A study of immunocompromised patients undergoing bone marrow transplants and given fluconazole as a "just in case" measure developed an increase in candida krusei colonies. This led led the researchers, writing in the New England Journal of Medicine (31 October 1991) to conclude that in patients at high risk for "disseminated candida infections" suppression of bacterial flora and more common candida pathogens "may permit some less pathogenic, but natively resistant candida species. . . to emerge as systemic pathogens."
What this could mean is that killing off candida albicans further disrupts the bowel flora, allowing other bugs to grow.Another unexplained phenomenon is that women who take oral Nystatin for systemic candida seem to suffer an increase in vaginal candida. But it could well be that the anti fungal disrupts the vaginal balance further, paving the way for the overrunning of other pathogens.