I should add another reason really.
-about 10 years ago, is when they used more antibiotics than they did now, since they had less drugs specific for crohn, those tests were not negative, but also not really positive
but, there were many issues with those tests, many of the tests used non-macrophage penetrating antibiotics, many used incredibly low doses, many stopped too soon, many built up the dose too slow which leads to resistance, they didn't use probiotics which leaves the mucosa vulnerable to colonisation, etc
basically antibiotics were discarted at that point, they argued that if it were bacteria, antibiotics should have helped
so, now, with much better tech available, they are discovering AIEC and other bugs, and they realise they're not normal bugs, they're macrophage penetrating, AIEC replicate inside macrophages, they're intracellular and if the antibiotic is not macrophage penetrating, it might not work very well against macrophage penetrating bacteria (it doesn't mean it's useless, flagyl has some, effect against some strains in limited numbers). What it does mean is that they can point to those old studies and explain why they're flawed.
That doesn't mean that antibiotics now suddenly would work, it just means, that people shouldn't base their facts on old studies done 10 years ago, because there are plenty of reasons that can explain why they failed outside of concluding that crohn is not related to specific strains of pathogenic bacteria.
10 years ago they tried antibiotics for crohn, and it didn't help enough, they concluded antibiotics didn't help for crohn, without knowing which bacteria they were targeting, with many flawed studies, without knowing the bacteria are macrophage penetrating (trojan horses if often used, they infitrate a magrophage and exploit it). When doctors say that antibiotics don't work for crohn, many base their opinion on those studies done long ago, which shouldn't be happening but it does.
(I'm not saying antibiotics work or even work for everyone, I'm just saying, many doctors don't have the right facts in front of them)