Novel metabarcoding diagnostics to safeguard against the incursion of emerging and novel canine and feline vector-borne zoonoses in Australia and Israel.

This joint PhD project will be based at the University of Melbourne, with a 12 month stay at Hebrew University of Jerusalem.

Supervision Team: Professor Rebecca Traub and Dr Vito Colella (University of Melbourne); Professor Gad Baneth (Hebrew University of Jerusalem)

Project description: Canine and feline vector-borne diseases (CVBDs) transmitted by ticks, fleas and biting-flies, are a significant cause of morbidity and mortality in companion animals. Some of these pathogens are also responsible for several well-recognized infectious diseases that are capable of being transmitted to humans (termed ‘zoonoses’), throughout the globe. In recent years, CVBDs have emerged at accelerated rates owing to increased movement of pets, exacerbated by suboptimal efficacies of anti-parasite formulations, incursions of human dwellings into previously sparsely populated habitats, and climate change, that have permitted previously exotic vectors and their pathogens to establish in new environments. This has been particularly evident in Israel (Baneth et al., 2017) and more recently Australia (https://www.agric.wa.gov.au/ehrlichiosis). Although biosecurity pathways may appear rigorous, there are several limitations, including diagnostic, that impact on risk-mitigation strategies for exotic CVBDs entering Australia and Israel. Current diagnostic methods only target a limited number of specific pathogens and are unable to detect or identify the many exotic or novel vector-borne pathogens emerging at accelerated rates globally. Early detection and recognition of these pathogens is crucial to mitigate incursion and establishment of these VBDs in Australia and Israel.

The aim of this PhD project will be to:
1. Design a portable, metabarcoding diagnostic tool based on nanopore sequencing technology, capable of highly accurate, rapid and cost-effective detection and characterisation of all known canine, and feline vector-borne parasitic and bacterial diseases in real-time.
2. Validate the accuracy and precision of this metabarcoding diagnostic tool using positive-control samples or samples experimentally seeded with known quantities of targeted disease agents.
3. Verify and compare the diagnostic test parameters of the metabarcoding diagnostic tools to traditional ‘reference’ diagnostic assays using samples from ‘high risk’ Canidae and Felidae in Australia (feral dogs, feral cats, foxes) and Israel (stray dogs, wild foxes, wolves, jackals, and feral cats).

Aim 1 will be carried out by the PhD student at UoM under Prof Traub and Dr Colella’s guidance. Prof Traub’s laboratory has strong track-record and expertise in the development and validation of diagnostic assays, in particular, next-generation sequencing-based metabarcoding methods (mNGS) for pathogen detection (Huggins et al., 2019a, b; Huggins et al., 2020). Following completion of Aim 1 and part of Aim 2 (estimated 15 months), the student will be hosted by Prof Baneth’s group at HUJ for the next 12 months, as Prof Baneth’s laboratory has access to archived library of genomic DNA and clinical samples from a broad range of pathogens otherwise unattainable in Australia, where they will complete Aim 2 and part of Aim 3. The final 9 months of the PhD will be spent back in UoM completing Aim 3 (using archived samples at Prof Traub’s lab) and finalizing thesis submission.

How to Apply

Minimum entry requirements for a PhD at Melbourne are summarised here, including visa and English language requirements. For information on applying for this project, please see here. Applications should be sent to Professor Rebecca Traub.

References: 1. Baneth, G., Yasur-Landau, D., Gilad, M., Nachum-Biala, Y., 2017. Canine leishmaniosis caused by Leishmania major and Leishmania tropica: comparative findings and serology. Parasit Vectors 10, 113.; 2. Huggins, L.G., Koehler, A.V., Ng-Nguyen, D., Wilcox, S., Schunack, B., Inpankaew, T., Traub, R.J., 2019a. Assessment of a metabarcoding approach for the characterisation of vector-borne bacteria in canines from Bangkok, Thailand. Parasit Vectors 12, 394.; 3. Huggins, L.G., Koehler, A.V., Ng-Nguyen, D., Wilcox, S., Schunack, B., Inpankaew, T., Traub, R.J., 2019b. A novel metabarcoding diagnostic tool to explore protozoan haemoparasite diversity in mammals: a proof-of-concept study using canines from the tropics. Sci Rep 9, 12644.; 4. Huggins, L.G., Koehler, A.V., Schunack, B., Inpankaew, T., Traub, R.J., 2020. A Host-Specific Blocking Primer Combined with Optimal DNA Extraction Improves the Detection Capability of a Metabarcoding Protocol for Canine Vector-Borne Bacteria. Pathogens 9. 5. Colella V, Nguyen VL, Tan DY, Lu N, Fang F, Zhijuan Y, Wang J, Liu X, Chen X, Dong J, Nurcahyo W, Hadi UK, Venturina V, Tong KBY, Tsai YL, Taweethavonsawat P, Tiwananthagorn S, Le TQ, Bui KL, Watanabe M, Rani PAMA, Annoscia G, Beugnet F, Otranto D, Halos L. 2020  Zoonotic Vectorborne Pathogens and Ectoparasites of Dogs and Cats in Eastern and Southeast Asia. Emerg Infect Dis.;26(6):1221-1233.