What other types of testing can be done to confirm with little doubt the origin of the food contamination?

Tryp synthetase A
Over the course of evolutionary history, mutations will occur, that will cause the amino acid sequence to change somewhat. Every time the bacteria replicates, there's a certain chance for error in duplicating the DNA. This could cause a change in the amino acid sequence. Even over the course of several months, if you are growing lots of bacteria to make protein, without going back to the stock of bacteria, you have to make sure that the amino acid sequence of the protein still has the correct sequence.
Food contamination 
This usually involves making comparisons about the sources of ingredients in the food and other foods that didn't make people ill, and eliminating possibilities. 

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Probably because you wake up early. even when i get a good nights sleep i still feel tired if i wake up early. or maybe you just need coffee.