Evaluation of a hierarchical ascendant clustering process implemented in a veterinary syndromic surveillance system.

Syndromic surveillance is considered as one of the surveillance components for early warning of health-related events, as it allows detection of aberrations in health indicators before laboratory confirmation. "MoSS-Emergences 2" (MoSS-E2), a tool for veterinary syndromic surveillance, aggregates groups of similar clinical observations by hierarchical ascendant classification (HAC). In the present study, this HAC clustering process was evaluated using a reference set of data that, for the purpose of this evaluation, was a priori divided and defined as Bluetongue (BTV) positive cases (PC) on the one hand and BTV negative cases (NC) on the other hand. By comparing the clustering result of MoSS-E2 with the expected outcome, the sensitivity (the ability to cluster PC together) and specificity (the ability to exclude NC from PC) of the clustering process were determined for this set of data. The stability of the classes obtained with the clustering algorithm was evaluated by comparing the MoSS-E2 generated dendrogram (applying complete linkage) with dendrograms of STATA® software applying average and single linkage methods. To assess the systems' robustness, the parameters of the distance measure were adjusted according to different scenarios and obtained outcomes were compared to the expected outcome based on the a priori known labels. Rand indexes were calculated to measure similarity between clustering outcomes. The clustering algorithm in its default settings successfully segregated the reference BTV cases from the non-BTV cases, resulting in a sensitivity of 100.0% (95% CI: 89.0-100.0) and a specificity of 100.0% (95% CI: 80.0-100.0) for this set of data. The different linkage methods showed similar clustering results indicating stability of the classes (Rand indexes of respectively 0.77 for average and 0.75 for single linkage). The system proved to be robust when changing the parameters as the BTV cases remained together in meaningful clusters (Rand indexes between 0.72 and 1). The configurable MoSS-E2 system demonstrated its suitability to identify meaningful clusters of clinical syndromes.

Reproducibility of local environmental factors for the abundance of questing Ixodes ricinus nymphs on pastures.

In ecology and epidemiology, exploratory field studies based on multivariate statistical models commonly are used to identify factors that are associated with a phenomenon. The challenge is to evaluate whether these factors are indeed correlated to the phenomenon or if the statistical significance results from fortuitous association or type 1 statistical error (probability of rejecting a null hypothesis when it is true). This is particularly the case when the phenomenon is linked to environmental factors that usually are more or less correlated to each other and when the phenomenon is itself highly variable. The abundance of Ixodes ricinus ticks, a major disease vector in Europe, is highly variable and depends on environmental conditions that define suitable habitat and host presence. Our objective was to identify reproducible factors in space and time that influenced the abundance of questing I. ricinus nymphs. We sampled questing nymphs in pastures in 4 settings, i.e. during 3 periods (2003, 2004, and 2006) in one region, and during one period (2006) in another region, both regions located in Central France. The same data collection, data selection, and model analysis using negative binomial distribution were applied independently in the 4 data sets to identify 'reproducible' factors, i.e. explanatory factors that were significant in different time periods and spaces. The 3 most reproducible factors suggested that woodland type vegetation and woodland vicinity constantly favoured nymph abundance on pastures. In addition, the presence of fruit trees was significantly associated with nymph abundance in one region. The other factors were not reproducible. The study confirmed the status of key factors for nymph abundance while avoiding having to redefine the statistical model to model the different sampling conditions. It also shows the difficulty to identify factors with general significance acting on a very variable phenomenon, based on a study made one year in one region. Relevant study design should consider appropriate repetitions based on the range of values of the studied factors. Furthermore, discussion of the results is essential to identify factors that have a general significance.

Ecological factors characterizing the prevalence of bacterial tick-borne pathogens in Ixodes ricinus ticks in pastures and woodlands.

Ecological changes are recognized as an important driver behind the emergence of infectious diseases. The prevalence of infection in ticks depends upon ecological factors that are rarely taken into account simultaneously. Our objective was to investigate the influences of forest fragmentation, vegetation, adult tick hosts, and habitat on the infection prevalence of three tick-borne bacteria, Borrelia burgdorferi sensu lato, Anaplasma phagocytophilum, and Rickettsia sp. of the spotted fever group, in questing Ixodes ricinus ticks, taking into account tick characteristics. Samples of questing nymphs and adults were taken from 61 pastures and neighboring woodlands in central France. The ticks were tested by PCR of pools of nymphs and individual adults. The individual infection prevalence was modeled using multivariate regression. The highest infection prevalences were found in adult females collected in woodland sites for B. burgdorferi sensu lato and A. phagocytophilum (16.1% and 10.7%, respectively) and in pasture sites for Rickettsia sp. (8.7%). The infection prevalence in nymphs was lower than 6%. B. burgdorferi sensu lato was more prevalent in woodlands than in pastures. Forest fragmentation favored B. burgdorferi sensu lato and A. phagocytophilum prevalence in woodlands, and in pastures, the B. burgdorferi sensu lato prevalence was favored by shrubby vegetation. Both results are probably because large amounts of edges or shrubs increase the abundance of small vertebrates as reservoir hosts. The Rickettsia sp. prevalence was maximal on pasture with medium forest fragmentation. Female ticks were more infected by B. burgdorferi sensu lato than males and nymphs in woodland sites, which suggests an interaction between the ticks and the bacteria. This study confirms the complexity of the tick-borne pathogen ecology. The findings support the importance of small vertebrates as reservoir hosts and make a case for further studies in Europe on the link between the composition of the reservoir host community and the infection prevalence in ticks.

A nation-wide epidemiological study of acute bovine respiratory disease in France.

Acute bovine respiratory disease (ABRD) is a respiratory syndrome caused by various infectious agents, and represents a major economic and health problem in cattle herds worldwide. The aim of the study was to present how we can describe the epidemiological characteristics of ABRD in France, including risk factor analysis and spatio-temporal pattern investigation. The data were collected by specialized surveyors during the 2001 animal survey conducted by the French Ministry for Agriculture and Fisheries, from a representative sample of cattle herds. The health questionnaire concerned farm characteristics, practice of BRD vaccination, presence of ABRD, time of occurrence and number of affected animals for the period November 2000-October 2001. After a descriptive analysis of the syndrome, a space-time scan statistic was performed to detect potential clusters, and a logistic regression model was used for analysis of risk factors. The study sample included 16,581 cattle herds as representative of the 260,000 French herds. The ABRD cumulative incidence at farm level was 9.8%, the cumulative incidence at animal level was 2.1%, the cumulative mortality 0.1% and the lethality proportion 6.5%. ABRD occurred mainly during cold months with an epidemic peak in December. Spatial repartition of the syndrome showed that the whole territory was affected, with a higher number of cases in the north-east region, the main bovine production area in France. Three space-time clusters were identified in the period November 2000-February 2001. ABRD was significantly associated with production type, herd size, and BRD vaccination. Beef herds were less affected than dairy herds, and increased herd size increased the risk of ABRD. The outbreak was clustered in space and time, suggesting a common infectious agent for the epidemic in the detected areas. The influence of production type and herd size on syndrome occurrence highlighted the importance of management practices, human movement and animal density.

The relationships between Ixodes ricinus and small mammal species at the woodland-pasture interface.

Ixodes ricinus, as vector, and small mammals, as reservoirs, are implicated in pathogen transmission between wild fauna, domestic animals and humans at the woodland-pasture interface. The ecological relationship between ticks and small mammals was monitored in 2005 on four bocage (enclosed pastureland) sites in central France, where questing ticks were collected by dragging and small mammals were trapped. Questing I. ricinus tick and small mammal locations in the environment were assessed through correspondence analysis. I. ricinus larval burden on small mammals was modeled using a negative binomial law. The correspondence analyses underlined three landscape features: grassland, hedgerow, and woodland. Seven small mammal species were trapped, while questing ticks were all I. ricinus, with the highest abundance in woodland and the lowest in pasture. The small mammals were overall more abundant in hedgerow, less present in woodland and sparse in grassland. They carried mainly I. ricinus, and secondarily I. acuminatus and I. trianguliceps. The most likely profile for a tick-infested small mammal corresponded to a male wood mouse (Apodemus sylvaticus) in woodland or hedgerow during a dry day. A. sylvaticus, which was the only species captured in grassland, but was also present in hedgerow and woodland, may be a primary means of transfer of I. ricinus larvae from woodland to pasture.

Mammal and bird species distribution at the woodland-pasture interface in relation to the circulation of ticks and pathogens.

The tick vector Ixodes ricinus can be found in pastures in landscapes where pasture and woodland intermix, such as in the bocage. To identify which mammal or bird species could potentially transport ticks between woodland and pasture, we did a species inventory on four French bocage sites in 2005. Fifty-eight species were observed, 21 of which were found in three different habitats: the middle of the pasture, the hedgerow ecotone, and the woodland. Because the bocage is a meeting point for wildlife, domestic animals, and humans, species using the three habitats could potentially be epidemiologic agents for circulation of tick vectors as well as of pathogens. Thus, the bocage could be used as a model landscape for the study of epidemiologic cycles and potential emergence of multiple-host pathogens.

A spatial hazard model for cluster detection on continuous indicators of disease: application to somatic cell score.

Methods for spatial cluster detection dealing with diseases quantified by continuous variables are few, whereas several diseases are better approached by continuous indicators. For example, subclinical mastitis of the dairy cow is evaluated using a continuous marker of udder inflammation, the somatic cell score (SCS). Consequently, this study proposed to analyze spatialized risk and cluster components of herd SCS through a new method based on a spatial hazard model. The dataset included annual SCS for 34 142 French dairy herds for the year 2000, and important SCS risk factors: mean parity, percentage of winter and spring calvings, and herd size. The model allowed the simultaneous estimation of the effects of known risk factors and of potential spatial clusters on SCS, and the mapping of the estimated clusters and their range. Mean parity and winter and spring calvings were significantly associated with subclinical mastitis risk. The model with the presence of 3 clusters was highly significant, and the 3 clusters were attractive, i.e. closeness to cluster center increased the occurrence of high SCS. The three localizations were the following: close to the city of Troyes in the northeast of France; around the city of Limoges in the center-west; and in the southwest close to the city of Tarbes. The semi-parametric method based on spatial hazard modeling applies to continuous variables, and takes account of both risk factors and potential heterogeneity of the background population. This tool allows a quantitative detection but assumes a spatially specified form for clusters.

Prevalence of Anaplasma phagocytophilum, Rickettsia sp. and Borrelia burgdorferi sensu lato DNA in questing Ixodes ricinus ticks from France.

A total of 4701 Ixodes ricinus, collected during the summer of 2003, were analyzed for three pathogens. DNA was detected from the three pathogens. Co-detection of more than one pathogen was observed.

Detecting emerging diseases in farm animals through clinical observations.

Predicting emerging diseases is among the most difficult challenges facing researchers and health managers. We present available approaches and tools to detect emerging diseases in animals based on clinical observations of farm animals by veterinarians. Three information systems are described and discussed: Veterinary Practitioner Aided Disease Surveillance in New Zealand, the Rapid Syndrome Validation Project-Animal in the United States, and "émergences" in France. These systems are based on syndromic surveillance with the notification of every case or of specific clinical syndromes or on the notification of atypical clinical cases. Data are entered by field veterinarians into forms available through Internet-accessible devices. Beyond challenges of implementing new information systems, minimizing economic and health effects from emerging diseases in animals requires strong synergies across a group of field partners, in research, and in international animal and public health customs and practices.

Broad-range PCR-TTGE for the first-line detection of bacterial pathogen DNA in ticks.

Ticks are known or suspected vectors for a wide range of bacterial pathogens. One of the first steps for tick-borne risk assessment is the detection of these pathogens in their vectors. In the present study, a broad-range PCR amplification of the eubacterial gene encoding the 16S rRNA gene combined with Temporal Temperature Gradient gel Electrophoresis (TTGE) was evaluated as a method allowing the one-step detection of bacterial pathogen DNA in ticks. Firstly, DNA extracts from bacteria known to be tick-borne pathogens, i.e., Borrelia burgdorferi lato sensu, Anaplasma phagocytophilum, Spotted Fever Group (SFG) Rickettsia spp., were used to establish a TTGE pathogen DNA reference marker. Secondly, we used broad-range PCR-TTGE to detect the presence of DNA from these three pathogens in 55 DNA extracts from pools of 10 nymphal Ixodes ricinus ticks, which have been previously shown to carry DNA from at least one of those bacteria by specific PCR. Among the 20 B. burgdorferi specific-PCR samples, 15 (75%) were also found to be positive using PCR-TTGE. Sixteen of the seventeen (94%) Rickettsia spp. PCR-specific samples were positive using PCR-TTGE detection and all PCR-specific positive extracts (11/11, 100%) for A. phagocytophilum were also positive using PCR-TTGE. Moreover, we identified unexpected bacterial sequences that were not related to any of the three pathogens such as a sequence related to Spiroplasma sp. Thus, broad-range PCR-TTGE allowed the single step detection of DNA from up to 3 pathogens in the same co-infected samples as well as detection of DNA from unexpected bacteria.

Statistical modelling for clinical mastitis in the dairy cow: problems and solutions.

Modelling case occurrence and risk factors for clinical mastitis, as a key multifactorial disease in the dairy cow, requires statistical models. The type of model used depends on the choice of perception or the study level: herd, lactation, animal, udder and quarter. The validity of the tests that are performed through these models is especially ensured when hypotheses of independence between statistical units are respected, and when the model adjustments do not involve overdispersion faced with the observed data. In the article, the main sources of overdispersion are identified according to the different levels of perception of mastitis risk. Then, the proposed solutions to control for overdispersion at each study level are discussed and the difficulty to compare the study results is highlighted through a variety of methodological choices of the authors. Two main categories of models are used for modelling clinical mastitis, i.e. generalist exploratory models and explanatory designed models. The contribution of the explanatory models to improve modelling accuracy and relevance is documented through the two main published methodological approaches, the first one being based on a states model, and the second on a survival model. The integration and optimisation of such explanatory modelling methods should be possible in the future in order to develop a more global explanatory model including herd risk factors, which could pertinently predict udder infections (both clinical and subclinical) at the cow, lactation, or even udder and quarter levels.