PMID- 26865050
OWN - NLM
STAT- MEDLINE
DCOM- 20161006
LR  - 20220318
IS  - 2049-2618 (Electronic)
IS  - 2049-2618 (Linking)
VI  - 4
DP  - 2016 Feb 11
TI  - Composition and dynamics of the respiratory tract microbiome in intubated 
      patients.
PG  - 7
LID - 10.1186/s40168-016-0151-8 [doi]
LID - 7
AB  - BACKGROUND: Lower 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. RESULTS: We 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. CONCLUSIONS: Longitudinal 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.
FAU - Kelly, Brendan J
AU  - Kelly BJ
AD  - Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 
      Philadelphia, PA, 19104, USA. brendank@mail.med.upenn.edu.
FAU - Imai, Ize
AU  - Imai I
AD  - Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 
      Philadelphia, PA, 19104, USA. imaii@mail.med.upenn.edu.
FAU - Bittinger, Kyle
AU  - Bittinger K
AD  - Department of Microbiology, Perelman School of Medicine, University of 
      Pennsylvania, Philadelphia, PA, 19104, USA. kbit@mail.med.upenn.edu.
FAU - Laughlin, Alice
AU  - Laughlin A
AD  - Department of Microbiology, Perelman School of Medicine, University of 
      Pennsylvania, Philadelphia, PA, 19104, USA. laugh.alice@gmail.com.
FAU - Fuchs, Barry D
AU  - Fuchs BD
AD  - Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 
      Philadelphia, PA, 19104, USA. barry.fuchs@uphs.upenn.edu.
FAU - Bushman, Frederic D
AU  - Bushman FD
AD  - Department of Microbiology, Perelman School of Medicine, University of 
      Pennsylvania, Philadelphia, PA, 19104, USA. bushman@mail.med.upenn.edu.
FAU - Collman, Ronald G
AU  - Collman RG
AD  - Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 
      Philadelphia, PA, 19104, USA. collmanr@mail.med.upenn.edu.
LA  - eng
GR  - R01 HL113252/HL/NHLBI NIH HHS/United States
GR  - U01HL098957/HL/NHLBI NIH HHS/United States
GR  - U01 HL098957/HL/NHLBI NIH HHS/United States
GR  - T32 AI055435/AI/NIAID NIH HHS/United States
GR  - L30 AI120149/AI/NIAID NIH HHS/United States
GR  - U01 HL112712/HL/NHLBI NIH HHS/United States
GR  - P30 AI045008/AI/NIAID NIH HHS/United States
GR  - T32 HL758627/HL/NHLBI NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
DEP - 20160211
PL  - England
TA  - Microbiome
JT  - Microbiome
JID - 101615147
RN  - 0 (DNA, Bacterial)
RN  - 0 (RNA, Ribosomal, 16S)
SB  - IM
MH  - Adult
MH  - Aged
MH  - Aged, 80 and over
MH  - Bronchoscopy
MH  - Case-Control Studies
MH  - Critical Illness
MH  - DNA, Bacterial/*genetics
MH  - Female
MH  - Genetic Variation
MH  - Humans
MH  - Intensive Care Units
MH  - *Intubation, Intratracheal
MH  - Longitudinal Studies
MH  - Male
MH  - Microbiota/*genetics
MH  - Middle Aged
MH  - Oropharynx/microbiology
MH  - Pneumonia, Ventilator-Associated/diagnosis/*microbiology/pathology
MH  - RNA, Ribosomal, 16S/*genetics
MH  - Respiration, Artificial
MH  - Respiratory Tract Infections/diagnosis/*microbiology/pathology
MH  - Sequence Analysis, RNA
MH  - Trachea/microbiology
PMC - PMC4750361
EDAT- 2016/02/13 06:00
MHDA- 2016/10/08 06:00
PMCR- 2016/02/11
CRDT- 2016/02/12 06:00
PHST- 2015/07/11 00:00 [received]
PHST- 2016/01/26 00:00 [accepted]
PHST- 2016/02/12 06:00 [entrez]
PHST- 2016/02/13 06:00 [pubmed]
PHST- 2016/10/08 06:00 [medline]
PHST- 2016/02/11 00:00 [pmc-release]
AID - 10.1186/s40168-016-0151-8 [pii]
AID - 151 [pii]
AID - 10.1186/s40168-016-0151-8 [doi]
PST - epublish
SO  - Microbiome. 2016 Feb 11;4:7. doi: 10.1186/s40168-016-0151-8.