Physical factors contributing to rural water supply functionality performance in Uganda

This report communicates the findings generated from one of the project surveys – deconstruction and forensic analysis of 50 individual water points in Uganda. The report presents the new data generated to Uganda’s groundwater resource potential; the nature and condition of hand-pump borehole installations; and the significance of both of these factors to service performance. Based on the evidence collected, the main physical factors affecting functionality performance within Uganda are the poor condition of handpump components, and the complex aquifer resource. The impact of these factors can be mitigated through appropriate material choice for handpump components (non GI), increased investment in borehole siting and testing, and adequate accessibility to repairs and maintenance capacity with breakdowns. These factors should not be considered to be the only driving forces of functionality outcomes in these regions of Uganda, however, and the results of this survey need to be examined alongside the wider project findings. Wider institutional arrangements, resources and dynamics, are likely to play a significant role in the implementation of appropriate borehole construction, siting and design; procurement processes; and the management capacity available for water points at national to local levels

Drinking water quality from rural handpump-boreholes in Africa

Groundwater provides a vital source of drinking water for rural communities in many parts of Africa, particularly in the dry season when there are few safe alternative sources. This paper summarises results from a study (n = 428) assessing dry season water quality, both microbiological and inorganic chemistry, in handpump equipped boreholes (HPBs) across the Ethiopia Highlands (n = 142), Malawi (n = 162) and Uganda (n = 124) using a stratified, randomised sampling design. This study seeks to examine general water quality by randomly sampling rural groundwater supplies across larger areas with different geology and climate. The majority, 72%, of HPBs surveyed provide good quality dry season drinking water as defined by WHO drinking water quality criteria. Within this overall picture, the most notable constraints were from thermotolerant coliforms (TTCs), which exceeded the WHO drinking water guideline of zero colony forming units (cfu/100 ml) in 21% of sites (range 0–626 cfu/100 ml). TTC contamination was found to have a significant and positive correlation with annual average rainfall (ρ = 0.2, p = 0.00003). Across all three countries, WHO health based chemical drinking water quality values were exceeded at 9% of sites and were found for manganese (4%), fluoride (2.6%) and nitrate (2.5%); arsenic concentrations were below the guideline value of 10 μg l−1 (range 400 μg l−1) found in drinking water sources in Uganda challenges the decision by WHO not to formalise a health-based guideline for Mn. While the overall level of microbiological contamination from HPBs is low, results from this study strongly suggest that at a national and regional level, microbiological contamination rather than chemical contamination will provide a greater barrier to achieving targets set for improved drinking water quality under the UN-SDG 6. Efforts should be made to ensure that boreholes are properly sited and constructed effectively to reduce pathogen contamination

UPGro Hidden Crisis Research Consortium. Survey 1 Country Report, Uganda

Statistics on the functionality of water points from the Hidden Crisis project in Uganda are presented. The survey, undertaken in 2016, was focussed on boreholes equipped with handpumps (HPBs) within the 112 districts of Uganda. A stratified two stage random sampling approach was adopted and 10 districts identified to sample. A tiered definition of functionality was applied, and all which enabled more nuanced definitions to be reported: The results from the survey indicate: • 55% of HPBs were working on the day of the survey (compared to national figure of 86% for rural water supply ) • 34% of HPBs passed the design yield of 10 litres per minute • 23% passed the design yield and also experienced < 1 month downtime within a year. • 18% passed the design yield and reliability criteria and also water quality criteria The results of the survey indicate the utility of carrying out more detailed assessments of functionality to help unpack national statistics. A linked survey of the performance of the water management arrangements at water points showed that for 70% of the sites water management arrangements were judged to be weak

Tryptophan-like and humic-like fluorophores are extracellular in groundwater: implications as real-time faecal indicators

Fluorescent natural organic matter at tryptophan-like (TLF) and humic-like fluorescence (HLF) peaks is associated with the presence and enumeration of faecal indicator bacteria in groundwater. We hypothesise, however, that it is predominantly extracellular material that fluoresces at these wavelengths, not bacterial cells. We quantified total (unfiltered) and extracellular (filtered at < 0.22 µm) TLF and HLF in 140 groundwater sources across a range of urban population densities in Kenya, Malawi, Senegal, and Uganda. Where changes in fluorescence occurred following filtration they were correlated with potential controlling variables. A significant reduction in TLF following filtration (ΔTLF) was observed across the entire dataset, although the majority of the signal remained and thus considered extracellular (median 96.9%). ΔTLF was only significant in more urbanised study areas where TLF was greatest. Beneath Dakar, Senegal, ΔTLF was significantly correlated to total bacterial cells (ρs 0.51). No significant change in HLF following filtration across all data indicates these fluorophores are extracellular. Our results suggest that TLF and HLF are more mobile than faecal indicator bacteria and larger pathogens in groundwater, as the predominantly extracellular fluorophores are less prone to straining. Consequently, TLF/HLF are more precautionary indicators of microbial risks than faecal indicator bacteria in groundwater-derived drinking water

Observed controls on resilience of groundwater to climate variability in sub-Saharan Africa

Groundwater in sub-Saharan Africa supports livelihoods and poverty alleviation, maintains vital ecosystems, and strongly influences terrestrial water and energy budgets. Yet the hydrological processes that govern groundwater recharge and sustainability—and their sensitivity to climatic variability—are poorly constrained. Given the absence of firm observational constraints, it remains to be seen whether model-based projections of decreased water resources in dry parts of the region are justified. Here we show, through analysis of multidecadal groundwater hydrographs across sub-Saharan Africa, that levels of aridity dictate the predominant recharge processes, whereas local hydrogeology influences the type and sensitivity of precipitation–recharge relationships. Recharge in some humid locations varies by as little as five per cent (by coefficient of variation) across a wide range of annual precipitation values. Other regions, by contrast, show roughly linear precipitation–recharge relationships, with precipitation thresholds (of roughly ten millimetres or less per day) governing the initiation of recharge. These thresholds tend to rise as aridity increases, and recharge in drylands is more episodic and increasingly dominated by focused recharge through losses from ephemeral overland flows. Extreme annual recharge is commonly associated with intense rainfall and flooding events, themselves often driven by large-scale climate controls. Intense precipitation, even during years of lower overall precipitation, produces some of the largest years of recharge in some dry subtropical locations. Our results therefore challenge the ‘high certainty’ consensus regarding decreasing water resources in such regions of sub-Saharan Africa. The potential resilience of groundwater to climate variability in many areas that is revealed by these precipitation–recharge relationships is essential for informing reliable predictions of climate-change impacts and adaptation strategies

Environmental tracers to evaluate groundwater residence times and water quality risk in shallow unconfined aquifers in sub Saharan Africa

In sub-Saharan Africa, shallow aquifer systems are relied on as the main safe and secure water resource available to rural communities. Information on the sustainability and vulnerability of groundwater abstraction is becoming increasingly important as groundwater development increases. As part of the UpGro Consortium Project- Hidden Crisis, 150 hand pumped boreholes (HPBs), ranging between 15 and 101 m depth were investigated to examine the resilience of aquifer systems in the Ethiopian Highlands, and the crystalline basement rocks of Uganda and Malawi. Environmental tracers (chlorofluorocarbons (CFCs), SF6, chloride and the stable isotopes of water), water quality indicators (nitrate and E. coli), and groundwater-level time series data were used to estimate groundwater residence time and recharge at a regional scale (100–10,000 km2) and investigate the risks to water quality and water supply over different timeframes, and geological and climatic environments. Average estimated recharge rates using three different techniques (CFCs, chloride mass balance, water table fluctuation method) were between 30 and 330, 27–110 and 30–170 mm y−1, for sites in Ethiopia, Uganda and Malawi, respectively. These estimates of recharge suggests abstraction from dispersed low-yielding HPBs is sustainable. Comparison of stable isotopes in rainfall and groundwater indicates that there is little evaporation prior to recharge, and recharge events are biased to months with greater rainfall and more intense rainfall events There was a weak correlation between nitrate and CFCs within all three countries, and no correlation between E. coli and CFCs within Ethiopia or Malawi. The presence of E. coli at a large proportion of the sites (Ethiopia = 38%, Uganda = 65% and Malawi = 47%) suggests rapid transit of contaminated surface water into the borehole and its presence in groundwater that has CFC-12 concentrations less than 75 pg kg−1 indicates mixing of very young water with water >40 years old. The rapid transit pathways are most likely associated with damaged HPB headworks and poor construction. In several monitored HPBs, daily drawdown due to pumping, drew the groundwater levels close to the base of the HPB, indicating that these HPBs were located in parts of the aquifer with low permeability, or were poorly designed, offering limited capacity for increased demand. Improved HPB siting and construction, coupled with groundwater level monitoring are required to capitalise on the more resilient groundwater within the shallow aquifers and safeguard adequate and good quality water supply for rural communities

Evidence that dicot-infecting mastreviruses are particularly prone to inter-species recombination and have likely been circulating in Australia for longer than in Africa and the Middle East

Viruses of the genus Mastrevirus (family Geminiviridae) are transmitted by leafhoppers and infect either mono- or dicotyledonous plants. Here we have determined the full length sequences of 49 dicot-infecting mastrevirus isolates sampled in Australia, Eritrea, India, Iran, Pakistan, Syria, Turkey and Yemen. Comprehensive analysis of all available dicot-infecting mastrevirus sequences showed the diversity of these viruses in Australia to be greater than in the rest of their known range, consistent with earlier studies, and that, in contrast with the situation in monocot-infecting mastreviruses, detected inter-species recombination events outnumbered intra-species recombination events. Consistent with Australia having the greatest diversity of known dicot-infecting mastreviruses phylogeographic analyses indicating the most plausible scheme for the spread of these viruses to their present locations, suggest that most recent common ancestor of these viruses is likely nearer Australia than it is to the other regions investigated.Department of HE and Training approved lis

UPGro Hidden Crisis Research Consortium : project approach for defining and assessing rural water supply functionality and levels of performance

This technical brief is aimed at sharing the learning and approaches developed by the UPGro Hidden Crisis Research Project to look at how the functionality and performance levels of boreholes equipped with handpumps (HPBs), can be assessed using a common set of definitions and methods. A tiered approach to defining and measuring functionality is found to be useful to examining functionality for different scales and purposes of monitoring. This report is aimed at national and regional actors involved in the provision and monitoring of rural water supply functionality. The brief sets out the tiered functionality definitions, and accompanying survey methods, which were developed by the project and have been applied in functionality surveys across Ethiopia, Uganda and Malawi [5-7]. The brief provides a summary of: • The tiered approach to defining and measuring the functionality and performance levels of boreholes equipped with handpumps (HPBs). • A series of survey methods which were found to be useful by the Hidden Crisis project to collect sufficient data to assess HPB functionality across the tiered definition approach. • A series of guidelines which could form core criteria for assessing functionality and performance levels of water points . This summary should be read in conjunction with the appendices which provide details of the methods and approaches described

Observed controls on resilience of groundwater to climate variability in sub-Saharan Africa

Groundwater in sub-Saharan Africa supports livelihoods and poverty alleviation1,2, maintains vital ecosystems, and strongly influences terrestrial water and energy budgets. Yet the hydrological processes that govern groundwater recharge and sustainability—and their sensitivity to climatic variability—are poorly constrained4. Given the absence of firm observational constraints, it remains to be seen whether model-based projections of decreased water resources in dry parts of the region4 are justified. Here we show, through analysis of multidecadal groundwater hydrographs across sub-Saharan Africa, that levels of aridity dictate the predominant recharge processes, whereas local hydrogeology influences the type and sensitivity of precipitation–recharge relationships. Recharge in some humid locations varies by as little as five per cent (by coefficient of variation) across a wide range of annual precipitation values. Other regions, by contrast, show roughly linear precipitation–recharge relationships, with precipitation thresholds (of roughly ten millimetres or less per day) governing the initiation of recharge. These thresholds tend to rise as aridity increases, and recharge in drylands is more episodic and increasingly dominated by focused recharge through losses from ephemeral overland flows. Extreme annual recharge is commonly associated with intense rainfall and flooding events, themselves often driven by large-scale climate controls. Intense precipitation, even during years of lower overall precipitation, produces some of the largest years of recharge in some dry subtropical locations. Our results therefore challenge the ‘high certainty’ consensus regarding decreasing water resources in such regions of sub-Saharan Africa. The potential resilience of groundwater to climate variability in many areas that is revealed by these precipitation–recharge relationships is essential for informing reliable predictions of climate-change impacts and adaptation strategies

Patterns of antibiotic use, pathogens, and prediction of mortality in hospitalized neonates and young infants with sepsis: A global neonatal sepsis observational cohort study (NeoOBS)

BACKGROUND: There is limited data on antibiotic treatment in hospitalized neonates in low- and middle-income countries (LMICs). We aimed to describe patterns of antibiotic use, pathogens, and clinical outcomes, and to develop a severity score predicting mortality in neonatal sepsis to inform future clinical trial design. METHODS AND FINDINGS: Hospitalized infants <60 days with clinical sepsis were enrolled during 2018 to 2020 by 19 sites in 11 countries (mainly Asia and Africa). Prospective daily observational data was collected on clinical signs, supportive care, antibiotic treatment, microbiology, and 28-day mortality. Two prediction models were developed for (1) 28-day mortality from baseline variables (baseline NeoSep Severity Score); and (2) daily risk of death on IV antibiotics from daily updated assessments (NeoSep Recovery Score). Multivariable Cox regression models included a randomly selected 85% of infants, with 15% for validation. A total of 3,204 infants were enrolled, with median birth weight of 2,500 g (IQR 1,400 to 3,000) and postnatal age of 5 days (IQR 1 to 15). 206 different empiric antibiotic combinations were started in 3,141 infants, which were structured into 5 groups based on the World Health Organization (WHO) AWaRe classification. Approximately 25.9% (n = 814) of infants started WHO first line regimens (Group 1-Access) and 13.8% (n = 432) started WHO second-line cephalosporins (cefotaxime/ceftriaxone) (Group 2-"Low" Watch). The largest group (34.0%, n = 1,068) started a regimen providing partial extended-spectrum beta-lactamase (ESBL)/pseudomonal coverage (piperacillin-tazobactam, ceftazidime, or fluoroquinolone-based) (Group 3-"Medium" Watch), 18.0% (n = 566) started a carbapenem (Group 4-"High" Watch), and 1.8% (n = 57) a Reserve antibiotic (Group 5, largely colistin-based), and 728/2,880 (25.3%) of initial regimens in Groups 1 to 4 were escalated, mainly to carbapenems, usually for clinical deterioration (n = 480; 65.9%). A total of 564/3,195 infants (17.7%) were blood culture pathogen positive, of whom 62.9% (n = 355) had a gram-negative organism, predominantly Klebsiella pneumoniae (n = 132) or Acinetobacter spp. (n = 72). Both were commonly resistant to WHO-recommended regimens and to carbapenems in 43 (32.6%) and 50 (71.4%) of cases, respectively. MRSA accounted for 33 (61.1%) of 54 Staphylococcus aureus isolates. Overall, 350/3,204 infants died (11.3%; 95% CI 10.2% to 12.5%), 17.7% if blood cultures were positive for pathogens (95% CI 14.7% to 21.1%, n = 99/564). A baseline NeoSep Severity Score had a C-index of 0.76 (0.69 to 0.82) in the validation sample, with mortality of 1.6% (3/189; 95% CI: 0.5% to 4.6%), 11.0% (27/245; 7.7% to 15.6%), and 27.3% (12/44; 16.3% to 41.8%) in low (score 0 to 4), medium (5 to 8), and high (9 to 16) risk groups, respectively, with similar performance across subgroups. A related NeoSep Recovery Score had an area under the receiver operating curve for predicting death the next day between 0.8 and 0.9 over the first week. There was significant variation in outcomes between sites and external validation would strengthen score applicability. CONCLUSION: Antibiotic regimens used in neonatal sepsis commonly diverge from WHO guidelines, and trials of novel empiric regimens are urgently needed in the context of increasing antimicrobial resistance (AMR). The baseline NeoSep Severity Score identifies high mortality risk criteria for trial entry, while the NeoSep Recovery Score can help guide decisions on regimen change. NeoOBS data informed the NeoSep1 antibiotic trial (ISRCTN48721236), which aims to identify novel first- and second-line empiric antibiotic regimens for neonatal sepsis. TRIAL REGISTRATION: ClinicalTrials.gov, (NCT03721302)