If you look at the rise of C. difficile infection rates in the US versus the amount of trehalose encountered in the food supply, it's far more likely that C. difficile rates are correlated to the increasing use of proton pump inhibitors rather than trehalose which is rare even 20 years after a relatively inexpensive commercial process to produce it was introduced.
Doctors have been passing out PPIs like candy for the last 20 years. The reason our stomach is an acidic environment is primarily as a defense against bacterial infection, not so much for digestion. It's well known that raising stomach pH opens the door to all sorts of gastrointestinal infections.
That original study linking trehalose to human infection rates of C. difficile was just bad science. They took correlation to imply causation. Then they did an in vitro test and said C. difficile likes trehalose. Not once in that study did I see any effort to link actual trehalose consumption to C. difficile infection in humans.
Again, I invite people to go to their local grocery store and see how many food products you can find that are sweetened with trehalose. Good luck with that because there are just about none. The reason is simple - while the Hayashibara process greatly lowered the cost of producing trehalose it is still many times more expensive than regular sugar. And, it takes about 2x as much trehalose at about 2x the calories to achieve the same level of sweetness. Aside from our interest in trehalose vis-à-vis atherosclerosis, about the only thing it has going for it is that it spikes insulin less than sucrose. But, you're still getting the calories (and twice as many of them) so it is remarkably uncompelling as a sweetener for most foodstuffs.