Urban groundwater quality in sub-Saharan Africa: current status and implications for water security and public health.

Groundwater resources are important sources of drinking water in Africa, and they are hugely important in sustaining urban livelihoods and supporting a diverse range of commercial and agricultural activities. Groundwater has an important role in improving health in sub-Saharan Africa (SSA). An estimated 250 million people (40% of the total) live in urban centres across SSA. SSA has experienced a rapid expansion in urban populations since the 1950s, with increased population densities as well as expanding geographical coverage. Estimates suggest that the urban population in SSA will double between 2000 and 2030. The quality status of shallow urban groundwater resources is often very poor due to inadequate waste management and source protection, and poses a significant health risk to users, while deeper borehole sources often provide an important source of good quality drinking water. Given the growth in future demand from this finite resource, as well as potential changes in future climate in this region, a detailed understanding of both water quantity and quality is required to use this resource sustainably. This paper provides a comprehensive assessment of the water quality status, both microbial and chemical, of urban groundwater in SSA across a range of hydrogeological terrains and different groundwater point types. Lower storage basement terrains, which underlie a significant proportion of urban centres in SSA, are particularly vulnerable to contamination. The relationship between mean nitrate concentration and intrinsic aquifer pollution risk is assessed for urban centres across SSA. Current knowledge gaps are identified and future research needs highlighted.

Les ressources en eaux souterraines sont des sources importantes d'eau potable en Afrique, et elles sont d'une énorme importance pour les êtres vivants en milieu urbain et pour le soutien d'une gamme diversifiée d'activités commerciales et agricoles. Les eaux souterraines jouent un rôle important en améliorant la santé en Afrique sub-saharienne (ASS). 250 millions de personnes environ (40% du total) vivent dans des centres urbains à travers l'ASS. L'ASS a connu une expansion rapide de ses populations urbaines depuis les années 1950, avec une augmentation à la fois des densités de population et de leur extension géographique. Les estimations prévoient un doublement de la population urbaine de l'ASS entre 2000 et 2030. L'état qualitatif des ressources en eau souterraine urbaines peu profondes est souvent très pauvre du fait de l'insuffisance de la gestion des déchets et de la protection de la ressource, et pose un risque sanitaire significatif pour les utilisateurs, alors que des ressources plus profondes captées par forage fournissent souvent une source importante d'eau potable de bonne qualité. Etant donné la croissance de la demande future de cette ressource limitée, ainsi que le changement climatique potentiel dans cette région dans le futur, une compréhension détaillée de la quantité et la qualité de cette ressource est exigée pour son utilisation durable. Cet article fournit une évaluation complète de l'état qualitatif, à la fois microbien et chimique, des eaux souterraines urbaines en ASS à travers une gamme de contextes hydrogéologiques et de différents types de point d'eaux souterraines. Les terrains du sous-sol de faible emmagasinement, qui sont situés sous une proportion significative de centres urbains en ASS, sont particulièrement vulnérables à la contamination. Le rapport entre la concentration moyenne en nitrate et le risque intrinsèque de pollution des aquifères est évalué pour les centres urbains de l'ASS. Des lacunes actuelles en matière de connaissances sont identifiées et les besoins de recherches futurs sont mis en évidence.

Los recursos hídricos subterráneos son una fuente importante de agua potable en África y son sumamente importantes para mantener los medios de subsistencia urbanos y para apoyar una amplia gama de actividades comerciales y agrícolas. El agua subterránea tiene un papel importante en la mejora de la salud en el África Subsahariana (SSA). Se calcula que 250 millones de personas (40% del total) viven en centros urbanos en el África Subsahariana. El SSA ha experimentado una rápida expansión en las poblaciones urbanas desde la década de 1950, con el aumento de la densidad de población, así como la ampliación de la cobertura geográfica. Las estimaciones sugieren que la población urbana en África Subsahariana se duplicará entre 2000 y 2030. El estado de calidad del agua subterránea somera es a menudo muy pobre debido a la gestión inadecuada de los desechos y de la protección de las fuentes, representando un riesgo significativo para los usuarios, mientras que los pozos más profundos proporcionan una fuente importante de agua potable de buena calidad. Dado el crecimiento de la demanda futura de este recurso finito, así como los cambios potenciales en el clima futuro en esta región, una comprensión detallada de su cantidad y calidad es necesaria para utilizar este recurso de manera sostenible. Este artículo ofrece una evaluación integral del estado de la calidad del agua, tanto microbiana como química, del agua subterránea urbana en el SSA a lo largo de una serie de terrenos hidrogeológicos y diferentes tipos de puntos de agua subterránea. Los basamentos de bajo almacenamiento, que subyacen a una proporción significativa de los centros urbanos del África Subsahariana, son particularmente vulnerables a la contaminación. Se evalúa la relación entre la concentración media de nitratos y el riesgo intrínseco de contaminación acuífera para los centros urbanos a través de la SSA. Se identifican las deficiencias actuales de conocimientos y se destacan las necesidades de futuras investigaciones.

As águas subterrâneas são fontes importantes de água para consumo na África, e são amplamente importantes para sustentar o modo de vida urbano e dar suporte a uma amplitude diversa de atividades comerciais e agrícolas. As águas subterrâneas têm um papel importante no desenvolvimento da saúde na África subsaariana (ASS). São estimadas 250 milhões de pessoas (40% do total) vivendo nos centros urbanos na ASS. ASS tem vivenciado uma rápida expansão na população urbana desde os anos 50, com aumento das densidades populacionais assim como expansão da cobertura geográfica. As estimativas sugerem que a população urbana na ASS dobrará entre 2000 e 2030. As condições de qualidade dos aquíferos livres em áreas urbanas estão frequentemente muito pobres por causa do gerenciamento de perdas e proteção das fontes inadequados, e apresenta um risco significativo à saúde dos usuários, enquanto poços mais profundos frequentemente fornecem fontes importantes de água potável de boa qualidade. Dado o crescimento na demanda futura desse recurso finito, assim como mudanças potenciais no clima futuro da região, um entendimento detalhado da sua quantidade e qualidade é necessário para o uso sustentável deste recurso. Esse estudo fornece uma avaliação compreensiva das condições de qualidade da água, tanto microbiológica quanto química, das águas subterrâneas urbanas na ASS por uma gama de terrenos hidrogeológicos e diferentes tipos pontuais de águas subterrâneas. Terrenos de menor armazenamento de base, que fundamentam uma porção significante dos centros urbanos da ASS, são particularmente vulneráveis a contaminação. A relação entre a concentração média de nitrato e o risco intrínseco de poluição do aquífero é avaliado para os centros urbanos na ASS. Lacunas do conhecimento atual foram identificadas e destaca-se a necessidade de pesquisas futuras.

Are sanitation interventions a threat to drinking water supplies in rural India? An application of tryptophan-like fluorescence.

Open defecation is practised by over 600 million people in India and there is a strong political drive to eliminate this through the provision of on-site sanitation in rural areas. However, there are concerns that the subsequent leaching of excreta from subsurface storage could be adversely impacting underlying groundwater resources upon which rural populations are almost completely dependent for domestic water supply. We investigated this link in four villages undergoing sanitary interventions in Bihar State, India. A total of 150 supplies were sampled for thermotolerant (faecal) coliforms (TTC) and tryptophan-like fluorescence (TLF): an emerging real-time indicator of faecal contamination. Sanitary risk inspections were also performed at all sites, including whether a supply was located within 10 m of a toilet, the recommended minimum separation. Overall, 18% of water supplies contained TTCs, 91% of which were located within 10 m of a toilet, 58% had TLF above detection limit, and sanitary risk scores were high. Statistical analysis demonstrated TLF was an effective indicator of TTC presence-absence, with a possibility of TTCs only where TLF exceeded 0.4 µg/L dissolved tryptophan. Analysis also indicated proximity to a toilet was the only significant sanitary risk factor predicting TTC presence-absence and the most significant predictor of TLF. Faecal contamination was considered a result of individual water supply vulnerability rather than indicative of widespread leaching into the aquifer. Therefore, increasing faecal contamination of groundwater-derived potable supplies is inevitable across the country as uptake of on-site sanitation intensifies. Communities need to be aware of this link and implement suitable decentralised low-cost treatment of water prior to consumption and improve the construction and protection of new supplies.

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 1.4µg/L in all contaminated sites.

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 thermotolerant (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 pollution alert systems for drinking water supplies throughout the world, as well as for mapping enteric pathogen risks in developing regions.

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 µg/L. Other compounds (n = 26) were detected in less than 15% of the sources and included the bactericide triclosan (up to 0.03 µg/L), chlorination by-products - trihalomethanes (up to 50 µg/L), and the surfactant 2,4,7,9-tetramethyl-5-decyne-4,7-diol (up to 0.6 µg/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.

Assessment of the stability of human viruses and coliphage in groundwater by PCR and infectivity methods.

AIM: To investigate the potential health hazard from infectious viruses where coliphages, or viruses by polymerase chain reaction (PCR), have been detected in groundwater. Two aspects were investigated: the relationship between infectivity and detection by PCR and the stability of coliphage compared to human viruses. METHODS AND RESULTS: Virus decay (1 year) and detection (2 years) studies were undertaken on groundwater at 12 degrees C. The order of virus stability from most to least stable in groundwater, based on first-order inactivation, was: coliphage PhiX174 (0.5 d(-1)) > adenovirus 2 > coliphage PRD1 > poliovirus 3 > coxsackie virus B1 (0.13 d(-1)). The order for PCR results was: norovirus genotype II > adenovirus > norovirus genotype I > enterovirus. CONCLUSIONS: Enterovirus and adenovirus detection by PCR and the duration of infectivity in groundwater followed similar trends over the time period studied. Adenovirus might be a better method for assessing groundwater contamination than using enterovirus; norovirus detection would provide information on a significant human health hazard. Bacteriophage is a good alternative indicator. SIGNIFICANCE AND IMPACT OF THE STUDY: PCR is a useful tool for identifying the health hazard from faecal contamination in groundwater where conditions are conducive to the survival of viruses and their nucleic acid.

A comparison of the extent and impacts of sewage contamination on urban groundwater in developed and developing countries.

In much of the world urban groundwater is an important resource for domestic and industrial use. In many developing countries, groundwater taken directly (untreated) from individual springs and wells is the only option available to communities where comprehensive, reliable reticulated supply systems are absent. A common feature of urban groundwater in both developing and developed countries is contamination by sewage. Current and recent research is presented that shows sewer leakage impacts groundwater in developed countries whilst on-site sanitation contaminates groundwater in developing countries. In the latter case, the competing demands of sanitation and groundwater protection must be addressed. Limitations on the usefulness of accepted standard sewage indicator species in groundwater are also highlighted. As sewage contamination of groundwater is usually addressed only if an actual health risk is posed, it is vital both to developed and developing countries to understand the movement of actual pathogens in groundwater in the context of groundwater management. Further research is required on microbial survival and health risks posed by sewage contamination.

A comparison of six cypovirus isolates by cross-hybridisation of their dsRNA genome segments.

Genetic relationships between the genome segments of six cypovirus (CPV) isolates were analysed by RNA cross-hybridisation. These included three type 1 viruses and single isolates of types 2, 5 and 12, which collectively are identical to those previously compared by serology and electrophoresis [Mertens et al. (1989), J Gen Virol 70: 173-185]. Since only genome segment 10 of three cypovirus types and segments 8 and 9 of a single virus strain (of type 1) have currently been sequenced, this initial study provides some additional information on sequence variation/similarity in each of the ten genome segments. The RNA of the type 1 viruses showed high levels of cross-hybridisation. Significant but much lower levels of cross-hybridisation were detected between type 1 and the related type 12 CPV. However, only very low levels of cross-hybridisation were detected between the other pairs of viruses. Apart from evidence of a slightly higher level of sequence similarity between the largest segments, the RNA sequence appeared to vary uniformly across the whole genome. There was no evidence for any type specific RNA sequences restricted to individual genome segment(s). The sequence variation, reflected in the levels of RNA sequence similarity and cross hybridisation, correlates well with serological data, showing large differences between CPV types and supports the continued use of electropherotype as one of the 'species parameters' for the classification of cypoviruses.

Helicobacter pylori infection rates in relation to age and social class in a population of Welsh men.

The seroprevalence of IgG antibodies to Helicobacter pylori was determined using a standard enzyme linked immunosorbent assay in a population of 749 randomly selected men, aged 30-75 years, from Caerphilly, South Wales. The overall prevalence of H pylori was 56.9%, increasing sharply in middle age from 29.8% in those aged 30-34 to over 59% in those aged 45 or older (p less than 0.0001). Age standardised seroprevalence rates were lowest in combined social class categories I and II (49.2%), intermediate in categories IIIN and M (57.5%), and highest in categories IV and V (62.2%) (p = 0.01). In those aged 30-34 years, the prevalence rate for those in combined social class categories IV and V was 57.9% - double the rate for social class categories IIIM and N (28.3%) and five times the prevalence rate in those in social class categories I and II (11.1%). These differences in the infection patterns of H pylori by social class are consistent with patterns of peptic ulcer disease and gastric cancer.

Analysis of the roles of bluetongue virus outer capsid proteins VP2 and VP5 in determination of virus serotype.

Analyses of reassortant and parental strains of BTV serotypes 3 and 10, in serum neutralization tests, confirmed the major role of outer capsid protein VP2 in determination of virus serotype and its involvement in serum neutralization. However, a reassortant BTV strain (R70), containing protein VP5 derived from BTV 3 and VP2 derived from BTV 10, cross-neutralized with both parental virus strains (BTV 3 and BTV 10). It is concluded that VP5 also plays some part in serotype determination of these virus isolates, as analyzed by serum-neutralization, but its role may be less significant than that of VP2.

Cytoplasmic polyhedrosis virus classification by electropherotype; validation by serological analyses and agarose gel electrophoresis.

Serological analyses of several different cytoplasmic polyhedrosis viruses (CPVs), including two type 1 CPVs from Bombyx mori, type 1 CPV from Dendrolimus spectabilis, type 12 CPV from Autographa gamma, type 2 CPV from Inachis io, type 5 CPV from Orgyia pseudotsugata and type 5 CPV from Heliothis armigera, demonstrated a close correlation between the antigenic properties of the polyhedrin or virus particle structural proteins and the genomic dsRNA electropherotypes. The dsRNAs of these viruses were analysed by electrophoresis in 3% and 10% polyacrylamide gels with a discontinuous Tris-HCl/Tris-glycine buffer system or by 1% agarose gel electrophoresis using a continuous Tris-acetate-EDTA buffer system. Electrophoretic analysis in agarose gels was found to be the most suitable for the classification of CPV isolates into electropherotypes, and the results obtained showed a close correlation with the observed antigenic relationships between different virus isolates. However, electrophoretic analysis in 10% polyacrylamide gels was most sensitive for the detection of intra-type variation and the presence of mixed virus isolates.

Analysis of genome segments from six different isolates of bluetongue virus using RNA-RNA hybridisation: a generalised coding assignment for bluetongue viruses.

Nucleic acid probes prepared directly from bluetongue virus (BTV) genomic double-stranded RNA (dsRNA) have been used to identify the functionally equivalent genome segments from six distinct isolates of BTV after their separation in both agarose and polyacrylamide gel electrophoresis systems. Variations in the rate, and in one case the order, of migration of the equivalent genome segments from different viruses was detected in the polyacrylamide gel system. However, the genomic dsRNA profiles of eleven BTV isolates were found to be identical when analysed by agarose gel electrophoresis. Functionally equivalent genome segments from the six viruses that were analysed were found to migrate in identical relative positions in this gel system. From these data we propose a modified version of the protein coding assignments published for BTV 1 South Africa (Mertens et al., 1984) in which the identification of the genome segments would be based upon their order of migration in the agarose rather than the polyacrylamide gel system. The modified coding assignments, unlike the original assignments, would be applicable to all of those viruses analysed and appear likely to be valid for all normal BTV isolates.

A comparison of six different bluetongue virus isolates by cross-hybridization of the dsRNA genome segments.

The relationship between six different isolates of BTV was analyzed by cross-hybridization of genomic dsRNA using blotting and probe techniques (using an alkali fragmented probe made from BTV dsRNA). The viruses compared in this way included BTV serotype 1 from South Africa, serotypes 3 and 4 from Cyprus, serotype 10 from North America, and serotypes 1 and 20 from Australia. Under the hybridization and washing conditions used, which were calculated to allow stable duplex formation between RNA molecules containing greater than 90% sequence homology, two of the genome segments (segments 2 and either 5 or 6, which encode the two major outer capsid proteins VP2 and VP5) appeared to contain serotype-specific RNA sequences. Significant cross-hybridization between these segments from different serotypes was detected only with serotypes 4 and 20, which are known to have a particularly close antigenic relationship. The amounts of homologous sequence that were detected in segments other than 2 and 5 between different viruses indicated some correlation between their geographical origins and a degree of relatedness, which is independent of the virus serotype. High levels of sequence homology were detected between the isolates from Cyprus and Africa and to a slightly lesser extent from North America, suggesting a common ancestry. These results also indicated that within the limited number of viruses studied, the Australian isolates form a separate interrelated group of bluetongue viruses.

Group C rotaviruses in humans.

Atypical rotaviruses obtained from human feces from Australia, Brazil, and the United Kingdom were shown by a combination of techniques--immunoelectron microscopy, immunofluorescence, genome profile analysis, terminal fingerprint analysis of genome segments, and dot-blot hybridization--to be related to group C porcine rotaviruses. The prevalence of antibody to group C rotaviruses was found to be low in human sera and immunoglobulin pools from six countries. No signs of infection were obtained when one of the human viruses was inoculated into gnotobiotic piglets. We conclude that the atypical human viruses are the first examples of group C rotaviruses in humans.

Definition of two new groups of atypical rotaviruses.

Comparative antigenic and nuclei acid analyses were carried out on two new atypical rotavirus isolates coming respectively from chickens (D/132) and pigs (E/DC-9). Indirect immunofluorescence showed that each virus carried different group antigens which were also distinct from those of previously described rotavirus groups. By genome profile analysis each virus had a pattern of genomic RNAs clearly distinct from those of the other rotavirus groups. Comparative terminal fingerprinting of corresponding genome segments from the two viruses showed large differences between them, indicating that all of their genomic RNAs had significant differences in sequence both from each other and from the three previously defined rotavirus groups. On the basis of these results, extension of the number of rotavirus groups from three to five is proposed, with isolates D/132 and E/DC-9 being the type members of groups D and E respectively.

A rapid screening assay for detecting individual RNA species in field isolates of rotaviruses.

A method is described that allows the rapid screening of field isolates of rotavirus for the detection of specific viral RNA segments. Cloned cDNA copies of viral genomic RNAs are employed for detection in the assay which makes use of the dot-hybridization technique of Thomas (1980). The assay developed was shown to be sufficiently sensitive and specific to allow the genetic composition of virions to be determined over a wide range of concentrations. The feasibility of using the method developed for both the analysis of genetic reassortants prepared in vitro and for screening field isolates to detect putative genome reassortment events is demonstrated.

The inhibition of HeLa cell RNA synthesis following infection with vaccinia virus.

Vaccinia virus WR induces an immediate and rapid inhibition of HeLa S3 cell RNA synthesis as determined by pulse-labelling with [3H]uridine. The inhibition was independent of the purity of the infecting virus preparation and the multiplicity of infection over the range of 4 to 200 pk.f.u./cell. Inhibition was not evident in cells pre-treated with cycloheximide or following infection with u.v.- or heat-inactivated virus, suggesting that viral protein synthesis was required. There was no apparent selective inhibition of any particular species of RNA. Following infection, the uptake of [3H]uridine into cellular pools and the subsequent biosynthesis of UTP proceeded at the same rate as in mock-infected control cells. The rate of degradation of pre-labelled RNA was not enhanced in infected cells compared to controls. Analysis of the nuclear DNA-dependent RNA polymerase (EC 2.7.7.6) activities revealed a progressive and eventually total loss of RNA polymerase B activity, no obvious effect on RNA polymerase A and the presence of a viral RNA polymerase, the possible significance of which is discussed.

The genomes of rotaviruses isolated from chronically infected immunodeficient children.

Abnormal RNA migration profiles were found in numerous rotavirus samples from two chronically infected children suffering from severe combined immunodeficiency. In both cases additional bands consisting of dsRNA were found migrating between RNA segments 1 and 7, and in one case RNA segment 11 was lost from the profile. Hybridization studies using segment-specific cloned cDNA probes indicated that some of the additional bands had sequence homologies with normal rotavirus dsRNA segments. In most cases these sequences were derived from genome segments of lower molecular weight by the formation of covalently linked concatemers.