so reluctance to 'change behaviour' from open defecation to using shared toilets is perfectly understandable.
In general, people might quite rationally choose open defecation, especially in the bush, as more hygienic for the individual defecator even though it's less hygienic for everyone else.

The short answer is I agree that in most cases microbial fingerprinting would not be practical for many public safety monitoring purposes. In our project we are using fingerprinting data to address methodological questions about the performance of general fecal indicators, individual pathogens, and combinations of pathogens at accurately detecting enteropathogens. Using Kisumu as a model, we are quantifying uncertainty associated with using any of these strategies to assess enteropathogens in publically-shared environments. As an example, let’s say Cryptosporidium has a 0.6 probability of accurately predicting whether any other pathogen is present or not present, Crypto and the ST toxin gene of ETEC achieves 0.75 accuracy, and Crypto, ST, and Adenovirus achieves 0.91 probability. Stakeholders like you mentioned can weigh the cost-benefits of progressively more expensive approaches and make informed decisions about how much uncertainty they are willing to accept.

The longer answer requires more space than reasonable for a blog, but is basically that no one really knows just yet whether the interactions between humans, the environment, and human pathogens or the indicators used as proxies can be easily reduced to simple relationships. I think that (mostly) everyone acknowledges that it is necessary - the WASH sector needs to get better about objectively evaluating policy and interventions/programs. Do shared latrines pose higher risks of exposure, and if so how? Are improvements in sanitation coverage reducing open defecation? How much impact will latrines have given all of the other sources of feces and pathways to infection?

Unfortunately, all the evidence suggests that in places like Kisumu, the story may be more complex than we hope. And the easiest to use, lowest cost indicators are not appropriate for many of these questions although they are quite useful for drinking water/food/hands where tolerance for any contamination is low. The starting point begins with using rigorous science like microbial fingerprinting to understand how humans, animals, etc. affect safety of the environment and to figure out which indicators best measure risks from different sources. Second is to validate those patterns across sites with similar developmental challenges. Then we will are equipped to have an evidence based discussion about observable factors or indicator assays for risk evaluation by utilities and others.

I hope that doesn't come across as a non-answer, but I think we have to be transparent about current knowledge gaps.

Kelly

Interesting update on the GEMS study:
www.cawst.org/blog/bydate/2016/12/diarrh...se-the-top-culprits/

It seems like more thought has to be put into preventing the spread of viruses especially regarding pitlatrines as viruses can travell quite far in groundwater compared to the typical ecoli indicators.