Long-Term Implications of Antibiotic Use on Gut Health and Microbiota in Populations Including Patients With Cystic Fibrosis

Since the commercialization of antibiotics in the 1940s, life expectancy has increased in parallel with their discovery. However, concerns regarding the collateral effects of antibiotic therapy on gut microbiota composition and functionality within the host have come to the fore. Antibiotic therapy disrupts the normal ecology of the gut microbiome, resulting in altered composition, and in some cases function. Cystic fibrosis (CF) is an ideal candidate group in which to examine antibiotic effects on the gut microbiota. Chronic antibiotic use, along with the typical high-fat CF diet, cystic fibrosis transmembrane conductance regulator malfunction itself, pancreatic enzyme supplementation, and suppression of gastric acid, play a key role in defining the unique composition of the CF intestinal microbiota. Most available studies focus on the short-term effects of an antibiotic course of limited duration (eg, 7 days) and the pattern of recovery after such treatments. Here we discuss the specific effects of different antibiotic families on the gut microbiota. We examine the multidrug-resistant, Clostridium difficile, and antibiotic-associated diarrhea risk and prevalence associated with chronic antibiotic use. We review the success to date of probiotics to ameliorate CF symptomology. Finally, we explore alternative therapies for infection control currently under research.