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IntroductionWithin the 2007–2014 programme for the surveillance of antimicrobial resistance (AMR) in livestock in France, mcr-1 prevalence average in commensal Escherichia coli was found to be 5.9% in turkeys and 1.8% in broilers, indicating that mobile colistin resistance had spread in farm animals. In 2017, the French national Ecoantibio2 plan was established to tackle AMR in veterinary medicine, with the objective of a 50% reduction in exposure to colistin in farm animals within 5 years (from 2014–2015 to 2020). Our objective was to update data concerning the prevalence and molecular epidemiology of colistin resistance, in consideration of colistin sales in poultry production in France.MethodsAntimicrobial susceptibility of commensal E. coli isolated from broilers and turkeys at slaughterhouse was determined by broth micro-dilution. The mcr genes were screened by polymerase chain reaction (PCR). Whole genome sequencing (WGS) was used to investigate the genetic diversity of colistin-resistant isolates. Transformation experiments enabled identification of the mcr-bearing plasmid replicon types. The correlation between prevalence of colistin resistance and colistin usage data was explored statistically.Results and discussionIn 2020, in France, the resistance prevalence to colistin in poultry production was 3% in turkeys and 1% in broilers, showing a significant highly positive correlation with a −68% decrease of poultry exposure to colistin since 2014. Only the mcr-1 gene was detected among the colistin-resistant E. coli. More than 80% of isolates are multi-drug resistant with 40% of isolates originating from turkeys and 44% originating from broilers co-resistant to the critically important antimicrobial ciprofloxacin. Most of the strains had no clonal relationship. The mcr gene was located in different plasmid types, carrying various other AMR genes. The decrease in colistin resistance among poultry in France can be considered a positive outcome of the national action plans for reduced colistin usage.

La quantité d’antibiotiques utilisés dans les filières monogastriques (porcs, volailles et lapins) a chuté fortement à partir des années 2000, et connaît une relative stabilisation depuis quelques années. Les plans EcoAntibio successifs ont renforcé la dynamique et contribué à réduire drastiquement l’usage des antibiotiques critiques. Cette évolution est la résultante combinée d’évolutions réglementaires, d’actions volontaires privées mises en œuvre dans les filières de production, et de démarches professionnelles collectives et individuelles. Différentes actions ont été mises en place, reposant sur une approche multifactorielle de la santé, l’établissement d’un diagnostic fin des troubles sanitaires de l’élevage, et un travail sur leurs causes sous-jacentes pour définir des mesures préventives adaptées. L’accent est mis sur la conduite d’élevage, l’assainissement vis à vis d’agents pathogènes particuliers, la biosécurité, la vaccination, la nutrition, et l’usage de substances alternatives. Les pratiques d’antibiothérapie ont aussi évolué, avec la mise en place de guides de bonnes pratiques consensuels, la généralisation de l’examen bactériologique et de l’antibiogramme, la bonne observance des posologies, et le suivi précis de la santé pour adapter les traitements. La mise en place de ces évolutions repose par ailleurs sur un bon rapport de confiance entre éleveur, vétérinaire et technicien d’élevage, l’accompagnement des éleveurs ayant aussi été renforcé via des dispositifs de sensibilisation et de formation. La poursuite de la rationalisation des usages reposera sur le ciblage des exploitations à risque au regard des usages d’antibiotiques et la mise en place d’actions sur-mesure.

Promouvoir un usage responsable et prudent des antibiotiques est un axe clé des plans d’action internationaux, européens et nationaux pour lutter contre l’antibiorésistance. De nombreuses recommandations et mesures visent à diminuer l’utilisation des antibiotiques en réservant leur usage dans les cas où il est strictement nécessaire. Dans une approche « Une seule santé », l’Agence européenne des médicaments a établi une catégorisation des antibiotiques à usage vétérinaire en prenant en compte à la fois le risque pour la santé humaine et les besoins en santé animale. Il est en effet particulièrement important de préserver les antibiotiques considérés comme critiques pour le traitement des maladies bactériennes chez l’Homme. Depuis 2011, des objectifs nationaux ont été définis afin de réduire l’utilisation des antibiotiques en médecine vétérinaire en France. Des initiatives prises par les filières et les plans Ecoantibio ont créé une dynamique qui a permis d’atteindre ces objectifs. La France fait d’ailleurs partie des pays européens qui ont le plus diminué ces dernières années l’usage des céphalosporines de 3e et 4e générations et des fluoroquinolones. La nouvelle règlementation européenne prévoit un ensemble de mesures qui vise à mieux encadrer et réduire l’usage de certains antibiotiques dans les élevages. Mesurer et suivre les usages contribue à favoriser une utilisation prudente des antibiotiques et à évaluer l’efficacité des actions menées à cet égard. Cet article présente différents systèmes de suivi de l’usage des antibiotiques qui ont été développés par différents acteurs dans la lutte contre l’antibiorésistance.

Abstract By 2010, systems set up to monitor the antimicrobial resistance of pathogenic bacteria and antimicrobial usage identified a sustained increase regarding third‐ and fourth‐generation cephalosporin resistance in French pig production. This sector mobilised and collectively committed to responsible action in the following months. This led to a multi‐professional voluntary stewardship programme that was started in 2011. A consensus of veterinary opinion led to the definition of restrictive rules on the prescription of the third‐ and fourth‐generation cephalosporins targeted by the antimicrobial stewardship programme (ASP). All pig sector professionals, including farmers, were informed. Existing monitoring systems for usage and resistance were supplemented by data from the records of veterinarians' cephalosporin deliveries and from individual pig farm surveys investigating antimicrobial usage. The second step, from 2014, entailed regulatory measures that consolidated the programme by setting quantitative reduction objectives and specifying the terms and conditions for prescribing and dispensing a list of critical antimicrobial molecules including cephalosporins. All the data sources confirmed a significant fall of more than 90% in cephalosporin usage in the French pig production sector between 2010 and 2016. Monitoring systems recorded that the resistance of commensal and pathogenic Escherichia coli isolates also tended to decrease over the same period. The stewardship programme proved highly effective in reducing usage and containing resistance, illustrating the efficiency of a well‐defined multi‐professional strategy.

International organizations encourage the monitoring of antimicrobial use and resistance in bacteria to manage and minimize further development of antimicrobial resistance. In France, the public policy plan Ecoantibio has underlined the need to collect data on antimicrobial use in all livestock production chains from direct, on-farm studies. To gain better knowledge on antimicrobial use in the aquaculture industry, we therefore conducted a cross-sectional study in 2014–2015 on a representative sample of 100 French freshwater salmonid farms. The health issues and medicinal products used during the reference year (full year preceding the visit, 2013 or 2014), were recorded by administering an on-farm questionnaire and by consulting documents, feed mills and prescribing veterinarians. Rainbow trout fry syndrome (RTFS), the most frequently reported disease, affected 41% of the fish farms at least once in the previous year. Parasitic diseases were also a cause of major concern, and finally furunculosis affecting 20% of the farms. Two-thirds (65%) of the farmers used antimicrobials at least once during this preceding year. Florfenicol was the most frequently used antimicrobial, mainly to treat outbreaks of RTFS, but it represented less than 20% of the treated fish biomass. Antimicrobials regarded as critical for public health reasons were used only exceptionally.

The acknowledgment of antimicrobial resistance (AMR) as a major health challenge in humans, animals and plants, has led to increased efforts to reduce antimicrobial use (AMU). To better understand factors influencing AMR and implement and evaluate stewardship measures for reducing AMU, it is important to have sufficiently detailed information on the quantity of AMU, preferably at the level of the user (farmer, veterinarian) and/or prescriber or provider (veterinarian, feed mill). Recently, several countries have established or are developing systems for monitoring AMU in animals. The aim of this publication is to provide an overview of known systems for monitoring AMU at farm-level, with a descriptive analysis of their key components and processes. As of March 2020, 38 active farm-level AMU monitoring systems from 16 countries were identified. These systems differ in many ways, including which data are collected, the type of analyses conducted and their respective output. At the same time, they share key components (data collection, analysis, benchmarking, and reporting), resulting in similar challenges to be faced with similar decisions to be made. Suggestions are provided with respect to the different components and important aspects of various data types and methods are discussed. This overview should provide support for establishing or working with such a system and could lead to a better implementation of stewardship actions and a more uniform communication about and understanding of AMU data at farm-level. Harmonization of methods and processes could lead to an improved comparability of outcomes and less confusion when interpreting results across systems. However, it is important to note that the development of systems also depends on specific local needs, resources and aims.

Livestock-associated methicillin resistant Staphylococcus aureus (LA-MRSA) colonizes livestock animals worldwide, especially pigs and calves. Although frequently carried asymptomatically, LA-MRSA can cause severe infections in humans. It is therefore important to better understand LA-MRSA spreading dynamics within pig farms and over pig movement networks, and to compare different strategies of control and surveillance. For this purpose, we propose a stochastic meta-population model of LA-MRSA spread along the French pig movement network (n = 10,542 farms), combining within- and between-farm dynamics, based on detailed data on breeding practices and pig movements between holdings. We calibrate the model using French epidemiological data. We then identify farm-level factors associated with the spreading potential of LA-MRSA in the network. We also show that, assuming control measures applied in a limited (n = 100) number of farms, targeting farms depending on their centrality in the network is the only way to significantly reduce LA-MRSA global prevalence. Finally, we investigate the scenario of emergence of a new LA-MRSA strain, and find that the farms with the highest indegree would be the best sentinels for a targeted surveillance of such a strain’s introduction.

Abstract Background There has been a strong implication of both the French swine industry and the national authorities on reducing the use of antimicrobials in swine production since 2010. The annual monitoring of antimicrobial sales by the French Veterinary Medicines Agency (Anses-ANMV) provides estimates but not detailed figures on actual on-farm usage of antimicrobials in swine production. Results In order to provide detailed information on the 2010 and 2013 antimicrobial use in the French swine industry, the methodology of cross-sectional retrospective study on a representative sample of at least 150 farms has been elected. The analysis of the collected data shows a strong and significant decrease in antimicrobial exposure of pigs between 2010 and 2013. Over three years, the average number of days of treatment significantly decreased by 29% in suckling piglets and by 19% in weaned piglets. In fattening pigs, the drop (− 29%) was not statistically significant. Only usage in sows did increase over that period (+ 17%, non-significant), which might be associated with the transition to group-housing of pregnant sows that took place at the time. Also, over that period, the use of third- and fourth generation cephalosporins in suckling piglets decreased by 89%, and by 82% in sows, which confirms that the voluntary moratorium on these classes of antimicrobials decided at the end of 2010 has been effectively implemented. Conclusions The methodology of random sampling of farms appears as a precise and robust tool to monitor antimicrobial use within a production animal species, able to fulfil industry and national authorities’ objectives and requirements to assess the outcome of concerted efforts on antimicrobial use reduction. It demonstrates that the use of antimicrobials decreased in the French swine industry between 2010 and 2013, including the classes considered as critical for human medicine.

Antimicrobial resistance (AMR) threatens our public health and is mainly driven by antimicrobial usage (AMU). For this reason the World Health Organization calls for detailed monitoring of AMU over all animal sectors involved. Therefore, we aimed to quantify AMU on turkey farms. First, turkey-specific Defined Daily Dose (DDDturkey) was determined. These were compared to the broiler alternative from the European Surveillance of Veterinary Antimicrobial Consumption (DDDvet), that mention DDDvet as a proxy for other poultry species. DDDturkey ranged from being 81.5% smaller to 48.5% larger compared to its DDDvet alternative for broilers. Second, antimicrobial treatments were registered on 60 turkey farms divided over France, Germany and Spain between 2014 and 2016 (20 flocks per country). Afterwards, AMU was quantified using treatment incidence (TI) per 100 days. TI expresses the percentage of the rearing period that the turkeys were treated with a standard dose of antimicrobials. Minimum, median and maximum TI at flock level and based on DDDturkey = 0.0, 10.0 and 65.7, respectively. Yet, a huge variation in amounts of antimicrobials used at flock level was observed, both within and between countries. Seven farms (12%) did not use any antimicrobials. Aminopenicillins, polymyxins, and fluoroquinolones were responsible for 72.2% of total AMU. The proportion of treating farms peaked on week five of the production cycle (41.7%), and 79.4% of the total AMU was administered in the first half of production. To conclude, not all DDDvet values for broilers can be applied to turkeys. Additionally, the results of AMU show potential for reducing and improving AMU on turkey farms, especially concerning the usage of critically important antimicrobials.

Food-producing animals are an important reservoir and potential source of transmission of antimicrobial resistance (AMR) to humans. However, research on AMR in turkey farms is limited. This study aimed to identify risk factors for AMR in turkey farms in three European countries (Germany, France, and Spain). Between 2014 and 2016, faecal samples, antimicrobial usage (AMU), and biosecurity information were collected from 60 farms. The level of AMR in faecal samples was quantified in three ways: By measuring the abundance of AMR genes through (i) shotgun metagenomics sequencing (n = 60), (ii) quantitative real-time polymerase chain reaction (qPCR) targeting ermB, tetW, sul2, and aph3′-III; (n = 304), and (iii) by identifying the phenotypic prevalence of AMR in Escherichia coli isolates by minimum inhibitory concentrations (MIC) (n = 600). The association between AMU or biosecurity and AMR was explored. Significant positive associations were detected between AMU and both genotypic and phenotypic AMR for specific antimicrobial classes. Beta-lactam and colistin resistance (metagenomics sequencing); ampicillin and ciprofloxacin resistance (MIC) were associated with AMU. However, no robust AMU-AMR association was detected by analyzing qPCR targets. In addition, no evidence was found that lower biosecurity increases AMR abundance. Using multiple complementary AMR detection methods added insights into AMU-AMR associations at turkey farms.

Pour réduire l’usage des antibiotiques en élevage, divers travaux en sciences biotechniques visent à concevoir et identifier des solutions zootechniques ou thérapeutiques alternatives aux antibiotiques. Cependant, au-delà de ces solutions techniques, des facteurs humains et sociaux déterminent les décisions de prescrire et d’administrer ou non des antibiotiques. L’article met l’accent sur ces facteurs et dresse une synthèse des travaux menés en sciences humaines et sociales en France sur la réduction de l’usage des antibiotiques dans différentes filières animales et leurs contributions pour relever ce défi. Trois contributions majeures ont émergé, à différentes échelles. La première consiste en une meilleure compréhension des processus de changement de pratiques opérés par les éleveurs pour réduire l’usage des antibiotiques dans leur élevage : identification des freins et motivations des éleveurs pour opérer ce changement, caractérisation de trajectoires de changement y compris les contextes dans lesquels elles sont réalisées, et des outils mobilisés par les éleveurs pour y parvenir. Une seconde contribution porte sur la compréhension du rôle des réseaux d’acteurs des éleveurs dans ces processus de changement : rôle du conseiller d’élevage et du vétérinaire et de leur relation de travail avec l’éleveur ; rôle des pairs pour expérimenter de nouvelles pratiques. La dernière contribution porte sur la compréhension et la conception de modes de gouvernance collectifs pour réduire l’usage des antibiotiques en élevage : analyse de la prescription vétérinaire et de ses évolutions, du rôle des acteurs des filières pour une action concertée et de la dynamique impulsée par le plan EcoAntibio. Quelques pistes sont évoquées pour approfondir ces travaux.

Outbreaks of poliomyelitis in African countries that were previously free of wild-type poliovirus cost the Global Polio Eradication Initiative US$850 million during 2003-2009, and have limited the ability of the program to focus on endemic countries. A quantitative understanding of the factors that predict the distribution and timing of outbreaks will enable their prevention and facilitate the completion of global eradication.Children with poliomyelitis in Africa from 1 January 2003 to 31 December 2010 were identified through routine surveillance of cases of acute flaccid paralysis, and separate outbreaks associated with importation of wild-type poliovirus were defined using the genetic relatedness of these viruses in the VP1/2A region. Potential explanatory variables were examined for their association with the number, size, and duration of poliomyelitis outbreaks in 6-mo periods using multivariable regression analysis. The predictive ability of 6-mo-ahead forecasts of poliomyelitis outbreaks in each country based on the regression model was assessed. A total of 142 genetically distinct outbreaks of poliomyelitis were recorded in 25 African countries, resulting in 1-228 cases (median of two cases). The estimated number of people arriving from infected countries and