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This document specifies a method for the detection of 16S ribosomal RNA (16S rRNA) of Escherichia coli (E. coli) in drinking water using real-time reverse transcription-polymerase chain reaction (RT-PCR) based on a defined Ct-value (cut-off point).
This document is applicable to drinking water, and it can be applied to other water matrices if the appropriate validation of performance of this method has been undertaken by the laboratory prior to use.
The presence or absence of E. coli 16S rRNA is detected with a relative limit of detection level of 1 colony forming unit (cfu)/100 ml, unless the nature and/or content of suspended matter and/or accompanying flora in the matrix interfere with the efficiency of the real-time RT-PCR reaction. If such interference adversely effects the detection limit, its presence can be determined by using an internal process control.
The genetic target used by this method is not fully specific for E. coli. Consequently, closely related Escherichia species (e.g. E. fergusonii, E. marmotae, E. ruysiae) and Shigella species cannot be distinguished and will be detected by this method.
Examination of water samples for the presence of Escherichia coli (E. coli) provides important information on the quality of water and the possible risk to human health. In situations where rapid insight regarding the presence of E. coli and the effect of corrective measures in the distribution network of drinking water is needed, a quick method is crucial. Culture-based methods are used in drinking water laboratories based on different parts of the ISO 9308 series ‘Water quality — Enumeration of Escherichia coli and coliform bacteria’, and the test result is available in 1 day or 2 days.
There are situations in which a faster result of detection of E. coli is needed, where every minute counts: for example, for maintenance and leaks in the drinking water distribution network or after cleaning of faecal contaminated water systems. Molecular diagnostics could be a solution. Therefore, several organizations in the Netherlands and Belgium developed a real-time reverse transcription-PCR (RT-PCR) for rapid detection of E. coli in drinking water. The test result for the detection of E. coli is available within 5 hours instead of 1 day. This method is standardized in the Netherlands (NEN 6234) with the method description and associated validation data published in Water Research (see doc. SC 4/N 951) – if needed, the raw data can be shared on demand: please contact laura.mout@nen.nl. Further information is given as well in the report ‘Validation of a real-time RT-PCR method for rapid detection of E. coli in distributed drinking water’ in doc. SC 4/N 952.
Other countries noted the need for an international guideline for real-time RT-PCR-based detection of E. coli to ensure consistent implementation across laboratories. The requirements, guidelines and performance characteristics mentioned in the proposed standardized reference method are intended to ensure that the results in various laboratories are reliable, comparable and reproducible. In summary, real-time RT-PCR is a rapid and reliable method for the detection of E. coli, particularly relevant during microbial contamination events in the distribution network of drinking water.
Please note that during the plenary meeting of ISO/TC 147/SC 4 ‘Water quality - Microbiological methods’ of 17 April 2026, resolution 47 was taken (see also the presentation from the Netherlands in doc. SC 4/N 903):
Resolution 47 (Pretoria-47/2026)
ISO/TC 147/SC 4 thanks Gabi van Pelt and Laura Mout for their presentation (see N 903) on the possible NWI Water quality – Detection of Escherichia coli by reverse transcription-polymerase chain reaction (RT-PCR) and invites The Netherlands to submit the draft and Form 4 for the NP-Ballot by the end of September 2026. The information that the raw data from related studies can be shared on demand will be provided with the NP-Ballot.
SC 4 decides to launch a CIB in parallel with the NP-Ballot to confirm the establishment of a new Working Group in ISO/TC 147/SC 4: “E. coli by RT-PCR” , led by The Netherlands. SC 4 agrees to invite CEN/TC 230 ‘Water analysis’ to develop this method in parallel under the ISO lead (Vienna agreement).
The Resolution is agreed on unanimously.
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