Being even more serious - the big problem with pathogen discovery studies in the past have just been the lack of sensible negative controls! But PCR studies are potentially even worse than sequencing because of false positives from mispriming and contamination from stuff being handled in the lab. Sequencing data at least lets you know you are on-target, and the sequence information helps you clue into whether you are looking at a natural population.
What would be nice about the field sequencing is that over time you’d build a nice picture of what is intrinsic to host, what is environment and what is reagent contamination. But yes, in the wrong hands I dread to think what you’d find