Composition and dynamics of the respiratory tract microbiome in intubated patients

Abstract

BackgroundLower respiratory tract infection (LRTI) is a major contributor to respiratory failure requiring intubation and mechanical ventilation. LRTI also occurs during mechanical ventilation, increasing the morbidity and mortality of intubated patients. We sought to understand the dynamics of respiratory tract microbiota following intubation and the relationship between microbial community structure and infection.ResultsWe enrolled a cohort of 15 subjects with respiratory failure requiring intubation and mechanical ventilation from the medical intensive care unit at an academic medical center. Oropharyngeal (OP) and deep endotracheal (ET) secretions were sampled within 24 h of intubation and every 48–72 h thereafter. Bacterial community profiling was carried out by purifying DNA, PCR amplification of 16S ribosomal RNA (rRNA) gene sequences, deep sequencing, and bioinformatic community analysis. We compared enrolled subjects to a cohort of healthy subjects who had lower respiratory tract sampling by bronchoscopy. In contrast to the diverse upper respiratory tract and lower respiratory tract microbiota found in healthy controls, critically ill subjects had lower initial diversity at both sites. Diversity further diminished over time on the ventilator. In several subjects, the bacterial community was dominated by a single taxon over multiple time points. The clinical diagnosis of LRTI ascertained by chart review correlated with low community diversity and dominance of a single taxon. Dominant taxa matched clinical bacterial cultures where cultures were obtained and positive. In several cases, dominant taxa included bacteria not detected by culture, including Ureaplasma parvum and Enterococcus faecalis.ConclusionsLongitudinal analysis of respiratory tract microbiota in critically ill patients provides insight into the pathogenesis and diagnosis of LRTI. 16S rRNA gene sequencing of endotracheal aspirate samples holds promise for expanded pathogen identification.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-016-0151-8) contains supplementary material, which is available to authorized users.

The dynamics of the pulmonary microbiome during mechanical ventilation in the intensive care unit and the association with occurrence of pneumonia

“…The spectrum of detected species and their diversity was not associated with antimicrobial treatment, even though all patients were treated with moderate-spectrum or broad-spectrum antibiotics at some point of mechanical ventilation. This result supports previous findings obtained in intubated patients 25. Sample collection from the trachea, very close to ETT may explain these findings and we speculate that the measured microbiome at least partly reflects the biofilm of microbes formed on the surface of the tube.…”

“…These results are in line with previous findings using molecular microbial detection methods 25. This study differs from previous attempts as we quantified the change in diversity per patient, rather than on a population basis.…”

Respiratory microbiota and lower respiratory tract disease

“…58,68 In studies with repeated sampling, the dominance of one taxon was maintained over time, and its relative abundance increased throughout the pneumonia episode, particularly if the patient was intubated. 51 Intubation was consistently a risk factor for bacterial disturbance in the lower respiratory tract (low diversity and evenness) supporting the hypothesis of a lung microbiota resulting from the equilibrium between microaspirations from the upper respiratory tract and clearance mechanisms. 34,51,58,63 Antibiotic administration seemed to have less effect on bacterial diversity than intubation, 58 and this effect was transitory, with recovery of a similar oropharyngeal microbiota a few days after antibiotic treatment compared to the microbiota before antibiotic administration.…”

“…51 Intubation was consistently a risk factor for bacterial disturbance in the lower respiratory tract (low diversity and evenness) supporting the hypothesis of a lung microbiota resulting from the equilibrium between microaspirations from the upper respiratory tract and clearance mechanisms. 34,51,58,63 Antibiotic administration seemed to have less effect on bacterial diversity than intubation, 58 and this effect was transitory, with recovery of a similar oropharyngeal microbiota a few days after antibiotic treatment compared to the microbiota before antibiotic administration. 52 However, most of the studies did not assess this effect, probably due to difficulties in assuming bacterial viability from DNA based measures.…”

“…80 On the other hand, Kelly et al reported similar results when comparing the performance of two sequencing platforms (Illumina MiSeq and Roche/454) on the same samples. 51 To avert these issues, it is necessary to standardize existing techniques, to keep establishing associations between the microbiota from different sampled respiratory sites, and ideally, to create a unique genome reference database. In addition, molecular biology tools to assess viability of bacteria identified by sequencing methods should be applied when possible.…”