Tracing enteric pathogen contamination in sub-Saharan African groundwater

Quantitative PCR (qPCR) can rapidly screen for an array of faecally-derived bacteria, which can be employed as tracers to understand groundwater vulnerability to faecal contamination. A microbial DNA qPCR array was used to examine 45 bacterial targets, potentially relating to enteric pathogens, in 22 groundwater supplies beneath the city of Kabwe, Zambia in both the dry and subsequent wet season. Thermotolerant (faecal) coliforms, sanitary risks, and tryptophan-like fluorescence, an emerging real-time reagentless faecal indicator, were also concurrently investigated. There was evidence for the presence of enteric bacterial contamination, through the detection of species and group specific 16S rRNA gene fragments, in 72% of supplies where sufficient DNA was available for qPCR analysis. DNA from the opportunistic pathogen Citrobacter freundii was most prevalent (69% analysed samples), with Vibrio cholerae also perennially persistent in groundwater (41% analysed samples). DNA from other species such as Bifidobacterium longum and Arcobacter butzleri was more seasonally transient. Bacterial DNA markers were most common in shallow hand-dug wells in laterite/saprolite implicating rapid subsurface pathways and vulnerability to pollution at the surface. Boreholes into the underlying dolomites were also contaminated beneath the city highlighting that a laterite/saprolite overburden, as occurs across much of sub-Saharan aquifer, does not adequately protect underlying bedrock groundwater resources. Nevertheless, peri-urban boreholes all tested negative establishing there is limited subsurface lateral transport of enteric bacteria outside the city limits. Thermotolerant coliforms were present in 97% of sites contaminated with enteric bacterial DNA markers. Furthermore, tryptophan-like fluorescence was also demonstrated as an effective indicator and was in excess of 1.4 μg/L in all contaminated sites

Emerging contaminants in urban groundwater sources in Africa

The occurrence of emerging organic contaminants within the aquatic environment in Africa is currently unknown. This study provides early insights by characterising a broad range of emerging organic contaminants (n > 1000) in groundwater sources in Kabwe, Zambia. Groundwater samples were obtained during both the dry and wet seasons from a selection of deep boreholes and shallow wells completed within the bedrock and overlying superficial aquifers, respectively. Groundwater sources were distributed across the city to encompass peri-urban, lower cost housing, higher cost housing, and industrial land uses. The insect repellent DEET was ubiquitous within groundwater at concentrations up to 1.8 mg/L. Other compounds (n ¼ 26) were detected in less than 15% of the sources and included the bactericide triclosan (up to 0.03 mg/L), chlorination by-products e trihalomethanes (up to 50 mg/L), and the surfactant 2,4,7,9-tetramethyl-5-decyne-4,7-diol (up to 0.6 mg/L). Emerging contaminants were most prevalent in shallow wells sited in low cost housing areas. This is attributed to localised vulnerability associated with inadequate well protection, sanitation, and household waste disposal. The five-fold increase in median DEET concentration following the onset of the seasonal rains highlights that more mobile compounds can rapidly migrate from the surface to the aquifer suggesting the aquifer is more vulnerable than previously considered. Furthermore it suggests DEET is potentially useful as a wastewater tracer in Africa. There was a general absence of personal care products, life-style compounds, and pharmaceuticals which are commonly detected in the aquatic environment in the developed world. This perhaps reflects some degree of attenuation within the subsurface, but could also be a result of the current limited use of products containing emerging contaminants by locals due to unaffordability and unavailability. As development and population increases in Africa, it is likely a wider-range of emerging contaminants will be released into the environment

In-situ tryptophan-like fluorescence: a real-time indicator of faecal contamination in drinking water supplies

Enteric pathogens are typically inferred from the presence of surrogate indicator organisms such as thermo-tolerant (faecal) coliforms (TTCs). The analysis of TTCs requires time-consuming incubation in suitable laboratories, which can limit sampling resolution, particularly during critical pollution events. Here, we demonstrate the use of in-situ fluorimeters targeting tryptophan-like compounds as a rapid, reagentless indicator of TTCs in groundwater-derived potable water supplies in Africa. A range of other common indicators of TTCs were also determined including nitrate, turbidity, and sanitary risk survey scores. Sampling was conducted during both the dry and wet seasons to investigate seasonality. Tryptophan-like fluorescence was the most effective predictor of both presence/absence and number of TTCs during both seasons. Seasonal changes in tryptophan-like fluorescence in deeper supplies suggest it is transported more efficiently through the aquifer than TTCs. Moreover, the perennial elevated concentrations in some wells suggest it is more resilient than TTCs in groundwater. Therefore tryptophan-like fluorescence could also be a better indicator of some smaller, more easily transported, and long-lived, pathogenic enteric viruses. These sensors have the potential to be included in real-time pollutionalert systems for drinking water supplies throughout the world, as well as for mapping enteric pathogen risks in developing regions

Large-scale survey of seasonal drinking water quality in Malawi using in situ tryptophan-like fluorescence and conventional water quality indicators

Faecally-contaminated drinking water is a risk to human health, with the greatest risks to those living in developing countries. UN Sustainable Development Goal 6 aims to address this issue. Tryptophan-like fluorescence (TLF) shows potential as a rapid method for detecting microbial contamination in drinking water, which could reduce the spread of waterborne diseases. This study is the first to investigate the effectiveness of TLF for a large-scale survey using a randomised, spot-sampling approach. The large-scale survey took place in Malawi, sub-Saharan Africa, in the dry season (n = 183). A subset of sources were revisited at the end of the following wet season (n = 41). The effectiveness of TLF was assessed by comparing TLF results to thermotolerant coliforms (TTC), humic-like fluorescence (HLF), inorganic hydrochemical data and sanitary risk scores. The most prominent differences in microbial water quality were observed between source types, with little variation between districts and seasons. TLF, TTCs, turbidity and sanitary risk scores were all elevated at alternative sources (shallow wells and tap stands) compared to hand-pumped boreholes. In the dry season, 18% of hand-pumped boreholes showed TTC contamination, which increase to 21% in the wet season. Groundwater recharge processes are likely responsible for seasonal variability of inorganic hydrochemistry at hand-pumped boreholes. TLF was able to distinguish no and low WHO risk classes (TTC 0–9 cfu/100 mL) from medium, high and very high risk classes (TTC 10 – >1000 cfu/100 mL). TLF failed to distinguish between no and low risk classes, which limits the use of TLF for assessing water quality to drinking water standards. This dataset indicates that HLF may raise baseline TLF for samples with low TLF values, increasing false positives. Therefore, TLF is better suited as a rapid high-level water quality screening tool to assess moderate and high levels of faecal contamination

Tryptophan-like fluorescence as a high-level screening tool for detecting microbial contamination in drinking water

Regular monitoring of drinking water quality is vital to identify contamination of potable water supplies. Testing for microbial contamination is important to prevent transmission of waterborne disease, but establishing and maintaining a water quality monitoring programme requires sustained labour, consumables and resources. In low resource settings such as developing countries, this can prove difficult, but measuring microbial contamination is listed as a requirement of reaching the UN's Sustainable Development Goal 6 for water and sanitation. A nine-month water quality monitoring programme was conducted in rural Malawi to assess the suitability of tryptophan-like fluorescence (TLF), an emerging method for rapidly detecting microbial contamination, as a drinking water quality monitoring tool. TLF data was compared with thermotolerant coliforms (TTCs, E. coli) and inorganic hydrochemical parameters. A large (n = 235) temporal dataset was collected from five groundwater drinking water sources, with samples collected once or twice weekly depending on the season. The results show that TLF can indicate a broader contamination risk but is not as sensitive to short term variability when compared to other faecal indicators. This is likely due to a broad association of TLF with elevated DOC concentrations from a range of different sources. Elevated TLF may indicate preferential conditions for the persistence of TTCs and/or E. coli, but not necessarily a public health risk from microbial contamination. TLF is therefore a more precautionary risk indicator than microbial culturing techniques and could prove useful as a high-level screening tool for initial risk assessment. For widespread use of TLF to be successful, standardisation of TLF values associated with different levels of risk is required, however, this study highlights the difficulties of equating TLF thresholds to TTCs or E. coli data because of the influence of DOC/HLF on the TLF signal

Groundwater recharge and age-depth profiles of intensively exploited groundwater resources in northwest India

Intensive irrigation in northwest India has led to growing concerns over the sustainability of current and future groundwater abstraction. Environmental tracers and measurements of groundwater residence times can help quantify the renewal processes. Results from 16 paired locations show the interquartile ranges for residence times in shallow alluvial groundwater (8–50 m deep) to be 1–50 years and significantly less than those from deeper groundwater (76–160 m deep) at 40–170 years. The widespread occurrence of modern tracers in deep groundwater (>60% of sites had >10% modern recharge) suggests that there is low regional aquifer anisotropy and that deep aquifers are recharged by a significant component of recent recharge via vertical leakage. Stable isotope and noble gas results at all depths conform to modern meteoric sources and annual average temperatures, with no evidence of significant regional recharge from canal leakage in this study area close to the Himalayas

Groundwater and resilience to drought in the Ethiopian Highlands

During drought, groundwater is often relied on to provide secure drinking water, particularly in rural Africa where other options are limited. However, the technology chosen to access groundwater significantly affects local water security. Here we examine the performance of springs, hand-dug- wells and boreholes in northern Ethiopia through direct high frequency monitoring of water-levels (n=19) and water quality (n=48) over an 18-month period and gathering information on community impacts of declining water access during the El Niño 2015/2016 drought. We found that shallow boreholes equipped with handpumps were the most reliable water supply, recovering within hours to daily abstraction throughout all conditions. Recovery and performance of most hand-dug-wells and springs declined significantly throughout the extended dry season, although in specific aquifer conditions they were reliable. All sources types had negligible measured contamination from Thermo-tolerant Coliforms through the extended dry season, but were contaminated during the rains marking drought cessation. Boreholes were least affected, median 10 cfu/100ml, compared to 190 and 59 cfu/100ml for hand-dug-wells and springs respectively. Many communities who relied solely on springs, wells or rivers experienced severe water shortage in the El Niño drought with mean daily collection times up to 12 hours and volumes collected reducing to 3-5 litre- per-capita- per-day. This led to reports of violent conflict, missed meals, reduction in school attendance and farm activity and increased health impacts. From this study there is a clear case for improving resilience to drought by installing boreholes equipped with handpumps where feasible even if collection times are >30 minutes

Seasonal, episodic and periodic changes in terrestrial water storage recorded By DEEP Piezometric Monitoring in the Ganges/Brahmaputra/Meghna DELTA

Piezometric monitoring in vertical profile at sites across the southern and coastal floodplains of the Ganges/Brahmaputra/Meghna (GBM) delta confirms gravitational flow in sediments of the Bengal Aquifer System (BAS) to a depth of at least 320 m (the maximum depth of measurement). Individual and paired records of groundwater head indicate seasonal recovery and recession of water storage, periodic and episodic ground surface loading, and earth tide responses. Lunar periodicity in groundwater head fluctuation coincident with tide height at one coastal site is consistent with tidal surface loading/unloading. Diurnal tidal fluctuations in the same record change amplitude and shift phase with depth, also indicative of surface loading/unloading. Transience in the surface loading signals with depth is governed by the vertically integrated hydraulic properties of the thick BAS sedimentary sequence. Inland, earth tide responses of smaller amplitude and lacking phase shift with depth are ubiquitous in the background signal. Most records include clearly resolvable episodic deflections in the order of 0.1 m water head and up to 0.5 m water head, near simultaneous with depth, corresponding to individual episodes of rainfall. The episodic head deflections provide a record of change in terrestrial water storage (ΔTWS) comprising undifferentiated surface water flooding, soil moisture and shallow groundwater recharge – a direct land-based equivalent of satellite estimates of ΔTWS. Enigmatic short-term recession from individual deflection peaks may be related to elastic deformation and ground surface lowering under terrestrial water storage loading