Probiotic organisms, in general, have an excellent safety profile and have been shown to be well-tolerated in hundreds of trials. Adverse events are rare with probiotic administration, with the most commonly experienced side effects being mild bloating and flatulence.
Infections and sepsis have been reported in adults when taking lactobacilli supplements[3, 4] and cases of infection in young children and infants have also been reported. These situations, however, are extremely rare. Cases of infection due to lactobacilli and bifidobacteria are estimated to represent only 0.05%-0.4% of cases of infective endocarditis and bacteremia and have generally only occurred in patients with underlying conditions that are of a severe nature. Given the rapidly increasing use of probiotics worldwide, it is of interest that increased consumption has not led to an increase in such infections in consumers. A recent review of the area concluded that opportunistic pathogenecity is considered very low.
Some argue that there is an increased risk of adverse events in the immunocompromised; whilst others maintain there is no published evidence that consumption of probiotics that contain lactobacilli or bifidobacteria increases the risk of opportunistic infection among such individuals. In immunocompromised patients, it would be prudent to weigh out the potential benefits and risk of administration of a specific probiotic strain prior to its prescription.
Worldwide there have been a small number of cases of fungemia reported in the literature associated with administration of preparations containing Saccharomyces cerevisae var. boulardii (aka Saccharomyces boulardii). These have occurred exclusively in immunocompromised or critically ill individuals, and in particular those with intravascular catheters. In the latter case, Saccharomyces organisms appear to have been introduced directly into the bloodstream by individuals handling both the probiotic preparation and the catheter. Hence, it is often recommended that prescription of Saccharomyces-based probiotic preparations be carefully considered in immunosuppressed or critically ill patients. 
Caution is warranted with the prescribing of all probiotic agents in critically ill patients with impaired gastrointestinal barrier function, as an infection could result due to bacterial translocation and impaired immune function.[3, 9, 10]
1. Didari, T., et al., A systematic review of the safety of probiotics. Expert Opinion on Drug Safety, 2014. 13(2): p. 227-239.
2. Williams, N.T., Probiotics. American Journal of Health-System Pharmacy, 2010. 67(6): p. 449-458.
3. Land, M.H., et al., Lactobacillus sepsis associated with probiotic therapy. Pediatrics, 2005. 115(1): p. 178-81.
4. Mackay, A.D., et al., Lactobacillus endocarditis caused by a probiotic organism. Clinical Microbiology and Infection, 1999. 5(5): p. 290-292.
5. Boyle, R.J., R.M. Robins-Browne, and M.L. Tang, Probiotic use in clinical practice: what are the risks? The American Journal of Clinical Nutrition, 2006. 83(6): p. 1256-1264.
6. Borriello, S.P., et al., Safety of Probiotics That Contain Lactobacilli or Bifidobacteria. Clinical Infectious Diseases, 2003. 36(6): p. 775-780.
7. Shanahan, F., A Commentary on the Safety of Probiotics. Gastroenterology Clinics of North America, 2012. 41(4): p. 869-876.
8. Kelesidis, T. and C. Pothoulakis, Efficacy and safety of the probiotic Saccharomyces boulardii for the prevention and therapy of gastrointestinal disorders. Therapeutic Advances in Gastroenterology, 2012. 5(2): p. 111-125.
9. Muñoz, P., et al., Saccharomyces cerevisiae Fungemia: An Emerging Infectious Disease. Clinical Infectious Diseases, 2005. 40(11): p. 1625-1634.
10. Besselink, M.G., et al., Probiotic prophylaxis in predicted severe acute pancreatitis: a randomised, double-blind, placebo-controlled trial. Lancet, 2008. 371(9613): p. 651-9.