CV

Research Interests

Microbes, Parasites, Genomics, Metabolomics, Bioinformatics, Phylogenetics, Infectious disease, Zoonoses, One Health, Multi-omics data integration.

Education

Doctor of Philosophy | Murdoch University, Perth, Australia, 2022

  • Ecology of Ticks and Microbes in Australian Wildlife. Supported by Research Training Program (PhD tuition and stipend) scholarship.
  • Supervisors: Dr. Charlotte Oskam, Prof. Peter Irwin, Prof. Una Ryan, and Prof. Peter Banks.
  • Use of molecular tools to investigate the epidemiology of tick (and other vector) associated microbes (bacteria and protozoa) present in Australian wildlife.

Bachelor of Science Honours (Molecular Biology) | Murdoch University, Perth, Australia, 2017

Bachelor of Science | Murdoch University, Perth, Australia, 2016

  • Distinction average – Double major in Animal Health and Conservation & Wildlife Biology
  • Research project final year – small mammal camera trapping in Dryandra woodlands. Supervisors: A/Prof Peter Spencer and Mark Cowan (Department of Parks and Wildlife, WA).

Employment

Postdoctoral research fellow | Murdoch University, Perth, Australia, 2021–Present

  • Application of metabolic profiling and genomic sequencing to understand the age associated changes linked with the changing gut microbiome.
  • Principal investigator – Prof. Elaine Holmes ARC laureate project Understanding host-microbiome signalling axes in ageing – Centre for Computational and Systems Medicine.
  • Roles: Development of culture and genomic tools to investigate and characterise the human microbiome; processing and integration of large multi-omic data sets; project coordination including ethics applications, establishment of new laboratory areas, liaising with external collaborators and stake-holders

Research assistant | Murdoch University and Western Australian Police, 2020

  • Molecular forensic DNA laboratory work and analysis
  • Principal investigator: Dr. Shanan Tobe
  • Roles: Processing of samples in clean laboratory, development of polymerase chain reactions (PCR), genomic sequencing, data processing and reporting.

Demonstrator | Murdoch University, 2020–2017

  • Sessional teaching and marking for undergraduate units: Veterinary Parasitology (VET278), Veterinary Microbiology (VET211), Forensic DNA Analysis (BIO352).

Research assistant | Murdoch University and Department of Primary Industries, 2018

  • Casual research role in the dietary analysis of feral pigs using high-throughput sequencing.
  • Principal investigators: Dr. Peter Adams and Dr. Charlotte Oskam
  • Roles: Wet laboratory processing of samples for amplicon high-throughput sequencing and data analysis.

Super computing internship | Pawsey Supercomputing Centre and CSIRO, 2018–2017

  • Summer internship role on the Meta-analysis of Australian tick microbiomes. Video of my experiences.
  • Principal investigator: Dr. Charlotte Oskam
  • Roles: Development and document of computational workflows for high-throughput sequencing, website.

Publications

Journal Articles

Sanabria, J., Egan, S., Masuda, R., Lee, A., Gibson, G. R., Nicholson, J. K., Wist, J., Holmes E. 2022. Overview of the Nomenclature and Network of Contributors to the Development of Bioreactors for Human Gut Simulation Using Bibliometric Tools: A Fragmented Landscape. Journal of Agricultural and Food Chemistry, 70(37), 11458–11467. DOI: 10.1021/acs.jafc.2c03597

Gutierrez, C. F., Romero A. N., Egan, S., Holmes, E., Sanabria, J. 2022. Exploiting the potential of bioreactors for creating spatial organisation in the soil microbiome: A strategy for increasing sustainable agricultural practices. Microorganisms, 10(7), 1464. DOI: 10.3390/microorganisms10071464

Egan, S., Lettoof, D., Oskam, C. 2022. First record of the stump-tailed lizard tick, Amblyomma albolimbatum (Ixodida, Ixodidae) parasitising a human. Ticks and Tick-Borne Diseases, 13(1), 101873. DOI: 10.1016/j.ttbdis.2021.101873

Egan, S., Taylor, C., Banks, P., Northover, A., Alhstrom, L., Ryan, U., Irwin, P., Oskam C. 2021. The bacterial biome of ticks and their wildlife hosts at the urban-wildland interface. Microbial Genomics, 7(12), 000730. DOI: 10.1099/mgen.0.000730

Egan, S., Taylor, C., Austen, J., Banks, P., Northover, A., Alhstrom, L., Ryan, U., Irwin, P., Oskam C. 2021. Haemoprotozoan surveillance in peri-urban native and introduced wildlife from Australia. Current Research in Parasitology & Vector-Borne Diseases, 1, 100052. DOI: 10.1016/j.crpvbd.2021.100052

Hall, J., Rose, K., Austen, J., Egan, S., Bilney, R., Kambouris, P., MacGregor, C., Dexter, N. 2021. Baseline health parameters for a newly established population of long-nosed potoroo (Potorous tridactylus) at Booderee National Park, Australia. Journal of Wildlife Diseases, 57(3), 515–524. DOI: 10.7589/JWD-D-20-00168

Braima, K., Zahedi, A., Egan, S., Austen, J., Xiao, L., Witham, B., Pingault, N., Perera, S., Oskam, C., Reid, S., Ryan, U. 2021. Molecular analysis of cryptosporidiosis cases in Western Australia in 2019 and 2020 supports the occurrence of two swimming pool associated outbreaks and reveals the emergence of a rare C. hominis IbA12G3 subtype. Infection, Genetics and Evolution, 92, 104859. DOI: 10.1016/j.meegid.2021.104859

Braima, K., Zahedi, A., Oskam, C., Austen, J., Egan, S., Reid, S., Ryan, U. 2021. Zoonotic infection by Cryptosporidium fayeri IVgA10G1T1R1 in a Western Australian human. Zoonoses and Public Health, 68(4), 358–360. DOI: 10.1111/zph.12806

Egan, S., Ruiz-Aravena, M., Austen, J., Barton, X., Comte, S., Hamilton, D., Hamede, R., Ryan, U., Irwin, P., Jones, M., Oskam, C. 2020. Blood parasites in endangered wildlife: trypanosomes discovered during a survey of haemoprotozoa from the Tasmanian devil. Pathogens, 9(11), 873. DOI: 10.3390/pathogens9110873

Boulet, C., Egan, S., Jones, L., Jonsdottir, T., Power, M., Ralph, S., Tran, L., White, M. 2020. Parasitravaganza 2020: Insights into a Virtual Parasitology Conference. Trends in Parasitology, 36(11), 867–875. DOI:
10.1016/j.pt.2020.09.009

Austen, J., Van Kampen E., Egan, S., O’Dea, M., Jackson, B., Ryan, U., Irwin, P., Prada, D. 2020. First report of Trypanosoma dionisii (Trypanosomatidae) identified in Australia. Parasitology, 147(14), 1801–1809. DOI:
10.1017/S0031182020001845

Egan, S., Taylor, C., Austen, J., Banks, P., Alhstrom, L., Ryan, M., Irwin, P., Oskam C. 2020. Molecular identification of the Trypanosoma (Herpetosoma) lewisi clade in black rats (Rattus rattus) from Australia. Parasitology Research, 119(5), 1691–1696. DOI: 10.1007/s00436-020-06653-z

Egan, S., Loh, S-M., Banks, P., Gillet, A., Alhstrom, L., Ryan, M., Irwin, P., Oskam C. 2020. Bacterial community profiling highlights complex diversity and novel organisms in wildlife ticks. Ticks and Tick-Borne Diseases, 11(3), 101407. DOI: 10.1016/j.ttbdis.2020.101407

Evans, M., Egan, S., Irwin, P., Oskam, C. 2019. Automatic Barcode Gap Discovery reveals large COI intraspecific divergence in Australian Ixodidae. Zootaxa, 4652(2), 393–396. DOI: 10.11646/zootaxa.4656.2.13

Irwin, P., Egan, S., Greay, T., Oskam C. 2018. Bacterial tick-associated infections in Australia: Current studies and future directions. Microbiology Australia, 39(4), 200-202. DOI: 10.1071/MA18063

Loh, S-M., Egan, S., Gillet, A., Banks, P. B., Ryan U. M., Irwin, P. J., Oskam, C. L. 2018. Molecular surveillance of piroplasms in ticks from small and medium-sized urban and peri-urban mammals in Australia. International Journal of Parasitology: Parasites and Wildlife 7(2), 197-203. DOI: 10.1016/j.ijppaw.2018.05.005

Conference presentations

Egan, S. 2022. Influence of the gut microbiome in metabolism of chiral amino acids. Precision Nutrition Symposium, Murdoch University.

Egan, S. 2022. Individual profiling substrate utilization of the gut microbiome. ASEAN Microbiome Nutrition Centre, Singapore.

Egan, S. 2021. The bacterial biome of ticks and their wildlife hosts at the urban-wildland interface. Global Microbiome: West Coast Microbiome Network, Perth, Western Australia. Award winner.

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 (ISTTBD-XIV), online, hosted by German Society for Parasitology (DGP). Award winner.

Egan, S., Fontaine, J., Ryan, U., Irwin., and Oskam C. . Molecular and ecological insights into the ornate kangaroo tick, Amblyomma triguttatum. 10th Tick and Tick-borne Pathogen Conference (TTP10), Romania.

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

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.

Egan, S., Evans, M., Irwin, P., and Oskam, C. 2019. Molecular barcoding of Australian hard ticks (Ixodidae). Australian Society for Parasitology Annual Conference, Adelaide, South Australia.

Egan, S., Siew-May, L., Gillet, A., Banks, P., Ryan U., Irwin, P., and Oskam, C. 2018. Ticks parasitizing Australian wildlife and surveillance of potential tick-borne pathogens. Australian Society for Parasitology Annual Conference, Melbourne, Victoria.

Poster presentations

Egan, S., Loh, S-M., Banks, P., Gillett, A., Ahlstrom, L., Ryan, U., Irwin. P., and Oskam C. . The Australian tick microbiome: highlighting the diversity down under. 10th Tick and Tick-borne Pathogen Conference (TTP10), Romania.

Egan, S., Greay, T., Gofton, A., Ryan U., Irwin, P., and Oskam, C. 2018. What’s in a tick? Meta-analysis of microbial diversity in Australian ticks. Global Microbiome II 2018 (West Coast Microbiome Network), Perth, Western Australia.

Egan, S., Siew-May, L., Gofton, A., Greay, T., Banks, P., Irwin, P., and Oskam, C. 2017. Are bandicoot ticks a reservoir for novel bacteria? Combined Biological Sciences Meeting, Perth, Western Australia.

Grants & Awards

  • Seed Grant (Research & Innovation), Murdoch University, awarded November 2021 (co-investigator)

  • Seed Grant (pool B), Spinnaker Health Research Foundation, awarded November 2021 (co-investigator)

  • Flash talk presentation winner, Global Microbiome Perth (West Coast Microbiome Network), awarded August 2021

  • Sinnecker-Kunz Award for early career researchers (ECRs) presented at the 14th International Symposium on Ticks and Tick-borne Diseases (ISTTBD-XVI), 1st place out of 12 ECRs selected to present, awarded March 2021 Murdoch Media write up

  • Holsworth Wildlife Research Endowment grant (Ecological Society Australia) awarded October 2020

  • Ticks and tick-borne pathogens (TTP10) conference student grant awarded February 2020 [postponed to 2022]

  • Concepts in Parasitology course sponsorship (Bayer Australia) awarded November 2019

  • Holsworth Wildlife Research Endowment grant (Ecological Society Australia) awarded July 2019

  • Australian Society for Parasitology Conference Travel Grant awarded July 2019

  • Australian Society for Parasitology Conference Travel Grant awarded September 2018

  • Holsworth Wildlife Research Endowment grant (Ecological Society Australia) awarded June 2018

  • Research Training Program (PhD tuition and stipend) scholarship (Australian Government) awarded 2018

  • Best poster design at the Combined Biological Sciences Meeting awarded August 2017

  • Myrtle AB Lamb Honours Scholarship (Murdoch University) awarded March 2017

Teaching

In addition to casual laboratory demonstrating for undergraduate units, I have also coordinated and written material for the following:

Research student supervision

  • Talya Conradie, Masters (Research) - Cataloguing the lung-associated virome using data from shotgun metagenomic studies.
  • Ash Peck, Doctor of Philosophy - Investigating mosquito-borne viruses and parasites in Western Australia using next-generation sequencing.
  • Ruby Dixon, Bachelor of Science Honours - Identification of unique microbial signatures pre- and post-coitus in male-female pairings by next generation sequencing and its potential to detect sexual contact.

Service and presentations

Conference Organising Committee, West Coast Microbiome Network, Global Microbiome, Present–2021

Statistical Bioinformatics Seminar, The University of Sydney, Sydney Precision Bioinformatics Alliance, 2022

Career Workshop, Murdoch University, Student Society Medical, Molecular and Forensic Science, 2022

International Woman’s Day, Murdoch University, #breakthebias video, 2022

Women in STEMM Research Symposium, Murdoch University, 2021

Volunteer ResBaz, Perth as workshop helper, Curtin University, 2021

WISE Women Outreach, STEMM Workshop for high school students, Murdoch University, 2021

What’s in the wildlife? Ticks & microbes, Online seminar series, Australian Society for Parasitology, 2021

Conference Organising Committee, Online Parasitravaganza, Australian Society for Parasitology, 2020

Student Chapter Committee, Wildlife Disease Association Australiasia, 2019–2018

Murdoch University Open Day, Parasitology display, 2019

STEM & Supercomputers - career’s night, Pawsey Supercomputing Centre, Event write up, 2018

Perth Royal Show, Parasitology Life Undercover Display, 2017

Field and Laboratory Assistant, Parasitology Department, Murdoch University, 2016–2014

Secretary, Western Australia Wildlife Rehabilitation Council Inc., 2016–2014

Animal attendant, Little Paws Animal Rescue, 2015–2014

Peer review

  • PeerJ (2019)
  • Parasites & Vectors (2020)
  • Microbial Ecology (2021)
  • PLoS One (2021)

Training & Skills

Training courses

A selection of relevant short courses and workshops

  • Concepts in Parasitology, November–December 2019
    • Held at the Australian National University, Canberra & Kioloa, Australia.
    • Coordinated by the Australian Society for Parasitology.
  • ASMI BioInfoSummer, December 2018
    • Held at the University of Western Australia, Perth, Australia.
    • Coordinated by the Australian Mathematical Sciences Institute (AMSI).
  • 5th National Postgraduate Training Workshop in Systematics, July 2018
    • Held at The University of Adelaide, Adelaide, Australia.
    • Coordinated by the Australian Centre for Evolutionary Biology & Biodiversity.
  • Scientific use of animals, March 2018
    • Held at Murdoch University, Perth, Australia.
    • Coordinated by the Animal Ethics Committee, Murdoch University, Perth, Australia.
  • Super computing and cloud resources, June 2017
    • Held at Murdoch University, Perth, Australia.
    • Coordinated by the Pawsey Supercomputing Centre.

Technical skills

  • Computational biology and bioinformatics
    • Advanced knowledge of R/RStudio with emphasis on reproducible documentation including Rmarkdown, tidyverse, RShiny and dashboards, data interactive visualisation.
    • Advanced knowledge of linux/unix platforms with emphasis on computational genomics.
    • Experienced in use of version control software such as git.
    • Additional coding languages with intermediate knowledge - python, SQL, html, JavaScript, LaTex.
    • Experience in management of computational workflow including use of high performance computing (HPC) and virtual machines. Use of scheduling tools for HPC (e.g. SLURM) and workflow management software (e.g. snakemake).
    • Experience in analysis of large data sets and integration of multi-omic biological data.
  • Laboratory and fieldwork skills
    • Advanced skills in genomics wet laboratory including high-throughput sequencing (Illumina platform), Sanger Sequencing, polymerase chain reactions (PCR), real-time PCR, library preparation for sequencing platforms such as Illumina, PacBio, Oxford nanopore.
    • General laboratory techniques - various skills in laboratory including PC2 areas, biosafety containment, workflows for ultra-clean laboratory (forensic and ancient DNA applications), culture and molecular biology techniques, microscopy, specimen archive including museum settings.
    • Fauna field work - experience in small-medium mammal trapping, administration of anaesthesia, animal handling and collection of biological samples using non-invasive and invasive procedures (e.g. punch biopsy, blood collection). Experience also in wildlife trapping and image data analysis.