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Six source water fountains in the community of Berne, Switzerland were sampled monthly over the period of 1 year. The samples were tested for total counts by flow cytometry, and for fecal contamination by using the Bacteroidales16S rRNA markers HF183, BacR and AllBac. The total counts varied considerably between the different fountains with a minimal value of 5115 counts/L and with a maximal count of 198,508 counts/L. The long-term patterns of total counts over 1 year were typical for each fountain. Comparison of rainfall data and data for the non-specific fecal marker AllBac was shown to be a suitable approach to highlight the vulnerability of sources to environmental influences. HF183, indicating contamination of human origin, occurred only sporadically and in insignificant amounts. Furthermore, as indicated by BacR, the studied fountains showed no evidence of contamination by ruminant feces. Further work is suggested in order to establish threshold values for molecular Bacteroidalesmarkers, which could in future replace the currently used criteria for fecal indicator bacteria.

Within 2 months, two water sources in a karst area in Switzerland were sampled 9 times each, and analyzed by real-time PCR for 6 EHEC O-types, Shiga-like-toxin (stx1 and stx2) and intimin (eae) genes. With the exception of O111, 5 O-types were recorded regularly and at high frequencies (O26: 33.3 %; O157: 33.3 %; O104: 66.6 %; O103: 72.2 %; O145: 94.4 %). Genes for Shiga-like-toxins and intimin were almost omnipresent (stx1: 77.8 %; stx2: 83.3 %; eae: 77.8 %). Strain isolation was undertaken for O-groups 26, 103, 104, 145 and 157. Sample selection for strain isolation was based on Cq-values for the O-groups and stx1, stx2 and eae. From selected samples, frozen enrichment cultures were cultivated on EHLY-agar and 50 typical colonies screened for the O-type and genes encoding for stx1, stx2 and eae. With this approach, only one virulent EHEC-strain could be isolated (Escherichia coliO103, stx1 +; stx2 −; eae+). We carried out one extensive testing with 800 colonies of O-group O145, and no virulent strain was isolated. Our findings showed that PCR-results are not sufficient to formulate epidemiological conclusions and that the isolation of strains is necessary. However, as the detection procedure of EHEC in foods is cumbersome and expensive, the appropriateness of such an approach in official food control is a matter of debate.