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Bacterial and fungal communities in tracheal aspirates of intubated COVID-19 patients : a pilot study

Ruiz-Rodriguez, Alicia ; Lusarreta-Parga, Paula ; de Steenhuijsen Piters, Wouter A A ; Koppensteiner, Lilian ; Balcazar-Lopez, Carlos E LU ; Campbell, Robyn ; Dewar, Rebecca ; McHugh, Martin P ; Dockrell, David and Templeton, Kate E , et al. (2022) In Scientific Reports 12(1).
Abstract

Co-infections with bacterial or fungal pathogens could be associated with severity and outcome of disease in COVID-19 patients. We, therefore, used a 16S and ITS-based sequencing approach to assess the biomass and composition of the bacterial and fungal communities in endotracheal aspirates of intubated COVID-19 patients. Our method combines information on bacterial and fungal biomass with community profiling, anticipating the likelihood of a co-infection is higher with (1) a high bacterial and/or fungal biomass combined with (2) predominance of potentially pathogenic microorganisms. We tested our methods on 42 samples from 30 patients. We observed a clear association between microbial outgrowth (high biomass) and predominance of... (More)

Co-infections with bacterial or fungal pathogens could be associated with severity and outcome of disease in COVID-19 patients. We, therefore, used a 16S and ITS-based sequencing approach to assess the biomass and composition of the bacterial and fungal communities in endotracheal aspirates of intubated COVID-19 patients. Our method combines information on bacterial and fungal biomass with community profiling, anticipating the likelihood of a co-infection is higher with (1) a high bacterial and/or fungal biomass combined with (2) predominance of potentially pathogenic microorganisms. We tested our methods on 42 samples from 30 patients. We observed a clear association between microbial outgrowth (high biomass) and predominance of individual microbial species. Outgrowth of pathogens was in line with the selective pressure of antibiotics received by the patient. We conclude that our approach may help to monitor the presence and predominance of pathogens and therefore the likelihood of co-infections in ventilated patients, which ultimately, may help to guide treatment.

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publishing date
type
Contribution to journal
publication status
published
subject
keywords
Bacteria/genetics, COVID-19, Coinfection, Humans, Mycobiome, Pilot Projects
in
Scientific Reports
volume
12
issue
1
article number
9896
publisher
Nature Publishing Group
external identifiers
  • pmid:35701442
  • scopus:85131948380
ISSN
2045-2322
DOI
10.1038/s41598-022-13482-w
language
English
LU publication?
no
additional info
© 2022. The Author(s).
id
cb517838-fa9b-4d04-b5ff-a5236be54e1d
date added to LUP
2022-07-06 01:10:14
date last changed
2025-07-13 19:42:07
@article{cb517838-fa9b-4d04-b5ff-a5236be54e1d,
  abstract     = {{<p>Co-infections with bacterial or fungal pathogens could be associated with severity and outcome of disease in COVID-19 patients. We, therefore, used a 16S and ITS-based sequencing approach to assess the biomass and composition of the bacterial and fungal communities in endotracheal aspirates of intubated COVID-19 patients. Our method combines information on bacterial and fungal biomass with community profiling, anticipating the likelihood of a co-infection is higher with (1) a high bacterial and/or fungal biomass combined with (2) predominance of potentially pathogenic microorganisms. We tested our methods on 42 samples from 30 patients. We observed a clear association between microbial outgrowth (high biomass) and predominance of individual microbial species. Outgrowth of pathogens was in line with the selective pressure of antibiotics received by the patient. We conclude that our approach may help to monitor the presence and predominance of pathogens and therefore the likelihood of co-infections in ventilated patients, which ultimately, may help to guide treatment.</p>}},
  author       = {{Ruiz-Rodriguez, Alicia and Lusarreta-Parga, Paula and de Steenhuijsen Piters, Wouter A A and Koppensteiner, Lilian and Balcazar-Lopez, Carlos E and Campbell, Robyn and Dewar, Rebecca and McHugh, Martin P and Dockrell, David and Templeton, Kate E and Bogaert, Debby}},
  issn         = {{2045-2322}},
  keywords     = {{Bacteria/genetics; COVID-19; Coinfection; Humans; Mycobiome; Pilot Projects}},
  language     = {{eng}},
  month        = {{06}},
  number       = {{1}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Scientific Reports}},
  title        = {{Bacterial and fungal communities in tracheal aspirates of intubated COVID-19 patients : a pilot study}},
  url          = {{http://dx.doi.org/10.1038/s41598-022-13482-w}},
  doi          = {{10.1038/s41598-022-13482-w}},
  volume       = {{12}},
  year         = {{2022}},
}