It seems that probiotic fungi, specifically Saccharomyces boulardii probably don’t prevent NEC. There is one previous study Costalos et al which showed no difference in NEC, but some benefits on secondary outcomes (it was very underpowered for NEC, 87 babies of 28 to 32 weeks).
A new study (Demirel G, Celik IH, Erdeve O, Saygan S, Dilmen U, Canpolat FE. Prophylactic Saccharomyces boulardii versus nystatin for the prevention of fungal colonization and invasive fungal infection in premature infants. Eur J Pediatr. 2013:1-6) randomized 181 very low birth weight babies to either S Boulardii or to oral Nystatin to prevent fungal colonization and invasive infections. In this trial the authors found not much difference in either skin colonization or stool colonization with Candida between the nystatin and the probiotic group. There was no difference in NEC, and there were 2 cases of invasive candidiasis, both in the nystatin group, which is obviously not statistically significant. There were some benefits in secondary outcomes regarding feeding tolerance, as Costalos had also showed.
Nystatin is probably effective as prophylaxis against invasive fungal disease, but there have been few trials. Only one of the nystatin/placebo trials had a substantial size of 948 VLBW infants, they showed a positive effect, (but the placebo group frequency of invasive fungal infections was 36%!!). The fluconazole and nystatin trials were well reviewed last year in a systematic review by Chrisopher Blyth and colleagues from Australia. (Blyth CC, Barzi F, Hale K, Isaacs D: Chemoprophylaxis of neonatal fungal infections in very low birthweight infants: Efficacy and safety of fluconazole and nystatin. Journal of Paediatrics and Child Health 2012, 48(9):846-851).
The new study doesn’t prove a lot, except that the probiotics didn’t seem substantially worse than nystatin, but it does suggest to me that the next round of probiotic studies, comparing different preparations, should have saccharomyces in one mixture, and should analyze fungal sepsis as one outcome. Saccharomyces doesn’t seem to prevent NEC, but it might be better in the long term for fungal prophylaxis than fluconazole, without a risk of our fungi evolving resistance, if we can prove that it works.