Assessment of Aquifer Vulnerability in South Africa
Report No: 1494/1/07
May 2007


A prototype implementation manual for the national microbial monitoring programme (NMMP) for groundwater was completed in 2004 [Murray et al., 2004a].  That mainly desktop study produced a general framework for the design of the monitoring programme.  Before the design can be formally adopted by the Department of Water Affairs and Forestry (DWAF), the core design and a number of specific issues contained therein needed to be tested.
This report describes the choice of pilot study sites, the location and drilling of monitoring boreholes, the data collected and the assessment thereof.  It also includes an examination and refinement of sampling and analysis protocols for bacteria and viruses.  The initial version of this report served as a preliminary "implementation manual" for this pilot study (supplementing the main manual).  This final version records the refinements required for the final implementation manual aimed at full-scale implementation.

Project objectives

The project objectives as indicated in the original project proposal are as follows:
In order to achieve the objectives of the NMMP, monitoring viruses will also be important.  However, a design framework for viruses was not included in the original design.  Accordingly, a separate project was created to run concurrently with the present one to address this.  This had the following objective:
Monitoring objectives and design philosophy

The Objectives of the NMMP for groundwater are as follows [Murray et al., 2004a]
National Microbial Monitoring Programme for Groundwater
National Objectives

To measure, assess and report on a regular basis
the status and trends
of the microbial water quality
that reflects the degree of faecal pollution
(because of the associated human health risks)
of South African groundwater resources
in a manner that is
soundly scientific and
that will support strategic management decisions
in the context of sustainable fitness for use of those water resources.

In essence, the philosophy of the design of the monitoring programme focuses on monitoring faecal contamination of groundwater in a manner in which local containment of the contamination can be confirmed.  If containment is indeed observed, then statements, although cautious, can be made about the aquifer down-gradient of the "containment" borehole perhaps being uncontaminated.  In this way it is hoped that general statements can be made about the status of aquifers without having to monitor the aquifer at many points.  The intention is to maximise information and minimise costs because the NMMP is a national programme.

Pilot study focal issues

To achieve the above project objectives, the following four specific issues were identified:
  1. Suitability of potassium as an indicator of flow path.
  2. Distance to containment borehole.
  3. Presence of viruses in containment borehole in the absence of E. coli.
  4. Suitability of E. coli.
Issues 1 and 2 relate directly to the first project objective above, namely to develop improved guidelines for defining the faecal pollution attenuation zones.  Issue 3 relates directly to a fundamental suspicion that viruses, being smaller than bacteria, may travel further than bacteria in groundwater.  This is an important issue for the project objective relating to virus monitoring protocols.  Issue 4 was investigated simply by comparing the occurrence of E. coli with that of enterococci because the latter is known to live longer in the environment (although the environment itself can be a source of enterococci, besides the faecal contamination in the pollution sources studied).

Monitoring sites

Three sites were chosen:
Monitoring variables

The bacteria E. coli and enterococci as well as two groups of viruses (adenoviruses and enteroviruses) and the cytopathogenic effect were monitored in this pilot study.  A number of chemical variables were also monitored to investigate whether some, like potassium, could be used to confirm that boreholes were indeed in the flow path of the groundwater contamination (since increases in at least potassium can be expected down-gradient of faecal pollution sources).  Water levels were also determined.

Data assessment

Ogies sewage treatment works
Brits water care works

Potsdam sewage treatment works
Overall assessment
Refined procedures

Guidelines for geohydrologists for the placement of the containment borehole in particular have been improved on the basis of experienced gained in this pilot study.

Borehole construction specifications have been recorded that can be used as a basis of future drilling contracts.

Sampling procedures have been documented in some detail and include the use of photographs.  Issues such as personal hygiene, personal health, the borehole sampling sequence (least contaminated first, more contaminated last), pump and pipe disinfection, borehole purging, actual sampling, sample preparation and sample transport have been addressed.

Inclusion of viruses

Inclusion of viruses in the national monitoring programme is likely to be essential if the stated objectives of the programme are to be achieved.  This is primarily because of their different properties from bacteria (like E. coil) and the unpredictability of their behaviour.  However, monitoring for viruses raises a number of unique problems.

Viruses require large sample volumes.  One hundred litres is usually recommended although due to the inevitable associated problems, 20 litres is often used.  A simple Monte Carlo model was developed to better understand why sample volume is such an issue.  In essence, very low concentrations of viruses (e.g. 1 viral particle per 100 litres) are still associated with significant human health risks when used for drinking purposes.  Using only 20 litres to "capture" a single particle in 100 litres obviously creates considerable potential for "false negative" results.  (A false negative result reports that there are no viruses present when actually there are some present.)  The model demonstrated the seriousness of this problem.  Nevertheless, in accordance with current practice, 20 litre sample volumes are recommended.  However, it is also recommended that an explicit statement be made regarding the likely decrease in information content in reports when zero viral particles are reported:

"These results are based on only 20 litre samples where at least 100 litre samples are theoretically more desirable.  There is therefore a significant probability that results reported as zero viral particle/100 litres may be erroneous, i.e. low, yet problematic, numbers of viral particles may have been present but not detected.  Firm conclusions cannot therefore be drawn directly about the extent to which such water is actually drinkable."

The problems associated with having to ensure samples (a) reach laboratories within 24 hours and (b) are kept cold were carefully considered.  It was decided that these requirements cannot be relaxed.

Consideration was also given to which virus group would be the single group of choice for a national monitoring programme.  Enteroviruses were recommended for a variety of reasons.

Analytical methods were also described and alternatives compared.  Concentration of the viruses from the 20 litre sample can be achieved by ultrafiltration or using a glass wool trap.  A comparison of recovery rates suggests that ultrafiltration is better than glass wool.  However, careful consideration of when this is actually relevant revealed the following useful insight:  If the detection of viruses is based on a presence/absence test, the difference between the recovery rates is only important when there are very few virus particles in the sample.  It is proposed that the glass wool technique will be an acceptable concentration technique in the context of national monitoring.  In this case, the loss of information content at low virus concentrations again necessitates an explicit statement to this effect in reports in which zero viral particles is reported.  This is to ensure that water management decisions based on such data are suitably informed.  The above statement can be modified as follows:

"These results are based on only 20 litre samples where at least 100 litre samples are theoretically more desirable.  Furthermore, the virus concentration technique has inherently low virus recovery rates.  There is therefore a significant probability that results reported as zero viral particles/100 litres may be erroneous (i.e. low, yet problematic, concentrations of viruses may have been present but not detected).  Firm conclusions cannot therefore be drawn directly about the extent to which such water is actually drinkable."

In respect of the subsequent analytical technique, it is proposed that using an analytical technique that only detects presence or absence, like PCR, is satisfactory for viruses in the context of national monitoring.

The financial requirements relating to sampling and analysis were also considered.  Various assumptions were made concerning:
These were used as the basis for a spreadsheet model which calculated the overall costs for sampling, transport and analyses for a series of scenarios.  The results indicated the following:

If ultrafiltration is used to concentrate 20 litre samples in the laboratory:
It is also important to consider the disadvantages of only having one centralised laboratory when deciding on the number of laboratories required.  These include a small pool of expertise, a possible inclination to inflate prices, and a lack of local inter-laboratory comparisons for quality control purposes.

If glass wool traps are used in the field to concentrate 20 litre samples:
Human resource requirements as well as capital costs for equipment are also described in this report.  It is noted that in the initial years of implementation in which up to about 100 samples per year are being analysed, the time required for both E. coli and viruses can probably be accommodated by existing laboratories.  In other words, it is unlikely to be necessary to employ extra staff at those laboratories.

The following conclusions are drawn:
It is recommended that monitoring of viruses (specifically the enteroviruses) be included in the national microbial monitoring programme for groundwater based on their high infectivity, their presence not being confidently indicated by a bacterial indicator such as E. coil, their having relatively small sizes and potentially long survival times under some conditions, and having a behaviour that is difficult to predict.


The following conclusions are drawn from this study:

The following recommendations are made: