Humans are colonizing planets, and at some point discover that the fungal-like infection that permeates several worlds each form a groupmind. IIRC, one of the initial encounters with one of these group minds goes VERY bad, and there is fear that if the groupminds are able to communicate (by pheromones?) that fact then there will be a slaughter. So, humanity is SLOWLY decolonizing these worlds in the hope they can get the humans out before one of these group minds learns what happened elsewhere and decides on genocide.
It might have been part of a series. (I think that the events with the groupmind gone wrong occur in one book, and the word that humanity is pulling out are in another.)
It sounds like it should be a Julie E. Czerneda novel, but I can’t match it to one.
It came out in the early 2000s, I think. I only saw it in paperback. I don’t have any other story details, because I never bought or read it.