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.

Antibiotic treatment at delivery shapes the initial oral microbiome in neonates

“…The acquisition of the first microbial colonizers may be altered by multiple maternal and infant factors, which may result in differences in oral microbiota development. These factors could include mode of delivery, breastfeeding, pregnancy outcomes, parental contact, antibiotics, host factors and living environment, all of which have been recognised to affect infant’s intestinal microbial habitat1926272829. It is however not clear if, and to what extent, these factors contribute to shaping the oral microbiome.…”

The Threat of Antimicrobial Resistance on the Human Microbiome

“…Furthermore, the presence of AMR elements in the infant gut does not seem to be influenced by selective pressures from foodborne or administered antibiotics [50]. However, in preterm infants, there is evidence of selective negative pressure on meconium bacterial richness depending on antibiotic administered, with ticarcillin-clavulanate, and cefotaxime showing the greatest effects [51, 52]. Thus, as antibiotics are prescribed routinely in preterm and low birthweight infants for preventing necrotizing enterocolitis, spread of AMR in the preterm infant gut should be a factor of concern in the context of long-term intestinal and immune health, and must be addressed in longitudinal studies.…”

Impact of Early-Life Antibiotic Use on Gut Microbiota of Infants

“…Infants, particularly those born prematurely, represent an interesting population because they received early and often extensive antibiotic therapy in the first months after birth [32]. Gibson et al recently demonstrated that children who had been exposed to antibiotic therapy had a dramatical reduction in the diversity of their microbial population.…”

“…More interestingly, the researchers also observed that some children harboured antibiotic resistance genes as early as 2 months of age, before any antibiotic treatments. In recent report, researchers from Washington University School of Medicine (WUSM) demonstrated that gut microbiota in healthy American children also carried a large number of antibiotic resistance genes, likely to make harmful effects [32].…”

“…Bile-salt metabolism (BSM) is an important function of intestinal microbes, which influences energy and metabolism of the host [48]. Frequent antibiotic intake will accelerate the production of antibiotic resistance in infants, particularly those born prematurely, because they received early and often extensive antibiotic therapy in the first months after birth [32].…”