There has been little assessment of the methodological quality of studies measuring the performance (sensitivity and/or specificity) of diagnostic tests for animal diseases. In a systematic review, 190 studies of tests for bovine tuberculosis (bTB) in cattle (published 1934-2009) were assessed by at least one of 18 reviewers using the QUADAS (Quality Assessment of Diagnostic Accuracy Studies) checklist adapted for animal disease tests. VETQUADAS (VQ) included items measuring clarity in reporting (n=3), internal validity (n=9) and external validity (n=2). A similar pattern for compliance was observed in studies of different diagnostic test types. Compliance significantly improved with year of publication for all items measuring clarity in reporting and external validity but only improved in four of the nine items measuring internal validity (p < 0.05). 107 references, of which 83 had performance data eligible for inclusion in a meta -analysis were reviewed by two reviewers. In these references, agreement between reviewers' responses was 71% for compliance, 32% for unsure and 29% for non-compliance. Mean compliance with reporting items was 2, 5.2 for internal validity and 1.5 for external validity. The index test result was described in sufficient detail in 80.1% of studies and was interpreted without knowledge of the reference standard test result in only 33.1%. Loss to follow-up was adequately explained in only 31.1% of studies. The prevalence of deficiencies observed may be due to inadequate reporting but may also reflect lack of attention to methodological issues that could bias the results of diagnostic test performance estimates. QUADAS was a useful tool for assessing and comparing the quality of studies measuring the performance of diagnostic tests but might be improved further by including explicit assessment of population sampling strategy. Crown Copyright (C) 2017 Published by Elsevier B.V.

A systematic review was conducted to identify studies with data for statistical meta-analyses of sensitivity (Se) and specificity (Sp) of ante-mortem and post-mortem diagnostic tests for bovine tuberculosis (bTB) in cattle. Members of a working group (WG) developed and tested search criteria and developed a standardised two-stage review process, to identify primary studies with numerator and denominator data for test performance and an agreed range of covariate data. No limits were applied to year, language, region or type of test in initial searches of electronic databases. In stage 1, titles and available abstracts were reviewed. References that complied with stage 1 selection criteria were reviewed in entirety and agreed data were extracted from references that complied with stage 2 selection criteria. At stage 1, 9782 references were reviewed and 261 (2.6%) passed through to stage 2 where 215 English language references were each randomly allocated to two of 18 WG reviewers and 46 references in other languages were allocated to native speakers. Agreement regarding eligibility between reviewers of the same reference at stage 2 was moderate (Kappa statistic = 0.51) and a resolution procedure was conducted. Only 119 references (published 1934-2009) were identified with eligible performance estimates for one or more of 14 different diagnostic test types; despite a comprehensive search strategy and the global impact of bTB. Searches of electronic databases for diagnostic test performance data were found to be nonspecific with regard to identifying references with diagnostic test Se or Sp data. Guidelines for the content of abstracts to research papers reporting diagnostic test performance are presented. The results of meta-analyses of the sensitivity and specificity of the tests, and of an evaluation of the methodological quality of the source references, are presented in accompanying papers (Nunez-Garcia et al., 2017; Downs et al., 2017).

Bovine Tuberculosis (bTB) in cattle is a global health problem and eradication of the disease requires accurate estimates of diagnostic test performance to optimize their efficiency. The objective of this study was, through statistical meta-analyses, to obtain estimates of sensitivity (Se) and specificity (Sp), for 14 different ante-mortem and post-mortem diagnostic tests for bTB in cattle. Using data from a systematic review of the scientific literature (published 1934-2009) diagnostic Se and Sp were estimated using Bayesian logistic regression models adjusting for confounding factors. Random effect terms were used to account for unexplained heterogeneity. Parameters in the models were implemented using Markov Chain Monte Carlo (MCMC), and posterior distributions for the diagnostic parameters with adjustment for covariates (confounding factors) were obtained using the inverse logit function. Estimates for Se and/or Sp of the tuberculin skin tests and the IFN-gamma blood test were compared with estimates published 2010-2015. Median Se for the single intradermal comparative cervical tuberculin skin (SICCT) test (standard interpretation) was 0.50 and Bayesian credible intervals (CrI) were wide (95% Cr1 0.26, 0.78). Median Sp for the SICCT test was 1.00 (95% Crl 0.99, 1.00). Estimates for the IFN-gamma blood test Bovine Purified Protein Derivative (PPD)-Avian PPD and Early Secreted Antigen target 6 and Culture Filtrate Protein 10 (ESAT-6/CFP10) ESAT6/CFP10 were 0.67 (95% Cr1 0.49, 0.82) and 0.78 (95% Cr1 0.60, 0.90) respectively for Se, and 0.98 (95% Cr1 0.96, 0.99) and 0.99 (95% Cr1 0.99, 1.00) for Sp. The study provides an overview of the accuracy of a range of contemporary diagnostic tests for bTB in cattle. Better understanding of diagnostic test performance is essential for the design of effective control strategies and their evaluation. Crown Copyright (C) 2017 Published by Elsevier B.V.

Abstract Fibroblast growth factor receptor (FGFR) genetic alterations are frequently observed in cancer, suggesting that FGFR inhibition may be a promising therapy in patients harboring these lesions. Identification of predictive and pharmacodynamic biomarkers to select and monitor patients most likely to respond to FGFR inhibition will be the key to clinical development of this class of agents. Sensitivity to FGFR inhibition and correlation with FGFR pathway activation status were determined in molecularly annotated panels of cancer cell lines and xenograft models. Pathway inhibition in response to FGFR inhibitor treatment was assessed in cell lines (both in vitro and in vivo) and in samples from patients treated with the FGFR inhibitor JNJ-42756493 (erdafitinib). Frequency of FGFR aberrations was assessed in a panel of NSCLC, breast, prostate, ovarian, colorectal, and melanoma human tumor tissue samples. FGFR translocations and gene amplifications present in clinical specimens were shown to display potent transforming activity associated with constitutive pathway activation. Tumor cells expressing these FGFR activating mutants displayed sensitivity to the selective FGFR inhibitor erdafitinib and resulted in suppression of FGFR phosphorylation and downstream signal transduction. Clinically, patients receiving erdafitinib showed decreased Erk phosphorylation in tumor biopsies and elevation of serum phosphate. In a phase I study, a heavily pretreated bladder cancer patient with an FGFR3–TACC3 translocation experienced a partial response when treated with erdafitinib. This preclinical study confirmed pharmacodynamics and identified new predictive biomarkers to FGFR inhibition with erdafitinib and supports further clinical evaluation of this compound in patients with FGFR genetic alterations. Mol Cancer Ther; 16(8); 1717–26. ©2017 AACR.

Un panel de anticuerpos monoclonales específicos para subpoblaciones linfoides fueron usados para caracterizar leucocitos periféricos y pulmonares derivados de animales clínicamente enfermos (n=10) y corderos experimentalmente infectados (n=9) con el retrovirus productor de la adenomatosis pulmonar ovina (APO). Parámetros hematológicos de sangre periféricas de animales afectados naturalmente mostraron una clara linfopenia (2.66±1.36 x 10.3 mL-1, p<0.05) y neutrofilia (7.96±3.84 x 103 mL-1, p<0.05)comparado con animales controles (n=6). La linfopenia periférica en estos animales se caracterizó por una reducción significativa en el número y proporciones de linfocitos TCD5+ y CD4+, observándose paralelamente un incremento significativo en las proporciones de células CD8+ y linfocitos B (CD45RA+ y sIgG+). Similares linfopenia y reducciones significativas de CD5+, CD2+ y CD4+ en sangre periférica fueron observadas en corderos experimentalmente infectados y que desarrollaron severas lesiones de la enfermedad a las 5-10 semanas pos inoculación. Los animales clínicamente enfermos mostraron alteraciones en la relación CD4+/CD8+ circulante, disminuyendo desde 3.9 en animales no afectados con APO a 1.4 en animales afectados con APO. Las alteraciones linfoides en los corderos produjeron reducciones significativas en el peso de tejidos linfoides principalmente en el timo de animales infectados y severa despoblaciones de células linfoide en la corteza tímica así como en 2/2 nódulos y manto periarteriolar esplénico.También se observó una evidencia de un acelerado proceso involutivo del timo de corderos infectados. Evaluaciones de lavados pulmonares en ambos tipos de animales infectados mostraron un incremento significativo de células leucocitarias presentes en fluidos pulmonares recuperados. Los animales clínicamente enfermos mostraron un significativo aumento en células totales y macrófagos alveolares (24 veces), neutrófilos (185 veces) y linfocitos (11 veces) comparados con animales controles. A pesar de este enorme flujo celular hacia pulmones neoplásicos, se detectó una significativa reducción en las proporciones de linfocitos T CD5+ y CD4+ así como una elevada proporción de CD8+ (p<0.05). Las muestras de lavados pulmonares de corderos severamente infectados (5/9 mostraron también un aumento de células totales (11 veces), macrófagos y linfocitos (8 veces) comparados a corderos de edades similares (n=7). En estos corderos, sin embargo, hubo solamente una reducción en las proporciones de células B (CD45RA+ y sIgG+) pulmonares. El gran flujo celular hacia pulmones afectados tal vez refleje parte de la respuesta inmune del hospedero hacia la infección viral y/o células transformadas. Sin embargo, la severa reducción en número y proporciones de linfocitos T CD4+ así como el incremento en las proporciones de linfocitos CD8 y células B en linfocitos periféricos observadas principalmente en animales naturalmente enfermos con APO sugiere la existencia de disfunciones inmunes similares a las reportadas en infecciones retrovirales humanas y felinas.

BACKGROUND:Mycobacterium avium subspecies paratuberculosis (MAP) whole cell vaccines have been widely used tools in the control of Johne's disease in animals despite being unable to provide complete protection. Current vaccine strains derive from stocks created many decades ago; however their genotypes, underlying mechanisms and relative degree of their attenuation are largely unknown.RESULTS:Using mouse virulence studies we confirm that MAP vaccine strains 316 F, II and 2e have diverse but clearly attenuated survival and persistence characteristics compared with wild type strains. Using a pan genomic microarray we characterise the genomic variations in a panel of vaccine strains sourced from stocks spanning over 40 years of maintenance. We describe multiple genomic variations specific for individual vaccine stocks in both deletion (26-32 Kbp) and tandem duplicated (11-40 Kbp) large variable genomic islands and insertion sequence copy numbers. We show individual differences suitable for diagnostic differentiation between vaccine and wild type genotypes and provide evidence for functionality of some of the deleted MAP-specific genes and their possible relation to attenuation.CONCLUSIONS:This study shows how culture environments have influenced MAP genome diversity resulting in large tandem genomic duplications, deletions and transposable element activity. In combination with classical selective systematic subculture this has led to fixation of specific MAP genomic alterations in some vaccine strain lineages which link the resulting attenuated phenotypes with deficiencies in high reactive oxygen species handling.

BACKGROUND:A common approach to the application of epidemiological models is to determine a single (point estimate) parameterisation using the information available in the literature. However, in many cases there is considerable uncertainty about parameter values, reflecting both the incomplete nature of current knowledge and natural variation, for example between farms. Furthermore model outcomes may be highly sensitive to different parameter values. Paratuberculosis is an infection for which many of the key parameter values are poorly understood and highly variable, and for such infections there is a need to develop and apply statistical techniques which make maximal use of available data.RESULTS:A technique based on Latin hypercube sampling combined with a novel reweighting method was developed which enables parameter uncertainty and variability to be incorporated into a model-based framework for estimation of prevalence. The method was evaluated by applying it to a simulation of paratuberculosis in dairy herds which combines a continuous time stochastic algorithm with model features such as within herd variability in disease development and shedding, which have not been previously explored in paratuberculosis models. Generated sample parameter combinations were assigned a weight, determined by quantifying the model's resultant ability to reproduce prevalence data. Once these weights are generated the model can be used to evaluate other scenarios such as control options. To illustrate the utility of this approach these reweighted model outputs were used to compare standard test and cull control strategies both individually and in combination with simple husbandry practices that aim to reduce infection rates.CONCLUSIONS:The technique developed has been shown to be applicable to a complex model incorporating realistic control options. For models where parameters are not well known or subject to significant variability, the reweighting scheme allowed estimated distributions of parameter values to be combined with additional sources of information, such as that available from prevalence distributions, resulting in outputs which implicitly handle variation and uncertainty. This methodology allows for more robust predictions from modelling approaches by allowing for parameter uncertainty and combining different sources of information, and is thus expected to be useful in application to a large number of disease systems.

Due to the great diversity of topics and the huge amount of scientific data, it was proposed that separate scientific opinions on different welfare subjects would be more adequate and effective. Therefore, it was agreed that a scientific report, an overall scientific opinion and four risk assessments on: i) metabolic and reproductive disorders, ii) udder disorders, iii) leg and locomotion problems and iv) behavioural disorders, fear and pain would be produced. This overall scientific opinion integrates conclusions and recommendations from the scientific report with the outcomes from the four separate risk assessments. In the resulting list of outcomes, conclusions and recommendations considered to have a high priority are evidenced.

SUMMARY Following a request from the European Commission, the Panel on Animal Health and Welfare was asked to deliver a scientific opinion on welfare aspects of the main systems of stunning and killing of farmed carp in the EU. A semi-quantitative risk assessment approach was used to rank the risks of poor welfare associated with the different commercially applied stunning and killing methods for carp. Areas of welfare concern were identified, as well as guidance for future research. The risk assessment was mainly based on expert opinion, due to the limited amount of quantitative and published peer reviewed data on the effects of the hazards associated with the stunning and killing of carp. Pre-slaughter stages, immediately before stunning and killing, which had a direct impact on carp welfare, were included in the risk assessment. Stunning and killing 1 For citation purposes: Scientific Opinion of the Panel on Animal Health and Welfare on a request from the European Commission on Species-specific welfare aspects of the main systems of stunning and killing of farmed carp. The EFSA

Following a request from the European Commission, the AHAW Panel was asked to deliver a Scientific Opinion on the welfare of dairy cows, considering whether current farming and husbandry systems comply with the requirements of and welfare of dairy cows from the pathological, zootechnical, physiological and behavioural points of view. Due to the great diversity of topics and the huge amount of scientific data, it was proposed that separate scientific opinions on different welfare subjects would be more adequate and effective. Therefore, it was agreed to subdivide the risk assessment process into four different subjects: i) metabolic and reproductive disorders, ii) udder disorders, iii) leg and locomotion problems and iiii) behaviour, fear and pain. A fifth scientific opinion integrates conclusions and recommendations from the scientific report with the outcomes from the four separate risk assessments. The scientific opinion on welfare of dairy cows in relation to behaviour, fear and pain, based on a risk assessment with special reference to the impact of housing, feeding, management and genetic selection, was adopted by the AHAW Panel on 05 June 2009. In the risk assessment four different farming scenarios were considered: 1) cubicle houses; 2) tie-stalls; 3) straw yards; 4) pasture. Identified hazards were classified under (a) housing, (b) nutrition and feeding, (c) management and (d) genetics. The risk assessment outcomes for each of these four classes of hazards were determined and the four different farming scenarios compared. When comparing the different farming systems it can be concluded that the risk of suffering behaviour problems, fear and pain can be dependent of the farming systems. In the risk assessment, the risk estimates for behavioural problems, fear and pain associated with housing were generally higher than the risk estimates observed for the other categories of hazards. The risk estimates for behavioural problems, fear and pain associated with housing were highest for tie-stalls and lowest for cows at pasture, and were lower in straw yards than in cubicle housing. According to the scoring system used in this analysis, among the highest ranked hazards in terms of risk estimate in relation to the housing were design of stalls and inadequate bedding in both tie-stalls and cubicle housing. In cubicle houses, inappropriate flooring where cows walk posed the largest risk estimate for behavioural problems whereas having fewer cubicles than cows was the hazard with the largest magnitude of the adverse effect, but the risk estimate was relatively low. Poor air quality was rated as a hazard with a large magnitude of the adverse effect in all types of indoor housing. However, the degree of exposure was low, resulting in low risks for behavioural problems. For cows at pasture, hazards associated with housing have much lower magnitude of the adverse effect than for cows housed indoors. For cows at pasture, the largest risk estimates for behavioural problems were associated with inappropriate temperature and humidity, lack of handling facilities and problems with the milking parlour and waiting areas. The highest ranked hazards associated with straw yards were inadequate bedding, lack of space, zero grazing and inadequate flooring where cows walk. Finally, zero-grazing was rated as a hazard with a large magnitude of the adverse effect on cow behaviour, fear and pain in tie-stalls, straw yards and cubicle housing, but the risk estimate was relatively low. In relation to the use of tie stalls, Panel members concluded that tie-stalls restrict the voluntary movement and social behaviour of dairy cows. When periods of exercise are possible some of the adverse effects are reduced. Therefore, systems of husbandry and management should involve a minimum time of restricted movement in order that all dairy cows are able to meet their need to show certain behaviours such as grooming, social interaction and exercise. While tie-stall use continues, cows should have daily exercise that involves walking freely inside or outside (except where there are adverse climatic conditions) and also the freedom to carry out other behaviours. A minority opinion on the use of tie-stalls was expressed by some Panel members. The risk assessment showed that nutrition and feeding hazards have a lower risk of causing behavioural problems compared with other factors. The risk estimates and magnitudes of the adverse effects of behavioural problems associated with nutrition and feeding were quite similar for cubicle housing, tie-stalls and straw yards; however there were fewer hazards identified for pasture. The highest risk estimate for behavioural problems due to nutrition and feeding was associated with improper ration composition and underfeeding in cubicle houses, tie-stalls and straw yards. However, the magnitudes of the adverse effects were highest for poor feed quality of the roughage, improper ration composition, underfeeding, and improper sensory quality of the water source. As regards the management aspects for dairy cows, the maintenance of stable groups ensures that long-lasting affiliative relationships can continue, reducing the overall stress level in cows. In the risk assessment, the hazard with the highest or second highest magnitude of the adverse effect in the three systems where animals are kept loose was mixing animals from different groups. Husbandry practices should avoid regrouping of dairy cows in order to facilitate continuation of long-lasting social bonds, avoid frequent disruption and provide social stability. If social mixing of dairy cows is unavoidable, stress should be reduced by providing larger space allowance during grouping in buildings or on pasture. Regrouping or mixing on pasture is ideal as it offers space and good flooring. Appropriate management, together with larger space allowance, can minimize social agonistic interactions in the herd in general. When cows have to calve in groups indoors, this may cause disturbance for the cow. An individual calving pen with some visual and auditory contact with other cows gives the cow the best possibility to show normal behaviour and calve without problems. Dairy cows allowed to stay with their calf after birth and separated within 24 h show a mild stress reaction after separation. After the mother-young bond has been established, i.e. 2 days or more, the cow shows a stronger reaction after separation, and this reaction becomes stronger the longer the time that they stay together. Some infectious diseases may be transmitted from the cow to the calf at birth, and then an important measure for reducing disease transmission is to separate the calf very shortly after birth. If the cow is placed out of hearing and sight of the calf, the stress reaction of the cow is lower. When cow and calf have been together for prolonged suckling, e.g. 6-12 weeks, weaning plates placed on the calves reduce the stress reaction in the cow after separation. In the risk assessment, genetic selection for high milk yield with insufficient emphasis on other traits relating to fitness showed a very low risk of causing behavioural problems compared with other factors and no differences were observed among the different housing systems analysed. The magnitude of the adverse effect and the risk estimate for behavioural problems was highest for cows with high genetic potential for production due to selection ignoring other traits when the housing, nutrition and management are not optimized

Following a request from the European Commission (DG Health and Consumer Protection), the Panel on Animal Health and Welfare (AHAW) was requested for an opinion on porcine brucellosis (Brucella suis).B. suis consists of five biovars, however infection in pigs is caused by the first three biovars (biovars 1, 2, and 3). Infection of animals caused by biovars 1 and 3 differs from that caused by biovar 2 in the host specificity and geographical distribution. In the context of public health, biovar 2 is very rarely pathogenic for humans, whereas biovars 1 and 3 are highly pathogenic causing severe disease in human beings.There is currently no requirement for monitoring and surveillance of B. suis in domestic pigs or in wild life and therefore a lack of systematic epidemiologic data on porcine brucellosis in most MS. The occurrence of the disease is mainly sporadic (with the exception of certain areas where the characteristics of the production systems allow B. suis to be endemic). Within the EU, the epidemiological situation is varied, with some countries free of the disease, others reporting sporadic outbreaks and yet others reporting this disease as an emergent problem. Available epidemiological evidence shows that B. suis biovar 2 is the most common agent, but biovars 1 and 3 can also occur.Available evidence also suggests that currently the wild boar seems to remain the main source of infection for domestic pigs because several outbreaks of B. suis occurred in outdoor rearing systems, even on fenced premises, with the source of infection traced to contacts with wild boars. Transmission from wild boars to pigs is thought to be through the venereal route, as crossed piglets (striped) have been reported, at least in France and Portugal. Other routes might also be possible. Hares have been considered as a possible source of B. suis outbreaks in domestic pigs via swill feeding with offal from hunted infected hares. Some reported outbreaks have also been traced to the introduction of infected live animals originating from holdings where the diseases had not been detected.Based on the data of a systematic literature review, meta-analytical estimates of diagnostic sensitivity (Se) and specificity (Sp) of diagnostic tests for B. suis infection in pigs were generated. Highly sensitive and reasonably specific testing systems with the potential to combine more than one test are required for a rigorous detection and slaughter policy. Currently, serological testing in pigs is mainly useful to monitor the status of a herd but not reliable enough for single animals. Evidence from the systematic review suggests that indirect Enzyme-Linked ImmunoSorbent Assay (iELISA) and competitive Enzyme-Linked ImmunoSorbent Assay (cELISA) could be suitable candidates because of their high Se and Sp. However, the ELISA tests have not been fully evaluated and standardised for use in pigs. Primary reference standards are currently being developed. Formal procedures such as those implemented by the OE should be considered for accreditation of candidate tests (e.g. iELISA and cELISA) for the purpose of control of B. suis in pigs. Little is known about the causes of false positive serological reactions to B. suis testing in pigs (FPSR), but it is believed that Yersinia enterocolitica 0: 9 could be the main factor of this problem. To address the FPSR issue it is important to improve the specificity of current diagnostic tests. Specific studies should also be conducted with the aim to identify the mechanisms of FPSR and to elaborate specific testing protocols to reduce this phenomenon. Further development of Brucellin-based tests should be encouraged since, in addition to bacteriology and molecular tools, these tests are the only confirmatory tests suitable to fully discriminate between true brucellosis infections and the infections caused by Y. enterocolitica 0: 9 or other crossreacting bacteria.The risk factors (RF) for B. suis introduction and spreading into domestic pigs (in particular through contact with wildlife, and subsequent spread within the EU by trade in pigs and pig semen) have been identified and qualitatively assessed. The presence of infected wild boars and hares and the potential for exposure of outdoor pig holdings remain the most important risk factors in the currently affected areas. Exposure to infected wild boar would be influenced by the level of biosecurity resulting in variable level of either direct or indirect contact. In addition to the level of biosecurity, direct contact would also be influenced by the type of pig housing (e.g. outdoor vs indoor). Should the infection become established in holdings participating to intra-Community trade (e.g. outdoor, indoor, semen collection centres), the most important risk factor for wider spread within the EU would the infection remains unrecognised. This would create the potential for further spread within the EU either by direct or indirect contact. Movement of live pigs (mainly breeding pigs) and semen would be the most important risk factor given the intensive level of intra-Community trade. Indirect contact would mainly depend on mechanical transmission by people and shared contaminated equipment. The role of other means of transmission (e.g. rodents, scavenging birds) remains hypothetical. Awareness should be raised in the pig industry for indicative clinical signs of porcine brucellosis and to the additional risk posed by illegal swill feeding including offal from hares and wild boars.Semen production is well controlled by legal requirements related to the introduction of boars in semen collection centres, continuous monitoring of disease freedom and semen preparation requirements. However, transmission through this route could constitute an important way of disease dissemination. Boars kept in semen collection centres should continue to be selected and introduced from holdings that are epidemiologically proven as free from B. suis. Donors should continue to be serologically tested on holding of origin and in quarantine before being placed in the centre as well as on a regularly basis afterwards. The results indicate that the iELISA and cELISA could have the potential of being used for testing of boars for admission to semen collection centres and for compulsory routine testing.

BACKGROUND:Mycobacterium avium subspecies paratuberculosis (Map) causes an infectious chronic enteritis (paratuberculosis or Johne's disease) principally of ruminants. The epidemiology of Map is poorly understood, particularly with respect to the role of wildlife reservoirs and the controversial issue of zoonotic potential (Crohn's disease). Genotypic discrimination of Map isolates is pivotal to descriptive epidemiology and resolving these issues. This study was undertaken to determine the genetic diversity of Map, enhance our understanding of the host range and distribution and assess the potential for interspecies transmission.RESULTS:164 Map isolates from seven European countries representing 19 different host species were genotyped by standardized IS900--restriction fragment length polymorphism (IS900-RFLP), pulsed-field gel electrophoresis (PFGE), amplified fragment length polymorphisms (AFLP) and mycobacterial interspersed repeat unit-variable number tandem repeat (MIRU-VNTR) analyses. Six PstI and 17 BstEII IS900-RFLP, 31 multiplex [SnaBI-SpeI] PFGE profiles and 23 MIRU-VNTR profiles were detected. AFLP gave insufficient discrimination of isolates for meaningful genetic analysis. Point estimates for Simpson's index of diversity calculated for the individual typing techniques were in the range of 0.636 to 0.664 but a combination of all three methods increased the discriminating power to 0.879, sufficient for investigating transmission dynamics. Two predominant strain types were detected across Europe with all three typing techniques. Evidence for interspecies transmission between wildlife and domestic ruminants on the same property was demonstrated in four cases, between wildlife species on the same property in two cases and between different species of domestic livestock on one property.CONCLUSION:The results of this study showed that it is necessary to use multiple genotyping techniques targeting different sources of genetic variation to obtain the level of discrimination necessary to investigate transmission dynamics and trace the source of Map infections. Furthermore, the combination of genotyping techniques may depend on the geographical location of the population to be tested. Identical genotypes were obtained from Map isolated from different host species co-habiting on the same property strongly suggesting that interspecies transmission occurs. Interspecies transmission of Map between wildlife species and domestic livestock on the same property provides further evidence to support a role for wildlife reservoirs of infection.

Within the European Union (EU), detailed legislation has been developed for cattle, but not deer, to minimise disease risks associated with trade in animals and animal products. This legislation is expressed as input-based standards, providing a detailed outline of the activity required (for example, testing of animals and application of defined control measures), on the expectation that an adequate output (for example, confidence in freedom) will be achieved. Input-based standards are at odds with the increasing shift towards output-based standards, particularly in OIE rules governing international trade. In this paper, we define output-based standards to achieve and maintain freedom from tuberculosis (TB) in farmed deer, with reference to EU member states. After considering the probability of freedom achieved for cattle under existing EU legislation, we defined a 'free farmed deer holding' as one with a probability of freedom from infection of at least 99%. We then developed an epidemiological model of TB surveillance systems for deer holdings, incorporating different surveillance strategies, including combinations of diagnostic tests, and a variety of different scenarios relating to the potential for introduction of infection. A range of surveillance strategies were identified to achieve and maintain a free farmed deer holding, and worked examples are presented. The surveillance system sensitivity for varying combinations of screening and confirmatory tests in live animals, animals at slaughter and on-farm deaths is also presented. Using a single test at a single point in time, none of the TB tests routinely used in farmed deer is able to achieve an acceptable probability of TB freedom. If repeat testing were undertaken, an acceptable probability of TB freedom could be achieved, with differing combinations of the surveillance system sensitivity, frequency of testing and risk of introduction. The probability of introduction of infection through the importation of infected deer was influenced by the use of a pre-movement test (assumed 90% test sensitivity and negative test results), the TB prevalence in the source herd and the number of animals imported. A surveillance system sensitivity of at least 81% was achieved with different combinations of annual live animal surveillance and surveillance of animals at slaughter or on-farm deaths. This methodology has broad applicability and could also be extended to other diseases in both deer and other species with relevance to trade in animals and animal products.

Classical swine fever (CSF) is a disease that has been causing major socio-economic damages in the EU during the last decades. Although considerable progress has been made in the eradication and prevention of the disease, the threat for an epidemic still exists.The virus is endemic in the wild boar population of several member states (MS). Wild boar cannot be managed as domestic pigs. Hunting and vaccination have been tentatively used in order to stop transmission by reducing the number of susceptibles. Oral vaccination of wild boar with modified live vaccine based on the C-strain (the only suitable) is used; this vaccine does not allow serological differentiation between vaccinated and infected animals.The aim of the control measures for CSF in wild boar is to reduce the risk of transmission to domestic pigs, to prevent an "endemic phase evolution" or to reduce the endemic phase duration.In order to support and to improve the control and eradication measures as regards CSF in wild boar, EFSA was requested by the Commission to provide scientific advice on the efficacy of the available surveillance, hunting and vaccination measures to control and eradicate CSF in feral pig populations (wild boar), considering the possible use of new diagnostic tests and vaccines.In order to reply to the mandate data were collected from MS through two questionnaires (CSF vaccines, hunting practices and CSF vaccination in wild boar). Data were also extracted from the EU CSF wild boar data base, after requesting permission from the participating MS.Considering that the data received were rather limited and not comparable, the WG decided to use a model in order to fill the gaps in the available knowledge. For the evaluation of the efficacy of CSF control in wild boar a continuous metapopulation compartmental model developed in an EU research project (FP6-5015599-CSFVACCINE&WILDBOAR) was applied.Although the disease manifests in the same manner in both domestic pig and wild boar it is more difficult to identify in wild boar because clinical monitoring of these is hardly possible. Wild boar found dead constitutes the main alert sign of CSF. Hunters and gamekeepers should be instructed to report the finding of each dead wild boar to the competent authority at all times. In case of high-risk situations, a passive surveillance should be complemented by an active serological surveillance. The active sampling of wild boar is not as efficient as in domestic pigs considering that hunting is the sole practical system to obtain samples and that the aim of hunting is quite different.Consequently, the sample size is not controlled by authorities and fits rarely the aim of the survey in terms of detecting the presence of disease at a certain level. In addition, the interpretation of serological results is confounded by maternal derived antibodies (until the 6th month of age), vaccination and the sampling quality.There is no definition at EU level of spatial and temporal units for surveillance, neither for criteria defining a disease free wild boar population. The sample size is not the only factor that dictates the overall sensitivity of surveillance systems. Indeed, wild boar habitat, hunting patterns, and disease distribution should be included when assessing surveillance system sensitivity.After a vaccination campaign, PCR positive animals can be due to modified live vaccines (MLV) but these MLV-vaccinated animals can be cross-checked for wild type CSF virus (genetic DIVA - discriminatory PCR). A positive PCR diagnosis should be considered to indicate that an animal is or has been infected with the wild type or MLV virus but it is not necessarly still infectious.According to previous field experience and to model simulations of a CSF epidemic in a wild boar population and the possible outcomes regarding vaccination:-the disease will fade out without any additional control measures in small populations (between 1000 and 1500);-hunting is not efficient for CSF control and should not exceed the normal 45% per year. Hunting is currently needed for sampling;-vaccination: -increases population immunity progressively. The maximum population immunity is only reached after three double campaigns;-by one isolated campaign cannot increase population immunity adequately to control CSF and might even aggravate the persistence of CSF;-mainly prevents the spread of the infection in neighbouring vaccinated patches;-promotes long-term eradication through a progressive reduction of virus transmission to neighbouring areas;-always reduces the epidemic peak (number of infected animals/time). Endemic evolution of infection may occur when a low rate of vaccination is achieved;-in both infected and not yet infected areas, reaching a minimum target of 40 % of susceptible animals is necessary to obtain a positive control effect, below 20% - will increase probability of endemic stability, above 60% - will always eradicate the infection.

Following a request from the European Commission, the AHAW Panel was asked to deliver a Scientific Opinion on the welfare of dairy cows, considering whether current farming and husbandry systems comply with the requirements of and welfare of dairy cows from the pathological, zootechnical, physiological and behavioural points of view.Due to the great diversity of topics and the huge amount of scientific data, it was proposed that separate scientific opinions on different welfare subjects would be more adequate and effective. Therefore, it was agreed to subdivide the risk assessment process into four different subjects: i) metabolic and reproductive disorders, ii) udder disorders, iii) leg and locomotion problems and