Emonet S, et al. - In this case–control study, researchers compared bacteria identified by standard cultures and metataxonomics—particularly with respect to ventilator-associated pneumonia (VAP) pathogens—and determined whether the presence of particular bacteria or microbiota in tracheal and oropharyngeal secretions during the course of intubation are related to the development of VAP. A strong association of a low relative abundance of Bacilli at the time of intubation in the oropharyngeal secretions, with subsequent VAP development, was revealed in metataxonomic analyses. A significantly higher quantity of human and bacterial DNA was found in both tracheal and oropharyngeal secretions, on the day of VAP, in patients with VAP vs in matched controls with similar ventilation times. The pathogen(s) of VAP detected on culture, as well as many more bacteria, classically difficult to culture (such as Mycoplasma spp. and anaerobes) were identified by using molecular techniques. Overall, markers related to VAP development as well as significant variations in the taxa abundance between VAP and controls were identified via molecular analyses of respiratory specimens.