Investigating genome variation within a South African wild dog (Lycaon pictus) population: Towards understanding their susceptibility to Mycobacterium bovis infection

Thesis (PhD)--Stellenbosch University, 2022.ENGLISH ABSTRACT: African wild dogs (Lycaon pictus) are one of the world’s most endangered species and their survival has been impacted by human and interspecific conflict, habitat loss and disease. This keystone species is now vulnerable to genetic impoverishment which may compromise the recovery of populations and limit long-term viability. Recently, the infectious disease bovine tuberculosis (bTB), caused by Mycobacterium bovis (M. bovis), has caused mortality in wild dogs across South Africa. Mycobacterium bovis exposure levels appear to be alarmingly high in the largest African wild dog population in the country, the Kruger National Park (KNP). Currently, there is a lack of knowledge regarding the epidemiology and transmission dynamics of M. bovis in African wild dogs. Additionally, genome variation of this species, a crucial component required to support the planning of conservation strategies, has not been assessed. This study had three broad aims, (i) to characterize the molecular epidemiology of M. bovis infection in South African wild dogs, (ii) to determine whether mycobacterial shedding occurs in African wild dogs, and (iii) to assess the level of genomic diversity in KNP African wild dogs. The M. bovis strains identified in South African wild dogs were epidemiologically linked to those found in other animal hosts in shared geographical areas. A novel strain was identified in wild dogs from Hluhluwe iMfolozi Park (HiP), which showed low diversity compared to a common HiP strain. Conversely, high genetic diversity of KNP wild dog isolates was observed, indicative of multiple exposure opportunities and ongoing transmission of M. bovis. The predominant routes of M. bovis infection in wild dogs appeared to be via ingestion (of infected prey) and aerosol inhalation, as the bacterium was present in the gastrointestinal- and respiratory tract. Opportunities exist for wild dogs to share respiratory secretions, which can therefore act as an infection source. In most wild dogs, infection disseminated to multiple organ systems, and generalised disease was observed in two juvenile wild dogs, indicating that M. bovis disease may be severe in this species. However, it is unclear if the severity of the disease in African wild dogs is primarily a function of the high infection prevalence, pathogenicity of the organism or host susceptibility. The first population-wide genome data set was generated for the African wild dog, enabling the identification of genomic features consistent with a population bottleneck, based on low genome variation and excess heterozygosity. Interestingly, patterns of recent inbreeding were not detected in this population and very few closely related individuals were identified. Shallow genetic structure was observed between packs, indicating that adequate levels of gene flow were present to hamper genetic isolation. Collectively, the genomic features observed in the KNP population may not impact short- term viability, however, the low levels of genomic variation may compromise population recovery. The consequences of an emerging infectious disease on a population with low levels of genome variation may threaten the long-term viability of African wild dogs. This is critical information to consider when planning future conservation actions for this species and should be used as a framework to develop strategies that will restore genome variation and mitigate the spread of bTB.AFRIKAANSE OPSOMMING: Afrika wildehonde (Lycaon pictus) is een van die wêreld se mees bedreigde spesies en hul voortbestaan word beïnvloed deur menslike en interspesifieke konflik, habitatverlies en siektes. Hierdie hoeksteen- spesie is tans kwesbaar vir genetiese verarming, wat die herstel van bevolkings in gevaar kan stel en lewensvatbaarheid op lang termyn kan beperk. Onlangs het die aansteeklike siekte beestuberkulose (bTB), wat deur Mycobacterium bovis (M. bovis) veroorsaak word, die dood van wildehonde regoor Suid-Afrika veroorsaak. Die blootstellingsvlakke van M. bovis blyk onrusbarend hoog te wees in die grootste Afrika wildehond bevolking in die land, die Krugerwildtuin (KNP). Daar is huidiglik ‘n gebrek aan kennis oor die epidemiologie en oordragdinamika van M. bovis in wildehonde in Afrika. Daarbenewens is die genoom variasie van hierdie spesie, 'n belangrike komponent wat nodig is om die beplanning van bewaringstrategieë te ondersteun, nie voorheen geëvalueer nie. Hierdie studie het drie oorhoofse doelwitte gehad, (i) om die kenmerke van die molekulêre epidemiologie van M. bovis-infeksie in wildehonde van Suid-Afrika te beskryf, (ii) om te bepaal of mykobakteriese vergieting in Afrika wildehonde plaasvind, en (iii) om die vlak van genomiese diversiteit in KNP Afrika wildehonde te bepaal. Die M. bovis-stamme wat in Suid-Afrikaanse wildehonde geïdentifiseer is, was epidemiologies gekoppel aan dié van ander gashere wat in gedeelde geografiese gebiede aangetref word. 'n Nuwe stam, wat 'n lae diversiteit getoon het in vergelyking met 'n algemene HiP-stam, is in wildehonde uit Hluhluwe iMfolozi Park (HiP) geïdentifiseer. In teenstelling is 'n hoë genetiese diversiteit van KNP-wildehond isolate waargeneem, wat dui op veelvuldige blootstellings geleenthede en voortdurende oordrag van M. bovis. Die oorheersende metodes van M. bovis-infeksie in wildehonde blyk deur die inname (van geïnfekteerde prooi) en inaseming van M. bovis-bevattende lug partikels te wees, aangesien die bakterie in die spysverteringskanaal en asemhalingstelsel gevind is. Wildehonde het ‘n geneigdheid om respiratoriese afskeidings te deel met mekaar en dit kan dus as infeksiebron dien. In die meeste wildehonde het infeksie na verskeie orgaanstelsels versprei, en verspreide siekte is by twee jong wildehonde waargeneem. Dit dui daarop dat M. bovis-siekte in hierdie spesie moontlik ernstig kan wees. Dit is egter onduidelik of die erns van die siekte in wildehonde hoofsaaklik die gevolg is van die hoë voorkoms van infeksie, die patogenisiteit van die organisme of die vatbaarheid van die gasheer. Die eerste bevolkingswye genoomdatastel vir die Afrika wildehond is gegenereer. Hierdie datastel het dit moontlik gemaak om genomiese kenmerke wat ooreenstem met 'n populasieknelpunt te identifiseer, gebaseer op die lae genoom variasie en oormatige heterosigositeit. Patrone van onlangse inteling is nie in hierdie populasie opgespoor nie en baie min naverwante individue is geïdentifiseer. Oppervlakkige genetiese struktuur is tussen troppe waargeneem, wat daarop dui dat voldoende vlakke van geen vloei teenwoordig was om genetiese isolasie te belemmer. Gesamentlik beïnvloed die genomiese kenmerke wat in die KNP-populasie waargeneem word nie lewensvatbaarheid in die kort termyn nie, maar die lae genomiese variasie kan bevolkingsherstel in gedrang bring. Die gevolge van 'n opkomende aansteeklike siekte op 'n bevolking met lae genoom variasie kan die lewensvatbaarheid van Afrika wildehonde bedreig. Dit is kritieke inligting wat in ag geneem moet word wanneer toekomstige bewaringsaksies vir hierdie spesie beplan word. Dit moet as 'n raamwerk gebruik word om strategieë te ontwikkel om genoom variasie te herstel en om die verspreiding van bTB te beperk.Doctora

Transpace : an architectural intervention for people in transition

Identity, belonging and being are some of the aspects inventively explored in this document. In times of fundamental change, people tend to find a space, lose it and then find another space as life and the world transform around them. What does this metamorphosis entail and in what ways are we affected by it? How do we live through it and what may we become on our journey towards each other, particularly when the space and places from which we depart are – at least on the surface – so vastly different? Within our voyages of transitional discovery, we too often repudiate the underlying structure from which our values, norms and standards are born – the configuration of beliefs that, when being threatened, results in conflict, bringing forth anger and dispute. The proposed discourse initiates another way of being by concretizing phenomenological philosopher Martin Heidegger’s notion of dwelling. It furthermore explores the contributions made by American architect Christopher Alexander, indicating important ways in which Heidegger’s dwelling can be translated into more grounded architectural meaning. Within the urban context, the design addresses these fundamental structures of being and the predicaments experienced between people and place.Dissertation (MArch(Prof))--University of Pretoria, 2008.Architectureunrestricte

TB Control in Humans and Animals in South Africa: A Perspective on Problems and Successes

Mycobacterium tuberculosis (M. tb) remains one of the most globally serious infectious agents for human morbidity and mortality, but with significant differences in prevalence across the globe. In many countries, the incidence is now low and declining, but control and eradication remain a distant view. Similarly, the prevalence of bovine TB caused by Mycobacterium bovis (M. bovis), varies significantly across regions, although unlike for M. tuberculosis, data are sparse. The reduction in incidence and prevalence and control of both human and bovine TB is difficult and costly, yet some countries have managed to do this with some success. This perspective will consider some of the critical control steps we now know to be important for the control of TB from M. tuberculosis in humans living in South Africa, where the incidence of TB is the highest currently experienced. Despite the high incidence of human TB, South Africa has been able to reduce this incidence remarkably in the past few years, despite limited resources and high HIV prevalence. We draw from our experience to ascertain whether we may learn useful lessons from control efforts for both diseases in order to suggest effective control measures for bovine TB

African wild dogs (Lycaon pictus) from the Kruger National Park, South Africa are currently not inbred but have low genomic diversity

African wild dogs (Lycaon pictus) have undergone severe population reductions and are listed as endangered on the International Union for Conservation of Nature Red List. Small, isolated populations have the potential to suffer from threats to their genetic diversity that may impact species viability and future survival. This study provides the first set of population-wide genomic data to address conservation concerns for this endangered species. Whole genome sequencing data were generated for 71 free-ranging African wild dogs from the Kruger National Park (KNP), South Africa, and used to estimate important population genomic parameters. Genomic diversity metrics revealed that variation levels were low; however, this African wild dog population showed low levels of inbreeding. Very few first- and second-order relationships were observed in this cohort, with most relationships falling into the third-order or distant category. Patterns of homozygosity could have resulted from historical inbreeding or a loss in genome variation due to a population bottleneck. Although the results suggest that this stronghold African wild dog population maintains low levels of inbreeding, likely due to their cooperative breeding system, it may lead to a continuous population decline when a reduced number of suitable mates are available. Consequently, the low genomic variation may influence species viability over time. This study highlights the importance of assessing population genomic parameters to set conservation priorities. Future studies should include the investigation of the potential of this endangered species.https://www.nature.com/srepdm2022Veterinary Tropical Disease

Characterizing epidemiological and genotypic features of Mycobacterium bovis infection in wild dogs (Lycaon pictus)

Mycobacterium bovis (M. bovis) infects a wide range of wildlife species and has recently been discovered in the endangered African wild dog (Lycaon pictus). This study aimed to characterize the epidemiology of tuberculosis (TB) in wild dogs in endemic areas of South Africa. We describe 12 TB cases in wild dogs from Kruger National Park (KNP), Hluhluwe–iMfolozi Park (HiP) and a private facility in Hoedspruit from 2015 to 2017. Spoligotyping was used to identify the disease-causing M. bovis strain in these cases, and whole-genome sequencing was performed on 5 M. bovis isolates (KNP = 2 and HiP = 3) to investigate genomic diversity as well as the relationship to other isolates found in these geographical areas. Three distinct strain types were responsible for the M. bovis infections in this species. The SB0121 strain was observed in wild dogs from KNP, whereas SB0130 was responsible for infection in wild dogs from HiP. A novel strain, SB2681, was also identified in the HiP wild dogs. Whole-genome sequence analysis suggests that different infection sources exist among these wild dogs and that inter-species transmission most likely occurred between wildlife predators and prey located within shared geographical areas. This study highlights the importance of regular disease surveillance to identify and characterize potential threats for successful control of infection and protection of endangered species.The South African Medical Research Council and the National Research Foundation.http://wileyonlinelibrary.com/journal/tbedhj2022Paraclinical Science

AIDS-related mycoses: the way forward.

The contribution of fungal infections to the morbidity and mortality of HIV-infected individuals is largely unrecognized. A recent meeting highlighted several priorities that need to be urgently addressed, including improved epidemiological surveillance, increased availability of existing diagnostics and drugs, more training in the field of medical mycology, and better funding for research and provision of treatment, particularly in developing countries

Search for new particles in events with energetic jets and large missing transverse momentum in proton-proton collisions at root s=13 TeV

A search is presented for new particles produced at the LHC in proton-proton collisions at root s = 13 TeV, using events with energetic jets and large missing transverse momentum. The analysis is based on a data sample corresponding to an integrated luminosity of 101 fb(-1), collected in 2017-2018 with the CMS detector. Machine learning techniques are used to define separate categories for events with narrow jets from initial-state radiation and events with large-radius jets consistent with a hadronic decay of a W or Z boson. A statistical combination is made with an earlier search based on a data sample of 36 fb(-1), collected in 2016. No significant excess of events is observed with respect to the standard model background expectation determined from control samples in data. The results are interpreted in terms of limits on the branching fraction of an invisible decay of the Higgs boson, as well as constraints on simplified models of dark matter, on first-generation scalar leptoquarks decaying to quarks and neutrinos, and on models with large extra dimensions. Several of the new limits, specifically for spin-1 dark matter mediators, pseudoscalar mediators, colored mediators, and leptoquarks, are the most restrictive to date.Peer reviewe

Combined searches for the production of supersymmetric top quark partners in proton-proton collisions at root s=13 TeV

A combination of searches for top squark pair production using proton-proton collision data at a center-of-mass energy of 13 TeV at the CERN LHC, corresponding to an integrated luminosity of 137 fb(-1) collected by the CMS experiment, is presented. Signatures with at least 2 jets and large missing transverse momentum are categorized into events with 0, 1, or 2 leptons. New results for regions of parameter space where the kinematical properties of top squark pair production and top quark pair production are very similar are presented. Depending on themodel, the combined result excludes a top squarkmass up to 1325 GeV for amassless neutralino, and a neutralinomass up to 700 GeV for a top squarkmass of 1150 GeV. Top squarks with masses from 145 to 295 GeV, for neutralino masses from 0 to 100 GeV, with a mass difference between the top squark and the neutralino in a window of 30 GeV around the mass of the top quark, are excluded for the first time with CMS data. The results of theses searches are also interpreted in an alternative signal model of dark matter production via a spin-0 mediator in association with a top quark pair. Upper limits are set on the cross section for mediator particle masses of up to 420 GeV

Probing effective field theory operators in the associated production of top quarks with a Z boson in multilepton final states at root s=13 TeV

Peer reviewe

MUSiC : a model-unspecific search for new physics in proton-proton collisions at root s=13TeV

Results of the Model Unspecific Search in CMS (MUSiC), using proton-proton collision data recorded at the LHC at a centre-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 35.9 fb(-1), are presented. The MUSiC analysis searches for anomalies that could be signatures of physics beyond the standard model. The analysis is based on the comparison of observed data with the standard model prediction, as determined from simulation, in several hundred final states and multiple kinematic distributions. Events containing at least one electron or muon are classified based on their final state topology, and an automated search algorithm surveys the observed data for deviations from the prediction. The sensitivity of the search is validated using multiple methods. No significant deviations from the predictions have been observed. For a wide range of final state topologies, agreement is found between the data and the standard model simulation. This analysis complements dedicated search analyses by significantly expanding the range of final states covered using a model independent approach with the largest data set to date to probe phase space regions beyond the reach of previous general searches.Peer reviewe