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1.  Defining syndromes using cattle meat inspection data for syndromic surveillance purposes: a statistical approach with the 2005–2010 data from ten French slaughterhouses 
Background
The slaughterhouse is a central processing point for food animals and thus a source of both demographic data (age, breed, sex) and health-related data (reason for condemnation and condemned portions) that are not available through other sources. Using these data for syndromic surveillance is therefore tempting. However many possible reasons for condemnation and condemned portions exist, making the definition of relevant syndromes challenging.
The objective of this study was to determine a typology of cattle with at least one portion of the carcass condemned in order to define syndromes. Multiple factor analysis (MFA) in combination with clustering methods was performed using both health-related data and demographic data.
Results
Analyses were performed on 381,186 cattle with at least one portion of the carcass condemned among the 1,937,917 cattle slaughtered in ten French abattoirs. Results of the MFA and clustering methods led to 12 clusters considered as stable according to year of slaughter and slaughterhouse. One cluster was specific to a disease of public health importance (cysticercosis). Two clusters were linked to the slaughtering process (fecal contamination of heart or lungs and deterioration lesions). Two clusters respectively characterized by chronic liver lesions and chronic peritonitis could be linked to diseases of economic importance to farmers. Three clusters could be linked respectively to reticulo-pericarditis, fatty liver syndrome and farmer’s lung syndrome, which are related to both diseases of economic importance to farmers and herd management issues. Three clusters respectively characterized by arthritis, myopathy and Dark Firm Dry (DFD) meat could notably be linked to animal welfare issues. Finally, one cluster, characterized by bronchopneumonia, could be linked to both animal health and herd management issues.
Conclusion
The statistical approach of combining multiple factor analysis with cluster analysis showed its relevance for the detection of syndromes using available large and complex slaughterhouse data. The advantages of this statistical approach are to i) define groups of reasons for condemnation based on meat inspection data, ii) help grouping reasons for condemnation among a list of various possible reasons for condemnation for which a consensus among experts could be difficult to reach, iii) assign each animal to a single syndrome which allows the detection of changes in trends of syndromes to detect unusual patterns in known diseases and emergence of new diseases.
doi:10.1186/1746-6148-9-88
PMCID: PMC3681570  PMID: 23628140
Syndromic surveillance; Animal health; Meat inspection; Slaughterhouses; Cattle
2.  Questionnaire-based survey on distribution and clinical incidence of canine babesiosis in France 
Background
The causative agent of canine babesiosis is the protozoan Babesia canis, transmitted by the tick Dermacentor reticulatus within France. While the parasite can be found everywhere in France however cases of infection are associated with distinct geographical foci. The aim of the study was to evaluate the clinical occurrence of canine babesiosis diagnosed in veterinary clinics in order to propose an updated map of the disease distribution in France.
Results
Questionnaires were sent via email to all canine veterinary clinics in continental France. Information collected included the number of babesiosis cases diagnosed in 2010, the number of veterinary practitioners and the location of the clinic. The total number of dogs and practitioners per administrative department were used to define the reference population. The annual incidence rate of canine babesiosis per department was calculated as the ratio between the number of babesiosis cases reported by the clinics and the total number of dogs in the clinics of the same department. Data were geo-referenced for map construction (Quantum GIS version 1.7.4). The overall annual incidence rate of clinical babesiosis among the surveyed population was 1.07% (CI95 1.05-1.09) with geographical variations between departments, ranging from 0.01% to 16.05%. Four enzootic areas were identified: South-West, Center, East and Paris area. The South-West region should be considered as a hyper-enzootic area with the higher incidence rates.
Conclusion
Our results confirmed the burden of canine babesiosis in France. In the context of tick-borne disease emergence in Europe, the risk for canine babesiosis may become more significant in other European countries in the coming years.
doi:10.1186/1746-6148-9-41
PMCID: PMC3599680  PMID: 23448544
Babesia canis; Canine babesiosis; Incidence rates; Geographic distribution; France
3.  Individual factors associated with L- and H-type Bovine Spongiform Encephalopathy in France 
Background
Cattle with L-type (L-BSE) and H-type (H-BSE) atypical Bovine Spongiform encephalopathy (BSE) were identified in 2003 in Italy and France respectively before being identified in other countries worldwide. As of December 2011, around 60 atypical BSE cases have currently been reported in 13 countries, with over one third in France. While the epidemiology of classical BSE (C-BSE) has been widely described, atypical BSEs are still poorly documented, but appear to differ from C-BSE. We analysed the epidemiological characteristics of the 12 cases of L-BSE and 11 cases of H-BSE detected in France from January 2001 to late 2009 and looked for individual risk factors. As L-BSE cases did not appear to be homogeneously distributed throughout the country, two complementary methods were used: spatial analysis and regression modelling. L-BSE and H-BSE were studied separately as both the biochemical properties of their pathological prion protein and their features differ in animal models.
Results
The median age at detection for L-BSE and H-BSE cases was 12.4 (range 8.4-18.7) and 12.5 (8.3-18.2) years respectively, with no significant difference between the two distributions. However, this median age differed significantly from that of classical BSE (7.0 (range 3.5-15.4) years). A significant geographical cluster was detected for L-BSE. Among animals over eight years of age, we showed that the risk of being detected as a L-BSE case increased with age at death. This was not the case for H-BSE.
Conclusion
To the best of our knowledge this is the first study to describe the epidemiology of the two types of atypical BSE. The geographical cluster detected for L-BSE could be partly due to the age structure of the background-tested bovine population. Our regression analyses, which adjusted for the effect of age and birth cohort showed an age effect for L-BSE and the descriptive analysis showed a particular age structure in the area where the cluster was detected. No birth cohort effect was evident. The relatively small number of cases of atypical BSE and the few individual data available for the tested population limited our analysis to the investigation of age and cohort effect only. We conclude that it is essential to maintain BSE surveillance to further elucidate our findings.
doi:10.1186/1746-6148-8-74
PMCID: PMC3514362  PMID: 22647660
Atypical bovine spongiform encephalopathy; L-BSE; H-BSE; Spatial analysis; Risk factors; France
4.  Comparison of strategies for substantiating freedom from scrapie in a sheep flock 
Background
The public health threat represented by a potential circulation of bovine spongiform encephalopathy agent in sheep population has led European animal health authorities to launch large screening and genetic selection programmes. If demonstrated, such a circulation would have dramatic economic consequences for sheep breeding sector. In this context, it is important to evaluate the feasibility of qualification procedures that would allow sheep breeders demonstrating their flock is free from scrapie. Classical approaches, based on surveys designed to detect disease presence, do not account for scrapie specificities: the genetic variations of susceptibility and the absence of live diagnostic test routinely available. Adapting these approaches leads to a paradoxical situation in which a greater amount of testing is needed to substantiate disease freedom in genetically resistant flocks than in susceptible flocks, whereas probability of disease freedom is a priori higher in the former than in the latter. The goal of this study was to propose, evaluate and compare several qualification strategies for demonstrating a flock is free from scrapie.
Results
A probabilistic framework was defined that accounts for scrapie specificities and allows solving the preceding paradox. Six qualification strategies were defined that combine genotyping data, diagnostic tests results and flock pedigree. These were compared in two types of simulated flocks: resistant and susceptible flocks. Two strategies allowed demonstrating disease freedom in several years, for the majority of simulated flocks: a strategy in which all the flock animals are genotyped, and a strategy in which only founders animals are genotyped, the flock pedigree being known. In both cases, diagnostic tests are performed on culled animals. The less costly strategy varied according to the genetic context (resistant or susceptible) and to the relative costs of a genotyping exam and of a diagnostic test.
Conclusion
This work demonstrates that combining data sources allows substantiating a flock is free from scrapie within a reasonable time frame. Qualification schemes could thus be a useful tool for voluntary or mandatory scrapie control programmes. However, there is no general strategy that would always minimize the costs and choice of the strategy should be adapted to local genetic conditions.
doi:10.1186/1746-6148-5-16
PMCID: PMC2697144  PMID: 19405956

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