:: New UPGro Paper :: Tryptophan-like fluorescence as a measure of microbial contamination

A new paper has been published from the UPGro Gro for GooD project, working in Kenya, which develops the work done under the UPGro Catalyst Project on mapping groundwater quality, which developed an exciting new low-cost, real-time method of measuring microbial contamination of groundwater.


  • Globally, 25% of people lack access to water that is free from microbial contamination, in some countries the proportion is much higher.  This has major health implications, particularly for children.
  • Monitoring water quality for disease-causing organisms is difficult, and the common method is take water samples to a lab to measure Coli bacteria. Although largely successful, it is an expensive in terms of time and materials, and cannot be relied on for some kinds of biological water quality risks – particularly in groundwater where the absence of E.Coli does not guarantee biological safety of the water.
  • Tryptophan-like fluorescence (TLF) is a relatively new way of rapidly measuring biological water quality in the field, without needing expensive and time-consuming lab equipment and consumables. It is better suited to groundwater than surface water monitoring.

Key Points: –

  • This is the first groundwater study to compare TLF with E. Coli specifically.
  • Tryptophan-like fluorescence (TLF) can complement E. coli as a risk indicator, but it is not proposed as a replacement.
  • Both TLF and coli distinguish low/intermediate, high and very high risk sources.
  • TLF has negligible variability due to the method, unlike bacteriological analyses.
  • TLF is useful for pre-screening, monitoring and demonstrating risk in groundwater.
  • Fieldwork for this research was done in rural Kwale Country, Kenya
  • Next steps include:
    • focus on how TLF relates to pathogens and health, rather than just focusing on the coincidence with E.Coli.
    • better understanding of TLF in different groundwater conditions
    • better computer software of processing and presenting TLF data
    • assess the usefulness of TLF in communicating water risks to groundwater users.

Read the full paper (open access) here:

Nowickia, S.,  D. J.Lapworth, J.S.T. Ward, P. Thomson & K. Charles (2019) Tryptophan-like fluorescence as a measure of microbial contamination risk in groundwater, Science of The Total Environment, Volume 646, 1 January 2019, Pages 782-791 https://doi.org/10.1016/j.scitotenv.2018.07.274

If you are interested in finding out more on safe water and water quality monitoring then you watch these RWSN webinar recordings from late last year:

  • Safe water in towns and peri-urban areas: challenges of self-supply and water quality monitoring: https://vimeo.com/266654585
  • La salubrité de l’eau dans les villes et zones péri-urbaines: le défis liés à l’auto-approvisionnement et le suivi de la qualité https://vimeo.com/266649345

Safe water in towns and peri-urban areas: challenges of self-supply and water quality monitoring

Millions of people in towns and cities across Sub-Saharan Africa depend on groundwater day-to-day – but is it safe to drink? How can we measure the safety quickly, cheaply and accurately?  In this RWSN-UPGro webinar, Dr Jenny Grönwall (SIWI/T-GroUP) and Dr Dan Lapworth (BGS) present the latest updates on their research into urban groundwater monitoring and use, and how it can be improved.

Groundwater – the earth’s renewable wealth

By Sean Furey, Skat Foundation/RWSN/UPGro

Where does wealth come from? At its most basic, it is the difference between how much you invest in a product or service and how much you get from selling it. If the difference is positive you get wealth, if it is negative then you get trouble.

For a country like Zambia, the biggest source of wealth comes from underground: copper, oil and many other minerals and metals. Every aspect of our lives, from fertilisers, to homes, to solar panels depends on what can be dug from the ground. The scale on which mining and quarrying is done varies from a single person digging a hole, to the world’s largest machines demolishing mountains. Mining is also an economic activity that stretches from the very local to the most globalised trade.

In that context, groundwater can also be seen as a mineral resource on which the wealth of a country depends, so it was great that UPGro and RWSN were invited by the University of Zambia to run a special session on hydrogeology in Africa at the International Conference on Geology, Mining, Mineral and Groundwater Resources of the Sub-Saharan Africa, held in Livingstone, Zambia, in July.

The conference was opened by the President of Zambia, HE Edgar Lungu, who stressed the importance of groundwater and mineral resources to the economy, society and environment of Zambia and Africa more widely.

He was followed by a keynote speech by UPGro Ambassador, Dr Callist Tindimugaya of the Ministry of Water & Environment Uganda who gave the 400+ audience an overview of exciting groundwater initiatives happening across Africa, in particular highlighting UPGro, GRIPP, RWSN’s work on drilling professionalisation,the Africa Groundwater Network and the re-boot of the AMCOW Africa Groundwater Commission which took place the following week in Dar es Salaam.

One of the eye-opening facts that was presented by the government during the event that more than half of electricity generated in Zambia is used by the mining industry and most of that is used for de-watering mines – pumping water out of the ground and dumping it – contaminated – into rivers. Clearly a change in mindset is needed to see groundwater as a source of wealth to be used wisely for the benefit of all, not a problem that sends money pouring down the drain.

photos: Dr Callist Tindimugaya gives a keynote presentation on Groundwater Resources Management in Sub-Saharan Africa: Status, Challenges and Prospects.

UPGro-RWSN Special Session on Hydrogeology in Africa and Drilling Professionalisation



New pollution risk maps for Africa to help with achieving safe water for everyone


Media Release: World Water Day 22 March

New pollution risk maps for Africa to help with achieving safe water for everyone.
Responding to UNICEF/WHO report on Safely managed drinking water

The United Nations Children’s Fund (UNICEF) and the World Health Organisation (WHO) have published a key Joint Monitoring Programme (JMP) report on “Safely managed drinking water”[1]. It explains the way that the progress in improving drinking water will be measured across the world in pursuit of the Sustainable Development Goal Target 6.1 of achieving universal and equitable access to safe and affordable drinking water for all by 2030[2]. This is an immensely challenging target, particularly in many countries in Sub-Saharan Africa, which failed to reach the Millennium Development Goal Target of halving the number of people without access to an “improved” water source between 1990 and 2015.

For governments, aid agencies and citizens, a key question has been – what do we mean by “safe” water? This new JMP report starts to provide some of those answers. They define it to mean water that is “free from pathogens and elevated levels of toxic substances at all times”.  For many areas, the most accessible safe water is from the ground – from boreholes, wells and springs. But this is not the case everywhere.

There is no question about the importance of groundwater in sub-Saharan Africa, where it provides drinking water supplies for at least 170 million people. In comparison with surface water, groundwater is widely known for its greater reliability, resilience to climate variations and reduced vulnerability to pollution. However, groundwater contamination does occur when waste from households, municipalities, livestock, agriculture, hospitals and industries (including mining) is able to make its way Inadequate management of household and industrial waste is leading to the pollution of groundwater resources in urban centres in sub-Saharan Africa.

In a new landmark study just published[3], reviewed all the available data and studies on urban groundwater across the continent and build up a map of aquifer pollution risk (Fig. 1)

The lead researcher, Dr Daniel Lapworth, of the British Geological Survey, said: “Despite the risk to the health of millions of people across the continent, very little is routinely monitored. If there is any chance of achieving the Sustainable Development Goal targets – and adapting to climate change – it is essential that governments and water utilities routinely monitor groundwater quality and take appropriate action to protect their precious water resources.”

“However, we are excited that our research through has developed a low-cost and robust way for measuring groundwater quality[4], and this approach is being rolled out in our work in Africa and India.”

Fig. 1: Relationship between urban centres in sub-Saharan Africa (SSA) and estimated aquifer pollution risk using an intrinsic aquifer modelling approach (Ouedraogo et al. 2016). The location of studies included in the paper are shown. Major cities in SSA are shown and are from the ESRI cities dataset (2006)

More information

UPGro is funded by UK Aid; the UK Natural Environment Research Council (NERC); and the UK Economic and Social Research Council (ESRC). Knowledge Broker: Skat Foundation, in partnership with the Rural Water Supply Network (RWSN) www.rural-water-supply.net

For more information:

NERC media office
01793 411939 / 07785 459139 /  pressoffice@nerc.ac.uk

More details can be found on http://upgro.org ; The Knowledge Broker for UPGro is Skat Foundation, based in St Gallen, Switzerland. Contact: Sean Furey (sean.furey@skat.ch ) for more information.

[1] https://data.unicef.org/resources/safely-managed-drinking-water/

[2] https://sustainabledevelopment.un.org/sdg6

[3] Lapworth, D.J., D. C. W. NkhuwaJ. Okotto-OkottoS. PedleyM. E. StuartM. N. TijaniJ. Wright “Urban groundwater quality in sub-Saharan Africa: current status and implications for water security and public health” Hydrogeol J (2017). doi:10.1007/s10040-016-1516-6

[4] Sorensen J, D.J. Lapworth, B.P. Marchant, D.C.W. Nkhuwa, S. Pedley, M.E. Stuart, R.A. Bell, M. Chirwa, J. Kabika, M. Liemisa, M. Chibesa (2015) “In-situ tryptophan-like fluorescence: A real-time indicator of faecal contamination in drinking water supplies” Water Research, Volume 81, 15 September 2015, Pages 38–46

Zambia: Study Finds Shallow Groundwater Unsafe.

Kabwe is a transport hub and old mining town in central Zambia. One resident, Joseph, recounted how when he was growing up in the town in the 1970s, most houses had a tap and a reliable water supply from the municipal system. Few children in the town now have this luxury; in the 1980’s the world price of copper collapsed and the mines closed. Many of the townspeople could no longer afford their water bills, and the lack of investment led the municipal water system into a spiral of decline.

Today, the town continues to grow, in a haphazard way and sanitation is poor – only 11% of low income households have access to a latrine or toilet. Most of the poorer residents get water from shallow wells, and richer households have given up on the unreliable municipal water system and have their own deeper boreholes. But are these self-supply water sources safe? Does the risk change between the wet season and the dry? Is there a safe distance between latrine and well that would prevent the water from being contaminated? These are just a few questions that hard-pressed local government staff need answers to urgently, but they just can’t get data from enough wells and boreholes during the year.

Poor water quality continues to pose a major threat to human health

Many types of bacteria found in wastewater and sewage cause diarrhoeal diseases and cholera, which kill 1.8 million people every year, 90% of whom are children under 5 according to the World Health Organisation (http://www.who.int/water_sanitation_health/publications/factsfigures04/en/ ) . These bacteria are hard to measure directly, so the most common method used is to focus on bacteria, called E. Coli, which is an indicator of how unsafe water is. However, this test takes time, skill and a laboratory because the E. Coli have to be encouraged to grow so that they can be counted. What is urgently needed is a quick, cheap, accurate way of measuring this type of pollution to guide efforts to provide safe drinking water.

An answer may now be available, for Kabwe, and for water supplies all over Africa and beyond: a team, led by Dan Lapworth, from the British Geological Survey (BGS), along with colleagues from the University of Zambia, University of Surrey and Lukanga Water and Sewerage Company Ltd has been collaborating to develop a new way to measure groundwater pollution. It is a new probe that measures a protein called tryptophan and this was the first study to investigate the biological quality in groundwater using this technique.

This research was funded by DFID, NERC and ESRC through the UPGro: Unlocking the Potential of Groundwater for the Poor programme (http://upgro.org )

What they found in the wells and boreholes of Kabwe was that the amount of tryptophan measured by the probe corresponded very closely with bacteriological contamination. It confirmed that most of the shallow groundwater, which the poorest people in the town were using, was unsafe throughout both the wet and dry season, but that the deeper groundwater is generally free from faecal pollution, unless the borehole had not been sealed properly.

The advantage of the tryptophan probe is that it is quick, needs no special chemicals and cheap, so it can enable rapid surveys across dozens of wells and boreholes across the town, that just isn’t practical with traditional E. Coli testing.

The Principal Investigator, Dan Lapworth: “In a place like Africa where data scarcity and institutional capacity is a massive issue this could quickly provide a step-change in our understanding of spatial and temporal water quality risks in drinking water sources, the processes that control these and be used as a tool to monitor interventions and water quality failures.”

Although the research from the UPGro Catalyst grant has finished, others are taking an interest: the US-based charity, Water for People, asked BGS to trial the probe in rural areas of India undergoing sanitary interventions. Here, the sensor was equally successful at identifying bacteriological contamination in drinking water and the team was able to rapidly test up to 6 different supplies per hour.

Having access to safe water and basic sanitation is vital to everyone's life

In Kabwe it is now possible for the health risks from groundwater to be monitored, both across the town and over time.

Dan said “There are a number of different sensors available which can map groundwater quality risks – we have done our research on what we think is the most sensitive of these, but there is certainly room for improvement and development of this technology further for practical field based applications.”

As the international community attending the Stockholm World Water Week turns its attention to the new Sustainable Development Goals – which include achieving universal access to safe water – it is practical contributions, like the tryptophan probe that can make all the difference. For the people of Kabwe, it offers the hope that future investment in water and sanitation will deliver reliable and safe water to meet their needs.

James Sorensen, from BGS, said “These sensors were the best indicators of bacteriological contamination and water supplies could be tested within seconds”

WaterSan Perspective

Water Journalists Africa (WJA)
August 18, 2015

Kabwe is a transport hub and old mining town in central Zambia. One resident, Joseph, recounted how when he was growing up in the town in the 1970s, most houses had a tap and a reliable water supply from the municipal system. Few children in the town now have this luxury; in the 1980’s the world price of copper collapsed and the mines closed. Many of the townspeople could no longer afford their water bills, and the lack of investment led the municipal water system into a spiral of decline.

Today, the town continues to grow, in a haphazard way and sanitation is poor – only 11% of low income households have access to a latrine or toilet. Most of the poorer residents get water from shallow wells, and richer households have given up on the unreliable municipal water system and have their…

View original post 715 more words

Groundwater Resources and Supplies in Africa

24th February 2015

Two research-based presentations by: Joy Obando (Kenyatta University, Kenya) and Dan Lapworth (British Geological Survey, UK). With a focus on selected sites in in Comoros, Tanzania and Kenya, Obando’s presentation sets out key social and economic issues with respect to groundwater resources in coastal East Africa. Lapworth’s presentation examines the changes in water access and realities of groundwater resources in Kabwe, Zambia. The examples, combined with the lively exchange with participants, provide insights into the realities of drinking water for the poor in urbanising Africa. The webinar is facilitated by Jan Willem Foppen (UNESCO-IHE, Netherlands).

A tale of two cities: How can we provide safe water for poor people living in African cities?

Dan Lapworth, Jim Wright and Steve Pedley are working to find out.

Reproduced from Planet Earth Winter 2014, p 22-23

Across much of Africa, cities are growing quickly. Current projections estimate that by 2050, 60 per cent of the population will be living in urban areas – half of them in slums. Many of these people have little access to services such as clean water and sanitation, and the UN has identified fixing this as a major priority.

Continue reading A tale of two cities: How can we provide safe water for poor people living in African cities?

Poster presentations about work in Zambia and Kenya (Video)

At the IAH Congress, we asked two of the UPGro researchers to present their posters:

Jacob Mutua, Rural Focus Ltd, Kenya, describing the “Risks and Institutional Responses for Poverty Reduction in Rural Africa” Catalyst project

Dr Dan Lapworth talks about the project that he has been leading: “Mapping groundwater quality degradation beneath growing rural towns in SSA” in Zambia

Tracking pollution from a small town in Zambia

James Sorenson (BGS) walked us through his poster presentation for his Catalyst Project: Mapping groundwater quality degradation beneath growing rural towns in Sub Saharan Africa.

The story starts with a pesticide found in slug pellets, which was unexpectedly detected in UK groundwater. This prompted this research to look for similar chemicals in African groundwater, What was found was relatively high levels of DEET, known to many travellers as “Jungle Formula” for keeping mosquitos at bay.

The implications are that these potentially health impacting chemicals are not being tested for. The levels detected were low, but DEET, and similar pesticides break down very slowly, if at all. In larger urban areas, these chemicals could be entering water supply wells and boreholes at potentially harmful levels.

The level of risk is just not known yet, but this research has raised an important warning flag. However, relatively simple measures, such as well protection is critical, especially for shallow self supply boreholes.

A risk that is understood better is that from pathogens coming from sewage-polluted groundwater. This can lead to outbreaks of cholera, typhoid and many other diseases.The challenge is how to map and track this pollution to see where it is coming from and where it is going to.

Pathogens can’t be measured directly. The most common approach is to measure concentrations of faecal coliforms, but doing this has drawbacks: Coliforms are micro-organisms that have to be grown in ‘culture’ so that they can be counted. Coliforms also die more quickly than pathogens so groundwater sample tests may come back showing nothing, but in reality still be potentially harmful to health.

Field measurements of an amino acid, found in sewage, called tryptophan can be used to map and monitor pathogen contamination. Monitoring is done using fluorescence – shining a light through the water sample – so it can be done in realtime and doesn’t need regents. The work demonstraed that this monitoring method is quicker, cheaper and more accurate that than measuring faecal coliforms.

The fieldwork also showed that the drawdown from the supply wells is pulling in contamination from under the city, Kabwe. This has helped the town authority prioritise the control of informal settlements to the west of the town that is encroaching towards the well field for the town’s water supply.