Early life antibiotic usage and impact on the gut microbiota, including emergence of antimicrobial resistant Enterococcus

The early life microbiota is an ‘immature’ and highly dynamic microbial ecosystem, which is central to infant health. Both perinatal and postnatal factors can impact the gut microbiota, with antibiotics proposed to cause short and longer-term disturbances. Antibiotics not only impact microbial community composition, they also contribute to the overall antibiotic resistance profile i.e. the ‘resistome’, and they may also enhance carriage of multi-drug resistant bacteria. Given high antibiotic prescription practices in pregnant women and new-borns this also contributes to the global threat of antimicrobial resistant. This review summarises the current literature on antibiotic usage and how this may impact the developing gut microbiota during early life, including the influence of horizontal gene transfer on contributions to pathogenicity and resistance of gut bacteria. We also focus on Enterococcus spp. given their high levels in infants and their link with opportunistic infections that are a significant cause of morbidity and mortality during early life. Finally, a perspective on the importance to antibiotic stewardship, and harnessing the microbiota itself for anti-infection therapies for reducing antibiotic usage are also covered.