BackgroundPatients in resourced-limited neonatal and pediatric intensive care units (NICU and PICU) are vulnerable to healthcare associated infections (HAI). We report the incidence of HAI, multidrug resistant microorganisms (MDROs) and the pattern of antibiotic usage in the first six years of a surveillance program in a teaching hospital in Turkey.MethodsBetween 2007 and 2012 surveillance data for HAI, MDROs and antibiotic usage were collected from the infection control department, pathology, hospital admissions and pharmacy. In 2009 hand hygiene auditing was introduced. Hand sanitizer usage was expressed as liters per 1000 patient-days. Antibiotic usage was presented as defined daily doses (DDD). Evidence of change in the incidence of HAI was tested using Poison regression modeling.ResultsThe rate of gram negative MDRO in PICU increased significant between 2007 and 2012 (IRR 1.5, P = 0.033) but remained unchanged in NICU (P = 0.824). By 2012 ceftriaxone prescribing in PICU had decreased while carbapenem prescribing increased by 80 %. In NICU carbapenem decreased by 42 % and betalactam decreased by 29 %. Hand hygiene compliance significantly improved in PICU (IRR 1.9, p < 0.001) and NICU (IRR 2.2, p < 0.001) but compliance remained modest after three years with inconsistent levels across the 5 moments.ConclusionThe early years of our infection control program highlights the endemicity of HAI and MDROs in our NICU and PICU. The consistent pattern of antibiotic usage, endemic MROs in PICU and modest hand hygiene clearly provide strategic focuses for intervention.