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1.  Not all cows are epidemiologically equal: quantifying the risks of bovine viral diarrhoea virus (BVDV) transmission through cattle movements 
Veterinary Research  2014;45(1):110.
Many economically important cattle diseases spread between herds through livestock movements. Traditionally, most transmission models have assumed that all purchased cattle carry the same risk of generating outbreaks in the destination herd. Using data on bovine viral diarrhoea virus (BVDV) in Scotland as a case example, this study provides empirical and theoretical evidence that the risk of disease transmission varies substantially based on the animal and herd demographic characteristics at the time of purchase. Multivariable logistic regression analysis revealed that purchasing pregnant heifers and open cows sold with a calf at foot were associated with an increased risk of beef herds being seropositive for BVDV. Based on the results from a dynamic within-herd simulation model, these findings may be partly explained by the age-related probability of animals being persistently infected with BVDV as well as the herd demographic structure at the time of animal introductions. There was also evidence that an epidemiologically important network statistic, “betweenness centrality” (a measure frequently associated with the potential for herds to acquire and transmit disease), was significantly higher for herds that supplied these particular types of replacement beef cattle. The trends for dairy herds were not as clear, although there was some evidence that open heifers and open lactating cows were associated with an increased risk of BVDV. Overall, these findings have important implications for developing simulation models that more accurately reflect the industry-level transmission dynamics of infectious cattle diseases.
doi:10.1186/s13567-014-0110-y
PMCID: PMC4206702  PMID: 25323831
2.  How commercial and non-commercial swine producers move pigs in Scotland: a detailed descriptive analysis 
BMC Veterinary Research  2014;10:140.
Background
The impact of non-commercial producers on disease spread via livestock movement is related to their level of interaction with other commercial actors within the industry. Although understanding these relationships is crucial in order to identify likely routes of disease incursion and transmission prior to disease detection, there has been little research in this area due to the difficulties of capturing movements of small producers with sufficient resolution. Here, we used the Scottish Livestock Electronic Identification and Traceability (ScotEID) database to describe the movement patterns of different pig production systems which may affect the risk of disease spread within the swine industry. In particular, we focused on the role of small pig producers.
Results
Between January 2012 and May 2013, 23,169 batches of pigs were recorded moving animals between 2382 known unique premises. Although the majority of movements (61%) were to a slaughterhouse, the non-commercial and the commercial sectors of the Scottish swine industry coexist, with on- and off-movement of animals occurring relatively frequently. For instance, 13% and 4% of non-slaughter movements from professional producers were sent to a non-assured commercial producer or to a small producer, respectively; whereas 43% and 22% of movements from non-assured commercial farms were sent to a professional or a small producer, respectively. We further identified differences between producer types in several animal movement characteristics which are known to increase the risk of disease spread. Particularly, the distance travelled and the use of haulage were found to be significantly different between producers.
Conclusions
These results showed that commercial producers are not isolated from the non-commercial sector of the Scottish swine industry and may frequently interact, either directly or indirectly. The observed patterns in the frequency of movements, the type of producers involved, the distance travelled and the use of haulage companies provide insights into the structure of the Scottish swine industry, but also highlight different features that may increase the risk of infectious diseases spread in both Scotland and the UK. Such knowledge is critical for developing more robust biosecurity and surveillance plans and better preparing Scotland against incursions of emerging swine diseases.
doi:10.1186/1746-6148-10-140
PMCID: PMC4082416  PMID: 24965915
Livestock movement; Risk of infection; Pig; Contingency planning
3.  E. coli O157 on Scottish cattle farms: Evidence of local spread and persistence using repeat cross-sectional data 
Background
Escherichia coli (E. coli) O157 is a virulent zoonotic strain of enterohaemorrhagic E. coli. In Scotland (1998-2008) the annual reported rate of human infection is 4.4 per 100,000 population which is consistently higher than other regions of the UK and abroad. Cattle are the primary reservoir. Thus understanding infection dynamics in cattle is paramount to reducing human infections.
A large database was created for farms sampled in two cross-sectional surveys carried out in Scotland (1998 - 2004). A statistical model was generated to identify risk factors for the presence of E. coli O157 on farms. Specific hypotheses were tested regarding the presence of E. coli O157 on local farms and the farms previous status. Pulsed-field gel electrophoresis (PFGE) profiles were further examined to ascertain whether local spread or persistence of strains could be inferred.
Results
The presence of an E. coli O157 positive local farm (average distance: 5.96km) in the Highlands, North East and South West, farm size and the number of cattle moved onto the farm 8 weeks prior to sampling were significant risk factors for the presence of E. coli O157 on farms. Previous status of a farm was not a significant predictor of current status (p = 0.398). Farms within the same sampling cluster were significantly more likely to be the same PFGE type (p < 0.001), implicating spread of strains between local farms. Isolates with identical PFGE types were observed to persist across the two surveys, including 3 that were identified on the same farm, suggesting an environmental reservoir. PFGE types that were persistent were more likely to have been observed in human clinical infections in Scotland (p < 0.001) from the same time frame.
Conclusions
The results of this study demonstrate the spread of E. coli O157 between local farms and highlight the potential link between persistent cattle strains and human clinical infections in Scotland. This novel insight into the epidemiology of Scottish E. coli O157 paves the way for future research into the mechanisms of transmission which should help with the design of control measures to reduce E. coli O157 from livestock-related sources.
doi:10.1186/1746-6148-10-95
PMCID: PMC4022360  PMID: 24766709
E. coli O157; Epidemiology; Risk factor; Transmission; Persistence; PFGE
4.  Systems Approaches to Animal Disease Surveillance and Resource Allocation: Methodological Frameworks for Behavioral Analysis 
PLoS ONE  2013;8(11):e82019.
While demands for animal disease surveillance systems are growing, there has been little applied research that has examined the interactions between resource allocation, cost-effectiveness, and behavioral considerations of actors throughout the livestock supply chain in a surveillance system context. These interactions are important as feedbacks between surveillance decisions and disease evolution may be modulated by their contextual drivers, influencing the cost-effectiveness of a given surveillance system. This paper identifies a number of key behavioral aspects involved in animal health surveillance systems and reviews some novel methodologies for their analysis. A generic framework for analysis is discussed, with exemplar results provided to demonstrate the utility of such an approach in guiding better disease control and surveillance decisions.
doi:10.1371/journal.pone.0082019
PMCID: PMC3857842  PMID: 24348922
5.  Vaccination against Foot-And-Mouth Disease: Do Initial Conditions Affect Its Benefit? 
PLoS ONE  2013;8(10):e77616.
When facing incursion of a major livestock infectious disease, the decision to implement a vaccination programme is made at the national level. To make this decision, governments must consider whether the benefits of vaccination are sufficient to outweigh potential additional costs, including further trade restrictions that may be imposed due to the implementation of vaccination. However, little consensus exists on the factors triggering its implementation on the field. This work explores the effect of several triggers in the implementation of a reactive vaccination-to-live policy when facing epidemics of foot-and-mouth disease. In particular, we tested whether changes in the location of the incursion and the delay of implementation would affect the epidemiological benefit of such a policy in the context of Scotland. To reach this goal, we used a spatial, premises-based model that has been extensively used to investigate the effectiveness of mitigation procedures in Great Britain. The results show that the decision to vaccinate, or not, is not straightforward and strongly depends on the underlying local structure of the population-at-risk. With regards to disease incursion preparedness, simply identifying areas of highest population density may not capture all complexities that may influence the spread of disease as well as the benefit of implementing vaccination. However, if a decision to vaccinate is made, we show that delaying its implementation in the field may markedly reduce its benefit. This work provides guidelines to support policy makers in their decision to implement, or not, a vaccination-to-live policy when facing epidemics of infectious livestock disease.
doi:10.1371/journal.pone.0077616
PMCID: PMC3815046  PMID: 24204895
6.  Identifying associations between pig pathologies using a multi-dimensional machine learning methodology 
Background
Abattoir detected pathologies are of crucial importance to both pig production and food safety. Usually, more than one pathology coexist in a pig herd although it often remains unknown how these different pathologies interrelate to each other. Identification of the associations between different pathologies may facilitate an improved understanding of their underlying biological linkage, and support the veterinarians in encouraging control strategies aimed at reducing the prevalence of not just one, but two or more conditions simultaneously.
Results
Multi-dimensional machine learning methodology was used to identify associations between ten typical pathologies in 6485 batches of slaughtered finishing pigs, assisting the comprehension of their biological association. Pathologies potentially associated with septicaemia (e.g. pericarditis, peritonitis) appear interrelated, suggesting on-going bacterial challenges by pathogens such as Haemophilus parasuis and Streptococcus suis. Furthermore, hepatic scarring appears interrelated with both milk spot livers (Ascaris suum) and bacteria-related pathologies, suggesting a potential multi-pathogen nature for this pathology.
Conclusions
The application of novel multi-dimensional machine learning methodology provided new insights into how typical pig pathologies are potentially interrelated at batch level. The methodology presented is a powerful exploratory tool to generate hypotheses, applicable to a wide range of studies in veterinary research.
doi:10.1186/1746-6148-8-151
PMCID: PMC3483212  PMID: 22937883
7.  Predicted costs and benefits of eradicating BVDV from Ireland 
Irish Veterinary Journal  2012;65(1):12.
Bovine viral diarrhoea virus (BVDV) causes an economically important endemic disease (BVD) of cattle in Ireland and worldwide. Systematic eradication by detection and removal of infectious (BVDV carrier) cattle has been successful in several regions. We therefore assessed the benefits (disease losses avoided) and costs (testing and culling regime) of a potential eradication programme in Ireland. Published bio-economic models of BVDV spread in beef suckler herds and dairy herds were adapted to estimate potential benefits of eradication in Ireland. A simple model of BVDV spread in beef finisher herds was devised to estimate the benefits of eradication in this sector. A six year eradication programme consisting of 5 inter-related virological and serological testing programmes is outlined and costed. We found that the annualised benefits of BVDV eradication in Ireland exceeded the costs by a factor of 5 in the beef suckler sector and a factor of 14 in the dairy sector. Corresponding payback periods were 1.2 and 0.5 years respectively. These results highlight the significant economic impact of BVDV on the Irish cattle industry and suggest a clear economic benefit to eradication using the proposed approach. This type of cost-benefit analysis is considered an essential prerequisite prior to undertaking an eradication campaign of this magnitude.
doi:10.1186/2046-0481-65-12
PMCID: PMC3443014  PMID: 22748235
BVDV; Eradication; Cost benefit analysis
8.  Temporal and spatial patterns of bovine Escherichia coli O157 prevalence and comparison of temporal changes in the patterns of phage types associated with bovine shedding and human E. coli O157 cases in Scotland between 1998-2000 and 2002-2004 
BMC Microbiology  2009;9:276.
Background
Escherichia coli O157 is an important cause of acute diarrhoea, haemorrhagic colitis and, especially in children, haemolytic uraemic syndrome (HUS). Incidence rates for human E. coli O157 infection in Scotland are higher than most other United Kingdom, European and North American countries. Cattle are considered the main reservoir for E. coli O157. Significant associations between livestock related exposures and human infection have been identified in a number of studies.
Results
Animal Studies: There were no statistically significant differences (P = 0.831) in the mean farm-level prevalence between the two studies (SEERAD: 0.218 (95%CI: 0.141-0.32); IPRAVE: 0.205 (95%CI: 0.135-0.296)). However, the mean pat-level prevalence decreased from 0.089 (95%CI: 0.075-0.105) to 0.040 (95%CI: 0.028-0.053) between the SEERAD and IPRAVE studies respectively (P < 0.001). Highly significant (P < 0.001) reductions in mean pat-level prevalence were also observed in the spring, in the North East and Central Scotland, and in the shedding of phage type (PT) 21/28. Human Cases: Contrasting the same time periods, there was a decline in the overall comparative annual reported incidence of human cases as well as in all the major PT groups except 'Other' PTs. For both cattle and humans, the predominant phage type between 1998 and 2004 was PT21/28 comprising over 50% of the positive cattle isolates and reported human cases respectively. The proportion of PT32, however, was represented by few (<5%) of reported human cases despite comprising over 10% of cattle isolates. Across the two studies there were differences in the proportion of PTs 21/28, 32 and 'Other' PTs in both cattle isolates and reported human cases; however, only differences in the cattle isolates were statistically significant (P = 0.002).
Conclusion
There was no significant decrease in the mean farm-level prevalence of E. coli O157 between 1998 and 2004 in Scotland, despite significant declines in mean pat-level prevalence. Although there were declines in the number of human cases between the two study periods, there is no statistically significant evidence that the overall rate (per 100,000 population) of human E. coli O157 infections in Scotland over the last 10 years has altered. Comparable patterns in the distribution of PTs 21/28 and 32 between cattle and humans support a hypothesized link between the bovine reservoir and human infections. This emphasizes the need to apply and improve methods to reduce bovine shedding of E. coli O157 in Scotland where rates appear higher in both cattle and human populations, than in other countries.
doi:10.1186/1471-2180-9-276
PMCID: PMC2808314  PMID: 20040112
9.  Bayesian inference for within-herd prevalence of Leptospira interrogans serovar Hardjo using bulk milk antibody testing 
Biostatistics (Oxford, England)  2009;10(4):719-728.
Leptospirosis is the most widespread zoonosis throughout the world and human mortality from severe disease forms is high even when optimal treatment is provided. Leptospirosis is also one of the most common causes of reproductive losses in cattle worldwide and is associated with significant economic costs to the dairy farming industry. Herds are tested for exposure to the causal organism either through serum testing of individual animals or through testing bulk milk samples. Using serum results from a commonly used enzyme-linked immunosorbent assay (ELISA) test for Leptospira interrogans serovar Hardjo (L. hardjo) on samples from 979 animals across 12 Scottish dairy herds and the corresponding bulk milk results, we develop a model that predicts the mean proportion of exposed animals in a herd conditional on the bulk milk test result. The data are analyzed through use of a Bayesian latent variable generalized linear mixed model to provide estimates of the true (but unobserved) level of exposure to the causal organism in each herd in addition to estimates of the accuracy of the serum ELISA. We estimate 95% confidence intervals for the accuracy of the serum ELISA of (0.688, 0.987) and (0.975, 0.998) for test sensitivity and specificity, respectively. Using a percentage positivity cutoff in bulk milk of at most 41% ensures that there is at least a 97.5% probability of less than 5% of the herd being exposed to L. hardjo. Our analyses provide strong statistical evidence in support of the validity of interpreting bulk milk samples as a proxy for individual animal serum testing. The combination of validity and cost-effectiveness of bulk milk testing has the potential to reduce the risk of human exposure to leptospirosis in addition to offering significant economic benefits to the dairy industry.
doi:10.1093/biostatistics/kxp026
PMCID: PMC2742498  PMID: 19628639
Bayesian; Latent class analysis; Leptospirosis
10.  Herd-level risk factors associated with the presence of Phage type 21/28 E. coli O157 on Scottish cattle farms 
BMC Microbiology  2006;6:99.
Background
E. coli O157 is a bacterial pathogen that is shed by cattle and can cause severe disease in humans. Phage type (PT) 21/28 is a subtype of E. coli O157 that is found across Scotland and is associated with particularly severe human morbidity.
Methods
A cross-sectional survey of Scottish cattle farms was conducted in the period Feb 2002-Feb 2004 to determine the prevalence of E. coli O157 in cattle herds. Data from 88 farms on which E. coli O157 was present were analysed using generalised linear mixed models to identify risk factors for the presence of PT 21/28 specifically.
Results
The analysis identified private water supply, and northerly farm location as risk factors for PT 21/28 presence. There was a significant association between the presence of PT 21/28 and an increased number of E. coli O157 positive pat samples from a farm, and PT 21/28 was significantly associated with larger E. coli O157 counts than non-PT 21/28 E. coli O157.
Conclusion
PT 21/28 has significant risk factors that distinguish it from other phage types of E. coli O157. This finding has implications for the control of E. coli O157 as a whole and suggests that control could be tailored to target the locally dominant PT.
doi:10.1186/1471-2180-6-99
PMCID: PMC1713242  PMID: 17140453
11.  Analysis of Feces Samples Collected from a Wild-Bird Garden Feeding Station in Scotland for the Presence of Verocytotoxin-Producing Escherichia coli O157 
Composite wild bird feces collected at regular intervals from a garden feeding station in southwest Scotland over a 3-year period were examined for verocytotoxin-producing Escherichia coli O157. One sample was positive for Escherichia coli O157. The isolate belonged to phage type 21/28 and possessed vtx2, eaeA, and enterohemorrhagic E. coli hlyA genes.
doi:10.1128/AEM.72.3.2265-2267.2006
PMCID: PMC1393181  PMID: 16517685
12.  Molecular Epidemiology of Antimicrobial-Resistant Commensal Escherichia coli Strains in a Cohort of Newborn Calves 
Applied and Environmental Microbiology  2005;71(11):6680-6688.
Pulsed-field gel electrophoresis (PFGE) was used to investigate the dissemination and diversity of ampicillin-resistant (Ampr) and nalidixic acid-resistant (Nalr) commensal Escherichia coli strains in a cohort of 48 newborn calves. Calves were sampled weekly from birth for up to 21 weeks and a single resistant isolate selected from positive samples for genotyping and further phenotypic characterization. The Ampr population showed the greatest diversity, with a total of 56 different genotype patterns identified, of which 5 predominated, while the Nalr population appeared to be largely clonal, with over 97% of isolates belonging to just two different PFGE patterns. Distinct temporal trends were identified in the distribution of several Ampr genotypes across the cohort, with certain patterns predominating at different points in the study. Cumulative recognition of new Ampr genotypes within the cohort was biphasic, with a turning point coinciding with the housing of the cohort midway through the study, suggesting that colonizing strains were from an environmental source on the farm. Multiply resistant isolates dominated the collection, with >95% of isolates showing resistance to at least two additional antimicrobials. Carriage of resistance to streptomycin, sulfamethoxazole, and tetracycline was the most common combination, found across several different genotypes, suggesting the possible spread of a common resistance element across multiple strains. The proportion of Ampr isolates carrying sulfamethoxazole resistance increased significantly over the study period (P < 0.05), coinciding with a decline in the most common genotype pattern. These data indicate that calves were colonized by a succession of multiply resistant strains, with a probable environmental source, that disseminated through the cohort over time.
doi:10.1128/AEM.71.11.6680-6688.2005
PMCID: PMC1287745  PMID: 16269697
13.  Age-Related Decline in Carriage of Ampicillin-Resistant Escherichia coli in Young Calves 
Applied and Environmental Microbiology  2004;70(11):6927-6930.
The presence of ampicillin-resistant Escherichia coli (Ampr E. coli) in the fecal flora of calves was monitored on a monthly basis in seven cohorts of calves. Calves were rapidly colonized by Ampr E. coli, with peak prevalence in cohort calves observed in the 4 months after the calves were born. The prevalence of calves yielding Ampr E. coli in cohorts consistently declined to low levels with increasing age of the calves (P < 0.001).
doi:10.1128/AEM.70.11.6927-6930.2004
PMCID: PMC525229  PMID: 15528566
14.  Distribution of the saa Gene in Strains of Shiga Toxin-Producing Escherichia coli of Human and Bovine Origins 
Journal of Clinical Microbiology  2003;41(4):1775-1778.
Certain strains of Shiga toxin-producing Escherichia coli (STEC) which do not have the locus of enterocyte effacement pathogenicity island carry the STEC autoagglutinating adhesin (saa) gene. The distribution of the saa gene in STEC isolates from patients with hemolytic-uremic syndrome (HUS), patients with less severe diarrheal disease, asymptomatic individuals, and healthy cattle was examined. saa-positive strains were detected more frequently (P < 0.001) in STEC strains from bovines (32 of 56 strains) than in those from humans (8 of 91 strains). No significant association (P = 0.135) was found between the saa gene and STEC isolated from patients with HUS (6 of 46 strains) or diarrhea (2 of 29 strains) and from healthy controls (0 of 16 strains).
doi:10.1128/JCM.41.4.1775-1778.2003
PMCID: PMC153935  PMID: 12682185
15.  Lymphoid Follicle-Dense Mucosa at the Terminal Rectum Is the Principal Site of Colonization of Enterohemorrhagic Escherichia coli O157:H7 in the Bovine Host  
Infection and Immunity  2003;71(3):1505-1512.
Escherichia coli O157:H7 causes bloody diarrhea and potentially fatal systemic sequelae in humans. Cattle are most frequently identified as the primary source of infection, and E. coli O157:H7 generally colonizes the gastrointestinal tracts of cattle without causing disease. In this study, persistence and tropism were assessed for four different E. coli O157:H7 strains. Experimentally infected calves shed the organism for at least 14 days prior to necropsy. For the majority of these animals, as well as for a naturally colonized animal obtained from a commercial beef farm, the highest numbers of E. coli O157:H7 were found in the feces, with negative or significantly lower levels detected in lumen contents taken from the gastrointestinal tract. Detailed examination demonstrated that in these individuals the majority of tissue-associated bacteria were adherent to mucosal epithelium within a defined region extending up to 5 cm proximally from the recto-anal junction. The tissue targeted by E. coli O157:H7 was characterized by a high density of lymphoid follicles. Microcolonies of the bacterium were readily detected on the epithelium of this region by immunofluorescence microscopy. As a consequence of this specific distribution, E. coli O157:H7 was present predominately on the surface of the fecal stool. In contrast, other E. coli serotypes were present at consistent levels throughout the large intestine and were equally distributed in the stool. This is a novel tropism that may enhance dissemination both between animals and from animals to humans. The accessibility of this site may facilitate simple intervention strategies.
doi:10.1128/IAI.71.3.1505-1512.2003
PMCID: PMC148874  PMID: 12595469

Results 1-15 (15)