we used a back-calculation method to reconstruct the longitudinal trend of BSE infections. Between July 1987 and June 1997, an estimated 51,300 (CI =[24,300-84,700]) cattle were infected in France. The comprehensive surveillance of BSE with rapid tests, set up in France since 2001 at the abattoir and fallen plant, allowed study of the relative exposure of the successive birth cohorts with nonconditional logistic regression models adjusted for possible confounding variables. The results were in agreement with those of the back-calculation model, estimating a decrease of the BSE exposure from the birth cohort July 1995-June 1996 that matched with the decrease of the infection after June 1996. In view of the long incubation period of BSE, it is not possible to precisely assess the impact of any control measure before several years. Modeling was therefore used to estimate prospectively the efficiency of the ban of meat and bone meal extended to all farm species in November 2000. Using parameters about age at infection and incubation time estimated earlier, we assessed the minimum time to first detection if infections still occurred. We have waited up to June 2007 to know if less than 100 infections occurred among French cattle during the 6 months following January 2001.

The Wip1 phosphatase (PPM1D) antagonizes activation of the Chk2 tumour suppressor kinase.

We previously demonstrated that type 2C protein phosphatases (PP2C) Ptc2 and Ptc3 are required for DNA checkpoint inactivation after DNA double-strand break repair or adaptation in Saccharomyces cerevisiae. Here, we show the conservation of this pathway in mammalian cells. In response to DNA damage, ataxia telangiectasia mutated (ATM) phosphorylates the Chk2 tumour suppressor kinase at threonine 68 (Thr68), allowing Chk2 kinase dimerization and activation by autophosphorylations in the T-loop. The oncogenic protein Wip1, a PP2C phosphatase, binds Chk2 and dephosphorylates phospho-Thr68. Consequently, Wip1 opposes Chk2 activation by ATM after ionizing irradiation of cells. In HCT15 colorectal cancer cells corrected for functional Chk2 activity, Wip1 overexpression suppressed the contribution of Chk2 to the G2/M DNA damage checkpoint. These results indicate that Wip1 is one of the phosphatases regulating the activity of Chk2 in response to DNA damage.

Milk yield, age at first calving, and the risk of BSE: an analysis at the farm level in France.

The epidemic of bovine spongiform encephalopathy (BSE) in France, as in the UK, has affected dairy cattle much more than beef cattle. However, the intensification of dairy herd management as a risk factor for BSE has not to date been analyzed. For this purpose, two databases were merged: the French Milk Records database, and the French BSE database, which can be considered as being devoid of notification bias since July 2001, when systematic tests were implemented. Only pure Holstein herds were considered, which represent the vast majority of total and BSE-affected dairy herds in France. A case-control study was designed so that 20 control herds were matched to each case herd according to the location of the farm and the year of birth of the index case. Three thousand and forty five farms were included, among which 145 with a BSE case notified between July 2001 and July 2003, and 2900 controls. With respect to the risk of BSE, odds ratios for each class of milk yield and age at first calving were estimated by using conditional logistic regression models with appropriate adjustments to herd size. The two main results were the following: firstly, whereas most Holstein herds, with average production between 7000 and 10,000kg, had nearly the same BSE risk, a small category of very intensive herds, with annual milk yields above 10,000kg, were significantly more at risk than the other herds. Secondly, a very early first calving (under 26 months of age) was found to be at risk for BSE as compared to other categories, independently of the milk yield. These results are discussed in the light of the known age-dependent susceptibility to BSE.

Estimates of the prevalence of transmissible spongiform encephalopathies in sheep and goats in France in 2002.

An active surveillance programme for transmissible spongiform encephalopathies (TSES) in sheep and goats was implemented in France in 2002 at abattoirs and rendering plants. The analysis of the results of this programme highlighted three biases: a potentially non-random sampling scheme in both rendering plants and abattoirs, a heterogeneous geographical sampling ratio, and the use of two diagnostic tests of unequal sensitivity. Simulations were run to estimate the prevalence of TSES by taking these biases into account. A comparison of the prevalence of TSES calculated from the raw data with the simulation results showed that the effects of non-random sampling were minor in comparison with the effects of the heterogeneous geographical sampling ratio and the use of two diagnostic tests.

[The bovine spongiform encephalopathy in the UK and France: an epidemiological perspective]. / Point de vue épidémiologique sur l'encéphalopathie spongiforme bovine au Royaume Uni et en France.

Epidemiology is aimed at the study of the health status of human and animal populations. The present review shows how epidemiologists in the UK and France, contributed to a better knowledge of the bovine spongiform encephalopathy (BSE), its probable origin, and its associated risk factors. Following case studies and case-control surveys, the role of meat and bone meal (MBM) as the source of infection for cattle has been well established. Other epidemiological studies have shown the absence of horizontal transmission, but on the other hand a cohort study concluded to a possible vertical transmission. Backcalculation models, which intend to infer the characteristics of infection from the observations, agree on two results : first, the BSE infects young animals, under 2 years. Secondly, the peak of the French BSE epizootic, probably in the nineteen-eighties, was ignored. Successive measures concerningMBMfailed to completely abolish the epizootic. The analysis of born-after-the-ban (BAB) cases shows that their spatial distribution in France is not random, which argues against a sporadic origin. The French BAB cases may result from two nonexclusive events : residual contaminations of cattle by feed intended for pigs and poultry, and mother-to-calf prion transmission, likely at a low rate. If a total eradication of BSE is not obtained, it will be the task of epidemiologists in particular, to figure out the source of the residual infection.

Prevalence of BSE in cattle found dead, euthanased or emergency slaughtered on farms in western France in 2000, 2001 and 2002.

The overall trend and the trend within birth cohorts of the prevalence of bovine spongiform encephalopathy (BSE) in cattle found dead, euthanased or emergency slaughtered on farms in the Bretagne, Basse Normandie and Pays de la Loire regions of France, during the periods from August 7 to December 22 in 2000, 2001 and 2002, were analysed by non-conditional logistic regression, adjusted for the region and for the type of animals. The overall prevalence of BSE during these three periods decreased from 2.71 per 1000 in 2000 to 1.41 per 1000 in 2001 and 0.42 per 1000 in 2002. The prevalence within birth cohorts started to decrease for the cohort born between July 1, 1995 and June 30, 1996 (cohort 95/96) and the trend was reinforced for cohort 96/97, suggesting that the exposure of animals to the BSE agent had started to decrease for animals born after July 1995, that is, one year before the ban on specified risk materials in meat and bone meal was implemented in France. However, considering that most of the animals would have been infected at between six and 18 months of age, the decrease may have been due, at least partly, to this control measure.

Past, present and future of bovine spongiform encephalopathy in France.

The bovine spongiform encephalopathy (BSE) epidemic has been monitored in France since the end of 1990. The surveillance has been considerably enhanced since 2000, and today every cow aged 2 years or more is tested at the time of slaughter, culling or death. As of 1 May 2002, 613 native cases have been identified, 287 of them by the mandatory reporting system of suspect clinical cases or complementary programs, 213 by active surveillance of fallen stock and 113 by testing at the abattoir. The analysis of reported BSE cases shows a higher number of cases born between 1993 and 1995, which can be linked to a greater exposure at that time and to an increase in surveillance efficiency. When the clinical onset related to overexposure ends, the future trend of the BSE epidemic in France will depend on the efficiency of the control measures implemented since 1996. An indicator of this will be the number of BSE cases born among recent cohorts. Bovine spongiform encephalopathy (BSE) was described first in 1987 in Great Britain (Wells et al. 1987), where a huge epidemic started, and more than 180,000 cases have been detected since then in this country. A risk analysis undertaken in France in 1990, in part because of the amount of meat and bone meal (MBM) imported from Great Britain during the 1980s, led to the conclusion that BSE might have spread to France, and that sporadic cases might be observed (Savey et al. 1991). Epidemiological surveillance was therefore set up at the end of 1990, and control measures were taken to prevent the development of the disease. The trends in the number of BSE cases detected in France must be analyzed in the light of both the detection system and the control measures, as well as their changes over time.