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Introduction {#Sec1} ============ *Escherichia coli* (*E. coli*) consists of both commensal (ComEC) and diarrhoeagenic (DEC) types. DEC not only indicate the presence of intestinal pathogens or parasites but also constitute a human health risk in themselves (Grabow et al. [@CR9]; Kaper et al. [@CR17]). At present, seven groups of pathogenic *E.coli* have been identified, of which five were selected for this study based on their importance for surface-water pathogenicity. The DEC types have been classified into the following: entero-pathogenic *E. coli* (EPEC), entero-toxigenic *E. coli* (ETEC), entero-haemorrhagic *E. coli* (EHEC), entero-aggregative *E. coli* (EAEC) and entero-invasive *E. coli* (EIEC) (Ashbolt [@CR2]; Kaper et al. [@CR17]). There are media available for the detection of specific EHEC 0157:H7 but traditional culture methods for *E. coli* were not designed for the detection of DEC (Iijima et al. [@CR16]) but rather ComEC. Further conformational steps are thus required after culturing to distinguish the DEC from the ComEC which increases cost and time in producing the results. Diarrhoeagenic bacteria such as *Campylobacter jejuni*, *Salmonella enterica* serovar, *Shigella* spp., and *Vibrio* spp., can be readily isolated using selective plating media, with the exception of STEC 0157. Serotyping is the predominant means of differentiating pathogenic strains of *E. coli,* and phenotypic assays based on virulence characteristics can also identify DEC. Genotypic assays targeting virulence genes, especially polymerase chain reaction (PCR), are becoming standard procedure (Iijima et al. [@CR16]). Diagnosis is currently recommended for cases of persistent diarrhoea, children with severe diarrhoea unresponsive to treatment and immunodeficient patients with moderate to severe diarrhoea, and in epidemic outbreaks of gastroenteritis (Vidal et al. [@CR32]). Methods in molecular biology have progressed and offer significant increases in speed and specificity in identifying micro-organisms according to their specific genetic makeup encoded in the genomic DNA (Horokova et al. [@CR14]). Technologies such as microarrays and PCR are used to explore the global virulence pattern of strains (Wu et al. [@CR34]). However, for developing countries microarray is an expensive method which laboratories cannot afford for routine analysis. M-PCR is a rapid and cost-effective method for screening and identifying DEC. The targets selected for each category were: EHEC (*stx1*, *stx2* and *eaeA*); Atypical EPEC (*eaeA*) and Typical EPEC (*bfp*); ETEC (*st* and *lt*); EIEC (*ial*); EAEC (*eagg*); Commensal *E. coli* (*mdh*); *E. coli* toxin (*astA*) and, for the external control, *gapdh*. The major obstacle to using PCR for the detection and identification of pathogenic organisms from clinical or environmental water samples is the presence of substances that are inhibitory to PCR such as humic substances (Shieh et al. [@CR28]; Wilson [@CR33]). In order to monitor PCR inhibition sufficient laboratory controls are required in the m-PCR. The majority of published studies report the addition of 16s rRNA gene as the internal control to monitor for false negative results in m-PCR (Sabat et al. [@CR27]; Grape et al. [@CR10]). However, these are not sufficient to monitor false negative results for *E. coli* specifically, since 16s rRNA is amplified from the *E. coli* DNA. It would not be