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

Abstract

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