Tick-borne-pathogensUncertainty about Australian Lyme disease-like illness requires evidence-based science to identify the microorganisms responsible and provide conclusive data about the speed of infection after tick attachment. This project will identify and characterise the microbial biodiversity in ticks and wildlife reservoir hosts, with the aim to ultimately improve diagnostic tests, treatment protocols, and the control of tick-borne diseases. Ticks transmit a greater variety of pathogenic microorganisms than any other arthropod group, are the second most important vector of zoonotic pathogens to humans (after mosquitoes) and the chief cause of VBD in livestock, companion animals, and wildlife. Worldwide, the list of pathogens transmitted by ticks to mammalian hosts is increasing and there is an urgency to develop new strategies to control ticks and impair tick-borne pathogen transmission to reduce infection prevalence. In Australia, in addition to tick paralysis of companion animals and livestock due to envenomation by the Australian paralysis ticks (Ixodes holocyclus and Ixodes cornuatus), several zoonotic tick-borne infections are well recognised, including zoonotic tick-borne rickettsial infections (e.g. Queensland tick typhus). However in recent years, public and government concern about the potential for other tick-borne diseases in people has increased considerably, with lobbying by patient advocacy groups, a parliamentary hearing into the so-called Lyme disease-like illness (Hansard, 2015) and the establishment of a Clinical Advisory Committee on Lyme disease in Australia (CACLD), by Prof. Chris Baggoley, former Chief Medical Officer (CMO) of Australia. With project funding from ARC Linkage grant (LP160100200: Linkage POs Bayer Australia Ltd. and Bayer HealthCare) and the Ecological Society of Australia my PhD project involves the use of high-throughput sequencing to characterise the suite of microbes (bacteria and haemoprotozoa) from blood, tissue and ticks collected from Australian wildlife
Principal investigatorSiobhon Egan firstname.lastname@example.org
Area of scienceBiology
Systems usedNimbus and Managed Storage
Applications usedUbuntu virtual instance
A total of 15 runs were performed in the illumina miseq generating ~125 GB of raw data. Due to the large number of samples analysed in the present study computational analysis on the university supplied laptop is not practical. For the most robust analysis it is important that some sections of the pipeline are performed in parellel (e.g. denoising step in DADA2 pipeline (Callahan et al. 2016 Nat Meth)). And therefore data must be analysed at the same time. Taxonomic assignment is also an computational intensive step in bioinformatics. In metabarcoding approaches and it is generally accepted that more than classifing method and database needs to be used to ensure accruacey (Balvočiūtė and Huson, 2017 BMC Genomics.
The nature of metabarocoding bioinformatics is that often several different programs are used at various steps of the pipeline. The large size of the dataset to analyse therefore means that Pawsey’s cloud computing platform Nimbus is an ideal tool for metabarcoding bioinformatics. The linux platform is ideal for bioinformatic analysis and allows for easy install of required packages. In conjunction with added volume storage, data can be stored at different steps along the analysis pipeline. This is particularly important to allow for quality inspection and beta testing. Volume storage can then be down or upgraded as required resulting in an efficient use of Pawsey facilities
My PhD enrollment is due to end in March 2022, however I have made good progress and am on track to submit my thesis within the next 2 months (by June 2021).
Two publications are soon to be submitted to journals:
1. Egan, S., Taylor, C., Austen, J., Banks, P., Northover, A., Alhstrom, L., Ryan, U., Irwin, P., and Oskam C. In prep. Haemoprotozoa in wildlife at the urban interface.
2. Egan, S., Taylor, C., Banks, P., Northover, A., Alhstrom, L., Ryan, U., Irwin, P., and Oskam C. In prep. Uncovering sylvatic cycles of tick microbes in Australia.
Both of these publications acknowledge the use of Pawsey facilities and I will notify Pawsey once they are published.
With additional publications in preparation and to be submitted by the end of the year,.
Related conference abstracts accepted for presentation in 2020/2021.
– (Oral) Egan, S. 2021. What’s in the wildlife? Surveillance of ticks and their associated microbes in Australian wildlife. 14th International Symposium on Ticks and Tick-borne Diseases (Sinnecker-Kunz Early Career Researcher Award Session), Germany (hosted online). Award winner – I was select 1st out of 20 presentations by Earler Career Researchers who presented during this session.
– (Oral) Egan, S., Fontaine, J., Ryan, U., Irwin., and Oskam C. [2020 – rescheduled to 2021]. Molecular and ecological insights into the ornate kangaroo tick, Amblyomma triguttatum. 10th Tick and Tick-borne Pathogen Conference (TTP10), Romania.
– (Oral) Egan, S., Fontaine, J., Veber, W., Ruthof, K., Ryan, U., Irwin, P., and Oskam, C. 2019. Insights into Amblyomma triguttatum. Combined Biological Sciences Meeting, Perth, Western Australia
– (Oral) Egan, S., Fontaine, J., Veber, W., Ruthof, K., Ryan, U., Irwin, P., and Oskam, C. 2019. The ecology of Amblyomma triguttatum triguttatum in Western Australia. Australian Society for Parasitology Annual Conference, Adelaide, South Australia.
– (Poster) Egan. S., Loh, S-M., Banks, P., Gillett, A., Ahlstrom, L., Ryan, U., Irwin. P., and Oskam C. 2020 – rescheduled to 2021. The Australian tick microbiome: highlighting the diversity down under. 10th Tick and Tick-borne Pathogen Conference (TTP10), Romania.
Pawsey has been vital to the progress of my research. The nature of bioinformatic analysis during my PhD is adhoc but through the use of Pawsey facilities it has been easy to pick up where I left off in terms of the analysis.
During my PhD I was successful at obtaining funding from the Ecological Society of Australia, and the Australian Society for Parasitology. Funding of both projects was in part thanks to the support of Pawsey facilities which have allowed me to analyse the data generated from these grants.
Fig 1. Maximum likelihood (ML) phylogenetic reconstruction of Ixodida ZOTUs based on a 377 bp alignment of the 12S rRNA locus. Sequences generated using high-throughout amplicon sequencing from over 250 tick specimens collected form Australian wildlife.