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.

Inadequate hygiene coupled with the conjunctive use of the shallow subsurface as both a source of water and repository of faecal matter pose substantial risks to human health in low-income countries undergoing rapid urbanisation. To evaluate water, sanitation and hygiene (WASH) conditions in a small, rapidly growing town in central Uganda (Lukaya) served primarily by on-site water supply and sanitation facilities, water-point mapping, focus group discussions, sanitary-risk inspections and 386 household surveys were conducted. Household surveys indicate high awareness (82%) of domestic hygiene (e.g. handwashing, boiling water) but limited evidence of practice. WHO Sanitary Risk Surveys and Rapid Participatory Sanitation System Risk Assessments reveal further that community hygiene around water points and sanitation facilities including their maintenance is commonly inadequate. Spot sampling of groundwater quality shows widespread faecal contamination indicated by enumerated thermo-tolerant coliforms (TTCs) (Escherichia coli) ranging from 0 to 104 cfc/100 mL and nitrate concentrations that occasionally exceed 250 mg/L. As defined by the WHO/UNICEF Joint Monitoring programme, there are no safely managed water sources in Lukaya; ∼55% of improved water sources comprising primarily shallow hand-dug wells show gross faecal contamination by E. coli; and 51% of on-site sanitation facilities are unimproved. Despite the critical importance of on-site water supply and sanitation facilities in low-income countries to the realisation of UN Sustainable Goal 6 (access to safe water and sanitation for all by 2030), the analysis highlights the fragility and vulnerability of these systems where current monitoring and maintenance of communal facilities are commonly inadequate.

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Shallow groundwater is vulnerable to faecal contamination, especially in low-income urban areas where use of on-site sanitation facilities is high. This paper explores statistical relationships between potential factors influencing contaminant pathways (i.e., variables) and observed faecal contamination of shallow groundwater, represented by nitrate concentrations and counts of Escherichia coli (i.e., response function) in a small, growing town in Uganda over dry and wet seasons in 2018 and 2019. A statistically significant (p = 0.004) multiple linear regression model from dry-season E. coli counts in 2018 identifies medium sanitary risk levels and modes of construction as significant pathways (p = 0.01). Water source depth (&lt;20 m) and proximity (&gt;10 m) to a pit latrine were also significant (p&lt;0.05) in both hydrogeological formations. No significant linear regression models were established for NO3 during both seasons due to low pH and rapid infiltration velocities; inconsistent sample timing during the wet season impaired the significance of the statistical models of E. coli counts. We show that modes of construction of water sources and pit latrines play key roles in determining the quality of the shallow groundwater in urban environments. Greater emphasis is therefore required to improve the functionality and sustainability of on-site water sources and pit latrines.