Several vector-borne and zoonotic diseases have emerged or re-emerged in Europe over these last decades. Besides climate change that influences disease risk at a regional scale, landscape changes could be responsible for local heterogeneities in disease risk. Spatial epidemiology tries to understand and predict spatial variations in disease risk by using spatial tools and spatially-explicit modelling methods. This study investigated the impact of fine-grained landscape patterns on the transmission of vector-borne and zoonotic infections in terms of habitat suitability for vectors and/or hosts and of exposure of people to infectious agents. This was studied through three human diseases emerging or at risk of re-emergence in Europe: the rodent-borne Puumala hantavirus, the tick-borne Lyme borreliosis and the mosquito-borne malaria infections. Statistical models were first used to study the relationships between environmental variables and host abundance, host prevalence, and human cases of Puumala hantavirus. Environmental factors were also combined with socio-economic factors to explain Puumala hantavirus and Lyme borreliosis incidence rates. The combination of factors explaining disease transmission and the complexity of such systems led to the development of an innovative, spatially-explicit modelling method: multi-agent simulation (MAS). The MALCAM simulation model was developed to assess the risk of malaria re-emergence in southern France and simulates spatial and temporal variations in contact rate between people and potential malaria vectors. The effect of changes in potential drivers of malaria re-emergence was also simulated. The different case studies showed that fine-grained landscape patterns influence the presence and abundance of vectors and hosts. Moreover, environmental conditions may also influence disease transmission through pathogen dispersal and the exposure of people to infectious agents. Finally, this study showed that people-vector contacts not only depend on the spatial distribution of people and potential vectors, but also on their behaviours and interactions.

Invasive species are generally problematic where they occur, especially in terms of ecology, economy and disease. Members of the genus Rattus Fischer, 1803 particularly, are known as one of the most destructive invasive species to date since they cause widespread damage on terrestrial and island ecosystems. Two Rattus species have historically been reported as invasive species in South Africa, Rattus rattus Linnaeus, 1758, which has a widespread distribution throughout the country and Rattus norvegicus Berkenhout, 1769 which is primarily distributed along the coast of South Africa. A third species, Rattus tanezumi Temminck, 1844 (which forms part of the R. rattus species complex), a south-east Asian endemic, was first reported in 2005 to also occur in South Africa (and Africa). As this species is morphologically similar to R. rattus, its identification is reliant on molecular typing approaches. In the current study, molecular, morphological and disease aspects of South African Rattus were assessed. The nature and extent of variation between the three species was investigated using cytochrome b sequences and extensive mitochondrial d-loop database for comparative purposes. D-loop data identified one, four and two haplotypes for R. tanezumi, R. rattus and R. norvegicus, respectively whereas cytochrome b data identified additional haplotypes for R. rattus and R. tanezumi. Pairwise sequence divergence was highest between R. norvegicus and R. tanezumi (12.5% for D-loop and 12.0% for cyt b). Rattus norvegicus was recovered in the central parts of South Africa for the first time and occurred sympatrically with R. tanezumi at one locality, whereas Rattus rattus and R. tanezumi occurred sympatrically at three localities. The external and qualitative cranial morphology of all three species was compared in an attempt to find differences that could be used to morphologically differentiate between these Rattus species. Whereas R. norvegicus can easily be distinguished from R. rattus and R. tanezumi, there are no discernible morphological differences to distinguish R. rattus and R. tanezumi. A taxonomic synthesis and an identification key of the three species of Rattus based on qualitative morphology, molecular and cytogenetic data using genetically-identified individuals is provided. Members of South African Rattus were also found to be carriers of the bacteria Bartonella Strong et al., 1915 and Helicobacter Goodwin et al., 1989 emend. Vandamme et al., 1991. Bartonella elizabethae (Daly et al., 1993) Brenner et al., 1993, occurring in Rattus around the world was for the first time recovered from South African Rattus. This bacterium has been associated with infective endocarditis in humans and may pose a threat to immuno-compromised individuals in rural South African communities where Rattus occurs commensally. Two Helicobacter species, H. rodentium Shen et al., 1997 and H. muridarum Lee et al., 1992, were identified neither of which have known zoonotic potential. Apart from contributing to general small mammal studies in Africa, the present study may have implications in epidemiological, agricultural, biological conservation, and invasion biology research associated with problem rodents in the southern African subregion and beyond. / Dissertation (MSc)--University of Pretoria, 2010. / Zoology and Entomology / unrestricted

The concept of One Health is a rather new term that is used to describe the need for collaboration across expert disciplines to ensure health for humans, animals and the environment. The concept of One Health covers many different aspects of problems that pose a threat to a sustainable planet, for example zoonotic diseases, food hygiene, antibiotic resistance and animal welfare. In recent years the interest in One Health issues has expanded in a truly amazing way, therefore, it is in our interest to present an overview of One Health projects globally, regarding the topics of zoonotic diseases and animal welfare. The aim of this literature study is to conduct an overview of published studies, in the areas of zoonotic diseases and animal welfare, from geographically distinct parts of the world, including Europe, Middle East, South America, South-East Asia and Sub-Saharan Africa. This will be done by answering questions regarding the analysed publications, to explore similarities and differences between the previously mentioned geographic areas, regarding the two topics of interest. PubMed was used as search engine to identify publications suitable for the aim of this literature overview. 178 publications within the area of zoonotic diseases and 139 publications within the area of animal welfare met the inclusion criteria and were analysed and evaluated according to a question-sheet. Cross-border collaborations appeared to be more common in the field of zoonotic diseases than in the field of animal welfare. Looking at the amount of published papers, there seemed to be an elevation in number of publications focusing on zoonotic diseases from the time interval 2012-2013 to 2014-2015, in contrast to animal welfare, where the publication numbers increased some years later, from 2014-2015 to 2016-2017. Sub-Saharan African and South American publications focused more on vector borne diseases than the other investigated geographic areas. Regarding the most common cause of animal welfare issues, it appeared to be housing and human management in all investigated geographical demarcations.

The main aim of the current study was to determine the prevalence and diversity of potentially zoonotic bacterial genera in accurately identified indigenous rodents from South Africa. Bacterial prevalence and diversity were determined by PCR amplification and sequence analyses. Rodents were molecularly identified by amplification and sequence analysis of the mitochondrial cytochrome b gene region. Three species (Aethomys ineptus, Mastomys coucha and Otomys angoniensis) belonging to murid species complexes were identified. Furthermore, phylogenetic analyses revealed that both the proposed subspecies (R. dilectus dilectus and R. d. chakae) within the recently erected Rhabdomys dilectus occur in Hammanskraal and at the University of Pretoria Experimental farm, both in the Gauteng Province of South Africa. An overall bacterial prevalence of 38.6 % was observed in kidney samples of commensal and natural indigenous rodents after molecular screening with broad range 16S rRNA gene primers. Nucleotide sequence analyses identified a diverse range of bacterial genera namely, Bartonella, Anaplasma, Helicobacter, Burkholderia, Streptococcus, Aerococcus and Lactobacillus. Some members of these genera have been identified as causative agents of human and animal diseases, being transmitted either through environmental contamination or through haematophagous arthropod vectors. Subsequent genus-specific bacterial screening focussed on vector-borne genera identified in the commensal and natural rodent populations sampled. Bartonella prevalence and genetic diversity was compared between a natural and commensal population of the southern multimammate mouse (M. coucha) using two gene regions (Citrate synthase gene and NADH dehydrogenase gamma subunit gene). A significantly higher infection prevalence was detected in the commensal population (92.9 %) as compared to the natural population (56.9 %). No differences however, were detected between infection status and the ectoparasite loads calculated for both rodent populations. Apart from several novel Bartonella strains identified in both M. coucha populations, phylogenetic analyses also identified a species of known zoonotic potential (B. elizabethae) in both populations. The present study represents one of the first to screen indigenous rodents for tick-borne members of the bacterial family Anaplasmataceae. Anaplasma bovis-like DNA was detected in five of the six rodent species sampled (A. ineptus, Lemniscomys rosalia, M. coucha, O. angoniensis and R. dilectus) at an overall prevalence of 39.2 %. The potentially zoonotic Ehrlichia ewingii was detected in M. coucha samples only at a prevalence of 5.3 %. The diverse bacterial genera detected in commensal and natural populations of indigenous rodents comprise members of zoonotic potential and agricultural significance, highlighting the importance of continuous disease surveillance of indigenous rodents. / Dissertation (MSc)--University of Pretoria, 2014. / National Research Foundation (NRF) / Zoology and Entomology / MSc / Unrestricted

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