Drinking-water under a "One Health" lens: quantifying microbial contamination pathways between livestock and drinking-water

Lead Research Organisation: University of Southampton
Department Name: Sch of Geography & Environmental Sci

Abstract

Diarrhoeal disease and lack of access to safe water remain significant public health issues in developing countries. There is also growing concern about the potential for disease, including diarrhoeal infections, to be transmitted from livestock to humans. This project addresses the potential drinking-water contamination risks to human health in rural sub-Saharan Africa, where people and livestock often live in close proximity. Preliminary fieldwork will be carried out in rural Kenya, building on an ongoing study that is simultaneously recording human and livestock disease in ten villages. The fieldwork will test different techniques to identify contamination hazards from livestock, alongside water quality testing and recording of diarrhoea in children. These techniques will include the use of GPS collars to track cattle movements, maps of hazardous areas created by the communities themselves, and also checklists for recording signs of livestock hazards at water sources and around water stored in the home. We will look at how feasible it is to record hazards using these techniques. We will also statistically assess whether we find greater water contamination and greater diarrhoea in children where there are more recorded hazards.

Since measurement of water contamination used in such areas is based on bacteria found in both livestock and humans, the project will also work on affordable ways of testing for micro-organisms that are specifically found in livestock faeces versus those found in human faeces. If successful, such techniques could be used to investigate the importance of different sources of faecal contamination of drinking-water. This in turn could help manage the safety of rural water sources like wells and rainwater and better protect drinking-water stored in the home from contamination through livestock.

Because this complex problem requires a wide range of expertise, during the project we will strength our academic team to include more disciplines, particularly specialists in child health and social sciences. The tools for identifying hazards from livestock will be made widely available at the end of the project and UK expertise in the microbiological laboratory techniques will be shared with Kenyan collaborators. The experience gained will be used to build up contacts and develop a plan and team for a larger-scale study of livestock hazards, water contamination, and diarrhoeal disease risk in several countries.

Technical Summary

Background: Diarrhoeal disease risk remains the fourth leading cause of years of life lost globally, but the role of livestock in contributing to this burden remains unclear.
Objective: To develop and validate livestock-related hazard assessment protocols including affordable microbial source-tracking methods, deliver preliminary evidence regarding drinking-water contamination by livestock and its implications for human health, and develop a related multi-country research plan for a future, follow-up longitudinal survey component.
Study design: Water quality and livestock hazard module embedded in ongoing longitudinal health and demographic surveillance system.
Participants: Household members aged 6 months of over from 200 rural households in Siaya County, Kenya.
Outcomes: Source and point-of-consumption drinking-water contamination with E. coli and cryptosporidium; Fortnightly prospective prevalence of reported diarrhoea.
Planned analysis: Multinomial logistic regression of E. coli and cryptosporidium counts in drinking-water in relation to livestock ownership, sanitary risk inspection scores, and hazard maps, controlling for confounders; log linear model of prospective 2-day diarrhoea prevalence in those aged >5 months in relation to E. coli and cryptosporidium in stored water, controlling for confounders.
Immediate outputs: validated livestock hazard assessment tools; preliminary evidence on livestock, water contamination and diarrhoea risks; local capacity-building, particularly in microbial source tracking methods
Long-term research plan: Development of a multi-country protocol and research network for a water quality and livestock hazard module, to be embedded in longitudinal health and demographic surveillance systems such as INDEPTH surveys

Planned Impact

The project's ultimate beneficiaries are rural households in LMICs (but particularly Kenya), particularly young children, using non-piped water and potentially exposed to faecal contamination from close contact with livestock, with the planned benefit being reduced child diarrhoea and disrupted zoonotic disease transmission in such households, balanced against economic benefits of livestock ownership. According to WHO/UNICEF, 26% of Kenya's 34,800,000 rural population currently use wells or rainwater. In the long-term (10 years after project), this group should benefit through improved water safety planning of rural water sources (e.g. wells; rainwater) and of stored water in the home via hazard identification and scientific understanding of livestock-related contamination risks generated. This project will provide the evidence required to develop effective interventions to reduce livestock-drinking-water transmission pathways (e.g. through source protection and safer storage of water in the home), with potential application in many water-insecure areas. This can ensure livestock continue to provide nutritional and financial benefits to the rural poor, while protecting drinking-water supplies and improving human health. During the project, 200 households in 10 villages in Siaya County participating in the study should benefit directly through contact with the project team, who should raise awareness about livestock-related hazards both to drinking-water stored in the home and at water sources, as will schoolchildren in this area via related education campaigns.

Direct intermediate beneficiaries include water sector NGOs, the Siaya County government, and community-based managers of rural point water sources, via development of microbial source tracking techniques, improved sanitary risk inspection protocols, and potentially also via hazard mapping exercise in the project's final 6 months and 3 years afterwards. The Kenya Vision 2030 policy strategy document highlights lack of capacity in water resources monitoring, better water quality, and catchments management as among eight key national challenges for the water sector. With its development of affordable microbial source tracking technology and hazard identification tools, the project should therefore address 3 key strategic challenges identified by the Kenyan government. In the final project year and 3 years following the project, the World Health Organization, with its remit to disseminate good practice in drinking-water management, could also benefit through the project's development of tools relevant to rural water safety planning. In the 3 years after the project, the scientific insights into livestock movements and related hazards could inform integrated water catchment management, e.g. by the Lake Basin Development Authority. The Zoonotic Disease Unit are a further intermediate beneficiary, who may benefit from development of livestock hazard identification tools and evidence on water-borne disease transmission.

The commercial benefits of the study are limited, but in the three years following the project, its findings could indirectly benefit makers of livestock GPS collars and microbiological companies (e.g. Idexx) via the development of new applications and markets for their products and the associated publicity from the project. During the project, MSc students in Kenya working with the Kenya Medical Research Institute will benefit from the project via capacity-building and training, particularly in the use of microbial source tracking techniques, with the future employers of these students (including government and NGOs as above) and project staff being the ultimate beneficiaries in the five years following the project. Finally, there are also obvious benefits to the academic team delivering the project, through skills development, collaboration network enhancement, and research profile development during and in the 3 years after the project.

Publications

10 25 50
 
Description The project findings are relevant to Sustainable Development Goal 6, which aims to ensure sustainable management and availability of water for all, particularly among rural communities still lacking piped water and especially such communities in Kenya. The paper by Mr. Okotto-Okotto (VIRED International) looked at a technique called sanitary risk inspection, which is a structured way of observing contamination hazards around rural water sources so that they can be managed and made safer, promoted by the World Health Organization. In a field experiment, members of his team visited the same set of water sources in Siaya County, Kenya, independently at different times, recording the hazards they observed. The most experienced observer recorded more hazards than less experienced colleagues, suggesting that his colleagues were missing some hazards during water source inspections. Some hazards proved particularly difficult to observe consistently, such as those on roof catchments of rainwater harvesting systems, signs of open defecation around water sources, or discarded solid waste and rubbish around water sources. This suggests that the protocols could be refined to make them easier to use consistently in rural areas of developing countries (for example through clearer instructions or photos of what to look for on a roof catchment area). We tested the quality of drinking water stored in people's home, comparing this to contamination risk factors such as lack of sanitation but also presence of livestock around the home. After taking account of other water contamination hazards, we also found that water stored in the home had greater microbiological contamination where we observed goats in the home or poultry roosting nearby.

Another project component led by University of Brighton looked to develop a technique for identifying whether faecal contamination of water is human or livestock in origin, with such techniques being known as microbial source tracking. This technique involves isolating bacterial strains found only in livestock or only in humans, then observing whether these bacteria are preyed upon by bacteriophages (viruses that attack bacteria) when exposed to water samples drawn from a particular source or wastewater body. Despite being lower cost than alternative methods, before our project, this technique had not previously been used in Africa where water contamination and related public health problems are widespread. Through our project, the University of Brighton team trained Kenyan microbiologists in how to recover viruses from water. The University of Brighton team also successfully isolated promising bacterial strains found in Kenyan cattle and humans (as opposed to European or North American cattle and humans), and the technique was implemented under field conditions in Africa for the first time. Relevant data have been made available to the research community.

Note that we anticipate reporting more in future years, since we have papers under review that look at contact between cattle and water sources via GPS collars attached to herds, and also the effect of piped water interruptions in our study area. However, we will not report these findings until they have been peer-reviewed.
Exploitation Route Our work on protocols for observing hazards around rural water sources could be taken further by refining the instructions concerning those observations that were hard to make consistently (e.g. hazards such as overhanging branches over the roof catchments of rainwater harvesting systems). That would mean that rural water supply managers could more robustly identify and manage contamination risks reducing the safety of rural water supplies.

In addition to bacteria, there is growing interest among agencies such as the US Environmental Protection Agency in the use of viruses, particularly bacteriophages, as viral indicators for monitoring the safety of surface, ground and bathing waters as well as shellfish. The training that University of Brighton provided to microbiologists in Kenya could help them enumerate phages in environmental samples in future, and thereby make the most of such emerging developments in environmental microbiology for public health protection. The bacterial hosts isolated through the project and now held within Kenya could be further tested against a range of environmental samples through subsequent experiments. This would enable scientists to assess how far phage attacks on these hosts signify faecal contamination from cattle as opposed to humans or vice versa. Were such experiments to prove successful, the technique would be valuable in diagnosing the causes of faecal contamination, unlike the bacteria-based monitoring that is widely practiced.

One way in which the outcomes of this funding could be taken forward is through implementers (e.g. NGOs) putting measures in place to address the specific water access challenges faced by the communities in our study area in Siaya County, Kenya. Our evidence suggests that enhancements to domestic rainwater harvesting and / or greater separation of livestock and people around water sources could protect these communities from exposure to faecal contamination. We have discussed such measures with the communities in our ten study villages, and there appears to be community demand for such measures, so we plan to explore this further with implementing bodies.

Finally, the GPS collars that we used on our project to track cattle has been used on a pilot basis by KEMRI to track dogs, so as to understand their movement and its impacts on dog population dynamics for rabies control particularly via vaccination campaigns. Rabies elimination is a priority for the government of Kenya.
Sectors Agriculture, Food and Drink,Communities and Social Services/Policy,Environment

 
Description VIRED International and KEMRI held feedback meetings with resident groups in ten villages in Siaya County, Kenya concerning our findings on the safety of domestic water sources. In each village, residents were presented with maps of water sources in their communities, generated through the previous project's fieldwork. This enabled discussion of options for increasing the safety of drinking-water with community members and leaders and related education around water safety management. Examples of such options include appropriate use of household water treatment (e.g. practice of home chlorination; fencing to separate livestock from water sources) and ways of reducing contamination in rainwater harvesting systems (e.g. through moveable inlet pipes). The meetings also enabled us to evaluate community demand for specific interventions to reduce water contamination in these locations. Following the meetings, 80% of villages formed action groups to promote household water treatment and safer siting of pit latrines and sanitation. We also provided community leaders with hard copies of maps of water sources and contamination hazards in the surrounding landscape, which can help in managing the safety of water sources used in the study areas.
First Year Of Impact 2020
Sector Agriculture, Food and Drink,Environment
Impact Types Policy & public services

 
Description GCRF Strategic Development Fund: Reduction of water-borne disease transmission in Kenya (VIRED/KEMRI/Southampton)
Amount £32,768 (GBP)
Organisation University of Southampton 
Sector Academic/University
Country United Kingdom
Start 06/2019 
End 12/2019
 
Title Bacteroides phages recovered from human and animal faecal matrices in rural Kenya 
Description This data describes the recovering and isolation processes of Bacteroides spp. strains from human and cattle faecal sources from rural areas in Siaya County (Kenya), and occurred between 7th and 28th of June 2018. The data also includes the detection of bacteriophages (infecting these Bacteroides spp. host strains) in conjunction with traditional faecal indicator organisms in water sources from Kisumu and Siaya County (Kenya) occurring between June 18th 2018 and June 13th 2019. Exact location (coordinates) of the sample points are also described in the data set. A microbiological technique using Bile Esculin Bacteroides (BBE) agar was used for the recovering and isolation processes of Bacteroides spp. strains. Standard ISO (7899-2, 9308-1, 10705-2 and 10705-4) techniques, such as membrane filtration and the double-agar-layer methods, were used for the detection of bacteriophages and traditional faecal indicator organisms. The purpose of data collection was to develop new markers that could identify cattle and/or human sources of faecal contamination, which could be used as part of a Microbial Source Tracking (MST) tool box. Technicians and researchers from the University of Brighton (UK), University of Southampton (UK), from the Victoria Institute for Research on Environment and Development (VIRED) (KE) and from the Kenya Medical Research Institute (KEMRI) (KE) were responsible for the collection and interpretation of data. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact These data formed the basis for a presentation by Dr. Diogo Gomes da Silva (University of Brighton) at the International Water Association Health-Related Water Microbiology Symposium in Vienna in September 2019. Isolated bacteroides strains are held within Kenya at the University of Maseno / KEMRI. 
URL https://catalogue.ceh.ac.uk/documents/02c8a6b0-e59e-4278-b9a2-9958cd5a2c3c
 
Title Longitudinal household and microbiological survey of livestock-related risk factors for contamination of household stored water in Siaya County, Kenya 2018-2019 
Description A questionnaire survey was conducted and observations were made concerning the presence of livestock in the home. The survey protocol also covered other known risk factors for contamination of household stored water, particularly water treatment, storage and handling behaviours, sanitation, and hygiene: these data form the basis of this collection. At the end of the questionnaire interview, a sample of household stored water was collected for subsequent microbiological testing, forming a related data set. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact The data set was used as the basis for a stakeholder workshop, in which project findings were presented and discussed by the county government, zoonotic disease unit, and community representatives. Based on these data, we also held feedback meetings with resident groups in ten villages in Siaya County, Kenya concerning our findings on the safety of domestic water sources. In each village, residents were presented with maps of water sources in their communities, generated through the previous project's fieldwork, together with information about their safety. The meetings also enabled us to evaluate community demand for specific interventions to reduce water contamination in these locations (e.g. fencing to separate livestock from water sources; remediation of rainwater harvesting systems). Following the meetings, 80% of villages formed action groups to promote household water treatment and safer siting of pit latrines and sanitation. 
URL http://reshare.ukdataservice.ac.uk/id/eprint/854302
 
Title Sanitary risk observation of hazards at and surrounding rural water sources in Siaya County, Kenya 2018-2019 
Description These data were collected to quantify hazards at water sources, particularly contact between livestock and water sources. In addition, they were collected to assess inter-observer agreement in hazard observations. Sanitary risk inspection is a structured means of observing and recording contamination hazards at and surrounding water sources, which has been promoted as a tool for water safety planning. It is however unclear how far different observers can consistently record hazards at a given water source. Water sources used for drinking, including rainwater systems, surface waters such as streams and dams, wells, boreholes and springs were all surveyed for hazards. Sources were visited twice, once in the wet season and again in the dry season, when the sample of sources visited was expanded. Six surveyors with varying backgrounds independently recorded the hazards they observed at each source, based on a structured observation protocol. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact The data led to the publication of an accompanying paper in the journal 'Exposure and Health'. 
URL http://reshare.ukdataservice.ac.uk/853860/
 
Title Water sources and contamination hazards in Siaya County, Kenya 2018 
Description Alongside scientific knowledge of hazards that may contaminate water sources, those living and working in rural sub-Saharan Africa may have detailed knowledge of potential contamination hazards and where they are located. Participatory mapping has been used as a component of the OneHealthWater project which aims to draw on that knowledge, to better understand geographic patterns of hazards that could contaminate water sources. The technique in this study involves working with small groups or individuals in 10 villages in Siaya County, who are then asked to map the domestic water sources and possible microbiological contamination hazards onto satellite imagery. The outputs may contribute to a better understanding of the potential hazards that may be found around rural water sources in sub-Saharan Africa and ultimately help to improve management of water safety. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Hard copy versions of the maps of water sources and hazards have been provided to the communities who participated in the original mapping exercises. 
URL https://beta.ukdataservice.ac.uk/datacatalogue/studies/study?id=853705
 
Description Feedback meetings with participants in study villages 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Study participants or study members
Results and Impact VIRED International and KEMRI organised a series of meetings to discuss the implications of the project findings in participating villages. After feeding back project findings, participants discussed potential interventions for addressing water contamination and their acceptability to the community. Examples of interventions discussed included fencing / separate drinking troughs to separate livestock from people at water sources; enhancements to protect domestic rainwater harvesting systems from contamination (e.g. movable inlet pipes and gravel boxes); and household water treatment and safe storage. Plans were made to approach implementing bodies concerning such interventions. All attendees were from Kenya (study participants / residents or community leaders in study villages) and meetings took place in Siaya County, Kenya.
Year(s) Of Engagement Activity 2020
 
Description Final project stakeholder workshop in Bondo, Kenya 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Study participants or study members
Results and Impact Preliminary study findings were presented to a group predominantly made up of community leaders from the study villages, but with county and regional government and local NGO representatives in attendance, alongside some postgraduate students. The session took place in Bondo, Kenya, and all participants were from Kenya.
Year(s) Of Engagement Activity 2019
 
Description Initial stakeholder workshop for OneHealthWater project 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact 52 participants (including county government representatives, community-based organisations, and study participants) attended a workshop presenting the study design for the project. Critical input into the study design was sought from participants, who provided valuable input as documented via a report on the project web site. All attendees were from Kenya and the event took place in Bondo, Kenya.
Year(s) Of Engagement Activity 2017
URL http://onehealthwater.org/news/start-up-workshop/
 
Description Key speaker presentation & panel debate, International Society for Neglected Tropical Diseases Water event: 'Onehealthwater - drinking-water under a one health lens' 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Third sector organisations
Results and Impact 120 delegates at the International Society for Neglected Tropical Diseases Water conference attended a presentation by Dr. Wright on the OneHealthWater project on 14 Nov 2018 at the Natural History Museum, London. Panel debate followed on linkages between zoonotic disease and Water, Sanitation and Hygiene. I estimate that perhaps 20 delegates were from DAC list countries.
Year(s) Of Engagement Activity 2018
URL https://www.isntdwater.com/programme
 
Description Laboratory training workshop to support microbial source tracking, Maseno University, Kisumu, Kenya 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact 18 staff from various government and academic laboratories across Kenya attended a 4-day training event at Maseno University organised by Dr. Gomes da Silva, University of Brighton with support from the OneHealthWater team. Delegates received hands-on experience of detecting, isolating and enumerating bacteriophages from environmental waters and learnt about microbial source tracking techniques. This sparked interest in taking the techniques further from delegates. The event took place at Maseno University, Kisumu, Kenya, with all delegates being from Kenyan institutions.
Year(s) Of Engagement Activity 2019
 
Description Presentation at the International Water Association Symposium on Health-Related Water Microbiology, Vienna 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Dr. Diogo Gomes Da Silva (University of Brighton) presented a poster entitled 'Phages of Bacteroidesspp. as a microbial source tracking (MST) tool for assessing drinking water sources in rural Kenya' to a group of microbiologists and environmental engineers, generating discussion around the potential for phage-based microbial source tracking in Africa.
Year(s) Of Engagement Activity 2019
URL https://www.jomay.at/hrwm/wp-content/uploads/2019/09/HRWM-2019_Programm_Web.pdf
 
Description Presentation by Dr. Thumbi Mwangi at the Wangari Maathai Institute, University of Nairobi 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact On 5th Dec 2018, Dr. Mwangi presented an overview of the project and linkages between human and livestock health to a mixed Japanese / Kenyan audience, generating discussion of how these linkages affect rural Kenyan populations. The event took place in University of Nairobi, Kenya, with some 25 audience members being Kenyan nationals.
Year(s) Of Engagement Activity 2018
 
Description Seminar at the International Water Management Institute, Accra, Ghana 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Other audiences
Results and Impact Dr. Wright presented a seminar on inter-observer agreement in sanitary risk assessment to a group of around 15 staff at the International Water Management Institute drawn from the Institute and GIZ, stimulating debate and discussion. The seminar took place in Accra, Ghana and approximately half the audience were from DAC countries.
Year(s) Of Engagement Activity 2019
 
Description Web site for OneHealthWater project 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact We developed a project web site, setting out the plans for the project to a general audience, leading to some queries via a web form from interested parties.
Year(s) Of Engagement Activity 2017
URL http://onehealthwater.org/