ScottScott Mitchell, PhD Student

The effect of microbiome composition on antibiotic resistance gene prevalence and horizontal gene transmission in the equine hindgut

Supervisors: Belinda Chapman (QB), Michelle Bull (QB), Nick Coleman (USyd)

Synopsis: The equine hindgut is a complex ecosystem (Dicks et al. 2014) where the effects of exogenous factors on the microbiome have not yet been fully characterized, but where there is evidence for both a core microbiome (e.g. Dougal et al. 2013) ) and dysbiosis (e.g. Costa et al. 2015) that mirrors concepts established for the human gastrointestinal tract. Like the human gut microbiome (Broaders et al. 2013; Ravi et al. 2015), the rich equine hindgut environment also appears to present ample opportunity for horizontal gene transfer (HGT), including acquisition and accumulation of antibiotic resistance (AR) determinants (Gronvøld et al. 2010). Acquisition of AR is a key area for HGT research, with much focus on the effect of anthropogenic activities (e.g. antibiotic overuse in humans and livestock, antibiotic contamination of grazing sites, etc.) (Davies & Davies, 2010). However, HGT is a much older response to competition and stress within complex microbial ecosystems that may also confer host advantages beyond the obvious AR (Davies & Davies, 2010). The equine hindgut, with its prokaryotic and eukaryotic diversity is a unique environment in which to study the evolutionary and ecological drivers and benefits of HGT. This study will contribute to an improved understanding of the broader problems of AR. The close interactions of horses and humans, including the use of horses in a variety of sporting pursuits, and the use of horse manures and bedding as fertilisers in large scale horticulture industries such as the mushroom industry, provide further reason for the study of AR gene transfer in horses, since these animals may be links in the chain of AR gene transfer in the environment.


Broaders, E., Gahan, C.G.M., Marchesi, J.R. 2013. Mobile genetic elements of the human gastrointestinal tract, potential for spread of antibiotic resistance genes. Gut Microbes, 4(4):271-280.

Costa, M.C, Stämpfli, H.R., Arroyo, L.G. Allen-Vercoe, E., Gomes, R.G., Weese, J.S. 2015. Changes in the equine fecal microbiota associated with the use of systemic antimicrobial drugs. BMC Veterinary Research, 11:19. doi:10.1186/s12917-015-0335-7.

Davies, J., Davies, D. 2010. Origins and evolution of antibiotic resistance. Microbiology and Molecular Biology Reviews, 74(3):417-433.

Dicks, L.M.T., Botha, M., Dicks, E., Botes, M. 2014. The equine gastro-intestinal tract: An overview of the microbiota, disease and treatment. Livestock Science, 160:69-81.

Dougal, K., de la Fuente, G., Harris, P.A., Girdwood, S.E., Pinloche, E., Newbold, C.J. 2013. Identification of a core bacterial community within the large intestine of the horse. PloS ONE, 8(10): e77660. doi:10.1371/journal.pone.0077660.

Gronvøld, A-M.R., Abée-Lund, T.M., Strand, E., Sørum, H., Yannarell, A.C., Mackie, R.I. 2010. Fecal microbiota in the clinical setting: potential effects of penicillin and general anesthesia. Veterinary Microbiology, 145:366-372.

Ravi, A., Avershina, E., Foley, S.L., Ludvigsen, J., Storrø, O., Øbien, T., Johnsen, R., McCartney, A.L., Abée-Lund, L., Rudi, K. 2015. The commensal infant gut meta-mobilome as a potential reservoir for persistent multidrug resistance integrons. Scientific Reports, 5:15317. doi:10.1038/srep15317.

Darcii Terre, Honours student

Clinically significant fungal species in the sand of NSW beaches, influenced by seasonality,  type of beach, tidal zone, human activities, animal presence and quantity of organic matter

Supervisors: Belinda Chapman (QB), Laszlo Irinyi (USyd), Wieland Meyer (USyd)

Synopsis: The impact of fungal infections are often neglected despite the fact that annually, more than 14.9 million people suffer from various fungal infections, with over 1.7 million deaths related to fungi worldwide (Jugessur & Denning, 2016). Recently, beach sand has been implicated as a possible reservoir or vector for microbial infections (Nestor et al., 1984), epidemiological studies are underway, investigating associations between contact with beach sand and risk of illness (Sabino et al., 2014; Whitman et al., 2014). As the Australia coastline consists of numerous beaches, regularly used for recreational activities by locals and tourist alike, the presence of potentially pathogenic fungi in sand has significance (Mendes, Nascimento & Oliveira, 1993) to public health (WHO & Organization, 2003) and data needs to be collected to asses this significance. It is important to investigate if there are any medically relevant fungal species present in beach sand in NSW and how their abundance is altered by the characteristics and seasonality of the beach. This study will assess the need for programs regularly monitoring the microbial presence in and around recreational waters in order to determine any implications and further actions to public health and safety (WHO & Organization, 2003).


Jugessur, J & Denning, D 2016, Hidden crisis, viewed August 14, 2017,

Mendes, B, Nascimento, M & Oliveira, J 1993, ‘Preliminary characterisation and proposal of microbiological quality standard of sand beaches’, Water Science and Technology, vol. 27, no. 3-4, pp. 453-456.

Nestor, I, Costin-LazÃ¥r, L, Sovrea, D & Ionescu, N 1984, ‘Detection of enteroviruses in seawater and beach sand’, Zentralblatt fur Bakteriologie, Mikrobiologie und Hygiene. 1. Abt. Originale B, Hygiene, vol. 178, no. 5-6, pp. 527-534.

Sabino, R, Rodrigues, R, Costa, I, Carneiro, C, Cunha, M, Duarte, A, Faria, N, Ferreira, FC, GargatÃ, MJ, JÃio, C, Martins, ML, Nevers, MB, Oleastro, M, Solo-Gabriele, H, Veríssimo, C, Viegas, C, Whitman, RL & BrandÃo, J 2014, ‘Routine screening of harmful microorganisms in beach sands: Implications to public health’, Science of The Total Environment, vol. 472, pp. 1062-1069.

Whitman, RL, Harwood, VJ, Edge, TA, Nevers, MB, Byappanahalli, M, Vijayavel, K, Brandão, J, Sadowsky, MJ, Alm, EW & Crowe, A 2014, ‘Microbes in beach sands: integrating environment, ecology and public health’, Reviews in Environmental Science and Bio/Technology, vol. 13, no. 3, pp. 329-368.

Who & Organization, WH 2003, Guidelines for safe recreational water environments. Volume 1: coastal and fresh waters, World Health Organization.