Ecological and epidemiological consequences of rapid urbanisation at wildlife-livestock-human interfaces

Urbanization is characterized by rapid intensification of agriculture, socioeconomic change, and ecological fragmentation, which can have profound impacts on the distributional ecology of host populations and epidemiology of infectious disease within them. In this thesis, results from a large-scale field study conducted in Nairobi, Kenya are used to explore how anthropogenic and ecological changes associated with urbanisation influence the structure of sympatric wildlife, livestock and human host populations, and dictate bacterial epidemiology in wildlife hosts. As likely points of contact (and thus parasite transmission) between vertebrate wildlife, livestock, and humans, household ‘interfaces’ were chosen as sampling units. The ecological and sociological status of households was characterised through ecological surveys, questionnaire data and geospatial mapping, and faecal samples were collected from wildlife occurring within the household compound, and livestock and human inhabitants. Escherichia coli was isolated from faecal samples, and characterised both phenotypically (through antimicrobial sensitivity testing) and genetically (through whole genome sequencing). In the first part of this thesis I consider the influence of urban land-use change on the structure of host populations at household interfaces. Using unsupervised machine learning I describe variation in the host composition of wildlife-livestockhuman interfaces and, through multivariate regression analysis, demonstrate that citywide variation in ecological and anthropogenic factors (such as biotic habitat diversity and wealth) drive structural changes in wildlife, livestock and human populations across the urban landscape of Nairobi. Utilising commensal E. coli as an exemplar organism, I proceed to explore epidemiological connectivity between wildlife, livestock and humans at household interfaces, and link epidemiological processes in urban wildlife to their drivers across the urban landscape. Firstly, I explore the epidemiology of clinically relevant antimicrobial resistant (AMR)-E. coli in urban wildlife in Nairobi. Comparing E. coli isolates in wildlife to livestock, humans and the environment, I find that E. coli isolated from wildlife have a lower diversity of resistance phenotypes, and are thus an unlikely source of AMR. At household interfaces, I find evidence of AMR-E. coli exchange between rodents/seed-eating birds, and cattle and humans, and demonstrate that transmission is facilitated through anthropogenic resource provision in households. Next, utilising high resolution sequencing data, I explore the response of microbial communities in wildlife hosts to urban land-use change. Specifically, I test the hypothesis that communities of bacterial mobile genetic elements (MGEs) are deterministically structured, according to changes in host community structure. I show that the diversity of genes encoding virulence and AMR in avian-borne E. coli is determined by variation in the distribution and density of birds, livestock and humans at household interfaces, and that this varies along gradients of urbanisation. To conclude, I relate the findings in this thesis across multiple scales, linking the influence of abiotic factors such as habitat alteration and socioeconomics to host community structure at household interfaces and the epidemiology of wildlife-borne E. coli. Using this framework, I suggest future directions for research on urban disease emergence, and discuss implications of my findings for public health and urban planning

Epilepsy diagnosis and management of children in Kenya: review of current literature

Introduction: The growing impact of non-communicable diseases in low- to middle-income countries makes epilepsy a key research priority. We evaluated peer-reviewed published literature on childhood epilepsy specific to Kenya to identify knowledge gaps and inform future priorities. Methodology: A literature search utilizing the terms “epilepsy” OR “seizure” as exploded subject headings AND “Kenya” was conducted. Relevant databases were searched, generating 908 articles. After initial screening to remove duplications, irrelevant articles, and publications older than 15 years, 154 papers remained for full-article review, which identified 35 publications containing relevant information. Data were extracted from these reports on epidemiology, etiology, clinical features, management, and outcomes. Results: The estimated prevalence of lifetime epilepsy in children was 21–41 per 1,000, while the incidence of active convulsive epilepsy was 39–187 cases per 100,000 children per year. The incidence of acute seizures was 312–879 per 100,000 children per year and neonatal seizures 3,950 per 100,000 live births per year. Common risk factors for both epilepsy and acute seizures included adverse perinatal events, meningitis, malaria, febrile seizures, and family history of epilepsy. Electroencephalography abnormalities were documented in 20%–41% and neurocognitive comorbidities in more than half. Mortality in children admitted with acute seizures was 3%–6%, and neurological sequelae were identified in 31% following convulsive status epilepticus. Only 7%–29% children with epilepsy were on antiseizure medication. Conclusion: Active convulsive epilepsy is a common condition among Kenyan children, remains largely untreated, and leads to extremely poor outcomes. The high proportion of epilepsy attributable to preventable causes, in particular neonatal morbidity, contributes significantly to the lifetime burden of the condition. This review reaffirms the ongoing need for better public awareness of epilepsy as a treatable disease and for national-level action that targets both prevention and management

Towards an ecosystem model of infectious disease

Increasingly intimate associations between human society and the natural environment are driving the emergence of novel pathogens, with devastating consequences for humans and animals alike. Prior to emergence, these pathogens exist within complex ecological systems that are characterized by trophic interactions between parasites, their hosts and the environment. Predicting how disturbance to these ecological systems places people and animals at risk from emerging pathogens-and the best ways to manage this-remains a significant challenge. Predictive systems ecology models are powerful tools for the reconstruction of ecosystem function but have yet to be considered for modelling infectious disease. Part of this stems from a mistaken tendency to forget about the role that pathogens play in structuring the abundance and interactions of the free-living species favoured by systems ecologists. Here, we explore how developing and applying these more complete systems ecology models at a landscape scale would greatly enhance our understanding of the reciprocal interactions between parasites, pathogens and the environment, placing zoonoses in an ecological context, while identifying key variables and simplifying assumptions that underly pathogen host switching and animal-to-human spillover risk. As well as transforming our understanding of disease ecology, this would also allow us to better direct resources in preparation for future pandemics

Publisher Correction: Towards an ecosystem model of infectious disease

Correction to: Nature Ecology & Evolution https://doi.org/10.1038/s41559-021-01454-8, published online 17 May 2021

Mobility promotes and jeopardizes biodiversity in rock-paper-scissors games

Biodiversity is essential to the viability of ecological systems. Species diversity in ecosystems is promoted by cyclic, non-hierarchical interactions among competing populations. Such non-transitive relations lead to an evolution with central features represented by the `rock-paper-scissors' game, where rock crushes scissors, scissors cut paper, and paper wraps rock. In combination with spatial dispersal of static populations, this type of competition results in the stable coexistence of all species and the long-term maintenance of biodiversity. However, population mobility is a central feature of real ecosystems: animals migrate, bacteria run and tumble. Here, we observe a critical influence of mobility on species diversity. When mobility exceeds a certain value, biodiversity is jeopardized and lost. In contrast, below this critical threshold all subpopulations coexist and an entanglement of travelling spiral waves forms in the course of temporal evolution. We establish that this phenomenon is robust, it does not depend on the details of cyclic competition or spatial environment. These findings have important implications for maintenance and evolution of ecological systems and are relevant for the formation and propagation of patterns in excitable media, such as chemical kinetics or epidemic outbreaks.Comment: Final submitted version; the printed version can be found at http://dx.doi.org/10.1038/nature06095 Supplementary movies are available at http://www.theorie.physik.uni-muenchen.de/lsfrey/images_content/movie1.AVI and http://www.theorie.physik.uni-muenchen.de/lsfrey/images_content/movie2.AV

“Excellence R Us”: university research and the fetishisation of excellence

The rhetoric of “excellence” is pervasive across the academy. It is used to refer to research outputs as well as researchers, theory and education, individuals and organisations, from art history to zoology. But does “excellence” actually mean anything? Does this pervasive narrative of “excellence” do any good? Drawing on a range of sources we interrogate “excellence” as a concept and find that it has no intrinsic meaning in academia. Rather it functions as a linguistic interchange mechanism. To investigate whether this linguistic function is useful we examine how the rhetoric of excellence combines with narratives of scarcity and competition to show that the hypercompetition that arises from the performance of “excellence” is completely at odds with the qualities of good research. We trace the roots of issues in reproducibility, fraud, and homophily to this rhetoric. But we also show that this rhetoric is an internal, and not primarily an external, imposition. We conclude by proposing an alternative rhetoric based on soundness and capacity-building. In the final analysis, it turns out that that “excellence” is not excellent. Used in its current unqualified form it is a pernicious and dangerous rhetoric that undermines the very foundations of good research and scholarship

The not-so-barren ranges

© Thesis Eleven Pty, Ltd., SAGE Publications. This is an impressionistic and informal essay written near the end of a novelist's Australia Research Council funded research project: 'Developing narratives from language and stories indigenous to the south coast of Western Australia', and informed by how that research project morphed into an emphasis on revitalization of Noongar language, and the attempt to restore connections between a particular Creation Story and landscape in an area regarded as 'massacre territory'. A sympathetic reader might think of the topic as 'The Wirlomin Noongar Language and Stories Project meets The Barren Ranges'

Does the early frog catch the worm? Disentangling potential drivers of a parasite age–intensity relationship in tadpoles

The manner in which parasite intensity and aggregation varies with host age can provide insights into parasite dynamics and help identify potential means of controlling infections in humans and wildlife. A significant challenge is to distinguish among competing mechanistic hypotheses for the relationship between age and parasite intensity or aggregation. Because different mechanisms can generate similar relationships, testing among competing hypotheses can be difficult, particularly in wildlife hosts, and often requires a combination of experimental and model fitting approaches. We used field data, experiments, and model fitting to distinguish among ten plausible drivers of a curvilinear age–intensity relationship and increasing aggregation with host age for echinostome trematode infections of green frogs. We found little support for most of these proposed drivers but did find that the parsimonious explanation for the observed age–intensity relationship was seasonal exposure to echinostomes. The parsimonious explanation for the aggregated distribution of parasites in this host population was heterogeneity in exposure. A predictive model incorporating seasonal exposure indicated that tadpoles hatching early or late in the breeding season should have lower trematode burdens at metamorphosis, particularly with simulated warmer climates. Application of this multi-pronged approach (field surveys, lab experiments, and modeling) to additional parasite–host systems could lead to discovery of general patterns in the drivers of parasite age–intensity and age–distribution relationships

Patient-centred measurement in ophthalmology – a paradigm shift

Ophthalmologists and researchers in ophthalmology understand what a rapidly evolving field ophthalmology is, and that to conduct good research it is essential to use the latest and best methods. In outcomes research, one modern initiative has been to conduct holistic measurement of outcomes inclusive of the patient's point of view; patient-centred outcome. This, of course, means including a questionnaire. However, the irony of trying to improve outcomes research by being inclusive of many measures is that the researcher may not be expert in all measures used. Certainly, few people conducting outcomes research in ophthalmology would claim to be questionnaire experts. Most tend to be experts in their ophthalmic subspecialty and probably simply choose a popular questionnaire that appears to fit their needs and think little more about it. Perhaps, unlike our own field, we assume that the field of questionnaire research is relatively stable. This is far from the case. The measurement of patient-centred outcomes with questionnaires is a rapidly evolving field. Indeed, over the last few years a paradigm shift has occurred in patient-centred measurement

Deterministic processes structure bacterial genetic communities across an urban landscape

Land-use change is predicted to act as a driver of zoonotic disease emergence through human exposure to novel microbial diversity, but evidence for the effects of environmental change on microbial communities in vertebrates is lacking. We sample wild birds at 99 wildlife-livestock-human interfaces across Nairobi, Kenya, and use whole genome sequencing to characterise bacterial genes known to be carried on mobile genetic elements (MGEs) within avian-borne Escherichia coli (n=241). By modelling the diversity of bacterial genes encoding virulence and antimicrobial resistance (AMR) against ecological and anthropogenic forms of urban environmental change, we demonstrate that communities of avian-borne bacterial genes are shaped by the assemblage of co-existing avian, livestock and human communities, and the habitat within which they exist. In showing that non-random processes structure bacterial genetic communities in urban wildlife, these findings suggest that it should be possible to forecast the effects of urban land-use change on microbial diversity