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The collective control programmes (CPs) that exist for many infectious diseases of farm animals rely on the application of diagnostic testing at regular time intervals for the identification of infected animals or herds. The diversity of these CPs complicates the trade of animals between regions or countries because the definition of freedom from infection differs from one CP to another. In this paper, we describe a statistical model for the prediction of herd-level probabilities of infection from longitudinal data collected as part of CPs against infectious diseases of cattle. The model was applied to data collected as part of a CP against bovine viral diarrhoea virus (BVDV) infection in Loire-Atlantique, France. The model represents infection as a herd latent status with a monthly dynamics. This latent status determines test results through test sensitivity and test specificity. The probability of becoming status positive between consecutive months is modelled as a function of risk factors (when available) using logistic regression. Modelling is performed in a Bayesian framework, using either Stan or JAGS. Prior distributions need to be provided for the sensitivities and specificities of the different tests used, for the probability of remaining status positive between months as well as for the probability of becoming positive between months. When risk factors are available, prior distributions need to be provided for the coefficients of the logistic regression, replacing the prior for the probability of becoming positive. From these prior distributions and from the longitudinal data, the model returns posterior probability distributions for being status positive for all herds on the current month. Data from the previous months are used for parameter estimation. The impact of using different prior distributions and model implementations on parameter estimation was evaluated. The main advantage of this model is its ability to predict a probability of being status positive in a month from inputs that can vary in terms of nature of test, frequency of testing and risk factor availability/presence. The main challenge in applying the model to the BVDV CP data was in identifying prior distributions, especially for test characteristics, that corresponded to the latent status of interest, i.e. herds with at least one persistently infected (PI) animal. The model is available on Github as an R package (https://github.com/AurMad/STOCfree) and can be used to carry out output-based evaluation of disease CPs. European Food Safety Authority (EFSA)

Professionals from seven European countries were interviewed to identify strategies used in surveillance and control of animal infections to influence behaviours such as programme enrolment, adoption of biosecurity measures, and engagement in surveillance. To find strategies that were well-designed from a theoretical perspective, three theoretical frameworks from nudge theory was were applied to the strategies; the Nuffield ladder to determine the strength of the interventions, EAST; to identify attributes of the strategies and, and MINDSPACE, to identify psychological mechanisms involved. We found that almost two thirds (91/120) of the strategies were designed in a manner likely to trigger multiple psychological mechanisms, which is in line with existing recommendations for successful effect i.e. achieving a desired behaviour. This was despite that the design of the strategies were based on professionals empirical understanding of requirements to achieve anticipated outcomes, rather than systematic use of methods from behavioural sciences and psychology. The most commonly used strategy was provision of information, and the least used mechanism was making a desired behaviour easy to perform. The findings in this study, with all the examples of strategies used, can serve as inspiration for others. The theoretical frameworks may also be beneficial to apply as a complement in future design of new strategies. This study did not include evaluation of how efficient different strategies have been, which would be an interesting area for future studies.

Based on Swedish legislation, all herds where Salmonella of any serotype is detected are put under restrictions, and measures aiming at eradication are required. Costs for sampling and control have increased in recent years and the aim of this study was to investigate the efficiency of different sampling strategies. We also compiled test results from recent surveillance activities and used these to complement and compare with calculated results. Sensitivities and specificities at group and herd level were calculated for different test strategies. A scenario-tree modeling approach was used to account for the hierarchy of animals within herds, and different relative risk of salmonella in different age groups. Negative and positive predictive values (NPV and PPV), and probability of freedom from Salmonella were calculated to compare the added value of different sampling strategies. Results showed that more fecal samples than serological samples per group are needed to reach a group sensitivity >0.50. This also means that serological testing leads to a higher NPV. For example, with 10 negative test-results from a group of 25 animals in a herd with a suspicion of Salmonella, the NPV based on serology was 0.75 and based on culture was 0.56. For the PPV, testing based on culture from fecal sampling was superior, as specificity of such testing was close to perfect. By changing the threshold for considering a group positive, from 1 test-positive animal to 2, the PPV of serological results could be increased without substantial loss in NPV. The herd sensitivity based on (1) bulk milk sampling, (2) fecal sampling of all animals, and (3) bulk milk sampling and individual sera from 20 animals within each age group was 0.53, 0.88, and 0.95, respectively. In low-prevalence regions, this sensitivity was enough to verify a high probability of freedom (>0.99), as the probability of infection in such Swedish regions has been shown to be 0.01. For herds with a higher prior probability of infection, repeated sampling (2–9 sampling occasions) was needed to reach the same level of confidence. Analysis of surveillance data indicated that boot swabs can be used to replace the standard fecal sampling presently used in Sweden. It was also confirmed that the individual specificity of the tests used for serological testing of Swedish calves is high (0.99). The results can form a basis for fit-for-purpose testing strategies (e.g., surveillance or prepurchase testing).

In this study associations between potential risk factors and salmonella status in Swedish dairy herds were investigated. A case-control study design was used, including existing as well as new cases. Herds were assigned a salmonella status on the basis of antibody analysis of bulk milk samples. Information on potential risk factors was collected from registry data and from farmers via a questionnaire. Univariable and multivariable logistic regression analyses were used to investigate associations between salmonella status and potential risk factors. In addition, multivariate analysis with Additive Bayesian Network (ABN) modelling was performed to improve understanding of the complex relationship between all the variables. Because of the difficulty in identifying associations between potential risk factors and infections with low prevalence and a large regional variation, exposure of potential risk factors in the high-prevalence region (Oland) were compared to exposure in other regions in Sweden. In total 483 of 996 (48%) farmers responded to the questionnaire, 69 herds had test-positive bulk milk samples. The strongest association with salmonella status was 'presence of salmonella test-positive herds

A national control program against bovine respiratory syncytial virus (BRSV) and bovine coronavirus (BCV) was launched in Norway in 2016. A key strategy in the program is to test for presence of antibodies and protect test-negative herds from infection. Because these viruses are endemic, the rate of re-introduction can be high, and a disease-free status will become more uncertain as time from testing elapses. The aim of this study was to estimate the probability of freedom (PostPFree) from BRSV and BCV antibodies over time by use of bulk tank milk (BTM) antibody-testing, geographic information and animal movement data, and to validate the herd-level estimates against subsequent BTM testing. BTM samples were collected from 1148 study herds in West Norway in 2013 and 2016, and these were analyzed for BRSV and BCV antibodies. PostPFree was calculated for herds that were negative in 2013/2014, and updated periodically with new probabilities every three months. Input variables were test sensitivity, the probability of introduction through animal purchase and local transmission. Probability of introduction through animal purchase was calculated by using real animal movement data and herd prevalence in the region of the source herd. The PostPFree from the final three months in 2015 was compared to BTM test results from March 2016 using a Wilcoxon Rank Sum Test. The probability of freedom was generally high for test-negative herds immediately after testing, reflecting the high sensitivity of the tests. It did however, decrease with time since testing, and was greatly affected by purchase of livestock. When comparing the median PostPFree for the final three months to the test results in 2016, it was significantly lower (p < 0.01) for test positive herds. Furthermore, there was a large difference in the proportion of test positive herds between the first and fourth quartile of PostPFree. The results show that PostPFree provides a better estimate of herd-level BTM status for both BRSV and BCV than what can be achieved by relying solely on the previous test-result.

Previous investigations suggest that the prevalence of Mycobacterium avium subsp. paratuberculosis (MAP) in Swedish cattle is low and all recent cases have been linked to imported animals. The aim of this study was to evaluate the surveillance system for MAP infection in Swedish cattle and to estimate the probability that the Swedish cattle population is free from this infection. Calculations of surveillance sensitivities and probability of freedom were made using stochastic scenario-tree modelling, which allows inclusion of information from several different sources, of complex surveillance data including results from non-representative sampling, as well as of documentations of differences in risk of being infected. The surveillance components included in the model were: (1) clinical surveillance, (2) fallen stock investigations, (3) the national surveillance programme (mainly beef herds), (4) a survey involving dairy herds and (5) a risk-based survey targeting herds with imported cattle. Previous or current presence of imported animals and participation in the on-going control programme was specified for each tested herd, in order to adjust for differences in risk. Calculations were made for each year from the start of 2005 to the end of 2008, and this formed the basis for a final estimate covering the whole study period and predictions of future probabilities of freedom from MAP. Results show that when applying a design prevalence of one animal in 0.1% of the herds, the probability of freedom at the end of 2008 was 0.63. At the design prevalence of one animal in 0.5% of herds, the estimated probability is >95% and it is demonstrated that the prevalence of MAP in Swedish cattle is below this level or absent. In order to increase the annual surveillance sensitivity in the future and thereby improve the probability of freedom, new surveillance activities or an intensification of current ones are needed.

Background : Whole genome sequencing (WGS) is becoming a routine tool for infectious disease outbreak investigations. The Swedish situation provides an excellent opportunity to test the usefulness of WGS for investigation of outbreaks with Salmonella Dublin ( S . Dublin) as epidemiological investigations are always performed when Salmonella is detected in livestock production, and index isolates from all detected herds are stored and therefore available for analysis. This study was performed to evaluate WGS as a tool in forward and backward tracings from herds infected with S. Dublin. Material and methods : In this study, 28 isolates from 26 cattle herds were analysed and the WGS results were compared with results from the epidemiological investigations, for example, information on contacts between herds. The isolates originated from herds in three different outbreaks separated geographically and to some extent also in time, and from the only region in Sweden where S. Dublin is endemic ( Oland ). Results : The WGS results of isolates from the three non-endemic regions were reliably separated from each other and from the endemic isolates. Within the outbreaks, herds with known epidemiological contacts generally showed smaller differences between isolates as compared to when there were no known epidemiological contacts. Conclusion : The results indicate that WGS can provide valuable supplemental information in S. Dublin outbreak investigations. The resolution of the WGS was sufficient to distinguish isolates from the different outbreaks and provided additional information to the investigations within an outbreak. Keywords: WGS; NGS; SNP; molecular epidemiology; zoonosis; Sweden (Published: 6 July 2016) Citation: Infection Ecology and Epidemiology 2016, 6: 31782 - http://dx.doi.org/10.3402/iee.v6.31782

In July 2007, PRRS was detected for the first time in Sweden. A total of eight positive herds were identified and various measures were taken to eradicate the disease, including restrictions and slaughter of infected herds. Subsequently, both active and passive surveillance activities were undertaken. This study describes stochastic scenario-tree modelling of all the various surveillance system components, to estimate the current probability that Sweden is free from PRRS. The model includes all actions taken after the first positive herd was detected. The surveillance system components included in the model were as follows: investigations undertaken in association with the outbreak, a serological study based on samples collected at slaughter, samples collected in the national PRRS surveillance programme and passive clinical surveillance. The probability of freedom was estimated in time steps of 1 month, from July to December 2007. After each time step, the calculated posterior probability of freedom from the previous month, combined with the probability of introduction, was used as a prior probability for the next month. The result from the model showed a 99.8% probability that Sweden was free from PRRS at the end of December 2007. The estimated total sensitivity of the surveillance system varied between 81.2% and 94.3% and was highest during the first months after the outbreak. For sensitivity analysis purposes, the model was also applied using higher risks of introduction. However, this did not make considerable difference to the final estimates.

Legislated Salmonella control in Sweden has been in place since the 1960s. The purpose of this study was to investigate presence of Salmonella antibodies in dairy cattle herds and to provide a basis for decisions on how surveillance and control can be improved. Bulk milk samples from all Swedish dairy herds (n=4 683) were analysed with two different ELISAs; one detecting antibodies against Salmonella Dublin (Dublin ELISA), and one detecting antibodies against several of the serotypes causing bovine salmonellosis including S. Dublin (Bovine ELISA). Information about herds, i.e. geographical location, local animal density, number of test positive herds within 5km, animal trade and herd size, was based on register data. The results confirm a very low prevalence of Salmonella in Swedish dairy herds throughout the country with the exception of an island in the southeast. The test positive herds split into two groups; 41 herds (1%) positive in the Dublin ELISA, and 101 herds (2%) positive in the Bovine ELISA but negative in the Dublin ELISA. Geographical location of positive herds, and comparison of the results of the screening with serotypes previously isolated from some of the herds, indicated that the first group represents herds presently or previously infected with S. Dublin while the second group represents herds presently or previously infected with other serotypes. Differences in serological status between herds in different regions, of different size, with different animal purchase patterns et cetera, were tested using logistic regression. Presence of positive herds within 5km was significantly associated to testing positive. For herds testing positive in the Dublin ELISA, significant associations were also seen with herd size. Purchase of animals during the last year was not significantly associated with the outcome in the final models. We conclude that for future surveillance, the Bovine ELISA can be used to help in identifying infected herds, and the Dublin ELISA can be used to distinguish herds with S. Dublin infections. The geographical clustering of test positive herds could facilitate future surveillance and disease control interventions. The results highlight differences between S. Dublin and other serotypes, e.g. concerning prevalence and degree of geographical clustering. Further studies on risk factors and potential local spread of Salmonella is warranted, particularly in the regions with clustering of S. Dublin infected herds.

Background The Swedish control program for salmonella includes restrictions and on-farm control measures when salmonella is detected in a herd. Required control measures are subsidised by the government. This provides an opportunity to study costs for on-farm salmonella control. The aim of this study was to describe the costs for on-farm salmonella control in Swedish cattle herds and to investigate the effects of herd factors on these costs in dairy herds. Results During the 15 years studied there had been a total of 124 restriction periods in 118 cattle herds; 89 dairy herds, 28 specialised fattening herds and three suckler herds. The average costs per herd for on-farm salmonella control was 4.60 million SEK with a median of 1.06 million SEK corresponding to approximately 490 000 and 110 000 EUR. The range was 0.01 to 41 million SEK corresponding to 1080 EUR to 4.44 million EUR per farm. The costs cover measures required in herd-specific control plans, generally measures improving herd hygiene. A mixed linear model was used to investigate associations between herd factors and costs for on-farm salmonella control in dairy herds. Herd size and length of the restriction period were both significantly associated with costs for on-farm control of salmonella with larger herds and longer periods of restrictions leading to higher costs. Serotype detected and administrative changes in the Swedish Board of Agriculture aiming at reducing costs were not associated with costs for on-farm salmonella control. Conclusions On-farm control of salmonella in Swedish cattle herds incurred high costs but the costs also varied largely between herds. Larger herds and longer restriction periods increased the costs for on-farm control of salmonella in Swedish dairy herds. This causes concern for future costs for the Swedish salmonella control program as herd sizes are increasing.

In September 2008, bluetongue virus serotype 8 (BTV-8) infection was detected for the first time in Sweden, in a dairy herd on the west coast. Two different previously published operational atmospheric dispersion models indicate that midges from infected regions in Europe are likely to have reached Sweden by atmospheric transport during an estimated infection window. Both models indicated that the likely dates for the incursion of midges were overnight on August 6 to 7 and August 14 to 15; however, the less constrained model indicated a number of additional possible dates. The distribution of infected herds detected by active surveillance coincides with the regions that were indicated by the models to have been reached by midges from regions in Denmark and Germany with infected herds. It is likely that several points of introduction of infected midges occurred, possibly on different occasions. No alternative routes for introduction of the infection to Sweden were identified, supporting the theory that BTV-8 was introduced by infected midges carried by the wind.

In this study we examined seven queens with normal oestrous cycles and a history of infertility after normal matings. We performed clinical examination, vaginal cytology, evaluation of oestradiol, progesterone and total T4 levels, vaginal bacterial culture, ultrasonography, and serum analyses for detection of antibodies against chlamydia and feline leukaemia virus (FeLV) antigenemia. Ovariohysterectomy (OHE) was recommended for 1/7 queens because of pathological uterine changes detected at ultrasonography and clinical examination. Four out of seven queens were treated with antibiotics and two of these had more litters. One of the queens that were treated was not mated again and one was mated without conceiving and was at a later OHE found to have degenerative uterine changes. No treatment was given and no diagnosis could be established in 2/7 queens. Both of them were later ovariohysterectomised and one showed degenerative uterine changes while the uterus of the other queen could not be obtained for follow-up. In summary, 4/7 cats were diagnosed with uterine pathology and no definitive diagnosis could be established for 3/7 queens.

Background: The Swedish Salmonella control program has been running for decades and has resulted in a low prevalence of Salmonella in Swedish food producing animals. Routine bacteriology is used to detect Salmonella, however, bacteriology is time consuming, costly and has a low sensitivity. Different enzyme-linked immunosorbent assays (ELISAs) have been developed for detection of antibodies against Salmonella Dublin and S. Typhimurium in bovine bulk milk, individual milk samples as well as in sera. Screening bulk milk for antibodies against Salmonella spp. could improve the cost-effectiveness of the surveillance in Swedish dairy cattle, but as characteristics of tests may vary in different populations, tests should always be evaluated in the specific population where they will be used. Hence, the aim of this study was to evaluate the specificities of three bovine ELISAs when used to analyse bulk milk samples from Swedish dairy cattle. A second aim was to compare the performance of the two Dublin ELISAs tested. Methods: Bulk milk samples for analysis were randomly selected from samples collected within the Swedish bulk milk sampling scheme and analyzed with the three ELISAs; a Danish in-house Dublin ELISA, PrioCHECK W Salmonella Ab bovine Dublin ELISA and PrioCHECK W Salmonella Ab bovine ELISA (hereafter named mixed ELISA). The specificities of the ELISAs were calculated assuming a disease-free status in Sweden i.e. that all test positive samples were assumed to be false positive results. This assumption can be used when a disease is known to be infrequent. Results: The calculated specificities of the two Dublin ELISAs and the mixed ELISA, when using the producer’s recommended cut-off value of the corrected optic-density percent (ODC%) were 99.4% (95% Confidence Interval (CI): 98.8% -99.8%), 99.4% (95% CI: 98.8% -99.8%) and 97.9% (95% CI: 96.8% -98.7%), respectively. The correlation between the ODC% values of the two Dublin ELISAs was 0.83. Conclusions: We conclude that the evaluated ELISAs have sufficiently high specificities to be used as supplement to bacteriological examinations in the Swedish Salmonella control program in cattle as well as a primary screening test in routine surveillance for S. Dublin.