I live in the Okanagan region of B.C., which is known for two things: wine and beaches. I might be exaggerating a bit on the "beaches" part, but the Okanagan is certainly a summer destination for a lot of people. The major municipalities and regional districts in the area have done a good job of maintaining public beach access, but with that access comes the risk of exposure to disease-causing bacteria. Historically, the local health authority would be responsible for sampling the water in close proximity to the beach, sampling the bacterial load (coliforms and fecal coliforms), and suggesting a beach closure if any individual sample was above a certain level, or if the running log mean of consecutive samples got too high. In the past couple of years, the local governments have taken on this sampling role but have used the same indicators and tests to determine whether or not a beach is "safe" for public access.
But are culture-based methods of counting coliforms really the best indicator of beach safety, or are there better methods out there? A (very large) group of researchers in the United Kingdom looked at this topic to determine whether molecular methods for enumerating coliform bacteria were better than traditional cultures. They bring up the very valid point that culture-based methods of enumeration can take a couple of days to get results back, whereas molecular methods (like quantitative polymerase chain reaction, or qPCR) can give results in a couple of hours. When dealing with beach water quality for bather safety, the quick turn-around time could be the difference between closing the beach while the hazard exists, and closing the beach once the hazard has already passed (and people have already been exposed to it).
One difficulty the paper points out with the use of qPCR is the current lack of epidemiological evidence between level of exposure and human illness. Because it's a relatively new technique, there isn't yet a strong link between a sample result and the potential for illness like there is for traditional culture counts. They also identify that the specificity of qPCR can be both a blessing and a curse: it's nice to not have to rely on indicator organisms (like E. coli) as catch-alls for human pathogens, but how do you identify the specific pathogens you want to target with the qPCR?
And of course, there's always the cost consideration. Implementing new testing methodologies can be exceedingly expensive, especially when you're talking about molecular biology. Add to that the fact that there would be a necessarily overlap between the two techniques as the transition took place, and you're looking at even higher costs. The researchers argue that the cost increase may not actually be associated with a significant benefit to public health: do people really need "real-time" beach data, or would time and money be better spent building predictive models using existing culture counts?
The researchers came up with a number of recommendations for the UK working group prior to implementation of a molecular method for determining beach safety, but the bottom line is that we're just not there yet. More research and evidence needs to be gathered, and the cost of transitioning to a new methodology needs to be reduced before local governments or health regions will consider the transition (given that there aren't that many concrete benefits).
It's also worth noting that as acute care costs rise, money for environmental health initiatives like beach monitoring necessarily decrease (see: local governments taking on sampling, as noted above). There has to be very real and clear benefits to the program to even keep health authorities involved, let alone getting them to invest new money.
Source: Oliver, David M. et al. (2014). Opportunities and limitations of molecular methods for quantifying microbial compliance parameters in EU bathing waters. Environment International, 64, 124-128.