Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): Japanese encephalitis (JE)

Non peer reviewe

Apport de l'épidémiologie dans le choix des outils d'aide à la prise de décision sanitaire en santé animale. (Evaluation des tests de dépistage en santé animale)

L étude et le choix des stratégies décisionnelles en santé animale nécessite de disposer d informations sur l efficacité des outils disponibles, qu il s agisse d un test unique, d une association de plusieurs tests ou d un ensemble de critères cliniques et épidémiologiques. La validation des tests de dépistage ou de diagnostic constitue donc un prérequis à la conception de protocoles d aide à la prise de décisions sanitaires. Lorsqu il existe une référence fournissant une information sur le statut infectieux des individus étudiés, l estimation des caractéristiques des tests peut être effectuée de manière directe. En santé animale, il est toutefois fréquent de ne pas disposer de cette information, lorsqu aucun test ne référence n est disponible ou lorsqu il n a pas pu être mis en œuvre, pour des raisons pratiques, économiques ou éthiques. Dans ce cas, l étude des tests requiert l utilisation de méthodes statistiques adaptées, telles l utilisation de modèles à classe latente implémentés par une approche bayésienne. Nous avons choisi, au cours de nos travaux, de nous intéresser à l estimation de la part d incertitude liée à l utilisation de tests en tant qu outils d aide à la prise de décision. Nous exposons dans un premier chapitre les enjeux et les modalités de la lutte contre les maladies animales, les outils épidémiologiques disponibles pour l élaboration de stratégies décisionnelles et les méthodes permettant l évaluation de ces outils et leur comparaison. Les trois chapitres suivants constituent une application de ces méthodes, dans des contextes différents correspondant à trois types de situations dans lesquelles il existe un besoin d aide à la décision sanitaire en santé animale : le dépistage de la brucellose porcine chez les porcs reproducteurs, le dépistage de l épididymite contagieuse du bélier chez les béliers destinés à l export et le dépistage de la tuberculose bovine dans les départements de Côte d Or et de Dordogne et dans la région camarguaise. Le dernier chapitre de ce manuscrit consiste en une discussion générale sur les modalités de choix d un outil d aide à la décision sanitaire.Knowing the efficacy of a diagnostic tool, whether it is a test used alone, a sequence of several tests or a group of clinical criteria, is essential to study and choose decision strategies. The validation of diagnostic and screening tests is thus necessary to conceive decision schemes. When a gold standard is available, the characteristics of a test can be estimated directly. However, the true individual disease status of the animals is often unknown, particularly in absence of a gold standard or when the gold standard cannot be used because of economical, practical or ethical constraints. In these cases, specific statistical methods like latent class models implemented through a Bayesian approach must be used. Our work aimed at estimating the uncertainty due to the use of diagnostic tests as decision tools. The first chapter presents the issues and practical details of the struggle against animal disease and the epidemiological tools available to estimate the characteristics of the tests and to compare them. In the three following chapters, these methods are applied to three different contexts in which the conception and the evaluation of decision tools are needed: the screening of porcine brucellosis in breeding hogs, the screening of Brucella ovis infection in exported rams and the screening of bovine tuberculosis in Côte d Or, Dordogne and Camargue (France). The last chapter consists in a global discussion about how to choose a decision tool.PARIS11-SCD-Bib. électronique (914719901) / SudocSudocFranceF

Vector-borne diseases

Non peer reviewe

Identification of Brucella sp. isolated in Brazil from 1976 to 2013 by Bruce-Ladder PCR

Background: Brucella sp. are the causative agents of brucellosis, an infectious disease that affects various species of animals and can be transmitted to humans through direct contact with infected animals, indirectly by the ingestion of rawmilk products, and during the handling of strains or infected material in the laboratory. Being a zoonosis, the detection of Brucella species in animals is essential for the prevention of the disease in humans and to perform a good program of control in infected herds. This study aimed at identifying Brucella field strains isolated from 1976 to 2013 in Brazil, using the modified Bruce-Ladder method, to evaluate the performance of this technique. Materials, Methods & Results: Eighty-three strains of Brucella sp. were included in the study, i.e. 21 reference strains (nine B. abortus, one B. canis, four B. melitensis, two B. ovis and five B. suis) and 62 field strains (six B. canis, one B. suis and 55 B. abortus). For the identification of the genus and/or species of Brucella, biochemical and physiological tests, including MacConkey-agar growth, glucose fermentation, haemolysis, catalase, oxidase and urease tests, nitrate reduction, citrate utilization, H2 S production and CO2 requirement, were performed. Genomic DNA was extracted from pure cultures through heat-lysis of bacterial cultures and the genus was confirmed by a genus-specific PCR (bcsp31 target gene), before performing the modified Bruce-Ladder PCR for the confirmation of the Brucella species. No problems of specificity were observed with the Bruce-Ladder PCR. However, the 1,682 bp fragment was not systematically amplified, even after several modifications such as the concentration of mix components, annealing temperatures and time. Therefore, an individual PCR using primers specific to this fragment was needed for complete identification of some strains. Also, only one kind of Polymerase gave the best results. All Brucella reference strains and negative controls gave the expected results. All field strains previously identified as B. abortus, B. canis and B. suis by biochemical and physiological tests were confirmed by the modified Bruce-Ladder PCR. All isolated Brucella abortus presented a Bruce-Ladder PCR profile expected for field strains, excluding the vaccine strains. Discussion: The modified Bruce-Ladder PCR identified properly all Brucella species (reference and field strains) and proved to be a reliable technique, thus facilitating the identification of the species in the laboratory, reducing the manipulation of these bacteria and the associated danger. Albeit the difficulties of amplification of one fragment for some strains, when using the multiplex technique, this method is fast and without risks after inactivation of the strains. Most studies on animal brucellosis in Brazil were only based on serological tests without identification of the pathogen; while the knowledge of the particular species and/or biovars that occur in Brazil, as well as their distribution, is important to monitor the spread of Brucella among sensitive species and among farms. Our results showed also that B. abortus is still the predominant species isolated in cattle in Brazil. The knowledge of the species that occur in Brazil can help to identify the source of infection and the measures of control to be applied, while it is also very important to trace the dispersion of strains among farms

Detecção de DNA de Brucella pela PCR em soros caninos positivos na imunodifusão dupla para brucelose

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Assessing the health status of managed honeybee colonies (HEALTHY-B): a toolbox to facilitate harmonised data collection

Tools are provided to assess the health status of managed honeybee colonies by facilitating further harmonisation of data collection and reporting, design of field surveys across the European Union (EU) and analysis of data on bee health. The toolbox is based on characteristics of a healthy managed honeybee colony: an adequate size, demographic structure and behaviour; an adequate production of bee products (both in relation to the annual life cycle of the colony and the geographical location); and provision of pollination services. The attributes ‘queen presence and performance’, ‘demography of the colony’, ‘in-hive products’ and ‘disease, infection and infestation’ could be directly measured in field conditions across the EU, whereas ‘behaviour and physiology’ is mainly assessed through experimental studies. Analysing the resource providing unit, in particular land cover/use, of a honeybee colony is very important when assessing its health status, but tools are currently lacking that could be used at apiary level in field surveys across the EU. Data on ‘beekeeping management practices’ and ‘environmental drivers’ can be collected via questionnaires and available databases, respectively. The capacity to provide pollination services is regarded as an indication of a healthy colony, but it is assessed only in relation to the provision of honey because technical limitations hamper the assessment of pollination as regulating service (e.g. to pollinate wild plants) in field surveys across the EU. Integrating multiple attributes of honeybee health, for instance, via a Health Status Index, is required to support a holistic assessment. Examples are provided on how the toolbox could be used by different stakeholders. Continued interaction between the Member State organisations, the EU Reference Laboratory and EFSA is required to further validate methods and facilitate the efficient use of precise and accurate bee health data that are collected by many initiatives throughout the EU.info:eu-repo/semantics/publishedVersio

Urgent advice on lumpy skin disease EFSA Panel on Animal Health and Welfare

In order to assess the effects on disease spread and persistence of partial stamping out of only clinically affected animals in holdings where the presence of lumpy skin disease has been confirmed, against total stamping-out policy of infected herds coupled with vaccination, a mathematical model for the transmission of LSDV between farms was developed and different scenarios explored. According to the model, vaccination has a greater impact in reducing LSDV spread than any culling policy, even when low vaccination effectiveness is considered. When vaccination is evenly applied so that 95% of the farms are vaccinated with 75% of vaccinated animals effectively protected, then total stamping out and partial stamping out result in a similar probability of eradicating the infection. When no vaccination is applied or when vaccination has a lower effectiveness (e.g. 40%), the probability of eradication is higher when total stamping out is performed as compared to partial stamping out. In general, partial stamping out results in limited increase of the number of farms affected as compared to total stamping out. Independently of the culling interventions applied in the model, vaccination was most effective in reducing LSDV spread if protection had already been developed at the time of virus entry, followed by protection of herds after virus entry. No vaccination is the least effective option in reducing LSDV spread. In order to reach the above described effects, it is necessary to implement vaccination of the entire susceptible population in regions at risk for LSDV introduction or affected by LSDV in order to minimise the number of outbreaks, and high animal- and farm-level vaccination coverage should be achieved. Farmers and veterinarians should be trained in the clinical identification of LSD in order to reduce underreporting, and the effectiveness of partial stamping out should be evaluated under field conditions.info:eu-repo/semantics/publishedVersio

Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): antimicrobial-resistant Escherichia coli in dogs and cats, horses, swine, poultry, cattle, sheep and goats

Escherichia coli (E. coli) was identified among the most relevant antimicrobial-resistant (AMR) bacteria in the EU for dogs and cats, horses, swine, poultry, cattle, sheep and goats in previous scientific opinions. Thus, it has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as in Article 9 and Article 8 for listing animal species related to the bacterium. The assessment has been performed following a methodology previously published. The outcome is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with uncertain outcome. According to the assessment here performed, it is uncertain whether AMR E. coli can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (33–66% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that the bacterium does not meet the criteria in Sections 1, 2, 3 and 4 (Categories A, B, C and D; 0–5%, 5–10%, 10–33% and 10–33% probability of meeting the criteria, respectively) and the AHAW Panel was uncertain whether it meets the criteria in Section 5 (Category E, 33–66% probability of meeting the criteria). The animal species to be listed for AMR E. coli according to Article 8 criteria include mammals, birds, reptiles and fish.info:eu-repo/semantics/publishedVersio

Welfare of pigs at slaughter

The killing of pigs for human consumption (slaughtering) can take place in a slaughterhouse or on farm. The processes of slaughtering that were assessed for welfare, from the arrival of pigs until their death, were grouped into three main phases: pre-stunning (including arrival, unloading from the truck, lairage, handling and moving of pigs); stunning (including restraint); and bleeding. Stunning methods were grouped into three categories: electrical, controlled atmosphere and mechanical. Twelve welfare consequences the pigs can be exposed to during slaughter were identified: heat stress, cold stress, fatigue, prolonged thirst, prolonged hunger, impeded movement, restriction of movements, resting problem, negative social behaviour, pain, fear and respiratory distress. Welfare consequences and relevant animal-based measures were described. In total, 30 welfare hazards that could occur during slaughter were identified and characterised, most of them related to stunning and bleeding. Staff were identified as the origin of 29 hazards, which were attributed to the lack of appropriate skill sets needed to perform tasks or to fatigue. Corrective and preventive measures for these hazards were assessed: measures to correct hazards were identified, and management was shown to have a crucial role in prevention. Outcome tables linking hazards, welfare consequences, animal-based measures, origins and preventive and corrective measures were developed for each process. Mitigation measures to minimise welfare consequences are proposed.info:eu-repo/semantics/publishedVersio

Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): antimicrobial-resistant Rhodococcus equi in horses

Rhodococcus equi (R. equi) was identified among the most relevant antimicrobial-resistant (AMR) bacteria in the EU for horses in a previous scientific opinion. Thus, it has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as in Article 9 and Article 8 for listing animal species related to the bacterium. The assessment has been performed following a methodology previously published. The outcome is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with uncertain outcome. According to the assessment here performed, it is uncertain whether AMR R. equi can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (10–66% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that the bacterium does not meet the criteria in Sections 1 and 2 (Categories A and B; 5–10% and 10–33% probability of meeting the criteria, respectively), and the AHAW Panel is uncertain whether it meets the criteria in Sections 3, 4 and 5 (Categories C, D and E; 10–66% probability of meeting the criteria in all three categories). The animal species to be listed for AMR R. equi according to Article 8 criteria are mainly horses and other species belonging to the Perissodactyla and Artiodactyla orders.info:eu-repo/semantics/publishedVersio