Scielo RSS <![CDATA[Water SA]]> vol. 36 num. 2 lang. en <![CDATA[SciELO Logo]]> <![CDATA[<B>Foreword</B>]]> <![CDATA[<B>Optimisation of methods for the collection and detection of bacterial pathogens from diarrhoeal human faecal samples using a novel stool collection kit</B>]]> Bacterial pathogens such as Escherichia coli, Salmonella-, Shigella- and Vibrio species are known to be common causative agents for diarrhoeal disease in humans. This study aimed to develop a culture-independent PCR assay for the detection of bacterial pathogens present in human faecal samples collected using a less intrusive faecal collection technique, the Bio-wipe kit. A multiplex-PCR (m-PCR) was optimised targeting the E. coli mdh gene, the Salmonella IpaB gene, the Vibrio sodB gene, and the Ial and IpaH genes present in entero-invasive E. coli and Shigella spp. The influence of the DNA extraction method, and sensitivity and specificity of the m-PCR and the Bio-wipe storage conditions on the detection of the bacterial pathogens was investigated. A guanidium thiocyanate DNA extraction method used with laboratory-prepared spin columns could successfully extract DNA from 93% of the samples analysed. The m-PCR could successfully identify and differentiate between the various pathogens tested and was specific for the selected pathogens. Faecal matter was successfully recovered from used Bio-wipes and the bacterial DNA could be detected from these samples at concentrations of 10 cfu. Bacterial DNA could be recovered from the Bio-wipes 5 to 10 d after use when the Bio-wipes were stored at 30°C and 14 d after usage when stored at ambient temperature. Thus the Bio-wipe kit, along with the m-PCR, can be used for collection and detection of bacterial pathogens during outbreaks and in rural settings. <![CDATA[<B>Detection of <I>Vibrio cholerae</I> O1 in animal stools collected in rural areas of the Limpopo Province</B>]]> Vibrio cholerae (V. cholerae), the causative agent of cholera, has been responsible for various outbreaks worldwide and may be associated with animal faeces. In an attempt to understand the occurrence of this organism in the environment, 230 faecal samples were collected from pigs, chickens, goats, donkeys, cows and pigeons in rural areas of the Limpopo Province. Bacterial DNA was extracted from the faecal samples using a guanidium thiocyanate-based method. The DNA was screened for the presence of the sodB, rfb, FlaE, 16S rRNA and ctxA genes associated with V. cholerae, V. cholerae O1, V. cholerae O139 using 2 multiplex polymerase chain reactions (m-PCR). The V. cholerae sodB gene was detected in 74 of the 230 samples tested. Detection rates for the faecal samples obtained from individual species were as follows: cows (55/74), chickens (8/74), goats (2/74), donkeys (4/74), pigs (3/74) and pigeons (2/74). V. cholerae O1 was detected in (17/74) cow and (3/74) chicken samples, of which (9/17) cow samples and (3/3) chicken samples tested positive for toxigenic V. cholerae O1. The presence of this organism in faecal samples, taken close to water sources used by the villagers, raises the possibility that the causative V. cholerae O1 strain of the most recent outbreak in South Africa was present in the area 6 months prior to the outbreak. <![CDATA[<B>The occurrence of pathogenic <I>Escherichia coli</I> in South African wastewater treatment plants as detected by multiplex PCR</B>]]> The aim of this study was to investigate the use of PCR to detect commensal and diarrhoeagenic Escherichia coli concentrated from water samples using membrane filtration. To achieve this, culture-based and PCR-based methods were compared for the detection of E. coli in raw sewage and primary, secondary and tertiary effluents from 6 wastewater treatment plants around Johannesburg, Gauteng. E. coli was concentrated from the samples using standard filtration techniques with subsequent incubation on E. coli/coliform chromogenic media to determine the E. coli levels. Bacterial DNA was isolated from bacterial colonies trapped on polyethersulphone membranes after filtration using a celite/guanidium thiocyanate method. A single multiplex PCR (m-PCR) assay was used that targeted the mdh, eaeA, stx1, stx2, st, lt, ial and eagg genes associated with diarrhoeagenic E. coli. The mdh gene was detected in all of the samples even if no culturable E. coli was detected. All the diarrhoeagenic E. coli types were detected in one or more of the raw sewage samples from the various plants. EPEC was present in 20% (2/10) of the samples, EHEC in 50% (5/10), ETEC in 80% (8/10), EIEC in 10% (1/10) and EAEC in 90% (9/10) of the samples. In the case of the primary and secondary treatment only ETEC (5/5; 100%) and EAEC (5/5; 100%) were detected in all of the samples. The results demonstrate that molecular techniques such as PCR have the potential to be used for the monitoring of water samples for the presence of pathogenic E. coli, without the need to culture the organisms. <![CDATA[<B>Large scale quantification of aquifer storage and volumes from the Peninsula and Skurweberg Formations in the southwestern Cape</B>]]> The Western Cape Province of South Africa is a relatively water-scarce area as a result of the Mediterranean climate experienced. Due to the increased usage of groundwater, and the requirement to know how much water is available for use, it is imperative as a 1st step to establish an initial estimate of groundwater in storage. The storage capacity, namely, the total available storage of the different aquifers, and the storage yield of the fractured quartzitic Peninsula and Skurweberg Formation aquifers of the Table Mountain Group (TMG), are calculated with a spreadsheet and Geographic Information System (GIS) model. This model is based on the aquifer geometry and estimated values (based on measured data) for porosity and specific storage (calculated using the classic Jacob relation). The aquifer geometry is calculated from 1:50 000 and 1:250 000 geological contacts, faults and major fractures, with dips and aquifer formation thickness calculated through structural geology 1st principles using a Digital Elevation Model (DEM). Balanced geological cross-sections constructed through the model areas provide an important check for the aquifer top and bottom surface depth values produced by the GIS model. The storage modelling undertaken here forms part of the City of Cape Town TMG Aquifer Feasibility Study and Pilot Project, with modelling focusing on the 3 main groundwater target areas at Theewaterskloof (Nuweberg), Wemmershoek and Kogelberg-Steenbras. In the storage models, the Peninsula and Skurweberg Formation aquifers have confined pore volumes ranging from approximately 29 bn. to 173 bn. m³ and 4 bn. to 26 bn. m3, respectively (based on using different porosity values ranging from 2.5% to 15%). Using an average head decline of 1 m across the confined aquifer areas across all 3 groundwater exploration areas, and confined pore volumes based on a porosity of 5%, 6.9 Mm³ and 1.1 Mm³ of groundwater, from the Peninsula and Skurweberg Formation aquifers, respectively, is available. The aquifer storage model intentionally makes use of low, geologically reasonable values for porosity and aquifer compressibility, so as to provide minimum large-scale 1st estimates of potential yields; however, when new data become available these initial porosity and compressibility assumptions will probably be revised upward. The storage yield approach is also very conservative, as it does not take into account the annual replenishment of the aquifer, and constitutes the yield potential during drought conditions (zero recharge) from the confined portion of the aquifer only. The yield model therefore provides a quantitative perspective on the common public and decision-maker perception that groundwater abstraction from the deep confined Peninsula Formation aquifer will significantly dewater the system, with (often unspecified) adverse ecological consequences. Even where the regionally-averaged decline in hydraulic head approaches 20 m, the volume released by aquifer compression generally remains in the order of 0.24% of the total volume in slow circulation within the deep groundwater flow system. A vastly greater volume of groundwater is essentially non-extractable by any practical and/or economical means. <![CDATA[<B>The impact of water quality on informally-declared heritage sites: a preliminary study</B>]]> The current study is an attempt to gauge the impact of water quality on 2 sacred sites in the eastern Free State, Mautse and Motouleng, which are informally-declared heritage sites, as well as the consequent implications for matters of living heritage as pertaining to the specific sites. The informally-constituted communities at the sacred sites are dependent on freshwater sources where water use, sanitation and waste disposal are unmanaged activities. The sustainability of informally-declared heritage sites may be uncertain due to factors relating to water quality. Water samples were collected for physical, chemical and biological analyses. The latter comprised algal and bacterial analyses which included testing for concentrations of faecal coliforms, where concentrations above 20 cfu/100 mℓ indicates a significant risk of infectious disease transmission (domestic use) and concentrations above 200 cfu/100 mℓ points to a significant infection risk for young livestock. Water quality is discussed in terms of human, animal and ecological risk, which may threaten the heritage and the economic subsistence based on the heritage at both sites.