TY - JOUR
T1 - Bacterial and fungal communities in tracheal aspirates of intubated COVID-19 patients
T2 - a pilot study
AU - Ruiz-Rodriguez, Alicia
AU - Lusarreta-Parga, Paula
AU - de Steenhuijsen Piters, Wouter A.A.
AU - Koppensteiner, Lilian
AU - Balcazar-Lopez, Carlos E.
AU - Campbell, Robyn
AU - Dewar, Rebecca
AU - McHugh, Martin P.
AU - Dockrell, David
AU - Templeton, Kate E.
AU - Bogaert, Debby
N1 - Funding Information:
DB reports grant from SCF-GCRF (UOE SFC-GCRF COVID-19- I200409-1800); grants from The Netherlands Organisation for Scientific research (NWO-VIDI; grant 91715359); Scottish Senior Clinical Fellowship award (CSO/SCF-GCRF grant: 9979491); DD reports grant from MRC SHIELD consortium (MR/N02995X/1); KT reports payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from Abbott diagnostics- to chair talk on SARS-antibody testing; None of the fees or grants listed here was received for the research described in this paper. No other authors report financial disclosures. None of the other authors report competing interests.
Funding Information:
The authors would like to thank all the patients who participated in this study. Also, we would like to thank professor Adilia Warris from the University of Exeter for sharing the fungal strains used to prepare the fungal mock community.
Publisher Copyright:
© 2022, The Author(s).
PY - 2022/6/14
Y1 - 2022/6/14
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85131948380&partnerID=8YFLogxK
U2 - 10.1038/s41598-022-13482-w
DO - 10.1038/s41598-022-13482-w
M3 - Article
C2 - 35701442
AN - SCOPUS:85131948380
SN - 2045-2322
VL - 12
JO - Scientific Reports
JF - Scientific Reports
IS - 1
M1 - 9896
ER -