The prospective open label two centre cluster randomised study was conducted in two neonatal intensive care units (NICU) in Estonia. We compared how antibiotics commonly used for empiric therapy of early onset sepsis influence the development of infants mucosal microbiota; identified other risk factors influencing the colonisation process; identified the relatedness of mucosal and blood isolates; defined the value of twice a week collected surveillance cultures in predicting late onset sepsis (LOS).Results showed that risk factors influencing nasopharyngeal and rectal colonisation are similar...