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Enterococcus cecorum , a commensal Gram-positive bacterium of the chicken gut, has emerged as a worldwide cause of lameness in poultry, particularly in fast-growing broilers. It is responsible for osteomyelitis, spondylitis, and femoral head necrosis, causing animal suffering, mortality, and antimicrobial use.

Enterococcus cecorum, a commensal Gram-positive bacterium of the chicken gut, has emerged as a worldwide cause of lameness in poultry, particularly in fast-growing broilers. It is responsible for osteomyelitis, spondylitis and femoral head necrosis, causing animal suffering, mortality and antimicrobial use. Research on the antimicrobial resistance ofE. cecorumclinical isolates in France is scarce, and epidemiological cut-off (ECOFF) values unknown. To determine tentative ECOFF (COWT) values forE. cecorumand to investigate the antimicrobial resistance patterns of isolates from mainly French broilers, we tested the susceptibility of a collection of commensal and clinical isolates (n=208) to 29 antimicrobials by the disc diffusion (DD) method. We also determined the minimum inhibitory concentrations (MICs) of 23 antimicrobials by the broth micro-dilution method. To detect chromosomal mutations conferring antimicrobial resistance, we investigated the genomes of 118E. cecorumisolates mainly obtained from infectious sites and previously described in the literature. We determined the COWTvalues for more than 20 antimicrobials and identified two chromosomal mutations explaining fluoroquinolone resistance. The DD method appears better suited for detectingE. cecorumantimicrobial resistance. Although tetracycline and erythromycin resistances were persistent in clinical and non-clinical isolates, we found little or no resistance to medically important antimicrobials.

On January 30, 2020, the World Health Organization (WHO) declared coronavirus disease 2019 (COVID-19) a Public Health Emergency of International Concern (1). On March 24, 2020, the Global Polio Eradication Initiative (GPEI) suspended all polio supplementary immunization activities and recommended the continuation of polio surveillance (2). In April 2020, GPEI shared revised polio surveillance guidelines in the context of the COVID-19 pandemic, which focused on reducing the risk for transmission of SARS-CoV-2, the virus that causes COVID-19, to health care workers and communities by modifying activities that required person-to-person contact, improving hand hygiene and personal protective equipment use practices, and overcoming challenges related to movement restrictions, while continuing essential polio surveillance functions (3). GPEI assessed the impact of the COVID-19 pandemic on polio surveillance by comparing data from January to September 2019 to the same period in 2020. Globally, the number of acute flaccid paralysis (AFP) cases reported declined 33% and the mean number of days between the second stool collected and receipt by the laboratory increased by 70%. Continued analysis of AFP case reporting and stool collection is critical to ensure timely detection and response to interruptions of polio surveillance.

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., This study details success conditions of an antimicrobial stewardship program in animal agriculture. Based on data provided by complementary and independent monitoring tools, success could be assessed on both usage and resistance. Results highlight the strong relationship between cephalosporins usage and resistance in pig production, supporting a containment perspective through usage restriction.

Standard disc diffusion and MIC test procedure were used to investigate the susceptibility of two hundred and fifty-one isolates collected from infected fish in France to florfenicol, oxolinic acid and tetracycline. The tests were performed at 22 ± 2℃ and for the 177 Yersinia ruckeri they were read after 24-28 hr incubation and for the 74 Aeromonas salmonicida isolates they were read after 44-48 hr. Applying epidemiological cut-off values to the susceptibility data generated in these tests, the isolates were categorized as wild-type or non-wild-type. The agent-specific categories into each isolate were placed on the basis of the data generated by the two methods were in agreement in 98% of the determinations made. It is argued that, with respect to categorising isolates, disc diffusion and MIC methods can be considered as equally valid at this temperature and after both periods of incubation.

The present article aims to present Boccaccio’s Buccolicum carmen as a main work in his latin production, inspired by Vergil and his followers during the Middle Age. Through the allegorical path, focused on the shepherd’s environment, Boccaccio first defines a model of power embodied by the king-shepherd. Moreover, he tries to convert his readers, as well as himself, into a better way of life related to Vergil’s one and close to the eremitic model. By doing so, he accomplishes himself as a poeta-theologus, as exposed by Dante.

Place: Hoboken Publisher: Wiley WOS:000556059500001; International audience; The aim of this study was to summarise the literature reporting the risk factors for mortality in the mussel speciesMytilus edulisandMytilus galloprovincialisin order to identify potential science-based solutions to prevent or mitigate mussel mortality outbreaks. We followed the PRISMA methodology: Preferred Reporting Items for Systematic Reviews and Meta-Analyses. The studied corpus of 91 publications (114 studies) was highly heterogeneous with respect to the methodological approaches used to define or estimate mussel mortality and the related putative risk factors. Results showed that the mortality risk of both mussel speciesM. edulisandM. galloprovincialisvaried across the seasons, increased with an elevated seawater temperature above a thermal threshold of 20 and 24 degrees C, respectively, decreased by protecting mussels from predation, and was associated with the presence of pathogens inM. edulis. ForM. galloprovincialis, using mussel spat from the same area where the farming is carried out and farming them together with another mussel species appears to reduce the mortality risk. However, forM. edulis, this could be achieved by using pure crosses and in particular mussel spat having a selected genotype. For wild bed conservation, sand accumulation and anthropogenic sedimentation should be minimised. Our analysis showed that current approaches to this research topic are limited and are unlikely to yield actionable evidence to identify mussel mortality prevention or mitigation strategies. Therefore, recommendations are offered to increase the ability of future eco-epidemiological research to identify multiple exposures associated with mussel mortality, underpinned by standardised efforts and cooperative initiatives.

Objectives To characterize and compare resistance trends in clinical Escherichia coli isolates from humans, food-producing animals (poultry, cattle and swine) and pets (dogs and cats). Methods Antibiogram results collected between January 2014 and December 2017 by MedQual [the French surveillance network for antimicrobial resistance (AMR) in bacteria isolated from the community] and RESAPATH (the French surveillance network for AMR in bacteria from diseased animals) were analysed, focusing on resistance to antibiotics of common interest to human and veterinary medicine. Resistance dynamics were investigated using generalized additive models. Results In total, 743 637 antibiograms from humans, 48 170 from food-producing animals and 7750 from pets were analysed. For each antibiotic investigated, the resistance proportions of isolates collected from humans were of the same order of magnitude as those from food-producing animals or pets. However, resistance trends in humans differed from those observed in pets and food-producing animals over the period studied. For example, resistance to third-generation cephalosporins and fluoroquinolones was almost always below 10% for both humans and animals. However, in contrast to the notable decreases in resistance observed in both food-producing animals and pets, resistance in humans decreased only slightly. Conclusions Despite several potential biases in the data, the resistance trends remain meaningful. The strength of the parallel is based on similar data collection in humans and animals and on a similar statistical methodology. Resistance dynamics seemed specific to each species, reflecting different antibiotic-use practices. These results advocate applying the efforts already being made to reduce antibiotic use to all sectors and all species, both in human and veterinary medicine.

Livestock-associated methicillin resistantStaphylococcus 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 farms 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-farm network (n=10,542 farms), combining within- and between-farms dynamics, based on detailed data on breeding practices and pig exchanges 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.

Colistin resistance associated with plasmidic resistance genes is a serious public health issue. We aimed at studying the transmission of an mcr-1 colistin- and rifampicin-resistant Escherichia coli strain between inoculated pigs and sentinels in different controlled conditions. Three groups of four pigs were bred in separated animal rooms and inoculated on Day 0 (D0). In each inoculated group, six contact pigs were introduced on D2. The first inoculated-and-contact group was left untreated. The ten pigs in the second inoculated-and-contact group received colistin (100 000 IU/kg) before inoculation or contact (D-7 to D-5), simulating prophylactic administration. Pigs in the third inoculated-and-contact group were treated just after inoculation or before transfer (D0 to D2), simulating metaphylactic administration. Faecal samples were regularly collected and segments of intestinal tracts were obtained at necropsy, on D20-D22. Samples were cultured on rifampicin-supplemented media, and PCR was used to detect the mcr-1 gene. The kinetics of infection, based on culture results, were analysed using an SIR model. The inoculated strain was detected in all inoculated and contact pigs. The SIR model showed that one infected pig could transmit the resistant bacteria to one susceptible individual in less than 3 h on average. Prophylactic administration significantly enhanced the transmission rate and resulted in more samples containing the mcr-1 resistance gene at necropsy. No effect of metaphylactic administration could be detected on the transmission rate, nor on the carriage of the resistant strain. Our study confirms that colistin should not be used in a prophylactic manner.

International audience; The statistical processing of analytical epidemiological data aims to determine the risk factors for a disease or veterinary public health problem. To meet this objective, generalized linear models are used. For observations from different sub-populations, these models exist as latent class models, also known as mixture models. However, in veterinary epidemiology in particular, these methods have three main limitations: (i) the number of observations in a sub-population must be greater than the number of variables, (ii) the variables must have a multi-normal distribution, and (iii) the variables must not have strong multi-collinearity, these hypotheses being rarely satisfied in practice. We propose an extension of the mixture models for a large number of variables that do not satisfy distributional hypothesis. These variables may also have the particularity of being organized into thematic blocks. The proposed method is called multiblock regression on latent classes. It combines the simultaneous search for sub-populations within the observations, as well as local (multiblock) regression models associated with each of these sub-populations. This new method is applied, for example, to the search for risk indicators for antibiotic consumption in French rabbit farms.; Le traitement statistique des données d'épidémiologie analytique vétérinaire vise à déterminer les facteurs de risque d'une maladie ou d'un problème de santé publique vétérinaire. Pour répondre à cet objectif, les modèles linéaires généralisés sont utilisés. Pour le cas où les observations proviennent de différentes sous-populations, ces modèles existent sous forme de modèles sur classes latentes, aussi connus sous le nom de modèles de mélange. Cependant, en épidémiologie vétérinaire notamment, ces méthodes présentent trois principales limites : (i) le nombre d'observations dans une sous-population doit être plus grand que nombre de variables, (ii) les variables doivent présenter une distribution multinormale, et (iii) les variables ne doivent pas présenter de multi-colinéarité marquées, ces hypothèses étant rarement vérifiées en pratique. Nous proposons une extension des modèles sur classes latentes pour le cas d'un grand nombre de variables ne vérifiant pas d'hypothèse distributionnelle. Ces variables peuvent présenter, de plus, la particularité d'être organisées en blocs thématiques. La méthode proposée est appelée régression multibloc sur classes latentes. Elle combine la recherche simultanée de sous-populations au sein des observations, ainsi que de modèles de régression (multibloc) locaux associés à chacune de ces sous-populations. Cette nouvelle méthode est appliquée, à titre d'exemple, à la recherche de marqueurs de risque de l'utilisation des antibiotiques dans des élevages français de lapins. Mots-clés : Epidémiologie analytique, facteurs de risque, modèles de mélange, régression sur classes latentes, utilisation d'antibiotiques, lapin.

This paper presents the impact on antimicrobial resistance (AMR) in poultry and pig bacteria of the French EcoAntibio plan, a public policy to reduce antimicrobial use in animals. The analysis was performed using sales data of veterinary antimicrobials and AMR data from bacteria obtained at slaughterhouse and from diseased animals. From 2011-2018, fluoroquinolones exposure decreased by 71.5 % for poultry and 89.7 % for pigs. For Campylobacter jejuni isolated from broilers at slaughterhouses, ciprofloxacin resistance increased from 51 % in 2010 to 63 % in 2018, whereas for turkeys the percentages varied from 56 % in 2014 to 63 % in 2018. For commensal E. coli isolated from the caecal content of broilers at slaughterhouses, the resistance to ciprofloxacin - assessed using an epidemiological cut-off value - increased in broiler isolates from 30.7 % in 2010 to 38.1 % in 2018. In turkeys, the percentage of resistant E. coli isolates decreased from 21.3 % in 2014 to 15.2 % in 2018, whereas in pigs, it increased from 1.9 % in 2009 to 5.5 % in 2017. However, for E. coli isolated from diseased animals, when the breakpoints of 2018 were applied, resistance to fluoroquinolones significantly decreased between 2010 and 2018 from 9.0%-5.4% for broilers/hens, from 7.4 % to 3.4 % for turkeys and from 9.4 % to 3.6 % for pigs. These data show that the major, rapid decrease in the exposition to fluoroquinolones had contrasting effects on resistance in the diverse bacterial collections. Co-selection or fitness of resistant strains may explain why changes in AMR do not always closely mirror changes in use.

Colistin resistance in Enterobacteriaceae is a public health problem. The present study was designed to evaluate the dissemination of a colistin-resistant Escherichia coli strain and its resistance gene, mcr-1, between orally inoculated pigs and their contacts. A non-inoculated control group, one low-dose and one high-dose group—both including two pens of two inoculated and three contact pigs—were raised in separate rooms. After inoculation of a colistin- and rifampicin-resistant E. coli suspension (2.5 × 105 CFU/pig for the low-dose group and 2.5 × 108 CFU/pig for the high-dose group), feces from inoculated and non-inoculated contact pigs were collected and inoculated on colistin- and rifampicin-supplemented media directly or after enrichment in rifampicin-supplemented media, then the isolates were characterized. PCR was used to detect the mcr-1 gene in lysates from feces cultivated in colistin-supplemented broth and DNA prepared from feces. Results showed that the low-dose inoculum was probably insufficient to obtain durable colonization, but could lead to the temporary presence of mcr-1-positive E. coli strains. The high-dose inoculum resulted in durable colonization of both inoculated and contact animals. In all groups, the mcr-1 gene was also detected in rifampicin-susceptible strains, suggesting its transfer to several commensal strains. A comparison of detection methods showed that more positive samples were obtained with cultures in rifampicin-supplemented media and suggests that current methods to evaluate the prevalence of colistin resistance in fecal samples suffer from poor sensitivity.

International audience; Categorized by WHO as critically important antibiotics, third-generation cephalosporins (3GCs) are one of the latest therapeutic alternatives to fight severe infectious diseases in humans. Some antibiotics belonging to this class are prescribed to treat food-producing animals in specific pathological contexts. Preserving the effectiveness of 3GCs requires characterization and careful monitoring of 3GCs resistance and the identification and implementation of measures that can limit this antimicrobial resistance (AMR). Here, we characterized the 3GCs resistance in Escherichia coli isolated from diseased animals. Using data collected from broilers, hens, calves, piglets, sows, turkeys and ducks between 2006 and 2016 by the French surveillance network of AMR in pathogenic bacteria of animal origin (called RESAPATH), we investigated the dynamics of resistance to 3GCs. Our non-linear analysis applied to time series showed that the evolution of E. coli resistance to 3GCs is specific to each animal category. From 2006 to 2010, resistance to 3GCs increased for most animal categories. We observed peaks of high-level of resistance for hens (21.5% in 2010) and broilers (26.7% in 2011), whereas trends stayed below 10% for the other animal categories throughout the study period. Resistance later decreased and, since 2014, 3GCs resistance has dropped below 10% for all animal categories. The parallel between trends and measures to limit AMR over the period shed lights on the impact of practices changes, public policies (EcoAntibio Plan) and sector-led initiatives (moratorium in swine sector). Finally, they highlight the usefulness and importance of AMR surveillance networks in animal health, such as RESAPATH.

The importance of the role of environment in the dissemination of antimicrobial resistant bacteria is now well recognized. Thus, bacterial indicators to monitor the phenomena are required. The Aeromonas genus is autochthonous in the aquatic environment and easy to detect in any water type, such as freshwater, or wastewater. These microorganisms are also causing infections in humans and animals (including fish). Furthermore, as Aeromonas spp. is able to acquire antimicrobial resistance mechanisms, it is candidate for indicator bacteria to follow antimicrobial resistance dissemination in aquatic environments. Unfortunately, to date, interpretation criteria for Aeromonas spp. for antimicrobial susceptibility tests are scarce in the literature. No epidemiological cut-off values for Aeromonas are currently available at EUCAST to interpret Minimum Inhibitory Concentrations (MIC). The only interpretation criteria available are clinical breakpoints from CLSI that are adapted from Enterobacteriaceae. Based on the results of MIC distributions obtained for a collection of environmental isolates of Aeromonas, this study aimed at proposing tentative epidemiological cut-off values (COWT) for Aeromonas spp. assessing whether the genus is an acceptable level of definition. Thus, 233 isolates collected from 16 rivers were identified at species level using Maldi-Tof (Bruker). Eleven different species were identified, the most abundant were A. bestiarum (n = 54), A. salmonicida (n = 45), A. sobria (n = 41), and A. eucrenophila (n = 37). 96-well micro-plates containing different concentrations of 15 antimicrobials, namely cefotaxime, ceftazidime, chloramphenicol, colistin, enrofloxacin, erythromycin, florfenicol, flumequine, gentamicin, nalidixic acid, oxolinic acid, streptomycin, temocillin, tetracycline, and trimethoprim-sulfamethoxazole, were prepared. The broth micro-dilution method was used to determine the antimicrobial susceptibility of each isolate. The estimation of COWT values was satisfactory obtained at genus level for all antimicrobials except cefotaxime and erythromycin. This first step is an invitation for other research teams to increase the amount of antimicrobial resistance data collected. Then, robustness of our proposed provisional generic epidemiological cut-off values could be assessed by testing antimicrobial susceptibility of various Aeromonas collections.

An increasing variety of indicators of antimicrobial usage has become available in human and veterinary medicine, with no consensus on the most appropriate indicators to be used. The objective of this review is therefore to provide guidance on the selection of indicators, intended for those aiming to quantify antimicrobial usage based on sales, deliveries or reimbursement data. Depending on the study objective, different requirements apply to antimicrobial usage quantification in terms of resolution, comprehensiveness, stability over time, ability to assess exposure and comparability. If the aim is to monitor antimicrobial usage trends, it is crucial to use a robust quantification system that allows stability over time in terms of required data and provided output; to compare usage between different species or countries, comparability must be ensured between the different populations. If data are used for benchmarking, the system comprehensiveness is particularly crucial, while data collected to study the association between usage and resistance should express the exposure level and duration as a measurement of the exerted selection pressure. Antimicrobial usage is generally described as the number of technical units consumed normalized by the population at risk of being treated in a defined period. The technical units vary from number of packages to number of individuals treated daily by adding different levels of complexity such as daily dose or weight at treatment. These technical units are then related to a description of the population at risk, based either on biomass or number of individuals. Conventions and assumptions are needed for all of these calculation steps. However, there is a clear lack of standardization, resulting in poor transparency and comparability. By combining study requirements with available approaches to quantify antimicrobial usage, we provide suggestions on the most appropriate indicators and data sources to be used for a given study objective.

A paralytic poliomyelitis outbreak occurred in Namibia in 2006, almost exclusively among adults. Nineteen cases were virologically confirmed as due to wild poliovirus type 1 (WPV1), and 26 were classified as polio compatible. Eleven deaths occurred among confirmed and compatible cases (24%). Of the confirmed cases, 97% were aged 15-45 years, 89% were male, and 71% lived in settlement areas in Windhoek. The virus was genetically related to a virus detected in 2005 in Angola, which had been imported earlier from India. The outbreak is likely due to immunity gaps among adults who were inadequately vaccinated during childhood. This outbreak underscores the ongoing risks posed by poliovirus importations, the importance of maintaining strong acute flaccid paralysis surveillance even in adults, and the need to maintain high population immunity to avoid polio outbreaks in the preeradication period and outbreaks due to vaccine-derived polioviruses in the posteradication era.

Current ante mortem inspection involves a check of relevant Food Chain Information (FCI) transmitted by the farmer to the slaughterhouse on a regulatory FCI document. Since 2000, a farm sanitary form with FCI data has been used for all consignments of broiler chickens in France. However, the FCI needs to be standardized for the collection and interpretation of data. A study was conducted to develop an expert system, undertaken to elaborate on a simple decision support system capable of predicting whether the flocks will present a high condemnation risk, based on FCI. For this, ‘optimal’ (i.e. on-farm survey data) and ‘worthy’ (i.e. farmers’ declaration on existing farm sanitary form) data quality conditions were considered to estimate the lower and upper reference bounds of the confidence that the decision-makers could have in such a tool. Chicken broiler flocks (404) were randomly selected in 15 slaughterhouses located in Western France in 2005. Condemnation proportion and farm sanitary form were collected for each selected flock. Information about health history and technical performances were also specifically collected on farm. Condemnation risk category was modelled from the on-farm collected information, using a Bayesian network and assuming this represented the optimal data quality conditions. Corresponding information declared by the farmer on the existing farm sanitary form was secondly used in the network to evaluate the impact of the uncertainty of such information on the condemnation classification obtained with the expert system. The learnt Bayesian network had 16 explanatory variables pertaining to technical characteristics and sanitary features of the flock. Using a threshold of 1% of condemned carcases to define high risk, the network sensitivity and specificity were 55% and 93%, respectively, corresponding to positive and negative predictive values of 70% and 87%. When declared existing information was used in the network, the sensitivity and specificity were 16% and 96%, respectively, corresponding to positive and negative predictive values of 57% and 80%. Results suggested that the predictive network developed may be insufficient for correctly classifying chicken flocks for targeting of management procedures, and in its current form, the expert system may be unlikely to be implemented in the field. However, it could help to improve the standardization of both form design and FCI interpretation at a national level.

Colistin has been used in veterinary medicine for decades, mainly for the prevention and treatment of Enterobacteriaceae infections. However, data regarding colistin resistance in bacteria from animals and food of animal origin are relatively scarce, partly because there are methodological difficulties hampering the analysis of susceptibility to colistin. Most data regarding clinical isolates are related to enteropathogenic Escherichia coli and Salmonella. The resistance percentages are sometimes high for pathogenic strains, and the mcr-1 gene has been detected in pathogenic E. coli isolates from pigs, cattle and poultry in different countries. The prevalence of colistin resistance in Salmonella from healthy animals is usually low but depends on the proportion of intrinsically colistin-resistant serotypes. For indicator E. coli, the resistance levels are often very low, although higher levels have been observed in Asia. The mcr-1 gene has been detected in indicator E. coli from pigs, cattle, poultry and their products. Thus, there is an urgent need to re-assess the use of colistin in livestock throughout the world to ensure a global strategy for preserving this last-resort antimicrobial.

Summary Aims: Methicillin-resistant Staphylococcus aureus (MRSA) ST398 has recently been described as a zoonotic agent. Its transmission between animals seems to be a pivotal factor in its emergence and dissemination. This experimental trial was performed to describe MRSA ST398 contamination and transmission in pigs after a low dose inoculation. Methods and results: Twelve specific pathogen-free (SPF) pigs were randomly divided between two separate pens. Three pigs in each pen received a nasal inoculation of 2 × 104 colony-forming units per animal, and three naive pigs were left in contact with them. Every 2 days and at necropsy, different samples were screened for MRSA. It was detected in nasal swabs from five inoculated and three naive contact pigs, as early as 1 day after inoculation. MRSA was also found in environmental wipes but never in faecal samples. At necropsy, MRSA was detected in the lymph nodes of two contact pigs and in the tonsils and lymph nodes of three inoculated pigs. Twelve other SPF pigs were included as negative control in a separate room. Conclusion: This experiment showed that inoculation of a low dose of MRSA ST398 could lead to the horizontal transmission of the bacterium between pigs, the contamination of mandibular lymph nodes and the contamination of the environment without faecal carriage. Significance and Impact of the Study: The minimal inoculated dose via nasal route to observe transmission of MRSA ST398 between pigs is equal or lower to 2 × 104 colony-forming units per animal, and faecal excretion seems not to be a necessary condition for horizontal transmission.

International audience; This work aims at introducing modelization, theoretical and numerical studies related to a new downscaling technique applied to Computational Fluid Dynamics. Our method consists in building a local model, forced by large scale information computed thanks to a classical numerical weather predictor. The local model, compatible with the Navier-Stokes equations, is used for the small scale computation (downscaling) of the considered fluid. It is inspired by S.B. Pope's works on turbulence, and consists in a so-called Langevin system of stochastic differential equations. We introduce this model and exhibit its links with classical RANS models. Well-posedness, as well as mean-field interacting particle approximations and boundary condition issues are addressed. We present the numerical discretization of the stochastic downscaling method and investigate the accuracy of the proposed algorithm on simplified situations.

A field study was conducted to estimate the sanitary condemnation proportion in male turkey broiler flocks, to describe the reasons for condemnation and the related macroscopic lesions, and to investigate whether primary production information would predict the risk of condemnation. Male turkey standard broiler flocks (117) were randomly selected in the 13 slaughterhouses located in Western France, from February to July 2006. The flocks were monitored from their arrival at the slaughterhouse until the results of the post mortem sanitary inspection. Information about rearing conditions, health history, catching and loading conditions, transportation to the slaughterhouse and slaughtering was also collected. Sampling design was considered in the calculations and the condemnation proportion was modelled using a negative binomial regression, accounting for clustering within slaughterhouse. The within-flock weighted average condemnation proportion was 1.8% (95% confidence interval, 1.3-2.3%). Emaciation, arthritis-polyarthritis and congestion were the main reported official reasons for condemnation, representing 76% of the condemned carcases. Three variables were significantly associated with increased risk of condemnation: observed locomotor disorders on the farm, high cumulative mortality 2 weeks before slaughter, and clinical signs observed by the Veterinary Services during the ante mortem inspection at the slaughterhouse. The final model explained 35% of the total variation in condemnation risk. Half of this explained variation could be attributed to locomotor disorders observed during rearing. The sensitivity and specificity of the model to predict a high flock condemnation risk were 80% and 74%, respectively, when using an optimum threshold of 0.95% to define high risk. The results of this study suggested that the variables found to be associated with condemnation proportion were markers of increased risk and could be used as indicators. These risk indicators can easily be retrieved from the pre-existing regulatory document transmitted before flock arrival at the slaughterhouse and could be used to screen flocks before slaughter, according to their expected risk of condemnation.

SUMMARYThe feasibility of using risk markers to screen broiler chicken flocks and anticipate their risk of condemnation at meat inspection was examined in 404 randomly selected flocks in 15 French slaughterhouses in 2005. Condemnation rate and information about rearing conditions, health history, catching and loading, transport and slaughtering were collected. The Poisson regression model of the condemnation rate consisted of six simple and biologically relevant predictors: production type, frequency of farmer's visits during the starting period, health disorders during rearing, on-farm mortality, mortality during transport, and slaughter-line speed. Although accurate prediction of the condemnation rate for a given flock was not feasible, flocks with low or high risk of condemnation could be distinguished. These findings could be useful at various stages of chicken production, to monitor and improve farm husbandry practices, minimize the impact of transport conditions, and optimize meat inspection procedures.

Several measurement units are available to quantify antimicrobial usage in veterinary medicine, to obtain diverse measures such as the weight of active substance used, the live weight (LW) treated, the fraction of animals exposed, the number of treatments recorded or the cost represented. These measures can be applied to study practices variability between farms, to characterize patterns of usage of the different antimicrobial classes or to follow evolution of antimicrobial usage with time. An investigation was carried out to specifically explore the influence of measurement units on the conclusions obtained from such studies. Antimicrobial exposure was explored in a sample of turkey and chicken broiler flocks, using six different units [kg of active compound, treatments, days of administration, kg of LW treated, animal daily dose to treat 1 kg of LW (ADD(kg)) and euros] to compare flocks usage variability and patterns of use of the different antimicrobial classes. Time-trends evolutions of macrolides usage in turkey broilers, characterized by percentage of flocks exposed and LW treated, were also compared. In all analyses, the measure gave different results without equivalences, highlighting the necessity for care in choosing the measurement unit and caution in interpreting the figures obtained.

International audience; We did a prospective observational 9-month long study to quantify risk factors of managerial and hygiene practices, and pig-health status for Salmonella seroconversion of fattening pigs reared in subclinically infected French farrow-to-finish farms. During the fattening phase, 2 649 pigs belonging to the same batch of contemporary pigs, from 89 conventional farrow-to-finish farms were individually followed and regularly blood sampled on a monthly basis. Farm recruitment was based on the farmer's willingness to cooperate. Pig status was assessed using an indirect ELISA test. Evolution of the serological status was studied by means of survival analysis. A Cox proportional-hazards model, taking into account the clustering of animals at the farm level, was used to examine the effects of explanatory variables on the time to Salmonella seroconversion of pigs. Applying group level antibiotic treatment to the pigs during the fattening period (Hazard Ratio (HR) = 2.4; 95% CI: 1.7, 3.4) was identified as a risk factor for Salmonella seroconversion, as the presence of residual Salmonella contamination in the fattening pen before placing the pigs into the pens (HR = 1.9; 95% CI: 1.2, 2.9). Porcine reproductive and respiratory syndrome virus (PRRSV) seropositivity during the fattening period also indicated an increased hazard for seroconversion (HR = 1.6; 95% CI: 1.1, 2.5). The batch size was identified as a risk factor for Salmonella seroconversion: the higher the number of pigs was in the fattening room followed, the higher was the risk (HR(+10 pigs) = 1.05 for a 10-pig increment; 95% CI: 1.03, 1.06). The biosecurity measures of wearing specific clothes before entering the facilities (HR = 0.5; 95% CI: 0.3, 0.9) and enclosing the pig farm facilities were protective (HR = 0.4; 95% CI: 0.2, 0.8).

International audience

Data collection at the flock level on a continuous basis, for antimicrobial use surveillance purposes, provides a complex challenge. Using existing on-farm records, produced as part of the regulations for meat inspection, a sampling scheme was implemented to collect on a simple, representative and continuous basis, the forms providing history of antimicrobial consumption of poultry flocks slaughtered in Brittany. Relational database-stored information provided by the forms includes treatment purpose, antimicrobial drug administered, age at treatment and treatment duration. The aim of this study was to collect information describing antimicrobial drug use quantitatively and qualitatively, by computing the frequency of antimicrobial use according to species, therapeutic class, treatment purpose, duration, and animal age at treatment. A study was carried out to check the validity of farmers' declarations. Examples of data and results are presented such as the relative importance of the different antimicrobial classes in relation to the live weight treated, which shows that beta-lactams and tetracyclines are the main classes used in broilers and turkeys respectively. Average bird weight at treatment was 0.5 kg for a broiler and 3 kg for a turkey. Nevertheless, several 'at-risk' periods could be identified. Initial results after 1 year of data collection showed that this surveillance system provides valid, detailed and useful data about antimicrobial drug use in poultry production at a low cost and with only a moderate time involvement.

Exposure measurement in pharmaco-epidemiological studies can be based on various sources that do not always concur. However, reliability is an important criterion when selecting the method used to assess exposure and interpreting the results obtained. An analysis based on invoices might be more informative and more accurate to assess vaccines exposure (yes/no) in turkey broiler production than a questionnaire administered to farmers, which is nevertheless more feasible and less time-consuming. We compared the two methods to assess vaccination exposure in 239 turkey broiler flocks reared in 129 farms in 2000-2001. The agreement (crude agreement and kappa) was calculated, and association between discrepancy and farm and flock characteristics was investigated. Marek's-disease vaccine, Newcastle-disease vaccine, turkey haemorrhagic-enteritis vaccine and turkey-rhinotracheitis vaccine exposures were reported on the questionnaire for 2.1, 27.6, 93.0, and 98.3% of flocks, respectively, and for 2.1, 29.3, 89.4, and 86.6%, of invoices for the flocks studied, respectively. A discrepancy was observed in 24.9% of flocks. A discrepancy was observed more frequently in specialised farms without any other animal production (OR = 3.6; CI = 1.5, 8.9) and when the farmer did not know whether vaccination had been performed in the hatchery (OR = 7.1; CI = 2.6, 19.7).

Fattening-pigs carriers of Salmonella enterica are believed to be a main source of carcass and pork contamination at the later steps of the meat process. We did a prospective study in 2000-2001 in 105 French farrow-to-finish pig farms. In each farm, a batch of contemporary fattening pigs housed in the same room was followed throughout the fattening period. Salmonella shedding was assessed on environmental samples of faecal material (taken by means of pairs of gauze socks) analysed by classical bacteriological methods. 36.2% of the batches studied had at least one contaminated environmental sample and therefore were classified as Salmonella-shedding batches. Logistic regression was used to assess the association between managerial and hygiene practices and health status and the shedding risk at the end of the finishing period. Emptying the pit below the slatted floor after the previous batch of sows was removed and frequent removal of sow dung during the lactation period were protective. Presence of residual Salmonella contamination of the floor and pen partitions in the fattening rooms before loading the growing pigs also was a risk factor. The risk for Salmonella shedding at the end of the fattening period was increased when dry feed (versus wet feed) was provided during the fattening period. Lastly, Lawsonia intracellularis seroconversion and PRRSV seropositivity during the fattening period also was a risk factor for Salmonella shedding.

It is shown how various ideas that are well established for the solution of Poisson's equation using plane wave and multigrid methods, can be combined with wavelet concepts. The combination of wavelet concepts and multigrid techniques turns out to be particularly fruitful. We propose a modified multigrid V cycle scheme that is not only much simpler, but also more efficient than the standard V cycle. Whereas in the traditional V cycle the residue is passed to the coarser grid levels, this new scheme does not require the calculation of a residue. Instead it works with copies of the charge density on the different grid levels that were obtained from the underlying charge density on the finest grid by wavelet transformations. This scheme is not limited to the pure wavelet setting, where it is faster than the preconditioned conjugate gradient method, but equally well applicable for finite difference discretizations.

Resistance of Escherichia coli to third-generation cephalosporin (3GC) in fecal samples representative of French egg production was studied. The susceptibility to cefotaxime of E. coli isolates obtained by culture on nonselective media was determined. Twenty-two nonsusceptible isolates were obtained (7.51%; 95% confidence interval, 4.49 to 10.54%), the majority of which came from young birds. Most isolates carried a bla CTX-M-1 group gene, and a few carried a bla CMY-2 -like gene. Control of 3GC resistance in laying hens is needed.

Colistin is a cyclic decapeptide bound to a fatty acid chain. It is active against many Gram-negative bacteria by destabilising the bacterial outer membrane. Bacteria can become resistant to colistin by modification of their lipopolysaccharide, thereby reducing the affinity of polymyxins. Colistin is often administered orally in poultry and pig production to control colibacillosis. Resistant isolates are sometimes recovered from pathological cases, particularly in piglets. However, in Europe the percentage of resistance to colistin in Escherichia coli strains isolated from the digestive tract microbiota of healthy animals remains

In recent years, broiler mortality during transport to the slaughterhouse has become a cause for concern because of animal welfare considerations and associated economic losses. A descriptive and analytical epidemiological study was carried out to estimate the extent of DoA in poultry broiler production in the main producing regions of France and to determine factors influencing the DoA rate. Data regarding animal characteristics and rearing, catching, transport and lairage conditions were collected on farm and at the slaughterhouse for 404 chicken broiler flocks processed during 2005. The average DoA rate was 0.18% (from 0% to 1.4%). Variables found to be associated (P < 0.05) with the DoA rate in a multivariable negative binomial model were flock cumulative mortality on farm, the catching system (mechanical being more at risk than manual), the density in crates (more space allowance being associated with less mortality) and climatic conditions (rain and wind being associated with more DoA). Mortality during transport is thus related to all production steps from the farm to the slaughterhouse. Efforts have therefore to be made by all professionals to contain mortality on farm and during catching and transportation.