Irish soil and land-use classifications as predictors of numbers of badgers and badger setts

Spatio-temporal models of bovine tuberculosis in the Irish cattle population, 2012-2019

INTRODUCTION

Bovine tuberculosis (bTB) is an important zoonotic disease which has serious and sometimes fatal effects on both human and non-human animals. In many countries it is endemic in the cattle population and has a considerable economic impact through losses in productivity and impacts on trade. The incidence rate in Ireland varies by herd and location and it is hoped that statistical disease-mapping models accounting for both spatio-temporal correlation and covariates might contribute towards explaining this variation.

METHODS

Ireland was divided into equally sized hexagons for computational efficiency (n = 997). Different spatio-temporal random-effects models (e.g. negative binomial Besag-York-Mollié) were explored, using comprehensive data from the national bTB eradication programme to examine the association between covariates and the number of bTB cattle. Leveraging a Bayesian framework, model parameter estimates were obtained using the integrated nested Laplace approximation (INLA) approach. Exceedance probabilities were calculated to identify spatial clusters of cases.

RESULTS

Models accounting for spatial correlation significantly improved model fit in comparison to non-spatial versions where independence between regions was assumed. In our final model at hexagon level, the number of cattle (IR = 1.142, CrI: 1.108 - 1.177 per 1000), the capture of badgers (IR = 5.951, CrI: 4.482 - 7.912), percentage of forest cover (IR = 1.031, CrI: 1.020 - 1.042) and number of farm fragments (IR = 1.012, CrI: 1.009 - 1.015 per 10 fragments) were all associated with an increased incidence of bTB. Habitat suitability for badgers, percentage of dairy herds and the number of cattle movements into the herd were not. As an epidemiological tool and to suggest future work, an interactive online dashboard was developed to monitor disease progression and disseminate results to the general public.

CONCLUSION

Accounting for spatial correlation is an important consideration in disease mapping applications and is often ignored in statistical models examining bTB risk factors. Over time, the same regions in Ireland generally show highest incidences of bTB and allocation of more resources to these areas may be needed to combat the disease. This study highlights national bTB incidence rates. Shifting from national level analysis to smaller geographical regions may help identify localised high-risk areas.

Altitude shapes the environmental drivers of large-scale variation in abundance of a widespread mammal species

AIM

Habitat quality and heterogeneity directly influence the distribution and abundance of organisms at different spatial scales. Determining the main environmental factors driving the variation in species abundance is crucial to understand the underlying ecological processes, and this is especially important for widely distributed species living in contrasting environments. However, the responses to environmental variation are usually described at relatively small spatial scales. Here, we studied the variation in abundance of a widely distributed mustelid, the European badger (Meles meles), across France.

LOCATION

The whole metropolitan France.

METHODS

We used (a) direct detections of 9,439 dead and living badgers, from 2006 to 2009, to estimate badger relative abundance in 703 small agricultural regions of metropolitan France and (b) a Bayesian modeling approach to identify the main environmental determinants influencing badger abundance.

RESULTS

Despite a continuous distribution of badger in France, we found large variation in badger abundance between regions, explained by environmental factors. Among a set of 13 environmental variables, we demonstrated that badger abundance in lowlands (<400 m a.s.l.) was mostly driven by biotic factors such as potential food resources (earthworm abundance and fruit crops) and forest fragmentation. Conversely, in mountainous areas, abiotic factors (i.e., soil texture and climate) drove the variation in badger relative abundance.

MAIN CONCLUSIONS

These results underline the importance of mapping the abundance of wildlife species based on environmental suitability and highlight the complexity of drivers influencing species abundance at such large spatial scales. Altitude shaped the environmental drivers (biotic vs. abiotic) that most influenced relative abundance of a widespread species. In the case of badger, such abundance maps are crucial to identify critical areas for species management as this mustelid is a main wild vector of bovine tuberculosis in several countries.

The population and landscape genetics of the European badger (Meles meles) in Ireland

The population genetic structure of free-ranging species is expected to reflect landscape-level effects. Quantifying the role of these factors and their relative contribution often has important implications for wildlife management. The population genetics of the European badger (Meles meles) have received considerable attention, not least because the species acts as a potential wildlife reservoir for bovine tuberculosis (bTB) in Britain and Ireland. Herein, we detail the most comprehensive population and landscape genetic study of the badger in Ireland to date-comprised of 454 Irish badger samples, genotyped at 14 microsatellite loci. Bayesian and multivariate clustering methods demonstrated continuous clinal variation across the island, with potentially distinct differentiation observed in Northern Ireland. Landscape genetic analyses identified geographic distance and elevation as the primary drivers of genetic differentiation, in keeping with badgers exhibiting high levels of philopatry. Other factors hypothesized to affect gene flow, including earth worm habitat suitability, land cover type, and the River Shannon, had little to no detectable effect. By providing a more accurate picture of badger population structure and the factors effecting it, these data can guide current efforts to manage the species in Ireland and to better understand its role in bTB.

Environmental dust inhalation in the European badger (Meles meles): Systemic distribution of silica-laden macrophages, pathological changes, and association with Mycobacterium bovis infection status

Chronic inhalation of crystalline silica and silicates may lead to severe lung disease in humans, termed silicosis. The disease is an occupational health concern in miners and related professions worldwide. Silicosis is also a strong risk factor for tuberculosis in humans. Due to its subterranean lifestyle, the European badger (Meles meles) is continuously exposed to environmental dust, while this species is also susceptible to tuberculosis, caused by Mycobacterium bovis. To date, a thorough investigation of mineral dust retention and its possible implication as a risk factor for mycobacterial infection in badgers has not been performed. The aims of this retrospective histological study were (1) to describe the systemic tissue distribution of silica-laden macrophages (SLMs) in badgers; (2) to compare the amount of SLMs in tissues of badgers of differing M. bovis infection status, pulmonary SLM burden and age; and (3) to assess whether inflammation was associated with SLMs. We assessed lung, lymph nodes, liver and spleen of 60 wild-caught badgers of known M. bovis infection status for the presence of SLMs using polarizing light microscopy. SLMs were consistently present within the lungs and were widely distributed throughout the lymphatic system. No inflammatory reaction to SLMs, as occurs in human silicosis, was observed in any tissue. Distribution and amount of SLMs were similar between M. bovis positive and negative badgers, and we were not able to show an association between the amount of SLMs and M. bovis infection status. The amount of SLMs within intra- and extrathoracic lymph nodes was positively associated with the amount of pulmonary SLMs, and with age. This is the first report of substantial and systemic tissue retention of mineral dust particles in a mammalian species lacking associated chronic inflammation (i.e. silicosis). We further highlight different pathogenetic mechanisms underlying silicosis and benign SLM accumulations following siliceous dust inhalation.

A review of risk factors for bovine tuberculosis infection in cattle in the UK and Ireland

Bovine tuberculosis (bTB) is an important disease of cattle caused by infection withMycobacterium bovis, a pathogen that may be extremely difficult to eradicate in the presence of a true wildlife reservoir. Our objective was to identify and review relevant literature and provide a succinct summary of current knowledge of risk factors for transmission of infection of cattle. Search strings were developed to identify publications from electronic databases to February 2015. Abstracts of 4255 papers identified were reviewed by three reviewers to determine whether the entire article was likely to contain relevant information. Risk factors could be broadly grouped as follows: animal (including nutrition and genetics), herd (including bTB and testing history), environment, wildlife and social factors. Many risk factors are inter-related and study designs often do not enable differentiation between cause and consequence of infection. Despite differences in study design and location, some risk factors are consistently identified, e.g. herd size, bTB history, presence of infected wildlife, whereas the evidence for others is less consistent and coherent, e.g. nutrition, local cattle movements. We have identified knowledge gaps where further research may result in an improved understanding of bTB transmission dynamics. The application of targeted, multifactorial disease control regimens that address a range of risk factors simultaneously is likely to be a key to effective, evidence-informed control strategies.

Factors affecting European badger (Meles meles) capture numbers in one county in Ireland

Understanding factors affecting the number of badgers captured at and around badger setts (burrows) is of considerable applied importance. These factors could be used to estimate probable badger densities for bovine tuberculosis (bTB) control and also for monitoring badger populations from a conservation perspective. Furthermore, badger management and vaccination programs would benefit by increasing the probability of efficiently capturing the target badger populations. Within this context, it was investigated whether badger capture numbers can be estimated from field signs and previous capture histories. Badger capture records (initial and repeated capture numbers at a sett) from a large-scale removal program (405 km(2), 643 setts) were used. Univariable count models indicated that there were a number of significant potential predictors of badger numbers, during initial capture attempts. Using a multivariable zero-inflated Poisson (ZIP) model of initial captures we found that badger capture numbers were significantly affected by sett type, season, year, and the number of sett entrances in active use. Badger capture numbers were also affected by the total previous catch during repeated capture events and by the number of previous capture attempts. There was a significant negative trend in badger captures across events. Measures of the ability of these models to estimate badger captures suggested that the models might be useful in estimating badger numbers across a population; however the confidence intervals associated with these predictions were large.

Variations in Badger (Meles meles) Sett Microclimate: Differential Cub Survival between Main and Subsidiary Setts, with Implications for Artificial Sett Construction

Maintaining homeothermy is essential for mammals, but has considerable energetic costs. In this study, we monitored the internal conditions of setts within five European badger (Meles meles) social groups during the cub-rearing season, that is, February to July, in 2004. Sett temperature showed substantial and significant variation over this period, while relative humidity remained stable throughout. Microclimate was least stable during the period for which cubs remain entirely below ground between February and April; however here the instrumented main sett demonstrated a much warmer and more stable temperature regime than did nearby subsidiary outliers. We thus postulate that the energy budget of reproducing females could be affected by even small temperature fluctuations, militating for optimal sett choice. For comparison we also report microclimatic data from two artificial setts and found them to be markedly inferior in terms of thermal insulative properties, suggesting that man-made setts may need more careful consideration in both thermal and spatial setts network in each territory to adequately compensate the loss (e.g., destruction due to development) of a natural sett, especially as a breeding den.

Habitat selection by European badgers at multiple spatial scales in Portuguese Mediterranean ecosystems

Different habitat features can limit animal populations at different spatial scales. We examined habitat selection by Eurasian badger in a montado landscape in southern Portugal at four scales: core area (1 km2), home range (4 km2), social group territory (25 km2), and local population (100 km2). Our goals were to identify important habitats for conservation at each spatial scale (cell size) using candidate variables shown to be important by previous research. As expected, across all scales, badger occurrence was consistently and strongly correlated with dominance of cork oak and deciduous woodlands, and badgers seemed to avoid cultivated fields. Contrary to expectation, monocultures of conifers contributed positively to badger detection. The predictive ability of the models was poor at all scales, probably owing to our inability to include factors such as food, competitors, predators, undercover vegetation, and roads. Nonetheless, the models illustrate the importance to badgers of the montado, an ancient human-modified ecosystem that is threatened by current European Union agricultural conversion policies.

The tuberculosis eradication programme in Ireland: a review of scientific and policy advances since 1988

A national programme to eradicate bovine tuberculosis commenced in Ireland in 1954. During the last 15-20 years, research has been conducted to address gaps in knowledge of disease epidemiology, to objectively evaluate alternative strategy options, and to critically assess the implementation of disease control strategies. This paper provides a review of scientific and policy advances in Ireland since 1988, relevant to the tuberculosis eradication programme in Ireland. There have been substantial advances in knowledge of aspects of disease epidemiology, relating to cattle-to-cattle transmission, the role of wildlife, transmission of infection from wildlife and methods to minimise wildlife-to-cattle transmission. Further, scientific advances have been made both in the detection and management of infected herds. With respect to policy, the paper describes current policy and policy advances in both the detection and management of infected herds, as well as current strategies to prevent herd breakdowns. The Irish programme is a useful example of science-informed policy in a national context.

Tuberculosis in cattle: the results of the four-area project

The four-area project was undertaken to further assess the impact of badger removal on the control of tuberculosis in cattle herds in Ireland. It was conducted between 1997 and 2002 in matched removal and reference areas in four counties, namely Cork, Donegal, Kilkenny and Monaghan, representing a wide range of Irish farming environments. In the removal areas, a proactive programme of badger removal was conducted, on two or three occasions each year, whereas in the reference areas, badger removal was entirely reactive following severe outbreaks of tuberculosis amongst cattle. A detailed statistical analysis of this study has already been presented by Griffin et al. [13]; this paper presents further, mainly descriptive, findings from the study. In total, 2,360 badgers were captured in the removal areas of which 450 (19.5%) were considered positive for tuberculosis and 258 badgers were captured in the reference areas, with 57 (26.1%) positive for tuberculosis. The annual incidence of confirmed herd restrictions was lower in the removal area compared to the reference area in every year of the study period in each of the four counties. These empirical findings were consistent with the hazard ratios found by Griffin et al. [13]. Further, the effect of proactive badger removal on cattle tuberculosis in the four-area project and in the earlier east-Offaly project, as measured using the number of reactors per 1,000 cattle tested, were very similar, providing compelling evidence of the role of badgers in the epidemiology of tuberculosis in Irish cattle herds. The validity of the four-area project was discussed in detail. Efforts to minimise badger-to-cattle transmission in Ireland must be undertaken in association with the current comprehensive control programme, which has effectively minimised opportunities for cattle-to-cattle transmission.

The impact of badger removal on the control of tuberculosis in cattle herds in Ireland

In Ireland, the herd prevalence of bovine tuberculosis has remained stable for several decades, and in common with several other countries, progress towards eradication has stalled. There is evidence in support of the potential role of infected badgers (Meles meles, a protected species) in bovine tuberculosis in Ireland and Britain. However, this evidence on its own has not been sufficient to prove disease causation. Field trials are likely to offer the best opportunity to define this role. Building on the earlier East Offaly project, our objectives were to assess the impact of badger removal on the control of tuberculosis in cattle herds in Ireland. The study was conducted from September 1997 to August 2002 in matched removal and reference areas (average area of 245.1km(2)) in four counties: Cork, Donegal, Kilkenny and Monaghan. Badger removal was intensive and proactive throughout the study period in the removal areas, but reactive (in response to severe tuberculosis outbreaks in cattle) in the reference areas. Removal intensity in the removal and reference areas during the first 2 years of the study averaged 0.57 and 0.07 badgers/km(2)/year, respectively. The outcome of interest was restriction of cattle herds due to confirmed tuberculosis, where tuberculous lesions were detected in one or more animals. Data were analysed using logistic regression (modelling the probability of a confirmed herd restriction) and survival analysis (modelling time to a confirmed herd restriction). During the study period, there was a significant difference between the removal and reference areas in all four counties in both the probability of and the time to a confirmed herd restriction due to tuberculosis. In the final year of the study, the odds of a confirmed herd restriction in the removal (as compared to the reference areas) were 0.25 in Cork, 0.04 in Donegal, 0.26 in Kilkenny and 0.43 in Monaghan. Further, the hazard ratios (removal over reference) ranged from 0.4 to 0.04 (a 60-96% decrease in the rate at which herds were becoming the subject of a confirmed restriction).

Bovine tuberculosis in badgers in four areas in Ireland: does tuberculosis cluster?

We described the distribution of badger populations in four different areas in the Republic of Ireland. The data came from periodic targeted badger-removal and subsequent post-mortem examinations conducted between 1989 and September 1997, and from a formal badger-removal project in the same areas from 1997 through 1999. Records were complete for 2292 badgers regarding the date of capture, tuberculosis status, geographical area and specific sett from where the badgers were snared. Of 3187 setts, 2290 had no badgers recorded against them (i.e. were inactive). The badger-level prevalence of tuberculosis differed among areas (range 13-29%). Badger populations were highly clustered by sett, and this result was similar over the four study areas. The median number of badgers per active sett was 2. Tuberculous badgers also clustered within a sett. The third quartile of tuberculous badgers was 1 per active sett. The prevalence of tuberculous badgers within a sett was not related to the total number of badgers. There was little evidence of spatial clustering with only one local cluster of tuberculous setts in each of three areas, and none in the fourth area. After adjusting for the number of badgers per sett, only one area had spatial clusters identified.