Integrating Survey and Molecular Approaches to Better Understand Wildlife Disease Ecology

Infectious wildlife diseases have enormous global impacts, leading to human pandemics, global biodiversity declines and socio-economic hardship. Understanding how infection persists and is transmitted in wildlife is critical for managing diseases, but our understanding is limited. Our study aim was to better understand how infectious disease persists in wildlife populations by integrating genetics, ecology and epidemiology approaches. Specifically, we aimed to determine whether environmental or host factors were stronger drivers of Salmonella persistence or transmission within a remote and isolated wild pig (Sus scrofa) population. We determined the Salmonella infection status of wild pigs. Salmonella isolates were genotyped and a range of data was collected on putative risk factors for Salmonella transmission. We a priori identified several plausible biological hypotheses for Salmonella prevalence (cross sectional study design) versus transmission (molecular case series study design) and fit the data to these models. There were 543 wild pig Salmonella observations, sampled at 93 unique locations. Salmonella prevalence was 41% (95% confidence interval [CI]: 37-45%). The median Salmonella DICE coefficient (or Salmonella genetic similarity) was 52% (interquartile range [IQR]: 42-62%). Using the traditional cross sectional prevalence study design, the only supported model was based on the hypothesis that abundance of available ecological resources determines Salmonella prevalence in wild pigs. In the molecular study design, spatial proximity and herd membership as well as some individual risk factors (sex, condition score and relative density) determined transmission between pigs. Traditional cross sectional surveys and molecular epidemiological approaches are complementary and together can enhance understanding of disease ecology: abundance of ecological resources critical for wildlife influences Salmonella prevalence, whereas Salmonella transmission is driven by local spatial, social, density and individual factors, rather than resources. This enhanced understanding has implications for the control of diseases in wildlife populations. Attempts to manage wildlife disease using simplistic density approaches do not acknowledge the complexity of disease ecology

Data from: An examination of the accuracy of a sequential PCR and sequencing test used to detect the incursion of an invasive species: the case of the red fox in Tasmania

1. Polymerase Chain Reaction (PCR) diagnostic tests are increasingly applied to the identification of wildlife. Yet rigorous verification is rare and the estimation of test accuracy (the probability that true positive and true negative samples are correctly identified – test sensitivity and specificity, respectively), particularly in combination with sequencing, is uncommon. This is important because PCR-based tests are prone to contamination in sampling and the laboratory. 2. Here, we use an experimental case–control approach to estimate the sensitivity and specificity of a sequential PCR-based wildlife detection test used to identify incursions of red foxes into Tasmania from predator faeces (scats). 3. Our results show that the sensitivity of the fox test is high (~94%) for the PCR-based test on its own, but this decreases to ~84% when combined with the DNA sequencing step. In contrast, the specificity increases from ~96% in the PCR only test to ~99.6% after inclusion of the DNA sequencing step. 4. The intense public scrutiny of the fox eradication program in Tasmania, has undoubtedly influenced the application of a sequential PCR test that maximises specificity at the expense of sensitivity and so increases the risk that scats containing fox DNA would not be detected. This could lead to the establishment of foxes in Tasmania as a consequence. 5. Synthesis and applications. Importantly, the estimation of the sensitivity and specificity of sequential tests enables decisions about the risk associated with mistaken identification (i.e. false negatives vs false positives) to be quantified for decision makers. The cost of false negative errors should be balanced against the costs of false positive errors, which could include the expenditure incurred in the application of unnecessary management actions were foxes not in fact present. Understanding the risks and costs associated with both false negative and false positive errors is therefore a key component to the decision making process for the management of the Tasmanian fox incursion

PCR_DNA_test_results

PCR_DNA_test_result

2016: From faeces to foxes: using genetics to manage an invasive predator for wildlife conservation

Slides from my talk at the Society for Molecular Biology and Evolution / Genetics Society of AustralAsia conference at the Gold Coast in 2016

2017: From faeces to foxes: using genetics to manage an invasive predator for wildlife conservation

Slides from my talk at the Australian Vertebrate Pest conference, Canberra, in 201

Host immunity hypothesis model formulation and coefficient estimates for molecular case series study designs.

<p>A fixed effect (indicator) covariate for herd and the distance between two pigs were included to control clustering and spatial autocorrelation.</p

Akaike information criterion (AIC) values and other model selection metrics for cross sectional prevalence logistic regression models using information theoretic approaches [29].

<p>The probability of the resource transmission model is very high (>0.99) and clearly the data support this model. Models are listed in AIC ranked order for each study design.</p