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The use of a living organism as therapy increases the potential risk in four general areas: transfer of antibiotic-resistance genes, translocation of the living organism from the intestine to other areas of the body, persistence in the intestines and the development of adverse reactions. The first three theorical concerns are of minimal impact on S. boulardii. Unlike other bacterial strains of probiotics, such as Enterococcus faecium and Lactobacillus rhamnosus, which have been shown to acquire antibiotic-resistance genes, S. boulardii has not developed any antibiotic or antifungal resistance[190,191]. Data from animal models shows reduced translocation with S. boulardii treatment[64,89], unlike other strains of S. cerevisiae[192]. As pharmacokinetic studies indicate, S. boulardii does not persist 3-5 d after oral ingestion is discontinued, so persistence is not a concern for this probiotic[118].

S. boulardii has been used as a probiotic since the 1950s in Europe and has been investigated in clinical trials worldwide. Safety and adverse event data collected during clinical trials, when patients are closely monitored for problems associated with the investigational treatment, has documented a remarkable safety profile of S. boulardii in adults. A wide diversity of adult patients have been followed up who were either randomized to S. boulardii as part of a clinical trial or were documented in case series or case reports for various disease indications (TD, n = 1596; AAD, n = 958; adult acute diarrhea, 156; enteral tube feeding, n = 103; IBD, n = 66; IBS, n = 16, HIV-related diarrhea, n = 18 and giardia infections, n = 50). These studies provide safety data for a total of 2963 adult patients and the only adverse reactions associated with S. boulardii was thirst (in 5 patients) and constipation (in 8 patients) in a trial of patients with C. difficile infections[53]. No case of S. boulardii fungemia has been reported in these diverse patient populations enrolled in clinical trials.

Infrequent cases of fungemia have been reported in case reports or case series in the literature. Most of the adult cases of S. boulardii fungemia are with serious co-morbidities and have central venous catheters. Most cases responded well to treatment with fluconazole or amphotericin B[193]. Some cases developed fungemia, not from the direct ingestion of S. boulardii probiotics, but acquired the yeast from contaminated environmental fomites[194]. Fungemia from S. cerevisiae (non-boulardii strains) have also been reported and are similar to S. boulardii cases, but have poorer prognosis[195,196]. A challenge to determining valid incidence of fungemia is the lack of available advanced yeast identification assays which can distinguish S. cerevisiae from S. boulardii.