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1.  Spatial multi-criteria decision analysis to predict suitability for African swine fever endemicity in Africa 
Background
African swine fever (ASF) is endemic in several countries of Africa and may pose a risk to all pig producing areas on the continent. Official ASF reporting is often rare and there remains limited awareness of the continent-wide distribution of the disease.
In the absence of accurate ASF outbreak data and few quantitative studies on the epidemiology of the disease in Africa, we used spatial multi-criteria decision analysis (MCDA) to derive predictions of the continental distribution of suitability for ASF persistence in domestic pig populations as part of sylvatic or domestic transmission cycles. In order to incorporate the uncertainty in the relative importance of different criteria in defining suitability, we modelled decisions within the MCDA framework using a stochastic approach. The predictive performance of suitability estimates was assessed via a partial ROC analysis using ASF outbreak data reported to the OIE since 2005.
Results
Outputs from the spatial MCDA indicate that large areas of sub-Saharan Africa may be suitable for ASF persistence as part of either domestic or sylvatic transmission cycles. Areas with high suitability for pig to pig transmission (‘domestic cycles’) were estimated to occur throughout sub-Saharan Africa, whilst areas with high suitability for introduction from wildlife reservoirs (‘sylvatic cycles’) were found predominantly in East, Central and Southern Africa. Based on average AUC ratios from the partial ROC analysis, the predictive ability of suitability estimates for domestic cycles alone was considerably higher than suitability estimates for sylvatic cycles alone, or domestic and sylvatic cycles in combination.
Conclusions
This study provides the first standardised estimates of the distribution of suitability for ASF transmission associated with domestic and sylvatic cycles in Africa. We provide further evidence for the utility of knowledge-driven risk mapping in animal health, particularly in data-sparse environments.
doi:10.1186/1746-6148-10-9
PMCID: PMC3918235  PMID: 24406022
African swine fever; Knowledge-driven risk mapping; Multi-criteria decision analysis
2.  The incidence of feline injection site sarcomas in the United Kingdom 
Background
Feline injection site sarcomas (FISS) are aggressive neoplasms that have been associated with vaccination. In North America the incidence estimates have varied from 1 case of FISS per 1,000-10,000 cats vaccinated. The aim of this study was to estimate the incidence of FISS in the United Kingdom (UK) in 2007. The ratio of FISS to vaccines sold in the UK was also estimated.
Fourteen FISS were diagnosed by a convenience sample of 34 small animal veterinary practices in the United Kingdom in 2007 and were used as the numerator for the incidence estimates. Denominator data was obtained from the computer systems of each practice. Considering that a single cause relationship with vaccination is not proven, three different denominators (number of cats registered, the number of cat consultations undertaken and the number of vaccination visits for cats at the practices) were used to express the potential variation in risk.
Results
The incidence risk of FISS per year was estimated to be 1/16,000 -50,000 cats registered by practices, 1/10,000-20,000 cat consultations and 1/5,000-12,500 vaccination visits.
Conclusion
When interpreting these findings, it needs to be taken into consideration that this sample of practices and their cats may not be representative of veterinary practices and cats at risk of FISS in the UK. However it can still be concluded with reasonable certainty that the incidence of FISS in the UK is very low.
doi:10.1186/1746-6148-9-17
PMCID: PMC3608079  PMID: 23339769
Feline injection site sarcomas; Incidence; Risk
3.  BPEX Pig Health Scheme: a useful monitoring system for respiratory disease control in pig farms? 
Background
Respiratory diseases account for significant economic losses to the UK pig industry. Lesions indicative of respiratory disease in pig lungs at slaughter e.g. pneumonia and pleuritis are frequently recorded to assess herd health or provide data for epidemiological studies. The BPEX Pig Health Scheme (BPHS) is a monitoring system, which informs producers of gross lesions in their pigs' carcasses at slaughter, enabling farm-level decisions to be made. The aim of the study was to assess whether information provided by the BPHS regarding respiratory lesions was associated with respiratory pathogens in the farm, farm management practices and each other.
Results
BPHS reports were obtained from a subset of 70 pig farms involved in a cross-sectional study conducted in 2008-09 investigating the epidemiology of post-weaning multi-systemic wasting syndrome. The reports were combined with data regarding the presence/absence of several pathogens in the herd and potential farm-level risk factors for respiratory disease. Principal component analysis (PCA) performed on BPHS reports generated three principal components, explaining 71% of the total variance. Enzootic pneumonia score, severe pleurisy and acute pleuropneumonia had the highest loadings for the principal component which explained the largest percentage of the total variance (35%) (BPHS component 1), it was thought that this component identifies farms with acute disease. Using the factor loadings a score for each farm for BPHS component 1 was obtained. As farms' score for BPHS component 1 increased, average carcass weight at slaughter decreased. In addition, farms positive for H1N2 and porcine reproductive and respiratory disease virus (PRRSV) were more likely to have higher levels of severe and mild pleurisy reported by the BPHS, respectively.
Conclusions
The study found statistical associations between levels of pleurisy recorded by BPHS at slaughter and the presence H1N2 and PRRSV in the herd. There is also some evidence that farms which submit pigs with these lesions may have reduced productivity. However, more research is needed to fully validate the scheme.
doi:10.1186/1746-6148-7-82
PMCID: PMC3285094  PMID: 22208847
4.  Evaluating the control of HPAIV H5N1 in Vietnam: virus transmission within infected flocks reported before and after vaccination 
Background
Currently, the highly pathogenic avian influenza virus (HPAIV) of the subtype H5N1 is believed to have reached an endemic cycle in Vietnam. We used routine surveillance data on HPAIV H5N1 poultry outbreaks in Vietnam to estimate and compare the within-flock reproductive number of infection (R0) for periods before (second epidemic wave, 2004-5; depopulation-based disease control) and during (fourth epidemic wave, beginning 2007; vaccination-based disease control) vaccination.
Results
Our results show that infected premises (IPs) in the initial (exponential) phases of outbreak periods have the highest R0 estimates. The IPs reported during the outbreak period when depopulation-based disease control was implemented had higher R0 estimates than IPs reported during the outbreak period when vaccination-based disease control was used. In the latter period, in some flocks of a defined size and species composition, within-flock transmission estimates were not significantly below the threshold for transmission (R0 < 1).
Conclusions
Our results indicate that the current control policy based on depopulation plus vaccination has protected the majority of poultry flocks against infection. However, in some flocks the determinants associated with suboptimal protection need to be further investigated as these may explain the current pattern of infection in animal and human populations.
doi:10.1186/1746-6148-6-31
PMCID: PMC2898779  PMID: 20525380
5.  Risk mapping of Rinderpest sero-prevalence in Central and Southern Somalia based on spatial and network risk factors 
Background
In contrast to most pastoral systems, the Somali livestock production system is oriented towards domestic trade and export with seasonal movement patterns of herds/flocks in search of water and pasture and towards export points. Data from a rinderpest survey and other data sources have been integrated to explore the topology of a contact network of cattle herds based on a spatial proximity criterion and other attributes related to cattle herd dynamics. The objective of the study is to integrate spatial mobility and other attributes with GIS and network approaches in order to develop a predictive spatial model of presence of rinderpest.
Results
A spatial logistic regression model was fitted using data for 562 point locations. It includes three statistically significant continuous-scale variables that increase the risk of rinderpest: home range radius, herd density and clustering coefficient of the node of the network whose link was established if the sum of the home ranges of every pair of nodes was equal or greater than the shortest distance between the points. The sensitivity of the model is 85.1% and the specificity 84.6%, correctly classifying 84.7% of the observations. The spatial autocorrelation not accounted for by the model is negligible and visual assessment of a semivariogram of the residuals indicated that there was no undue amount of spatial autocorrelation. The predictive model was applied to a set of 6176 point locations covering the study area. Areas at high risk of having serological evidence of rinderpest are located mainly in the coastal districts of Lower and Middle Juba, the coastal area of Lower Shabele and in the regions of Middle Shabele and Bay. There are also isolated spots of high risk along the border with Kenya and the southern area of the border with Ethiopia.
Conclusions
The identification of point locations and areas with high risk of presence of rinderpest and their spatial visualization as a risk map will be useful for informing the prioritization of disease surveillance and control activities for rinderpest in Somalia. The methodology applied here, involving spatial and network parameters, could also be applied to other diseases and/or species as part of a standardized approach for the design of risk-based surveillance activities in nomadic pastoral settings.
doi:10.1186/1746-6148-6-22
PMCID: PMC2873515  PMID: 20426843
6.  Associations between attributes of live poultry trade and HPAI H5N1 outbreaks: a descriptive and network analysis study in northern Vietnam 
Background
The structure of contact between individuals plays an important role in the incursion and spread of contagious diseases in both human and animal populations. In the case of avian influenza, the movement of live birds is a well known risk factor for the geographic dissemination of the virus among poultry flocks. Live bird markets (LBM's) contribute to the epidemiology of avian influenza due to their demographic characteristics and the presence of HPAI H5N1 virus lineages. The relationship between poultry producers and live poultry traders (LPT's) that operate in LBM's has not been adequately documented in HPAI H5N1-affected SE Asian countries. The aims of this study were to document and study the flow of live poultry in a poultry trade network in northern Vietnam, and explore its potential role in the risk for HPAI H5N1 during 2003 to 2006.
Results
Our results indicate that LPT's trading for less than a year and operating at retail markets are more likely to source poultry from flocks located in communes with a past history of HPAI H5N1 outbreaks during 2003 to 2006 than LPT's trading longer than a year and operating at wholesale markets. The results of the network analysis indicate that LPT's tend to link communes of similar infection status.
Conclusions
Our study provides evidence which can be used for informing policies aimed at encouraging more biosecure practices of LPT's operating at authorised LBM's. The results suggest that LPT's play a role in HPAI H5N1 transmission and may contribute to perpetuating HPAI H5N1 virus circulation amongst certain groups of communes. The impact of current disease prevention and control interventions could be enhanced by disseminating information about outbreak risk and the implementation of a formal data recording scheme at LBM's for all incoming and outgoing LPT's.
doi:10.1186/1746-6148-6-10
PMCID: PMC2837645  PMID: 20175881
7.  Peste des Petits Ruminants (PPR) in Ethiopia: Analysis of a national serological survey 
Background
Peste des petits ruminants (PPR) is a contagious viral disease of small ruminants in Africa and Asia. In 1999, probably the largest survey on PPR ever conducted in Africa was initiated in Ethiopia where 13 651 serum samples from 7 out of the 11 regions were collected and analyzed by competitive enzyme-linked immunosorbent assay (cELISA). The objective of this paper is to present the results of this survey and discuss their practical implications for PPR-endemic regions.
Methods
We explored the spatial distribution of PPR in Ethiopia and we investigated risk factors for positive serological status. Intracluster correlation coefficients (ρ), were calculated for 43 wereda (administrative units).
Results
Seroprevalence was very heterogeneous across regions and even more across wereda, with prevalence estimates ranging from 0% to 52.5%. Two groups of weredas could be distinguished on the basis of the estimated ρ: a group with very low ρ (ρ < 0.12) and a group with very high ρ (ρ > 0.37).
Conclusion
The results indicate that PPRV circulation has been very heterogeneous, the values for the ρ may reflect the endemic or epidemic presence of the virus or the various degrees of mixing of animals in the different areas and production systems. Age appears as a risk factor for seropositive status, the linear effect seeming to confirm in the field that PPRV is highly immunogenic. Our estimates of intracluster correlation may prove useful in the design of serosurveys in other countries where PPR is of importance.
doi:10.1186/1746-6148-4-34
PMCID: PMC2561016  PMID: 18786275
8.  Use of data mining techniques to investigate disease risk classification as a proxy for compromised biosecurity of cattle herds in Wales 
Background
Biosecurity is at the forefront of the fight against infectious diseases in animal populations. Few research studies have attempted to identify and quantify the effectiveness of biosecurity against disease introduction or presence in cattle farms and, when done, they have relied on the collection of on-farm data. Data on environmental, animal movement, demographic/husbandry systems and density disease determinants can be collated without requiring additional specific on-farm data collection activities, since they have already been collected for some other purposes. The aim of this study was to classify cattle herds according to their risk of disease presence as a proxy for compromised biosecurity in the cattle population of Wales in 2004 for risk-based surveillance purposes.
Results
Three data mining methods have been applied: logistic regression, classification trees and factor analysis. Using the cattle holding population in Wales, a holding was considered positive if at least bovine TB or one of the ten most frequently diagnosed infectious or transmissible non-notifiable diseases in England and Wales, according to the Veterinary Investigation Surveillance Report (VIDA) had been diagnosed in 2004. High-risk holdings can be described as open large cattle herds located in high-density cattle areas with frequent movements off to many locations within Wales. Additional risks are associated with the holding being a dairy enterprise and with a large farming area.
Conclusion
This work has demonstrated the potential of mining various livestock-relevant databases to obtain generic criteria for individual cattle herd biosecurity risk classification. Despite the data and analytical constraints the described risk profiles are highly specific and present variable sensitivity depending on the model specifications. Risk profiling of farms provides a tool for designing targeted surveillance activities for endemic or emerging diseases, regardless of the prior amount of information available on biosecurity at farm level. As the delivery of practical evidence-based information and advice is one of the priorities of Defra's new Animal Health and Welfare Strategy (AHWS), data-driven models, derived from existing databases, need to be developed that can then be used to inform activities during outbreaks of endemic diseases and to help design surveillance activities.
doi:10.1186/1746-6148-4-24
PMCID: PMC2488331  PMID: 18601728

Results 1-8 (8)