Aim: To analyze gram-negative isolates obtained from the oral cavity after prophylactic administration of antibiotics and their mechanisms of resistance and to compare them with isolates obtained from tracheal aspirates of the same patients. Materials and methods: Samples were collected in three intensive care units: surgical, neurosurgical and cardiosurgical, KBC Zagreb for 10 months. A swab of the oral cavity was taken before the prophylactic administration of antibiotics and on the 5th day after it, when the tracheal aspirate was also taken. The sample was subjected to Gram and methylene blue staining and seeded on blood and MacConkey agar for quantitative analysis. Bacteria were identified by conventional biochemical tests and MALDI-TOFF. The diagnosis of pneumonia was based on X-ray, CRP, and polymorphonuclear count. Isolates from the oral cavity underwent detailed antimicrobial susceptibility testing and resistance gene analysis and were compared with those obtained from tracheal aspirates. Results: A marked diversity of gram-negative bacteria and their mechanisms of resistance was found. High resistance rates and acquired genes encoding ESBL and carbapenemase were found among isolates of Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii. The main finding of the study is that the prophylactic use of antibiotics in surgical intensive care units is associated with colonization of the oral cavity and lower respiratory tract by gram-negative bacteria, leading to the conclusion that oral swab as a noninvasive sample may predict colonization of the lower respiratory tract with resistant gram-negative bacteria and the risk of developing pneumonia. Conclusion: Prophylactic administration of broad-spectrum antibiotics in surgery can alter the oral microbiome and cause colonization of the oral cavity with gram-negative bacteria, including multiple drugs or drug-resistant pathogens that can lead to lower respiratory tract infections in patients on mechanical ventilation.