Tracking over time the developing gut microbiota in newborns admitted to a neonatal intensive care unit during an outbreak caused by ESBL-producing Klebsiella pneumoniae

The establishment of gut microbiota is reportedly aberrant in newborns admitted to neonatal intensive care units (NICUs), with detrimental long-term health impacts. Here, we vertically tracked the developing gut bacterial communities of newborns hosted in an NICU during an outbreak sustained by ESBL Klebsiella pneumoniae and compared colonized and non-colonized patients. Most communities were highly variable from one sampling point to the next, and dominated by few taxa, often Proteobacteria and Enterobacteriaceae, with marked interindividual variability. This picture was retrieved independently of colonization status or clinical covariates. Our data support the emerging idea of preterm infants as a population in which no defined microbial signatures are clearly associated to clinical status. Instead, the strong pressure of the nosocomial environment, antibiotics and, in this case, the ongoing outbreak, possibly drive the evolution of microbiota patterns according to individual conditions, also in non-colonized patients.