Antibiotic perturbation of the preterm infant gut microbiome and resistome

Abstract

The gut microbiota plays important roles in nutrient absorption, immune system development, and pathogen colonization resistance. Perturbations early in life may be detrimental to host health in the short and the long-term. Antibiotics are among the many factors that influence the development of the microbiota. Because antibiotics are heavily administered during the first critical years of gut microbiota development, it is important to understand the effects of these interventions. Infants, particularly those born prematurely, represent an interesting population because they receive early and often extensive antibiotic therapy in the first months after birth. Gibson et al. recently demonstrated that antibiotic therapy in preterm infants can dramatically affect the gut microbiome. While meropenem, ticarcillin-clavulanate, and cefotaxime treatments were associated with decreased species richness, gentamicin and vancomycin had variable effects on species richness. Interestingly, the direction of species richness response could be predicted based on the abundance of 2 species and 2 genes in the microbiome prior to gentamicin or vancomycin treatment. Nonetheless, all antibiotic treatments enriched the presence of resistance genes and multidrug resistant organisms. Treatment with different antibiotics further resulted in unique population shifts of abundant organisms and selection for different sets of resistance genes. In this addendum, we provide an extended discussion of these recent findings, and outline important future directions for elucidating the interplay between antibiotics and preterm infant gut microbiota development.

Keywords: antibiotic resistance; antibiotics; gut microbiota; preterm infants.

Figure 1.

Antibiotics are the most prescribed medications in the neonatal intensive care unit. Data adapted from Clark et al. Pediatrics 2006. Frequency defined as the number of times a unique medication name was reported in the medications table in 220 NICUs in the United States and Puerto Rico between January 1996 and April 2005.

Figure 2.

Antibiotic treatment significantly alters preterm infant gut microbiota development. Preterm infant gut microbiota species richness (top) and composition (bottom) for the 3 individuals with samples analyzed directly before and after depicted antibiotic treatments for (A) meropenem, (B) vancomycin and meropenem, and (C) ticarcillin-clavulanate. Red bars (left) represent species richness for example individual. Black bars (right) represent average species richness for age matched preterm infants with no antibiotic treatment. Error bars depict one standard deviation.