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Does E. coli survive in rivers on its way from the farm to the fork?

Primary Supervisor: Dr Joshua Larsen, GEES

Secondary supervisor: Dr Jan-Ulrich Kreft, School of Bioscience & Dr Jen Drummond, GEES

PhD project title: Does E. coli survive in rivers on its way from the farm to the fork?

University of Registration: University of Birmingham

Project outline:

Escherichia coli (E. coli) are not only resident in animal and human guts but can also make their way through various environmental pathways back to other animal and human guts. Most E. coli are commensal bacteria that pose no significant health risk, but some are pathogens and/or carry antimicrobial resistance (AMR) genes, which could transfer to other strains. Given their ubiquity, the risk of agricultural produce becoming contaminated with strains of E. coli is sufficient to drive a multi-billion dollar food security program.

Despite the severity of this risk, we know little about the survival and transport of E. coli in the environment. Some studies have suggested that it can survive much longer than commonly thought (e.g., up to six weeks in riverbed sediments). However, it is unclear whether strains that reside in the environment for long times become adapted to the environment and are still competitive enough to establish themselves in the guts of warm-blooded organisms.

Once E. coli leaves the warm animal or human colon, it is transported through sewage pipelines to a wastewater treatment plant, where many E. coli will be removed but a few will enter river networks, especially during heavy rainfall when the capacity of treatment plants is exceeded and raw sewage can enter rivers. Additional pathways of E. colicontamination include direct surface runoff and groundwater seepage from farms and fields, and in some cases from animals that have direct access to river water. This river water may then be subsequently used for field irrigation, which if contaminated can lead toE. coli washed onto crops. Of particular concern are vegetable crops that are eaten raw such as lettuce. Once in rivers, E. coli can be inactivated or killed by the UV in sunlight but survives in the river bed sediments. The interface between water and sediments is therefore particularly important as heavy rain will resuspend sediment containing E. coli and transport this downstream while the water is turbid and with limited direct sunlight. Our hypothesis is that E. coli can survive for a long time in river sediments, such that it can eventually be resuspended into the water body, flood onto fields or be used for irrigation, and eventually ending up on a dinner table.

We will take samples from the environment (river water and sediment) to isolate and sequence resistant E. colistrains. We will also incubate these samples in the lab to track changes over time under controlled conditions in mesocosms (basically containers with sediment or water samples) to quantify survival or growth of E. coli in different habitats. We will also apply a mathematical model of the transport and short- and long-term retention of bacteria (particles) in rivers that incorporates the important exchange between water and underlying sediments, that can account for both low and high flow conditions. Using inputs of continuous river flow data and the E. coli water and sediment measurements, the model can be calibrated through multiple storm events to help improve predictions of E. coli transport, survival and persistence. This hydrodynamic model will be combined with a simple model of the growth and survival of E. coli based on the abundance data and mesocosm time series. The combined model can then predict the transport and fate of E. coli in the environment. This information will be vital for analysing the risk for a consumer to ingest resistant strains of E. coli and informing future government policy. This project will also allow the public to be better informed regarding the use of contaminated water sources and whether they pose a risk to food security, we would therefore prioritise disseminating our findings in both outreach activities as well as scientific publications.


  1. Jamieson, R.C., Joy, D.M., Lee, H., Kostaschuk, R., Gordon, R.J., 2004. Persistence of enteric bacteria in alluvial streams. J. Environ. Eng. 3, 203e212.
  2. Drummond, J. D. et al. Microbial transport, retention, and inactivation in streams – a combined experimental and stochastic modeling approach. Environ. Sci. and Technol. 49, 7825–7833 (2015).
  3. Brennan FP, O’Flaherty V, Kramers G, Grant J, Richards KG (2010). Long-Term Persistence and Leaching of Escherichia coli in Temperate Maritime Soils. Appl. Environ. Microbiol. 76: 1449–1455
  4. Ravva SV, Sarreal CZ, Mandrell RE (2014). Strain differences in fitness of Escherichia coli O157:H7 to resist protozoan predation and survival in soil. PLoS ONE 9: e102412

BBSRC Strategic Research Priority: Sustainable Agriculture and Food: Microbial Food Safety

Techniques that will be undertaken during the project:

  • Environmental sampling and field work
  • Isolation and culturing
  • Sequencing, bioinformatics, phylogenomics, epidemiology
  • Laboratory mesocosm experiments
  • Mathematical model design, simulation, combination, and analysis of hydrology and E. coli models.
  • Statistical analysis

Contact: Dr Joshua Larsen, University of Birmingham