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Challenges in the culture-independent analysis of oral and respiratory samples from intubated patients.

ABSTRACT: The spread of microorganisms in hospitals is an important public health threat, and yet few studies have assessed how human microbial communities (microbiota) evolve in the hospital setting. Studies conducted so far have mainly focused on a limited number of bacterial species, mostly pathogenic ones and primarily during outbreaks. We explored the bacterial community diversity of the microbiota from oral and respiratory samples of intubated patients hospitalized in the intensive care unit and we discuss the technical challenges that may arise while using culture-independent approaches to study these types of samples.

SUBMITTER: Lazarevic V

PROVIDER: S-EPMC4033159 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Challenges in the culture-independent analysis of oral and respiratory samples from intubated patients.

Lazarevic Vladimir V Gaïa Nadia N Emonet Stéphane S Girard Myriam M Renzi Gesuele G Despres Lena L Wozniak Hannah H Yugueros Marcos Javier J Veyrieras Jean-Baptiste JB Chatellier Sonia S van Belkum Alex A Pugin Jérôme J Schrenzel Jacques J

Frontiers in cellular and infection microbiology 20140523

The spread of microorganisms in hospitals is an important public health threat, and yet few studies have assessed how human microbial communities (microbiota) evolve in the hospital setting. Studies conducted so far have mainly focused on a limited number of bacterial species, mostly pathogenic ones and primarily during outbreaks. We explored the bacterial community diversity of the microbiota from oral and respiratory samples of intubated patients hospitalized in the intensive care unit and we ...[more]

PMID: 24904840

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Project description:BackgroundThere is very limited evidence identifying factors that increase respiratory drive in hypoxemic intubated patients. Most physiological determinants of respiratory drive cannot be directly assessed at the bedside (e.g., neural inputs from chemo- or mechano-receptors), but clinical risk factors commonly measured in intubated patients could be correlated with increased drive. We aimed to identify clinical risk factors independently associated with increased respiratory drive in intubated hypoxemic patients.MethodsWe analyzed the physiological dataset from a multicenter trial on intubated hypoxemic patients on pressure support (PS). Patients with simultaneous assessment of the inspiratory drop in airway pressure at 0.1-s during an occlusion (P0.1) and risk factors for increased respiratory drive on day 1 were included. We evaluated the independent correlation of the following clinical risk factors for increased drive with P0.1: severity of lung injury (unilateral vs. bilateral pulmonary infiltrates, PaO2/FiO2, ventilatory ratio); arterial blood gases (PaO2, PaCO2 and pHa); sedation (RASS score and drug type); SOFA score; arterial lactate; ventilation settings (PEEP, level of PS, addition of sigh breaths).ResultsTwo-hundred seventeen patients were included. Clinical risk factors independently correlated with higher P0.1 were bilateral infiltrates (increase ratio [IR] 1.233, 95%CI 1.047-1.451, p = 0.012); lower PaO2/FiO2 (IR 0.998, 95%CI 0.997-0.999, p = 0.004); higher ventilatory ratio (IR 1.538, 95%CI 1.267-1.867, p < 0.001); lower pHa (IR 0.104, 95%CI 0.024-0.464, p = 0.003). Higher PEEP was correlated with lower P0.1 (IR 0.951, 95%CI 0.921-0.982, p = 0.002), while sedation depth and drugs were not associated with P0.1.ConclusionsIndependent clinical risk factors for higher respiratory drive in intubated hypoxemic patients include the extent of lung edema and of ventilation-perfusion mismatch, lower pHa, and lower PEEP, while sedation strategy does not affect drive. These data underline the multifactorial nature of increased respiratory drive.

Project description: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.

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Challenges in the culture-independent analysis of oral and respiratory samples from intubated patients.

Publications

Challenges in the culture-independent analysis of oral and respiratory samples from intubated patients.

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