We are regularly doing bacterial transformation and subculture from plate to liquid media to extract DNA. This usually goes very well and is straightforward, but occasionally, the colonies that grew well on a plate, will not grow in liquid culture (with the same antibiotics that were in the plate). This has happened now to three persons on multiple plasmids.
For example, I was trying to ligate an ampicillin resistance gene (with its promoter) inside pENTR4 plasmid (already with Kanamycin resistance). My plate and LB both contained the two antibiotics, but the colonies only manage to get slightly turbid at a 16h timepoint.
Phage contamination is very unlikely, and the effect cannot be due to a toxicity of the inserted fragment, as both insert and vector have been grown in these same bacteria multiple times without problem.
EDIT1 - We use Carbenicillin in place of ampicillin in the plate, but not in the liquid media.
EDIT2 - After managing to grow some colonies in liquid, I managed to get a small amount of the plasmid (profile was good; concentration = 70ng/ul). The weird thing is that when I retransformed this DNA in Stbl3 bacteria, I had absolutely no trouble. Do you think the bacteria stock could be responsible?