Efficient modelling of infectious diseases in wildlife: A case study of bovine tuberculosis in wild badgers.

Bovine tuberculosis (bTB) has significant socio-economic and welfare impacts on the cattle industry in parts of the world. In the United Kingdom and Ireland, disease control is complicated by the presence of infection in wildlife, principally the European badger. Control strategies tend to be applied to whole populations, but better identification of key sources of transmission, whether individuals or groups, could help inform more efficient approaches.

The utility of whole-genome sequencing to identify likely transmission pairs for pathogens with slow and variable evolution.

Pathogen whole-genome sequencing (WGS) has been used to track the transmission of infectious diseases in extraordinary detail, especially for pathogens that undergo fast and steady evolution, as is the case with many RNA viruses. However, for other pathogens evolution is less predictable, making interpretation of these data to inform our understanding of their epidemiology more challenging and the value of densely collected pathogen genome data uncertain. Here, we assess the utility of WGS for one such pathogen, in the "who-infected-whom" identification problem.

Use of an expert elicitation methodology to compare welfare impacts of two approaches for blood sampling European badgers () in the field.

In the UK and Republic of Ireland, the European badger () is considered the most significant wildlife reservoir of the bacterium , the cause of bovine tuberculosis (bTB). To expand options for bTB surveillance and disease control, the Animal and Plant Health Agency developed a bespoke physical restraint cage to facilitate collection of a small blood sample from a restrained, conscious badger in the field. A key step, prior to pursuing operational deployment of the novel restraint cage, was an assessment of the relative welfare impacts of the approach.

Tissue distribution of angiotensin-converting enzyme 2 (ACE2) receptor in wild animals with a focus on artiodactyls, mustelids and phocids.

Natural cases of zooanthroponotic transmission of SARS-CoV-2 to animals have been reported during the COVID-19 pandemic, including to free-ranging white-tailed deer () in North America and farmed American mink () on multiple continents. To understand the potential for angiotensin-converting enzyme 2 (ACE2)-mediated viral tropism we characterised the distribution of ACE2 receptors in the respiratory and intestinal tissues of a selection of wild and semi-domesticated mammals including artiodactyls (cervids, bovids, camelids, suids and hippopotamus), mustelid and phocid species using immunohistochemistry. Expression of the ACE2 receptor was detected in the bronchial or bronchiolar epithelium of several European and Asiatic deer species, Bactrian camel (), European badger (), stoat (), hippopotamus (), harbor seal (), and hooded seal ().

Patterns and consequences of age-linked change in local relatedness in animal societies.

The ultimate payoff of behaviours depends not only on their direct impact on an individual, but also on the impact on their relatives. Local relatedness-the average relatedness of an individual to their social environment-therefore has profound effects on social and life history evolution. Recent work has begun to show that local relatedness has the potential to change systematically over an individual's lifetime, a process called kinship dynamics.

Uptake of baits by wild badgers: Influences of deployment method, badger age and activity patterns on potential delivery of an oral vaccine.

In parts of the United Kingdom and Ireland, the European badger is a wildlife host for Mycobacterium bovis (the causative agent of bovine tuberculosis). Badger vaccination is one management option for reducing disease spread. Vaccination is currently achieved by parenteral vaccination of captured badgers, but an oral vaccine delivered in a bait may provide an additional approach in the future.

A Scoping Review of Interventions Designed to Support Parents With Mental Illness That Would Be Appropriate for Parents With Psychosis.

The experience of psychosis can present additional difficulties for parents, over and above the normal challenges of parenting. Although there is evidence about parenting interventions specifically targeted at parents with affective disorders, anxiety, and borderline personality disorder, there is currently limited evidence for parents with psychotic disorders. It is not yet known what, if any, interventions exist for this population, or what kinds of evaluations have been conducted.

Spatial and temporal variation in proximity networks of commercial dairy cattle in Great Britain.

The nature of contacts between hosts can be important in facilitating or impeding the spread of pathogens within a population. Networks constructed from contacts between hosts allow examination of how individual variation might influence the spread of infections. Studying the contact networks of livestock species managed under different conditions can additionally provide insight into their influence on these contact structures.

Differential susceptibility of SARS-CoV-2 in animals: Evidence of ACE2 host receptor distribution in companion animals, livestock and wildlife by immunohistochemical characterisation.

Angiotensin converting enzyme 2 (ACE2) is a host cell membrane protein (receptor) that mediates the binding of coronavirus, most notably SARS coronaviruses in the respiratory and gastrointestinal tracts. Although SARS-CoV-2 infection is mainly confined to humans, there have been numerous incidents of spillback (reverse zoonoses) to domestic and captive animals. An absence of information on the spatial distribution of ACE2 in animal tissues limits our understanding of host species susceptibility.

Serologic responses correlate with current but not future bacterial shedding in badgers naturally infected with Mycobacterium bovis.

Bovine tuberculosis is a challenging cattle disease with substantial economic costs in affected countries. Eradication in parts of the United Kingdom and Ireland is hindered by transmission of the causative agent Mycobacterium bovis between cattle and European badgers (Meles meles). Diagnostic tests in badgers are of limited accuracy but may help us understand and predict disease progression.

Assessing the risks of SARS-CoV-2 in wildlife.

The novel coronavirus SARS-CoV-2 likely emerged from a wildlife source with transmission to humans followed by rapid geographic spread throughout the globe and severe impacts on both human health and the global economy. Since the onset of the pandemic, there have been many instances of human-to-animal transmission involving companion, farmed and zoo animals, and limited evidence for spread into free-living wildlife. The establishment of reservoirs of infection in wild animals would create significant challenges to infection control in humans and could pose a threat to the welfare and conservation status of wildlife.

Genetic, social and maternal contributions to Mycobacterium bovis infection status in European badgers (Meles meles).

Within host populations, individuals can vary in their susceptibility to infections and in the severity and progression of disease once infected. Though mediated through differences in behaviour, resistance or tolerance, variation in disease outcomes ultimately stems from genetic and environmental (including social) factors. Despite obvious implications for the evolutionary, ecological and epidemiological dynamics of disease traits, the relative importance of these factors has rarely been quantified in naturally infected wild animal hosts.

Identifying likely transmissions in Mycobacterium bovis infected populations of cattle and badgers using the Kolmogorov Forward Equations.

Established methods for whole-genome-sequencing (WGS) technology allow for the detection of single-nucleotide polymorphisms (SNPs) in the pathogen genomes sourced from host samples. The information obtained can be used to track the pathogen's evolution in time and potentially identify 'who-infected-whom' with unprecedented accuracy. Successful methods include 'phylodynamic approaches' that integrate evolutionary and epidemiological data.

Rapid growth inhibitory activity of a YafQ-family endonuclease toxin of the Helicobacter pylori tfs4 integrative and conjugative element.

Prokaryotic and archaeal chromosomes encode a diversity of toxin-antitoxin (TA) systems that contribute to a variety of stress-induced cellular processes in addition to stability and maintenance of mobile elements. Here, we find DinJ-YafQ family TA systems to be broadly distributed amongst diverse phyla, consistent with other ParE/RelE superfamily TAs, but more unusually occurring as a multiplicity of species-specific subtypes. In the gastric pathogen Helicobacter pylori we identify six distinct subtypes, of which three are predominantly associated with the mobilome, including the disease-associated integrative and conjugative element (ICE), tfs4.

Toll-like Receptor 5 Activation by the CagY Repeat Domains of Helicobacter pylori.

Helicobacter pylori (Hp) is an important human pathogen associated with gastric inflammation and neoplasia. It is commonly believed that this bacterium avoids major immune recognition by Toll-like receptors (TLRs) because of low intrinsic activity of its flagellin and lipopolysaccharides (LPS). In particular, TLR5 specifically detects flagellins in various bacterial pathogens, while Hp evolved mutations in flagellin to evade detection through TLR5.

Characterization of potential superspreader farms for bovine tuberculosis: A review.

Background: Variation in host attributes that influence their contact rates and infectiousness can lead some individuals to make disproportionate contributions to the spread of infections. Understanding the roles of such 'superspreaders' can be crucial in deciding where to direct disease surveillance and controls to greatest effect. In the epidemiology of bovine tuberculosis (bTB) in Great Britain, it has been suggested that a minority of cattle farms or herds might make disproportionate contributions to the spread of Mycobacterium bovis, and hence might be considered 'superspreader farms'.

Estimating wildlife vaccination coverage using genetic methods.

Vaccination is a useful approach for the control of disease in wildlife populations. However, its effectiveness is dependent in part on delivery to a sufficient proportion of the target population. Measuring the proportions of wild animal populations that have been vaccinated is challenging and so there is a need to develop robust approaches that can contribute to our understanding of the likely efficacy of wildlife vaccination campaigns.

Quantification of the Animal Tuberculosis Multi-Host Community Offers Insights for Control.

Animal tuberculosis (TB) is a multi-host zoonotic disease whose prevalence in cattle herds in Europe has been increasing, despite a huge investment in eradication. The composition of the host community is a fundamental driver of pathogen transmission, and yet this has not been formally quantified for animal TB in Europe. We quantified multi-host communities of animal TB, using stochastic models to estimate the number of infected domestic and wild hosts in three regions: officially TB-free Central-Western Europe, and two largely TB-endemic regions, the Iberian Peninsula and Britain and Ireland.

Evaluation of the Dual Path Platform (DPP) VetTB assay for the detection of Mycobacterium bovis infection in badgers.

Bovine tuberculosis (bTB), caused by Mycobacterium bovis, represents a major animal health issue. In the United Kingdom and the Republic of Ireland, European badgers (Meles meles) have been shown to act as a reservoir of M. bovis infection, hindering the eradication of bTB in livestock.

Genetic evidence further elucidates the history and extent of badger introductions from Great Britain into Ireland.

The colonization of Ireland by mammals has been the subject of extensive study using genetic methods and forms a central problem in understanding the phylogeography of European mammals after the Last Glacial Maximum. Ireland exhibits a depauperate mammal fauna relative to Great Britain and continental Europe, and a range of natural and anthropogenic processes have given rise to its modern fauna. Previous Europe-wide surveys of the European badger () have found conflicting microsatellite and mitochondrial DNA evidence in Irish populations, suggesting Irish badgers have arisen from admixture between human imported British and Scandinavian animals.

Effects of trading networks on the risk of bovine tuberculosis incidents on cattle farms in Great Britain.

Trading animals between farms and via markets can provide a conduit for spread of infections. By studying trading networks, we might better understand the dynamics of livestock diseases. We constructed ingoing contact chains of cattle farms in Great Britain that were linked by trading, to elucidate potential pathways for the transmission of infection and to evaluate their effect on the risk of a farm experiencing a bovine tuberculosis (bTB) incident.

Combining genomics and epidemiology to analyse bi-directional transmission of in a multi-host system.

Quantifying pathogen transmission in multi-host systems is difficult, as exemplified in bovine tuberculosis (bTB) systems, but is crucial for control. The agent of bTB, , persists in cattle populations worldwide, often where potential wildlife reservoirs exist. However, the relative contribution of different host species to bTB persistence is generally unknown.

Wildlife surveillance using deep learning methods.

Wildlife conservation and the management of human-wildlife conflicts require cost-effective methods of monitoring wild animal behavior. Still and video camera surveillance can generate enormous quantities of data, which is laborious and expensive to screen for the species of interest. In the present study, we describe a state-of-the-art, deep learning approach for automatically identifying and isolating species-specific activity from still images and video data.

No energetic cost of tuberculosis infection in European badgers (Meles meles).

Energy availability and energy use directly influence an organism's life history, fitness and ecological function. In wild animals, abiotic factors such as ambient temperature, season and rainfall, and biotic factors such as body mass, age, social group size and disease status, all potentially influence energy balance. Relatively few studies have examined the effects of disease on the energy expenditure of wild animals.