An interesting read around food forensics (a significantly growing field).
In answering the ultimate question being asked, vastly different results are shown based on the use of two different methodologies. I would assume that different products have been tested, which would have been accounted for in the technical findings.
I guess it really comes down to 'what was the initial testing authority asked to do ?', and what was the responding organisations asked to do?. Was it in fact the same question? And what is the appropriate methodology to be employed to respond to the respective questions?
The implication for reputations could affect both the company being tested (in this case Subway) and the testing authority (in this case Trent University Wildlife Forensic DNA Laboratory).