Airway microbiome dynamics and relationship to ventilator-associated infection in intubated pediatric patients.
airway microbiome
pediatrics
ventilator-associated infections
Journal
Pediatric pulmonology
ISSN: 1099-0496
Titre abrégé: Pediatr Pulmonol
Pays: United States
ID NLM: 8510590
Informations de publication
Date de publication:
02 2022
02 2022
Historique:
revised:
31
10
2021
received:
22
06
2021
accepted:
20
11
2021
pubmed:
24
11
2021
medline:
26
3
2022
entrez:
23
11
2021
Statut:
ppublish
Résumé
Little is known about the airway microbiome in intubated mechanically ventilated children. We sought to characterize the airway microbiome longitudinally and in association with clinical variables and possible ventilator-associated infection (VAI). Serial tracheal aspirate samples were prospectively obtained from mechanically ventilated subjects under 3 years old from eight pediatric intensive care units in the United States from June 2017 to July 2018. Changes in the tracheal microbiome were analyzed by sequencing bacterial 16S ribosomal RNA gene relative to subject demographics, diagnoses, clinical parameters, outcomes, antibiotic treatment, and the Ventilator-Associated InfectioN (VAIN) score. A total of 221 samples from 58 patients were processed and 197 samples met the >1000 reads criteria (89%), with an average of 43,000 reads per sample. The median number of samples per subject was 3 (interquartile range [IQR]: 2-5), with a median VAIN score of 2 (IQR: 1-3). Proteobacteria was the highest observed phyla throughout the intubation period, followed by Firmicutes and Actinobacteria. Alpha diversity was negatively associated with days of intubation (p = .032) and VAIN score (p = .016). High VAIN scores were associated with a decrease of Mycobacterium obuense, and an increase of Streptococcus peroris, Porphyromonadaceae family (unclassified species), Veillonella atypica, and several other taxa. No specific pattern of microbiome composition related to clinically diagnosed VAIs was observed. Our data demonstrate decreasing alpha diversity with increasing VAIN score and days of intubation. No specific microbiome pattern was associated with clinically diagnosed VAI.
Sections du résumé
BACKGROUND
Little is known about the airway microbiome in intubated mechanically ventilated children. We sought to characterize the airway microbiome longitudinally and in association with clinical variables and possible ventilator-associated infection (VAI).
METHODS
Serial tracheal aspirate samples were prospectively obtained from mechanically ventilated subjects under 3 years old from eight pediatric intensive care units in the United States from June 2017 to July 2018. Changes in the tracheal microbiome were analyzed by sequencing bacterial 16S ribosomal RNA gene relative to subject demographics, diagnoses, clinical parameters, outcomes, antibiotic treatment, and the Ventilator-Associated InfectioN (VAIN) score.
RESULTS
A total of 221 samples from 58 patients were processed and 197 samples met the >1000 reads criteria (89%), with an average of 43,000 reads per sample. The median number of samples per subject was 3 (interquartile range [IQR]: 2-5), with a median VAIN score of 2 (IQR: 1-3). Proteobacteria was the highest observed phyla throughout the intubation period, followed by Firmicutes and Actinobacteria. Alpha diversity was negatively associated with days of intubation (p = .032) and VAIN score (p = .016). High VAIN scores were associated with a decrease of Mycobacterium obuense, and an increase of Streptococcus peroris, Porphyromonadaceae family (unclassified species), Veillonella atypica, and several other taxa. No specific pattern of microbiome composition related to clinically diagnosed VAIs was observed.
CONCLUSIONS
Our data demonstrate decreasing alpha diversity with increasing VAIN score and days of intubation. No specific microbiome pattern was associated with clinically diagnosed VAI.
Identifiants
pubmed: 34811963
doi: 10.1002/ppul.25769
pmc: PMC8809006
mid: NIHMS1773321
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
508-518Subventions
Organisme : NCATS NIH HHS
ID : UL1 TR002649
Pays : United States
Informations de copyright
© 2021 Wiley Periodicals LLC.
Références
Thorax. 2017 Sep;72(9):803-810
pubmed: 28100714
Pediatr Infect Dis. 1983 Nov-Dec;2(6):472-4
pubmed: 6657504
BMC Genomics. 2012;13 Suppl 8:S17
pubmed: 23282177
Infect Genet Evol. 2018 Sep;63:316-325
pubmed: 29225146
Genome Inform. 2009 Oct;23(1):205-11
pubmed: 20180275
Bioinformatics. 2010 Oct 1;26(19):2460-1
pubmed: 20709691
Pediatr Crit Care Med. 2017 Jan;18(1):e24-e34
pubmed: 27828898
Arch Oral Biol. 2018 Jan;85:64-69
pubmed: 29031240
Genome Biol. 2011 Jun 24;12(6):R60
pubmed: 21702898
Intensive Care Med. 2000 Jul;26(7):959-66
pubmed: 10990113
BMC Bioinformatics. 2016 Dec 1;17(1):491
pubmed: 27905885
Pediatr Crit Care Med. 2011 May;12(3):286-96
pubmed: 21037503
Am J Respir Crit Care Med. 2020 Mar 1;201(5):555-563
pubmed: 31973575
Database (Oxford). 2010 Jul 06;2010:baq013
pubmed: 20624719
Nat Med. 2019 Jun;25(6):1012-1021
pubmed: 31142849
Nature. 2012 Jun 13;486(7402):215-21
pubmed: 22699610
New Microbiol. 2016 Jan;39(1):1-12
pubmed: 26922981
J Oral Microbiol. 2017 Sep 15;9(1):1368848
pubmed: 29081911
Nat Med. 2019 Jun;25(6):1001-1011
pubmed: 31142850
Pediatr Crit Care Med. 2017 Sep;18(9):e395-e405
pubmed: 28661973
Cell Host Microbe. 2015 May 13;17(5):704-15
pubmed: 25865368
Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6
pubmed: 23193283
FEBS Lett. 2016 Nov;590(21):3721-3738
pubmed: 27637588
PLoS Pathog. 2015 Jul 09;11(7):e1004923
pubmed: 26158874
Eur Respir J. 2021 Mar 18;57(3):
pubmed: 33008935
Intensive Care Med. 2019 Aug;45(8):1082-1092
pubmed: 31209523
PLoS Pathog. 2018 Jan 18;14(1):e1006798
pubmed: 29346420
Eur Respir J. 2016 Nov;48(5):1329-1339
pubmed: 27799386
Microbiome. 2016 Feb 11;4:7
pubmed: 26865050
Am J Respir Crit Care Med. 2011 Oct 15;184(8):957-63
pubmed: 21680950
J Med Microbiol. 1995 Aug;43(2):92-8
pubmed: 7629859
Pediatr Infect Dis J. 2011 Jul;30(7):580-4
pubmed: 21233782
Pediatr Crit Care Med. 2019 Aug;20(8):697-706
pubmed: 30985606
Am J Respir Crit Care Med. 2013 Jun 15;187(12):1382-7
pubmed: 23614695
Emerg Infect Dis. 2019 May;25(5):1015-1016
pubmed: 31002048
Chest. 2013 Nov;144(5):1448-1452
pubmed: 24189858