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Profiling the Bacterial Microbiome of Ticks That Parasitise Bandicoots in Australia

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Profiling the Bacterial Microbiome of Ticks That Parasitise Bandicoots in Australia Profiling the bacterial microbiome of ticks that parasitise bandicoots in Australia by Siobhon Egan Bachelor of Science This thesis is presented for the degree of Bachelor of Science Honours in Molecular Biology School of Veterinary and Life Sciences Murdoch University, Perth 2017 Author’s Declaration I declare that this thesis is my own account of my research and contains as its main content work which has not previously been submitted for a degree at any tertiary education institution. Siobhon Egan ii Abstract Molecular methods have recently revealed novel organisms inhabiting native Australian ticks, some of which are potentially pathogenic due to their similarity to causes of known tick-borne diseases (TBDs) worldwide. Australian bandicoots (Order: Peramelemorphia) are hosts of ticks that are known to bite humans. The persistence of bandicoots in urban and peri-urban areas results in increased exposure of humans to bandicoot ticks, and the bacterial diversity of ticks parasitising bandicoots is therefore of public health interest and requires further investigation. This study analysed 290 ticks parasitising bandicoots from New South Wales (NSW; n = 125), Queensland (QLD; n = 26), Northern Territory (NT; n = 15), Tasmania (TAS; n = 80), and Western Australia (WA; n = 44). A total of seven tick species (Haemaphysalis bancrofti, H. humerosa, Ixodes australiensis, I. fecialis, I. holocyclus, I. myrmecobii and I. tasmani) were identified from four Australian bandicoot species; the eastern barred bandicoot (Perameles gunnii), the long-nosed bandicoot (P. nasuta), the northern brown bandicoot (Isoodon macrourus), and the southern brown bandicoot (I. obesulus). Next Generation Sequencing (NGS) targeting the ubiquitous bacterial 16S rRNA gene was applied to a sub-sample of ticks (n = 66). Analysis of sequence data revealed the presence of Anaplasma, Borrelia, Ehrlichia and ‘Ca. Neoehrlichia’. Anaplasma bovis was detected in two ticks (H. bancrofti and H. humerosa) from the same bandicoot in NSW. A likely novel Ehrlichia sp. was identified from a single I. fecialis tick in WA. In addition to the confirmation of the recently described ‘Ca. Neoehrlichia arcana’ and ‘Ca. N. australis’ inhabiting I. holocyclus and I. tasmani from NSW and QLD, a novel ‘Ca. Neoehrlichia’ species was detected in ticks (I. australiensis and I. fecialis) from WA. Furthermore, sequences 98.8% similar to ‘Ca. Borrelia tachyglossi’ provide the first molecular description of Borrelia inhabiting ticks (H. humerosa and I. tasmani) parasitising Australian bandicoots. This study has provided an interesting insight into the microbial communities present in ticks parasitising Australian bandicoots and raises questions about the potential for tick-associated illness in people parasitised by these ticks. An investigation iii into the characterisation, prevalence, pathogenicity and transmission dynamics of these candidate tick-borne pathogens is required to establish the significance of this study. iv Acknowledgements My first acknowledgement must go to my supervisors, Dr. Charlotte Oskam (Primary) and Prof. Peter Irwin (Co-supervisor). Charlotte your generous support and advice has been the foundation of this project, thank you for being so approachable and providing the perfect balance of guidance and freedom. Peter, thank you for your inspiring ideas, big picture thinking and sharing your immense knowledge. Thank you to the team at the Vector and Water Borne Pathogen Research Group for your ongoing encouragement and advice. It has been a privilege to be a part of such a diverse and motivated group. In particular, I’d thank to thank Kimberly (Siew-May) Loh, Alexander Gofton and Telleasha Greay. Kim, thank you for being so patient during my first steps in the lab and making me feel so welcome. Alex, your all-round expertise and advice has been invaluable, I apologise for the constant interrupts and questions. Telleasha, thank you for ever so patiently guiding me through my NGS run and your help throughout. I would also like to thank Dr. Amanda Ash for your assistance in tick identification components. This research would not be possible without the many contributions by individuals and organisations. I would like to thank the following for donating specimens for this research; Prof. Peter Banks and Jenna Bytheway (University of Sydney), Dr. David Forshaw (Department of Agriculture and Food), Dr. Amy Northover (Murdoch University), Renata Phelps (WIRES), Dr. Bob Clippingdale (Forbes St Veterinary Clinic), Dr. Amber Gillet (Australia Zoo Wildlife Hospital), Trine Kruse (Territory Wildlife Park), Dr. Stephen Cutter (AMRIC) and Jacqui van Teulingen. I would also like to thank Dr. Amy Northover and A/Prof. Peter Spencer for their guidance and advice during my undergraduate years. I would have never considered further research if not for the inspiration and support you both provided. This research was kindly supported through the Myrtle AB Lamb Honours Scholarship provided by Murdoch University. Of course, a big thank you to my family for giving all this meaning. I would not be where I am today without your enduring support. To my partner Ray, thank you for continually reminding me that there is always time to laugh. Finally, to my big brother Rhys Egan, the source of my anguish but more overwhelming my inspiration. You made me want to make sure that I spent my 24th year on this earth achieving something worthwhile, and I hope I made you proud. You are so incredibly missed. I dedicate this to your memory. Until we meet again. v Table of Contents Author’s Declaration ......................................................................................................................................................... ii Abstract ................................................................................................................................................................................. iii Acknowledgements ............................................................................................................................................................ v List of Figures ................................................................................................................................................................... viii List of Tables ......................................................................................................................................................................... x List of Abbreviations ........................................................................................................................................................ xi Chapter 1 Introduction ..................................................................................................................................................... 1 1.1 Ticks ............................................................................................................................................................................. 2 1.1.1 Taxonomy and evolution ........................................................................................................................... 2 1.1.2 Identification of ticks ................................................................................................................................... 3 1.1.3 Life cycle ........................................................................................................................................................... 4 1.1.4 Host requirements and specificity ........................................................................................................ 5 1.2 The tick microbiome ............................................................................................................................................. 7 1.2.1 Bacterial composition in ticks ................................................................................................................. 7 1.2.2 Factors influencing the tick bacterial microbiome ......................................................................... 8 1.2.3 Methods to characterise these bacterial communities ................................................................. 9 1.2.4 NGS – understanding caveats & limitations ................................................................................... 11 1.3 Tick borne diseases ............................................................................................................................................ 12 1.3.1 Australian tick-borne diseases ............................................................................................................. 13 1.3.2 Emerging infectious diseases and novel bacteria – a critical approach ............................. 15 1.3.3 Identification of novel organisms inhabiting Australian ticks ............................................... 16 1.4. Australian bandicoots (Family Peramelidae) ........................................................................................ 17 1.4.1 Taxonomy & geographic distribution ............................................................................................... 17 1.4.2 Bandicoot-tick associations ................................................................................................................... 21 1.5 Conclusion & further research ...................................................................................................................... 24 1.6 Thesis aims and hypothesis ...........................................................................................................................
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