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Rice farming and rodent-borne zoonoses

Primary Supervisor: Dr. Erin Gorsich, School of Life Sciences

Secondary supervisor: Professor Mike Tildesley

PhD project title: Rice farming and rodent-borne zoonoses

University of Registration: University of Warwick

Project outline:

Land-use changes due to intensified agricultural practices are a concern in the Philippines (Dirzo et al, 2014). The replacement of forests by mixed agroecosystems and high-value crops has led to biodiversity loss and increased contact of humans with wild animal populations. Consequently, changes in the ecology of wild animals have led to changes in the epidemiology of diseases and emergence of novel livestock and human pathogens, e.g. zoonotic diseases (Olival et al, 2017).

In the Philippines, 4.7 million hectares of land are dedicated to rice farming alone (PhilRice, 2020). Rice is a vital dietary component in the Philippines that provides an estimated 109-kilogram of food per-capita each year. However, the rise of rice production has also provided generalist rodent species increased availability of food sources (Singleton et al, 2008). Due to their role as disease vectors, increases in their abundance and anthropogenically driven shifts in their distribution pose a significant threat to the public health (Baker, 2007). A study investigating the effect of land cover data on rodent pathogen prevalence identified a positive association between synanthropic rodent abundance and increased habitat fragmentation and agricultural land cover (Morand et al, 2019). The study also revealed an association between these human-altered landscapes and the presence of zoonotic pathogens. While it is known that human-altered landscapes, particularly agroecosystems influence the transmission of infectious diseases in general, a mechanistic understanding of how changes from agricultural practices influence disease risk is needed. This information could inform current surveillance efforts as well contribute to a broader understanding of disease spill-over.  

Therefore, this project will investigate the transmission ecology of rodent borne disease in agroecosystems. It will apply an interdisciplinary and systems approach to uncover key mechanisms influencing pathogen dynamics within the rodent vectors as well as the pathways / barriers to disease spill-over from rodents to humans or livestock. Specifically, the study aims to:

  1. Identify how agricultural practices and the environment (weather and landscape) influence of rodent population growth and their spatial distribution.
  2. Evaluate the effects of rodent population dynamics on pathogen prevalence?
  3. Identify the demographics and knowledge, attitude, and practice (KAP) of rice farmers that contribute to their exposure to rodent-borne zoonoses; and
  4. Create a predictive risk map of disease incidence and intensity for rodents and rice farmers based on the evaluated risk factors that drive ecological pathways of pathogens.


  1. Baker, D.G. (2007). Flynn’s parasites of laboratory animals (2nd edition). Blackwell.
  2. Dirzo, R.H.S., Young, M., Galetti, G., Ceballos, N., Isaac, J., & Collen, B. (2014). Defaunation in the Anthropocene. Science 345:401–416.
  3. Morand, S., Blasdell, K., Bordes, F., Buchy P., Carcy, B., Chaisiri, K., Chaval, Y., Claude, J., Cosson, J., & Desquesnes, M. (2019). Changing landscapes of Southeast Asia and rodent-borne diseases: decreased diversity but increased transmission risks. Ecological Applications DOI: 10.1002/eap.1886.hal-02105014.
  4. Olival, K.J., Hosseini, P.R., Zambrana-Torrelio, C., Ross, N., Bogich, T.L., & Daszak, P. (2017). Host and viral traits predict zoonotic spill-over from mammals. Nature 546:646–650.
  5. Philippine Rice Research Institute. (n.d.). Rice Statistics - PalayStat System (2021): Estimated production, area harvested and yield per hectare (PAY). Retrieved September 4, 2021, from
  6. Singleton, G.R., Joshi, R.C., & Sebastian, L.S. (2008). Philippine Rats: Ecology and Management. Philippine Rice Research Institute: Science City of Muñoz, Nueva Ecija.

BBSRC Strategic Research Priority: Sustainable Agriculture and Food:Animal Health and Welfare & Plant and Crop Science

Techniques that will be undertaken during the project:

Identifying the effects agricultural practices on rodent abundance and density will require a range of computational techniques applied to existing datasets collected by IRRI. These include mapping and statistical methodologies such as longitudinal data analysis and mark-recapture models. Data collection to estimate zoonotic pathogen prevalence will require a combination of molecular and traditional parasitology, as well as rodent trapping and identification. Finally, linking the animal density data with the pathogen data will build on traditional epidemiology methods to model disease spread, e.g. SIR models. Additional techniques are possible if the applicant is interested in model fitting or sustainable development.

Contact: Dr Erin Gorsich, University of Warwick