Microbial source tracking


Faecal contamination of drinking water poses an obvious hazard to human health. Faeces may contain a variety of microbes that can make us sick (pathogens). Blocking the spread of these organisms from animals and humans to drinking water supplies is a public health priority everywhere, particularly given the United Nations Sustainable Development Goal of safe and affordable water for all by the year 2030. Achieving this ambitious target will require a concerted long-term effort by all those working in the field of water, sanitation and hygiene. It will also need new ways of thinking.

Drinking water quality monitoring is one approach that can support efforts to expand safe water access. Traditionally, testing for bacteria commonly found in warm-blooded animals, sometimes called ‘faecal indicator bacteria’, is used to identify when water is contaminated with faeces. However, because these bacteria are found in both people and livestock, such tests do not identify the source of faecal contamination. To overcome this problem, a set of more experimental techniques known as ‘microbial source tracking’ has been established. The contamination source can be important – animal faeces may contain ‘zoonotic’ pathogens (e.g., Cryptosporidium and toxigenic E. coli) that can cause serious diseases in humans, particularly among the very young and the elderly.
In recent years, microbial source tracking (MST) has been proposed as a way of identifying the source of faecal contamination of drinking and bathing waters. Many different methods have been proposed, which vary widely in cost and their ability to pin-point specific contamination sources. A method recently developed at the University of Brighton (in collaboration with the University of Barcelona) uses traditional laboratory methods to identify contamination sources at relatively low cost.

Box 1 – Using bacteriophages to track sources of water contamination: University of Brighton’s method works by detecting bacteriophages (‘phages’), a class of viruses that attack bacteria. Phages have a limited bacterial host range and by using bacterial host strains that are only found in humans (or cattle), it is possible to distinguish phages in the environment that demonstrate faecal pollution from these sources. To detect these phages, samples are taken from animal slurry and wastewater facilities such as latrines, but also from water at risk of contamination. Using the slurry and wastewater samples, strains of common gut bacteria from specific sources (e.g. cattle; humans) are grown as a ‘lawn’ within agar in petri plates, to which a few millilitres of the water sample to be tested are added. If phages from a particular source (e.g. cattle) are present in the water to be tested, they will produce clear zones or ‘plaques’ in the lawn. This happens as the bacteria from that source are attacked and disintegrate through a process known as lysis. Counting these plaques is a way of indirectly counting the concentration of the viruses in the water and so estimating the degree of pollution from a specific animal source.


Although the method has been used fairly widely in Europe to investigate sources of pollution in rivers, coastal bathing waters and shellfisheries, it remains essentially a research tool at this stage. It requires further investigation to adapt it to the needs of areas of the world where contaminated drinking water is a major cause of human suffering.

MST is a novel and key component of this project, and will be used to investigate the impact of cattle rearing on drinking water supplies in rural Kenya. In combination with a variety of other approaches, our team hope that it will contribute to better rural water safety planning in Africa and support strategies for maintaining safe drinking water for all. MST will also be an important element of the capacity building aspects of the project. Experts from the University of Brighton will work closely with their Kenyan collaborators to adapt the method and to establish it within a Kenyan research laboratory as a basis for Africa-based research developments in the future.