- Our study investigates the causative pathogens of hospital-acquired conjunctivitis in our neonatal intensive care unit and their susceptibility patterns. Coagulase-negative Staphylococcus was the most common bacterium, 22.1% of all isolates. The frequency of the pathogens changed during neonates' stay; Klebsiella pneumoniae (from 18% to 6.9%) and Escherichia coli (from 16% to 4.8%) decreased, whereas methicillin-susceptible Staphylococcus aureus (from 4% to 12.7%) and Enterococcus spp (from 1% to 5.3%) increased. Gram-positive cocci showed high resistant patterns. Our study indicates that the distribution of bacteria causing hospital-acquired conjunctivitis in our neonates shifted from gram-negative to gram-positive microorganisms during their neonatal intensive care unit stay. The resistance patterns are worrisome among gram-positive cocci.