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The answers are revealing, and illustrate the complex situation. I would first suggest you consider a different type of toilet, such as UDDT.

If you must have a pit latrine, dig a deep square hole, line it with stone, or a thick layer of clayish soil, so the seepage is deeper; put a berm around it. Then use a telltale indicator, easier to detect than e.coli or coliform.

Just an idea...