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Colonization of the digestive tract has been supposed to be the source of many hospital-acquired infections, especially nosocomial pneumonia. To assess the relationship between oropharyngeal and gastric colonization and subsequent occurrence of nosocomial pneumonia, we prospectively studied 86 ventilated, intensive care unit (ICU) patients. Oropharyngeal or gastric colonizations were detected and quantified on admission and twice weekly during ICU stay. When nosocomial pneumonia was suspected on clinical grounds (new chest X-ray infiltrate and purulent tracheal secretions), diagnosis was assessed on fiberoptic bronchoscopy with quantitative cultures of a protected specimen brush sampling and/or a plugged telescoping catheter sampling yielding ≥ 103 cfu/ml of at least one microorganism. Bacterial strains responsible for colonization and infection (Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacteriaceae, and Staphylococcus aureus) were compared using pulsed-field electrophoresis. A total of 31 cases (36%) of pneumonia were diagnosed. Oropharyngeal colonization, detected either on admission or from subsequent samples, was a predominant factor of nosocomial pneumonia as compared with gastric colonization. For instance, oropharyngeal colonization with A. baumannii yielded a 7.45-fold estimated increased risk of pneumonia as compared with patients not yet or not identically colonized (p = 0.0004). DNA genomic analysis demonstrated that an identical strain was isolated from oropharyngeal or gastric samples and bronchial samples in all but three cases of pneumonia, due to S. aureus. These findings provide better knowledge of the pathophysiology of nosocomial pneumonia in mechanically ventilated patients. Garrouste-Orgeas M, Chevret S, Arlet G, Marie O, Rouveau M, Popoff N, Schlemmer B. Oropharyngeal or gastric colonization and nosocomial pneumonia in adult intensive care unit patients: a prospective study based on genomic DNA analysis.