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1.  Data-driven network modelling of disease transmission using complete population movement data: spread of VTEC O157 in Swedish cattle 
Veterinary Research  2016;47:81.
European Union legislation requires member states to keep national databases of all bovine animals. This allows for disease spread models that includes the time-varying contact network and population demographic. However, performing data-driven simulations with a high degree of detail are computationally challenging. We have developed an efficient and flexible discrete-event simulator SimInf for stochastic disease spread modelling that divides work among multiple processors to accelerate the computations. The model integrates disease dynamics as continuous-time Markov chains and livestock data as events. In this study, all Swedish livestock data (births, movements and slaughter) from July 1st 2005 to December 31st 2013 were included in the simulations. Verotoxigenic Escherichia coli O157:H7 (VTEC O157) are capable of causing serious illness in humans. Cattle are considered to be the main reservoir of the bacteria. A better understanding of the epidemiology in the cattle population is necessary to be able to design and deploy targeted measures to reduce the VTEC O157 prevalence and, subsequently, human exposure. To explore the spread of VTEC O157 in the entire Swedish cattle population during the period under study, a within- and between-herd disease spread model was used. Real livestock data was incorporated to model demographics of the population. Cattle were moved between herds according to real movement data. The results showed that the spatial pattern in prevalence may be due to regional differences in livestock movements. However, the movements, births and slaughter of cattle could not explain the temporal pattern of VTEC O157 prevalence in cattle, despite their inherently distinct seasonality.
doi:10.1186/s13567-016-0366-5
PMCID: PMC4982012  PMID: 27515697
2.  Epidemiology of Campylobacter jejuni infections in Sweden, November 2011–October 2012: is the severity of infection associated with C. jejuni sequence type? 
Infection Ecology & Epidemiology  2016;6:10.3402/iee.v6.31079.
Background
Campylobacter jejuni is among the most frequent causes of bacterial gastroenteritis in Europe. Over 8,000 C. jejuni multilocus sequence typing sequence types (STs) have been described; ST-21 and ST-45 have been identified as the most frequent types in all human studies so far. In contrast to other STs, ST-22 has been associated with the Guillain–Barré syndrome and ST-677 was recently linked to severe systemic infections in Finland. We investigated risk factors associated with hospitalisation in individuals with C. jejuni infections acquired in Sweden.
Methods
A total of 1,075 individuals with domestically acquired C. jejuni infection diagnosed between November 2011 and October 2012 in Sweden were included in this retrospective cohort study. Typing data for the isolates as well as clinical data including hospitalisation dates and diagnosis codes for individuals with C. jejuni infection were obtained. Factors associated with hospitalisation and length of hospitalisation were investigated by multivariable analysis.
Results
A total of 289 individuals were hospitalised due to C. jejuni infection (26.8%); those with co-morbidities were over 14 times more likely to become hospitalised than those without (odds ratio [OR]: 14.39, 95% confidence interval [CI]: 6.84–30.26). Those with underlying co-morbidities were also hospitalised longer than those without (4.22 days vs. 2.86 days), although this was not statistically significant. C. jejuni ST-257 (OR: 2.38; CI: 1.08–5.23), but not ST-22 or ST-677, was significantly associated with hospitalisation.
Conclusion
ST-677 was not associated with increased hospitalisation or a longer hospital stay in our study whilst ST-257 was. However, individuals with C. jejuni infections were generally more frequently hospitalised than previously demonstrated; this requires further consideration including possible targeted interventions.
doi:10.3402/iee.v6.31079
PMCID: PMC4826459  PMID: 27059819
gastrointestinal pathogens; epidemiology; sequence type; Campylobacter
3.  Evaluation of farm-level parameters derived from animal movements for use in risk-based surveillance programmes of cattle in Switzerland 
BMC Veterinary Research  2015;11:149.
Background
This study focused on the descriptive analysis of cattle movements and farm-level parameters derived from cattle movements, which are considered to be generically suitable for risk-based surveillance systems in Switzerland for diseases where animal movements constitute an important risk pathway.
Methods
A framework was developed to select farms for surveillance based on a risk score summarizing 5 parameters. The proposed framework was validated using data from the bovine viral diarrhoea (BVD) surveillance programme in 2013.
Results
A cumulative score was calculated per farm, including the following parameters; the maximum monthly ingoing contact chain (in 2012), the average number of animals per incoming movement, use of mixed alpine pastures and the number of weeks in 2012 a farm had movements registered. The final score for the farm depended on the distribution of the parameters. Different cut offs; 50, 90, 95 and 99 %, were explored. The final scores ranged between 0 and 5. Validation of the scores against results from the BVD surveillance programme 2013 gave promising results for setting the cut off for each of the five selected farm level criteria at the 50th percentile. Restricting testing to farms with a score ≥ 2 would have resulted in the same number of detected BVD positive farms as testing all farms, i.e., the outcome of the 2013 surveillance programme could have been reached with a smaller survey.
Conclusions
The seasonality and time dependency of the activity of single farms in the networks requires a careful assessment of the actual time period included to determine farm level criteria. However, selecting farms in the sample for risk-based surveillance can be optimized with the proposed scoring system. The system was validated using data from the BVD eradication program. The proposed method is a promising framework for the selection of farms according to the risk of infection based on animal movements.
doi:10.1186/s12917-015-0468-8
PMCID: PMC4499910  PMID: 26170195
Cattle movements; Risk score; Bovine viral diarrhoea; Animal movement database; Risk-based surveillance
4.  Surveillance systems evaluation: a systematic review of the existing approaches 
BMC Public Health  2015;15:448.
Background
Regular and relevant evaluations of surveillance systems are essential to improve their performance and cost-effectiveness. With this in mind several organizations have developed evaluation approaches to facilitate the design and implementation of these evaluations.
Methods
In order to identify and to compare the advantages and limitations of these approaches, we implemented a systematic review using the PRISMA guidelines (Preferred Reporting Items for Systematic Reviews and Meta-Analyses).
Results
After applying exclusion criteria and identifying other additional documents via citations, 15 documents were retained. These were analysed to assess the field (public or animal health) and the type of surveillance systems targeted; the development process; the objectives; the evaluation process and its outputs; and the attributes covered. Most of the approaches identified were general and provided broad recommendations for evaluation. Several common steps in the evaluation process were identified: (i) defining the surveillance system under evaluation, (ii) designing the evaluation process, (iii) implementing the evaluation, and (iv) drawing conclusions and recommendations.
Conclusions
A lack of information regarding the identification and selection of methods and tools to assess the evaluation attributes was highlighted; as well as a lack of consideration of economic attributes and sociological aspects.
doi:10.1186/s12889-015-1791-5
PMCID: PMC4418053  PMID: 25928645
Surveillance; Evaluation approaches; Health
5.  Prevalence of thermophilic Campylobacter species in Swedish dogs and characterization of C. jejuni isolates 
Background
The aims of this study were to investigate the prevalence of Campylobacter species in Swedish dogs, to identify the species of the Campylobacter isolates and to genotype the C. jejuni isolates. Young and healthy dogs were targeted and the sampling was performed at 11 veterinary clinics throughout Sweden from October 2011 to October 2012. Faecal swab samples were collected and sent to the laboratory at the National Veterinary Institute (SVA) for isolation of Campylobacter, speciation and genotyping.
Results
Campylobacter spp. were isolated from 67 of the 180 sampled dogs which yields an overall prevalence of 37%. The most prevalent species of Campylobacter among the participating dogs was C. upsaliensis with 52 of the 67 identified isolates. A lower prevalence was observed for C. jejuni with seven identified isolates and one isolate was identified as C. helveticus. Multi-locus sequence typing (MLST) was carried out on the seven C. jejuni isolates and all sequence types that were found are also commonly found in humans. The dogs were divided into three age groups; 1) under 12 months, 2) 12 to 23 months and 3) 24 months and older. The highest prevalence was found in the two younger age groups. Dogs shedding C. jejuni were between 3–12 months of age while dogs shedding C. upsaliensis were found in all ages.
Conclusions
The present investigation finds that Campylobacter spp. known to cause campylobacteriosis in humans are present in Swedish dogs. The results suggest an age predisposition where dogs under 2 years of age are more likely to shed Campylobacter spp. than older dogs. The most commonly isolated species was C. upsaliensis followed by C. jejuni, which was only detected in dogs up to 12 months of age. All C. jejuni isolates identified in the present study were of the same MLST types that have previously been described both in humans and in animals. The awareness of the Campylobacter risk of healthy young dogs may be an important way to reduce the transmission from dogs to infants, young children and immunocompromised adults.
doi:10.1186/s13028-015-0108-0
PMCID: PMC4389321  PMID: 25884591
Dog; Campylobacter; C. upsaliensis; C. jejuni; MLST; Prevalence
6.  Multivariate Statistical Assessment of Predictors of Firefighters’ Muscular and Aerobic Work Capacity 
PLoS ONE  2015;10(3):e0118945.
Physical capacity has previously been deemed important for firefighters physical work capacity, and aerobic fitness, muscular strength, and muscular endurance are the most frequently investigated parameters of importance. Traditionally, bivariate and multivariate linear regression statistics have been used to study relationships between physical capacities and work capacities among firefighters. An alternative way to handle datasets consisting of numerous correlated variables is to use multivariate projection analyses, such as Orthogonal Projection to Latent Structures. The first aim of the present study was to evaluate the prediction and predictive power of field and laboratory tests, respectively, on firefighters’ physical work capacity on selected work tasks. Also, to study if valid predictions could be achieved without anthropometric data. The second aim was to externally validate selected models. The third aim was to validate selected models on firefighters’ and on civilians’. A total of 38 (26 men and 12 women) + 90 (38 men and 52 women) subjects were included in the models and the external validation, respectively. The best prediction (R2) and predictive power (Q2) of Stairs, Pulling, Demolition, Terrain, and Rescue work capacities included field tests (R2 = 0.73 to 0.84, Q2 = 0.68 to 0.82). The best external validation was for Stairs work capacity (R2 = 0.80) and worst for Demolition work capacity (R2 = 0.40). In conclusion, field and laboratory tests could equally well predict physical work capacities for firefighting work tasks, and models excluding anthropometric data were valid. The predictive power was satisfactory for all included work tasks except Demolition.
doi:10.1371/journal.pone.0118945
PMCID: PMC4361601  PMID: 25775243
7.  Biosecurity level and health management practices in 60 Swedish farrow-to-finish herds 
Background
Biosecurity measures are important tools to maintain animal health in pig herds. Within the MINAPIG project, whose overall aim is to evaluate strategies to raise pigs with less antimicrobial use, biosecurity was evaluated in medium to large farrow-to-finish pig herds in Sweden. In 60 farrow-to-finish herds with more than 100 sows, the biosecurity level was evaluated using a previously developed protocol (BioCheck). In a detailed questionnaire, internal and external biosecurity was scored in six subcategories each. An overall score for biosecurity was also provided. Information regarding production parameters as well as gender and educational level of personnel working with the pigs was also collected. Descriptive statistics were used to examine the recorded data.
Results
The median scores for external and internal biosecurity were 68 and 59, respectively, where 0 indicates total absence of biosecurity and 100 means maximal possible biosecurity. The subcategories for external and internal biosecurity that had the highest scores were “Purchase of animals” (external) and “Nursery unit”/“Fattening unit” (internal), while “Feed, water and equipment supplies” (external) and “Measures between compartments and equipment”/“Cleaning and disinfection” (internal) received the lowest scores. A female caretaker in the farrowing unit, a farmer with fewer years of experience and more educated personnel were positively associated with higher scores for some of the external and internal subcategories. In herds with <190 sows, fattening pigs were mixed between batches significantly more often than in larger herds.
Conclusions
The herds in this study had a high level of external biosecurity, as well as good internal biosecurity. Strong biosecurity related to the purchase of animals, protocols for visitors, the use of all-in, all-out systems, and sanitary period between batches. Still, there is room for improvement in preventing both the introduction of disease to herds (external) and the spread of infections within herds (internal). Systems for animal transport can be improved and with respect to internal biosecurity, there is especially room for improvement regarding hygiene measures in and between compartments, as well as the staff’s working procedures between different groups of pigs.
Electronic supplementary material
The online version of this article (doi:10.1186/s13028-015-0103-5) contains supplementary material, which is available to authorized users.
doi:10.1186/s13028-015-0103-5
PMCID: PMC4359795  PMID: 25887040
Pig production; Biosecurity; Health management
8.  Vetsyn: Veterinary Syndromic Surveillance Streamlined into one R Package 
doi:10.5210/ojphi.v7i1.5683
PMCID: PMC4512328
Animal health; syndromic surveillance; R programming
9.  Standardising Syndromic Classification in Animal Health Data 
doi:10.5210/ojphi.v7i1.5789
PMCID: PMC4512370
Animal health; syndromic surveillance; ontology
10.  Veterinary syndromic surveillance in practice: costs and benefits for governmental organizations 
Infection Ecology & Epidemiology  2015;5:10.3402/iee.v5.29973.
Background
We describe a veterinary syndromic surveillance system developed in Sweden based on laboratory test requests.
Materials and methods
The system is a desktop application built using free software.
Results
Development took 1 year. During the first year of operation, utility was demonstrated by the detection of statistically significant increases in the number of laboratory submissions. The number of false alarms was considered satisfactory in order to achieve the desired sensitivity.
Discussion
Besides the demonstrated benefit for disease surveillance, the system contributed to improving data quality and communication between the diagnostic departments and the epidemiology department.
doi:10.3402/iee.v5.29973
PMCID: PMC4669311  PMID: 26634845
animal health; laboratory data; aberration detection
11.  Surveys on Coxiella burnetii infections in Swedish cattle, sheep, goats and moose 
Background
Q fever is a zoonotic disease caused by the bacterium Coxiella burnetii. Prevalence data in ruminant species are important to support risk assessments regarding public and animal health. The aim was to investigate the presence of or exposure to C. burnetii in cattle, sheep, goats and moose, and to compare two enzyme-linked immunosorbent assays (ELISAs). National surveys of antibodies against C. burnetii were performed for dairy cattle (n=1537), dairy goats (n=58) and sheep (n=518). Bovine samples consisted of bulk milk, caprine of pooled milk, and ovine of pooled serum. Antibodies were investigated in moose samples (n=99) from three regions. A one-year regional cattle bulk milk survey was performed on the Isle of Gotland (n=119, four occasions). Cattle, sheep and goat samples were analysed with indirect ELISA and moose samples with complement fixation test. For the sheep, goat, and parts of the cattle survey, samples were run in parallel by ELISAs based on antigens from infected ruminants and ticks. Bulk milk samples from the regional cattle survey and vaginal swabs from a subset of the sheep herds (n=80) were analysed for the agent by polymerase chain reaction. Spatial clustering was investigated in the national cattle survey.
Results
The prevalence of antibodies in dairy herds was 8.2% with large regional differences. High risk clusters were identified in the southern regions. The prevalence among dairy herds on the Isle of Gotland varied from 55.9% to 64.6% and 46.4% to 58.9.0% for antibodies and agent, respectively, overall agreement between agent and antibodies was 85.2%. The prevalence of antibodies in sheep was 0.6%, the agent was not detected the vaginal swabs. Antibodies were not detected in goats or moose, although parts of the moose samples were collected in an area with high prevalence in cattle. The overall agreement between the two ELISAs was 90.4%.
Conclusions
The prevalence of antibodies against C. burnetii in dairy cattle in Sweden shows large regional differences. The results suggest that C. burnetii is a rare pathogen among Swedish moose, dairy goat and sheep. ELISAs based on ruminant and tick antigen performed in a similar manner under Swedish conditions.
doi:10.1186/1751-0147-56-39
PMCID: PMC4112654  PMID: 25007979
Coxiella burnetii; Surveillance; Epidemiology; Cattle; Goat; Sheep; Moose; Cervids; Antibodies; Test evaluation
13.  Laboratory or Field Tests for Evaluating Firefighters' Work Capacity? 
PLoS ONE  2014;9(3):e91215.
Muscle strength is important for firefighters work capacity. Laboratory tests used for measurements of muscle strength, however, are complicated, expensive and time consuming. The aims of the present study were to investigate correlations between physical capacity within commonly occurring and physically demanding firefighting work tasks and both laboratory and field tests in full time (N = 8) and part-time (N = 10) male firefighters and civilian men (N = 8) and women (N = 12), and also to give recommendations as to which field tests might be useful for evaluating firefighters' physical work capacity. Laboratory tests of isokinetic maximal (IM) and endurance (IE) muscle power and dynamic balance, field tests including maximal and endurance muscle performance, and simulated firefighting work tasks were performed. Correlations with work capacity were analyzed with Spearman's rank correlation coefficient (rs). The highest significant (p<0.01) correlations with laboratory and field tests were for Cutting: IE trunk extension (rs = 0.72) and maximal hand grip strength (rs = 0.67), for Stairs: IE shoulder flexion (rs = −0.81) and barbell shoulder press (rs = −0.77), for Pulling: IE shoulder extension (rs = −0.82) and bench press (rs = −0.85), for Demolition: IE knee extension (rs = 0.75) and bench press (rs = 0.83), for Rescue: IE shoulder flexion (rs = −0.83) and bench press (rs = −0.82), and for the Terrain work task: IE trunk flexion (rs = −0.58) and upright barbell row (rs = −0.70). In conclusion, field tests may be used instead of laboratory tests. Maximal hand grip strength, bench press, chin ups, dips, upright barbell row, standing broad jump, and barbell shoulder press were strongly correlated (rs≥0.7) with work capacity and are therefore recommended for evaluating firefighters work capacity.
doi:10.1371/journal.pone.0091215
PMCID: PMC3948787  PMID: 24614596
14.  Field Tests for Evaluating the Aerobic Work Capacity of Firefighters 
PLoS ONE  2013;8(7):e68047.
Working as a firefighter is physically strenuous, and a high level of physical fitness increases a firefighter’s ability to cope with the physical stress of their profession. Direct measurements of aerobic capacity, however, are often complicated, time consuming, and expensive. The first aim of the present study was to evaluate the correlations between direct (laboratory) and indirect (field) aerobic capacity tests with common and physically demanding firefighting tasks. The second aim was to give recommendations as to which field tests may be the most useful for evaluating firefighters’ aerobic work capacity. A total of 38 subjects (26 men and 12 women) were included. Two aerobic capacity tests, six field tests, and seven firefighting tasks were performed. Lactate threshold and onset of blood lactate accumulation were found to be correlated to the performance of one work task (rs = −0.65 and −0.63, p<0.01, respectively). Absolute (mL·min−1) and relative (mL·kg−1·min−1) maximal aerobic capacity was correlated to all but one of the work tasks (rs = −0.79 to 0.55 and −0.74 to 0.47, p<0.01, respectively). Aerobic capacity is important for firefighters’ work performance, and we have concluded that the time to row 500 m, the time to run 3000 m relative to body weight (s·kg−1), and the percent of maximal heart rate achieved during treadmill walking are the most valid field tests for evaluating a firefighter’s aerobic work capacity.
doi:10.1371/journal.pone.0068047
PMCID: PMC3699487  PMID: 23844153
15.  Completeness of the disease recording systems for dairy cows in Denmark, Finland, Norway and Sweden with special reference to clinical mastitis 
Background
In the Nordic countries Denmark, Finland, Norway and Sweden, the majority of dairy herds are covered by disease recording systems, in general based on veterinary registration of diagnoses and treatments. Disease data are submitted to the national cattle databases where they are combined with, e.g., production data at cow level, and used for breeding programmes, advisory work and herd health management. Previous studies have raised questions about the quality of the disease data. The main aim of this study was to examine the country-specific completeness of the disease data, regarding clinical mastitis (CM) diagnosis, in each of the national cattle databases. A second aim was to estimate country-specific CM incidence rates (IRs).
Results
Over 4 months in 2008, farmers in the four Nordic countries recorded clinical diseases in their dairy cows. Their registrations were matched to registrations in the central cattle databases. The country-specific completeness of disease registrations was calculated as the proportion of farmer-recorded cases that could be found in the central database. The completeness (95% confidence interval) for veterinary-supervised cases of CM was 0.94 (0.92, 0.97), 0.56 (0.48, 0.64), 0.82 (0.75, 0.90) and 0.78 (0.70, 0.85) in Denmark, Finland, Norway and Sweden, respectively. The completeness of registration of all CM cases, which includes all cases noted by farmers, regardless of whether the cows were seen or treated by a veterinarian or not, was 0.90 (0.87, 0.93), 0.51 (0.43, 0.59), 0.75 (0.67, 0.83) and 0.67 (0.60, 0.75), respectively, in the same countries. The IRs, estimated by Poisson regression in cases per 100 cow-years, based on the farmers’ recordings, were 46.9 (41.7, 52.7), 38.6 (34.2, 43.5), 31.3 (27.2, 35.9) and 26.2 (23.2, 26.9), respectively, which was between 20% (DK) and 100% (FI) higher than the IRs based on recordings in the central cattle databases.
Conclusions
The completeness for veterinary-supervised cases of CM was considerably less than 100% in all four Nordic countries and differed between countries. Hence, the number of CM cases in dairy cows is underestimated. This has an impact on all areas where the disease data are used.
doi:10.1186/1746-6148-8-131
PMCID: PMC3489834  PMID: 22866606
Bovine mastitis; Disease recording; Completeness; Nordic; Database; Validation
16.  Can pre-collected register data be used to identify dairy herds with good cattle welfare? 
Acta Veterinaria Scandinavica  2011;53(Suppl 1):S8.
Abstract
Background
Pre-recorded register data from dairy herds are available in almost all Nordic countries. These databases can be used for research purposes, and one of the research areas is animal welfare. The aim of this study was to investigate if pre-recorded register data could be used to identify herds with good welfare, and to investigate if a combination of register data sets could be used to be able to more correctly distinguish between herds with good welfare and herds with welfare deficiencies.
Methods
As a first step, nine animal-based measurements on calves, young stock and cows in 55 randomly selected herds were performed on-farm as the basis for a classification of welfare at the herd level. The definition for being a case herd with “good welfare” was no score lying among the 10% worst in any of the nine welfare measurements. Twenty-eight of the 55 herds were cases according to this definition. As a second step, 65 potential welfare indicators, based on register data in a national dairy database, were identified by expert opinion. In the final step, the extent to which the suggested welfare indicators predicted farms’ as having good welfare according to the stated definition was assessed. Moreover, the effect of combining in sequence a previously developed model that identified herds with poor welfare with the present model identifying herds with good welfare was investigated.
Results
The final set of welfare indicators used to identify herds with good animal welfare included two fertility measures, cow mortality, stillbirth rate, mastitis incidence and incidence of feed-related diseases (including gastrointestinal disturbances but excluding paralyses and cramps). This set had a test sensitivity of correctly classifying herds with no score lying among the 10% worst of the nine welfare measurements of 96 %. However, the specificity of the test was only 56% indicating difficulties for the test to correctly classifying herds with one or more scores lying among the 10% worst. Combining the previously developed model with the present model, improved the welfare classification.
Conclusions
This study shows that pre-collected register data may be used to give approval to dairy farms with “good welfare” and that combining different sets of register data can improve the classification of herd welfare.
doi:10.1186/1751-0147-53-S1-S8
PMCID: PMC3194127  PMID: 21999569
17.  Herd and cow characteristics affecting the odds of veterinary treatment for disease – a multilevel analysis 
Background
Research has indicated that a number of different factors affect whether an animal receives treatment or not when diseased. The aim of this paper was to evaluate if herd or individual animal characteristics influence whether cattle receives veterinary treatment for disease, and thereby also introduce misclassification in the disease recording system.
Methods
The data consisted mainly of disease events reported by farmers during 2004. We modelled odds of receiving veterinary treatment when diseased, using two-level logistic regression models for cows and young animals (calves and heifers), respectively. Model parameters were estimated using three procedures, because these procedures have been shown, under some conditions, to produce biased estimates for multi-level models with binary outcomes.
Results
Cows located in herds mainly consisting of Swedish Holstein cows had higher odds for veterinary treatment than cows in herds mainly consisting of Swedish Red cows. Cows with a disease event early in lactation had higher odds for treatment than when the event occurred later in lactation. There were also higher odds for veterinary treatment of events for cows in January and April than in July and October. The odds for veterinary treatment of events in young animals were higher if the farmer appeared to be good at keeping records. Having a disease event at the same date as another animal increased the odds for veterinary treatment for all events in young animals, and for lameness, metabolic, udder and other disorders, but not for peripartum disorders, in cows. There were also differences in the odds for veterinary treatment between disease complexes, both for cows and young animals.
The random effect of herd was significant in both models and accounted for 40–44% of the variation in the cow model and 30–46% in the young animal model.
Conclusion
We conclude that cow and herd characteristics influence the odds for veterinary treatment and that this might bias the results from studies using data from the cattle disease database based on veterinary practice records.
doi:10.1186/1751-0147-51-34
PMCID: PMC2736961  PMID: 19698112

Results 1-17 (17)