Endemic foot and mouth disease: pastoral in-herd disease dynamics in sub-Saharan Africa.

Foot and mouth disease (FMD) burden disproportionally affects Africa where it is considered endemic. Smallholder livestock keepers experience significant losses due to disease, but the dynamics and mechanisms underlying persistence at the herd-level and beyond remain poorly understood. We address this knowledge gap using stochastic, compartmental modelling to explore FMD virus (FMDV) persistence, outbreak dynamics and disease burden in individual cattle herds within an endemic setting. Our analysis suggests repeated introduction of virus from outside the herd is required for long-term viral persistence, irrespective of carrier presence. Risk of new disease exposures resulting in significant secondary outbreaks is reduced by the presence of immune individuals giving rise to a period of reduced risk, the predicted duration of which suggests that multiple strains of FMDV are responsible for observed yearly herd-level outbreaks. Our analysis suggests management of population turnover could potentially reduce disease burden and deliberate infection of cattle, practiced by local livestock keepers in parts of Africa, has little effect on the duration of the reduced risk period but increases disease burden. This work suggests that FMD control should be implemented beyond individual herds but, in the interim, herd management may be used to reduced FMD impact to livestock keepers.

British Escherichia coli O157 in Cattle Study (BECS): to determine the prevalence of E. coli O157 in herds with cattle destined for the food chain.

Escherichia coli O157 are zoonotic bacteria for which cattle are an important reservoir. Prevalence estimates for E. coli O157 in British cattle for human consumption are over 10 years old. A new baseline is needed to inform current human health risk. The British E. coli O157 in Cattle Study (BECS) ran between September 2014 and November 2015 on 270 farms across Scotland and England & Wales. This is the first study to be conducted contemporaneously across Great Britain, thus enabling comparison between Scotland and England & Wales. Herd-level prevalence estimates for E. coli O157 did not differ significantly for Scotland (0·236, 95% CI 0·166-0·325) and England & Wales (0·213, 95% CI 0·156-0·283) (P = 0·65). The majority of isolates were verocytotoxin positive. A higher proportion of samples from Scotland were in the super-shedder category, though there was no difference between the surveys in the likelihood of a positive farm having at least one super-shedder sample. E. coli O157 continues to be common in British beef cattle, reaffirming public health policy that contact with cattle and their environments is a potential infection source.

Prevalence of antibodies to bovine viral diarrhoea virus in bulk tank milk and associated risk factors in Scottish dairy herds.

Bulk tank milk samples were collected from 374 dairy farms in Scotland in 2007/2008 along with questionnaire data relating to the management of the farm. Milk samples were tested for antibodies to bovine viral diarrhoea virus (BVDV) using a commercially available (Svanova) kit and percentage positivity scores calculated according to the manufacturer's guidelines. There were 220 farms that did not routinely vaccinate for bovine viral diarrhoea (BVD), and these were distributed according to the Swedish BVD eradication classes as 12.7 per cent, 22.3 per cent, 44.5 per cent and 20.5 per cent for Classes 0, 1, 2 and 3, respectively. A more sophisticated statistical method (finite mixture modelling) which does not depend on arbitrary thresholds and categories suggested a 73 per cent prevalence of herds with high mean levels of antibodies. Risk factor analysis suggested that routine vaccination for BVD, suspicion of BVD, housing of pregnant cows with calves, total number of cows and the proportion of cows that were dry were all associated with increased BVDV antibodies in bulk milk. The inclusion of BVD within the farm's health plan was associated with decreased BVDV antibodies in the bulk milk.

Quantifying the sources of variability in equine faecal egg counts: implications for improving the utility of the method.

The faecal egg count (FEC) is the most widely used means of quantifying the nematode burden of horses, and is frequently used in clinical practice to inform treatment and prevention. The statistical process underlying the FEC is complex, comprising a Poisson counting error process for each sample, compounded with an underlying continuous distribution of means between samples. Being able to quantify the sources of variability contributing to this distribution of means is a necessary step towards providing estimates of statistical power for future FEC and FECRT studies, and may help to improve the usefulness of the FEC technique by identifying and minimising unwanted sources of variability. Obtaining such estimates require a hierarchical statistical model coupled with repeated FEC observations from a single animal over a short period of time. Here, we use this approach to provide the first comparative estimate of multiple sources of within-horse FEC variability. The results demonstrate that a substantial proportion of the observed variation in FEC between horses occurs as a result of variation in FEC within an animal, with the major sources being aggregation of eggs within faeces and variation in egg concentration between faecal piles. The McMaster procedure itself is associated with a comparatively small coefficient of variation, and is therefore highly repeatable when a sufficiently large number of eggs are observed to reduce the error associated with the counting process. We conclude that the variation between samples taken from the same animal is substantial, but can be reduced through the use of larger homogenised faecal samples. Estimates are provided for the coefficient of variation (cv) associated with each within animal source of variability in observed FEC, allowing the usefulness of individual FEC to be quantified, and providing a basis for future FEC and FECRT studies.

Diagnostic accuracy of PCR for Jaagsiekte sheep retrovirus using field data from 125 Scottish sheep flocks.

Using a representative sample of Scottish sheep comprising 125 flocks, the sensitivity and specificity of PCR for Jaagsiekte sheep retrovirus (JSRV) was estimated. By combining and adapting existing methods, the characteristics of the diagnostic test were estimated (in the absence of a gold standard reference) using repeated laboratory replicates. As the results of replicates within the same animal cannot be considered to be independent, the performance of the PCR was calculated at individual replicate level. The median diagnostic specificity of the PCR when applied to individual animals drawn from the Scottish flock was estimated to be 0.997 (95% confidence interval [CI] 0.996-0.999), whereas the median sensitivity was 0.107 (95% CI 0.077-0.152). Considering the diagnostic test as three replicates where a positive result on any one or more replicates results in a positive test, the median sensitivity increased to 0.279. Reasons for the low observed sensitivity were explored by comparing the performance of the test as a function of the concentration of target DNA using spiked positive controls with known concentrations of target DNA. The median sensitivity of the test when used with positive samples with a mean concentration of 1.0 target DNA sequence per 25µL was estimated to be 0.160, which suggests that the PCR had a high true (analytical) sensitivity and that the low observed (diagnostic) sensitivity in individual samples was due to low concentrations of target DNA in the blood of clinically healthy animals.

Quantitative assessment of increased sensitivity of chronic laminitic horses to hoof tester evoked pain.

REASONS FOR PERFORMING STUDY: To evaluate quantitative sensory testing (QST) of the feet of laminitic horses using a power-assisted hoof tester. HYPOTHESIS: Hoof Compression Thresholds (HCTs) can be measured reliably and are consistently lower in horses with chronic laminitis than in normal horses. METHODS: HCTs of chronic laminitic (n=7) and normal horses (n=7) were repeatedly measured using a hydraulically powered and feedback controlled hoof tester. Data from 2 tests, at 3 sites in both forefeet, during 3 sessions were collected and statistically analysed using linear mixed models. RESULTS: The mean±s.e. HCT for the laminitic horses was 29.6±3.5 kg/cm2 and for horses in the normal group was 59.8±4.3 kg/cm2. Residual variance was the largest of the error components and was greater (P<0.001) for the normal horses; none of the other components significantly differed between the 2 groups. Averaging of HCTs from each foot could produce a test with intraclass correlation coefficients of 0.83 for the normal group and 0.87 for the laminitic group, with an estimated sensitivity of 0.94 and a specificity of 0.93. This test would permit detection with 80% power and 95% confidence of a reduction of over 40% in the difference in mean HCTs between laminitic and normal horses following effective treatment provided that the experimental groups are of 9 or more horses. CONCLUSIONS: HCTs can be safely and reliably measured experimentally using this hoof tester. The level of variability found indicates that, under these conditions, treatments may need to produce at least a 40% improvement to be detected. Simplification of the hoof tester, training of the horse and repeated testing may permit the method to be used clinically to detect changes in the HCTs of individual laminitic horses but these potential improvements will require further investigation. POTENTIAL RELEVANCE: Measurement of HCTs can provide an additional means for assessing the effectiveness of treatments for alleviation of chronic equine laminitis.

Prevalence of Pasteurella multocida and other respiratory pathogens in the nasal tract of Scottish calves.

The prevalence of Pasteurella multocida, a cause of bovine respiratory disease, was studied in a random sample of beef suckler and dairy farms throughout Scotland, by means of a cross-sectional survey. A total of 637 calves from 68 farms from six geographical regions of Scotland were sampled between February and June 2008. Deep nasal swabs were taken, and samples that were culture-positive for P multocida were confirmed by PCR. Prevalence of P multocida was 17 per cent (105 of 616 calves); 47 per cent of farms had at least one positive animal. A higher prevalence was detected in dairy calves than beef calves (P=0.04). It was found that P multocida was associated with Mycoplasma-like organisms (P=0.06) and bovine parainfluenza type 3 virus (BPI-3) (P=0.04), detected by culture and quantitative PCR of nasal swabs, respectively. Detection of P multocida was not associated with bovine respiratory syncytial virus (BRSV), bovine herpesvirus type 1 (BoHV-1) or bovine viral diarrhoea virus (BVDV). Mycoplasma-like organisms, BPI-3, BRSV, BoHV-1 and BVDV were detected in 58, 17, four, 0 and eight calves, on 25, five, two, 0 and five of the 68 farms, respectively.

Comparison of three alternative methods for analysis of equine Faecal Egg Count Reduction Test data.

The Faecal Egg Count Reduction Test (FECRT) is the most widely used method of assessing the efficacy of anthelmintics, and is the only in vivo technique currently approved for use with horses. Equine Faecal Egg Count (FEC) data are frequently characterised by a low mean, high variability, small sample size and frequent zero count observations. Accurate analysis of the data therefore depends on the use of an appropriate statistical technique. Analyses of simulated FECRT data by methods based on calculation of the empirical mean and variance, non-parametric bootstrapping, and Markov chain Monte Carlo (MCMC) are compared. The MCMC method consistently outperformed the other methods, independently of the distribution from which the data were generated. Bootstrapping produced notional 95% confidence intervals containing the true parameter as little as 40% of the time with sample sizes of less than 50. Analysis of equine FECRT data yielded inconclusive results in 53 of 63 (84%) datasets, suggesting that the routine use of prior sample size calculations should be adopted to ensure sufficient data are collected. The authors conclude that computationally intensive parametric methods such as MCMC be used for analysis of FECRT data with sample sizes of less than 50, in order to avoid erroneous inference about the true efficacy of anthelmintics in the field.

The prevalence of bovine viral diarrhoea virus infection in beef suckler herds in Scotland.

Bovine viral diarrhoea (BVD) is an endemic disease of cattle that causes substantial losses to both beef and dairy production worldwide. The goal of this study was to estimate the prevalence of active BVD virus (BVDV) infection in beef suckler herds in Scotland. Information was collected from 301 herds using a stratified random sampling design based on agricultural census data. Herds were classified as with and without active infection based on the within-herd BVDV seroprevalence in young stock using Bayesian finite mixture modelling. This method accounted for within- and between-herd variability and allowed for classification error by the diagnostic tests. The observed sample data enabled the discrimination of three distinct seroprevalence cohorts. The results provided evidence of active BVDV infection in 16% of herds and no evidence of recent exposure in approximately two thirds of herds. The epidemiological significance of the further 16% of herds containing young stock with a median BVDV seroprevalence of 26.3-38.5% remains unclear. The fact that a large percentage of herds did not show evidence of recent infection is encouraging from an animal health and welfare perspective and the study provides a model for the further exploration of strategies aimed at BVD control at national level.

Failure to transmit scrapie infection by transferring preimplantation embryos from naturally infected donor sheep.

The objective of the study was to examine whether or not the preimplantation embryo can act as a carrier of classic scrapie infection. The study was carried out on quarantined premises with sheep of highly susceptible scrapie genotypes. Uninfected embryos, collected from New Zealand-derived Suffolk ewes, were surgically transferred into recipient ewes that were also of New Zealand origin. Seventeen negative control lambs were born on the study premises from these embryo transfers. Thirty-nine experimental lambs were from embryos collected from naturally infected donor ewes. The experimental lambs were also born on the study premises after their surgical transfer into recipient ewes of New Zealand origin. These embryos had been collected from donor ewes in a scrapie-infected flock where the ewes were clinically sick with scrapie or developed clinical scrapie after embryo collection. All lambs were confirmed as scrapie susceptible of the ARQ/ARQ genotype. Twenty-eight experimental animals survived to the end point of the study at 5 yr of age with a mean survival of 1579 d. In the negative control group, 12 of 17 sheep survived to 5 yr of age with a mean survival of 1508 d. Postmortem examinations were carried out on all animals derived by embryo transfer, and in none was histologic or immunohistochemical evidence of scrapie found. In contrast, in the originating flock the majority of scrapie cases occurred in ARQ/ARQ genotyped animals where a 56% mortality from scrapie had been recorded in animals of this genotype. Thus, the study provides no evidence for transmission of scrapie and reinforces published evidence that vertical transmission of scrapie may be circumvented by embryo transfer procedures.

An investigation of factors associated with the prevalence of verocytotoxin producing Escherichia coli O157 shedding in Scottish beef cattle.

The prevalence of verocytotoxin-producing Escherichia coli (VTEC) O157 in 12-30-month-old beef finishing cattle in Scotland was determined using 1g faeces samples enriched in buffered peptone water, followed by immunomagnetic separation (IMS) and isolation on sorbitol MacConkey agar with cefixime and tellurite supplement (CT-SMAC). A validated questionnaire was used to collect information that could be associated with the samples. Generalised Linear Models and Generalised Linear Mixed Models were used to identify factors associated with shedding both between and within groups. A total of 14,856 samples were collected from 952 farms, of which 1231 were positive for VTEC O157. Prevalence levels were calculated with 95% confidence intervals as follows: 7.9% (6.5%, 9.6%) of animals sampled were estimated to be shedding VTEC O157, while 22.8% (19.6%, 26.3%) of farms were estimated as having at least one animal shedding in the group sampled. The median percentage of animals shedding in positive groups was 25% (20%, 32%). An increased probability of a group containing a shedding animal was associated with larger numbers of finishing cattle, the presence of pigs on the farm, or the farm being classed as a dairy unit stocking beef animals. Farms that spread slurry on grazing land were more likely to have shedding animals, while those that spread manure were at lower risk. Groups with older animals were less likely to be identified as positive. There was no significant regional difference in group shedding probabilities, but the proportion of positive groups dropped over two successive years of the study. Higher mean levels of shedding in positive groups were associated with animals being housed rather than at pasture, and this effect was stronger in groups which had recently had a change in housing or diet. Farms with animals at pasture had lower mean prevalence where water was supplied from a natural source, as had farms with higher numbers of finishing cattle. There remained unexplained variability in mean prevalence levels on positive farms in different areas of Scotland.

Prevalence, spatial distribution and the effect of control measures on louping-ill virus in the Forest of Bowland, Lancashire.

The complex pathogen-host-vector system of the tick-borne louping-ill virus causes economic losses to sheep and red grouse in upland United Kingdom. This paper examines the spatial distribution, incidence and effect of control measures on louping-ill virus in the Bowland Fells of Lancashire. Seroprevalence in sheep at the beginning of the study varied within the area and was affected significantly by the frequency of acaricide treatment. There was a clear decrease over 5 years in the effective force of infection on farms implementing a vaccination programme, irrespective of acaricide treatment regime, however, only one third of farms apparently eliminated infection. On farms where vaccination did not occur or where vaccination was carried out intermittently, the estimated force of infection was variable or possibly increased. Thus, as befits a complex host-pathogen system, reductions in prevalence were not as dramatic as predicted; we discuss the potential explanations for these observations.

The interaction between dam methylation sites and Xba1 restriction digest sites in Escherichia coli O157:H7 EDL933.

AIMS: The aim of this study was to gain a better understanding of the reason for the predicted pulsed-field gel electrophoresis (PFGE) pattern for the sequenced Escherichia coli O157:H7 EDL933 (EDL933) being different from that observed in practice, using the restriction enzyme Xba1. METHODS AND RESULTS: Primers were designed that flanked either side of each of the predicted Xba1 restriction sites, and the resultant PCR products were sequenced. No sequencing errors were found in the published genome. The distribution of dam methylation sites within the genome was investigated, and a new PFGE pattern was predicted by assuming that any Xba1 restriction site that coincided with a dam methylation site would not be cut. The estimated mean band sizes were obtained from six replicate gels. It was found that the observed and predicted PFGE patterns were in good agreement. CONCLUSIONS: The difference between the observed and the predicted PFGE patterns for EDL933, using Xba1, could be accounted for by assuming that the methylated restriction sites were not cut. SIGNIFICANCE AND IMPACT OF THE STUDY: PFGE is commonly used as a subtyping method. This study provides additional information about the basic technique that could enhance the interpretation of PFGE patterns in comparative studies of the E. coli isolates.

A simulation model to assess herd-level intervention strategies against E. coli O157.

A simulation model of a herd of grazing cattle, which has been developed to provide insight into the infection dynamics of E. coli O157 is described. The spatially explicit model enables the modelling of the infection transmission processes to be realistically addressed under field management conditions. The model is used to explore the efficacy of various potential control strategies in reducing the levels of within-herd infection. These measures include restricting the size of herds, niche engineering, improving housing hygiene and vaccination. While a vaccination strategy remains a hypothetical option, it has the potential to be particularly effective. It is likely that the most successful strategy will involve the implementation of a combination of measures.

Prevalence of 'head shooting' and the characteristics of the wounds in culled wild Scottish red deer.

The carcases of 230 wild, culled red deer (Cervus elaphus) were examined for the presence of bullet wounds and permanent wound tracts to determine the prevalence and significance of wounds involving the head, legs or carcase trunk. Head wounds were found in 17 (7.4 per cent) of the carcases and were classified into two groups: nine in which the marksman was considered to have specifically targeted the head, and eight carcases in which the head wound was considered to have resulted from a ;coup de grace' shot to dispatch a previously wounded animal. The analysis of the wound data from the carcase trunks, in combination with data collected in a previous study, indicates that the initial wound tracts in all the deer appeared to have lower mean terminal probabilities than subsequent wound tracts, and that this effect is exacerbated during the rut.

Assessing the efficacy of within-animal control strategies against E. coli O157: a simulation study.

A stochastic simulation model was used to assess the efficacy of potential measures to control the levels of Escherichia coli O157 within the bovine host. The model described E. coli O157 population sizes at several sites along the bovine gut and therefore only interventions that operate at an individual animal level could be evaluated. In order to use the model to evaluate the control strategies, it was necessary to make assumptions about how each strategy affected E. coli O157 populations in vivo. The within-animal conditions under these control strategies were modelled by adjusting the growth rates of E. coli O157 at specific sites of interest in the gut, based on these assumptions. The model simulated the population dynamics of an initial dose of E. coli O157 inoculated into an animal in the presence of inhibitory probiotics or antibiotics, bactericidal antibiotics or probiotics, and following fasting. Of the control strategies considered, the use of inhibitory probiotics appeared most promising and continued development of a suitable product is to be encouraged.

A simulation model for the study of the within-animal infection dynamics of E. coli O157.

Escherichia coli 0157 can cause serious illness, even death, in humans. There is some consensus that the main reservoirs of this harmful bacterium are the rumens and intestines of cattle. Hence, a stochastic model of the bovine gut was developed to investigate the in vivo population dynamics of E. coli O157. Because bacterial numbers can reach minimal levels, a stochastic system was considered, with a birth-death process being used to represent bacterial growth and decay dynamics throughout the gastrointestinal tract. Reinfection through ingestion of bacteria present in the environment was allowed to occur and the required clustered distribution of inter-event times was implemented through the use of a random hazard doubly stochastic Poisson process. Due to the inclusion of multiple compartments, a feedback mechanism and an interest in the non-equilibrium dynamics of the process, it was not possible to obtain an analytical representation of the process and therefore, a simulation study was used to obtain results. The within-animal model can be used to explore the efficacy of control measures which act at an individual animal level.

Prevalence and virulence factors of Escherichia coli serogroups O26, O103, O111, and O145 shed by cattle in Scotland.

A national survey was conducted to determine the prevalence of Escherichia coli O26, O103, O111, and O145 in feces of Scottish cattle. In total, 6,086 fecal pats from 338 farms were tested. The weighted mean percentages of farms on which shedding was detected were 23% for E. coli O26, 22% for E. coli O103, and 10% for E. coli O145. The weighted mean prevalences in fecal pats were 4.6% for E. coli O26, 2.7% for E. coli O103, and 0.7% for E. coli O145. No E. coli O111 was detected. Farms with cattle shedding E. coli serogroup O26, O103, or O145 were widely dispersed across Scotland and were identified most often in summer and autumn. However, on individual farms, fecal shedding of E. coli O26, O103, or O145 was frequently undetectable or the numbers of pats testing positive were small. For serogroup O26 or O103 there was clustering of positive pats within management groups, and the presence of an animal shedding one of these serogroups was a positive predictor for shedding by others, suggesting local transmission of infection. Carriage of vtx was rare in E. coli O103 and O145 isolates, but 49.0% of E. coli O26 isolates possessed vtx, invariably vtx1 alone or vtx1 and vtx2 together. The carriage of eae and ehxA genes was highly associated in all three serogroups. Among E. coli serogroup O26 isolates, 28.9% carried vtx, eae, and ehxA-a profile consistent with E. coli O26 strains known to cause human disease.

Super-shedding cattle and the transmission dynamics of Escherichia coli O157.

The prevalence of Escherichia coli O157 displays striking variability across the Scottish cattle population. On 78% of farms, in a cross-sectional survey of 952, no shedding of E. coli O157 was detected, but on a small proportion, approximately 2%, very high prevalences of infection were found (with 90-100% of pats sampled being positive). We ask whether this variation arises from the inherent stochasticity in transmission dynamics or whether it is a signature of underlying heterogeneities in the cattle population. A novel approach is taken whereby the cross-sectional data are viewed as providing independent snapshots of a dynamic process. Using maximum-likelihood methods to fit time-dependent epidemiological models to the data we obtain estimates for the rates of immigration and transmission of E. coli O157 infection - parameters which have not been previously quantified in the literature. A comparison of alternative model fits reveals that the variation in the prevalence data is best explained when a proportion of the cattle are assumed to transmit infection at much higher levels than the rest - the so-called super-shedders. Analysis of a second dataset, comprising samples taken from 32 farms at monthly intervals over a period of 1 year, additionally yields an estimate for the rate of recovery from infection. The pattern of prevalence displayed in the second dataset also strongly supports the super-shedder hypothesis.

Factors influencing the shedding of verocytotoxin-producing Escherichia coli O157 by beef suckler cows.

A study was designed to investigate management factors that might influence the shedding of verocytotoxin-producing Escherichia coli (VTEC) O157 by beef cows in Scotland, where there is a particularly high rate of human infection. Thirty-two herds were visited at least monthly over approximately 1 year for collection of fresh faecal pat samples and information on management factors. The faecal pat samples were tested for VTEC O157 by established culture and immunomagnetic separation methods. Questionnaires were completed at the monthly visits to record management factors. Data were analysed using both univariate and multi-factor (GLMM) analysis. Changes in the number of cows in a group, dogs, wild geese, housing, and the feeding of draff (distillers' grains) were statistically significant as risk factors. The event of calving appeared to reduce the likelihood of shedding. Any effects of weaning or turnout were not statistically significant. It appears that the rate of shedding of VTEC O157 is influenced by several factors but possibly the most important of these are the circumstances of animals being housed, or, when outside, the presence of wild geese.