What are the two major problems with testing for pathogens in water?

The presence or absence of pathogens in water cannot be directly tested for. Instead, the water is assessed by determining the presence of so-called indicator organisms, which point to potential contamination.

There are two difficulties in using indicator organisms to assess water quality. First, the absence of indicator organisms does not necessarily indicate the absence of pathogens. This can occur if there are a number of pathogens present that are not detected by the indicator organisms, or if the indicator organisms are not present at the time of sampling. Second, the presence of indicator organisms does not necessarily indicate the presence of pathogens. This can occur if the indicator organisms are not directly associated with the pathogen of interest, or if the indicator organisms are more resistant to the environmental conditions than the pathogen of interest.