Assessing the Bacterial Microbiome on Endotracheal Tubes From Ventilated Subjects

Objectives: In the United States ventilator associated pneumonia (VAP) has a high mortality rate. In this study we assess the microbiome and biofilm from oral and tracheal sections of endotracheal tubes from ICU subjects. Microbiome content was compared between sites and subjects, to determine if oral bacteria were a component of endotracheal biofilms.
Methods: Upon extubation, endotracheal tubes (ETT) were frozen and transported to a BSL-2 facility for processing. ETT tubes were sectioned to retain tubing from the oral cavity and the trachea. Oral and tracheal sections were further divided for DNA extraction and fluorescent staining. Bacterial DNA was extracted using MOBIO Powersoil DNA extraction kit, and 16S rDNA sequencing was performed by LC Biosciences. Microbiome data analysis was performed with CLC Genomics Workbench v10. For confocal imaging, tubes were fixed in formaldehyde and stained with calcafluor, hexidium iodide, and Syto9. Confocal images were quantified using Imaris software.
Results: Collectively, the most common bacteria present was Klebsiella pneumonia, which was present in the oral cavity and the tracheal samples. Oral bacteria were also present at both sites, and the most common were oral pathogens Porphyromonas gingivalis and Streptococcus constellatus. Using PERMANOVA analysis, no significant differences were detected in microbiome composition between oral and tracheal sites. Collectively, 295 operational taxonomic units were identified. Additionally, the appearance of oral and tracheal biofilms was similar as assessed by confocal imaging.
Conclusions: Pathogenic oral bacteria and nosocomial pathogens are ubiquitous on ETT, and colocalize to the ETT in both the oral cavity and the lower trachea in intubated subjects.