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Journal Articles Critical Care Year : 2022

Oropharyngeal and intestinal concentrations of opportunistic pathogens are independently associated with death of SARS-CoV-2 critically ill adults

Juliette Patrier (1) , Khanh Villageois-Tran (2) , Piotr Szychowiak (3) , Stéphane Ruckly (4) , Rémi Gschwind (5) , Paul-Henri Wicky (1) , Signara Gueye (1) , Laurence Armand-Lefevre (4, 1) , Mehdi Marzouk (1) , Romain Sonneville (1, 4) , Lila Bouadma (4, 1) , Marie Petitjean (4) , Fariza Lamara (4, 1) , Etienne de Montmollin (4, 1) , Jean-Francois Timsit (1, 4) , Etienne Ruppé (1, 4) , Laurent Abel (6) , Amal Abrous , Claire Andrejak , François Angoulvant (7, 8) , Delphine Bachelet , Marie Bartoli , Sylvie Behilill (9, 10) , Marine Beluze , Krishna Bhavsar , Lila Bouadma , Minerva Cervantes-Gonzalez , Anissa Chair , Charlotte Charpentier , Léo Chenard , Catherine Chirouze , Sandrine Couffin-Cadiergues , Camille Couffignal , Marie-Pierre Debray , Dominique Deplanque , Diane Descamps , Alpha Diallo , Fernanda Dias da Silva , Céline Dorival , Xavier Duval , Philippine Eloy , Vincent Enouf (9, 10) , Hélène Esperou , Marina Esposito-Farese , Manuel Etienne , Aline-Marie Florence , Alexandre Gaymard , Jade Ghosn , Tristan Gigante , Morgane Gilg , François Goehringer , Jérémie Guedj , Ikram Houas , Isabelle Hoffmann , Jean-Sébastien Hulot , Salma Jaafoura , Ouifiya Kafif , Antoine Khalil , Nadhem Lafhej , Cédric Laouénan , Samira Laribi , Minh Le , Quentin Le Hingrat , Soizic Le Mestre , Sophie Letrou , Yves Levy , Bruno Lina , Guillaume Lingas , Denis Malvy , France Mentré , Hugo Mouquet , Nadège Neant , Christelle Paul , Aurélie Papadopoulos , Christelle Paul , Ventzislava Petrov-Sanchez , Gilles Peytavin , Valentine Piquard , Olivier Picone , Manuel Rosa-Calatrava , Bénédicte Rossignol , Patrick Rossignol , Carine Roy , Marion Schneider , Richa Su , Coralie Tardivon , Jean-François Timsit , Sarah Tubiana , Sylvie van der Werf (9, 10) , Benoit Visseaux , Aurélie Wiedemann
Amal Abrous
  • Function : Author
Claire Andrejak
Delphine Bachelet
  • Function : Author
Marie Bartoli
  • Function : Author
Marine Beluze
  • Function : Author
Krishna Bhavsar
  • Function : Author
Lila Bouadma
  • Function : Author
Minerva Cervantes-Gonzalez
  • Function : Author
Anissa Chair
  • Function : Author
Charlotte Charpentier
  • Function : Author
Léo Chenard
  • Function : Author
Catherine Chirouze
Sandrine Couffin-Cadiergues
  • Function : Author
Camille Couffignal
  • Function : Author
Marie-Pierre Debray
  • Function : Author
Dominique Deplanque
  • Function : Author
Diane Descamps
  • Function : Author
Alpha Diallo
  • Function : Author
Fernanda Dias da Silva
  • Function : Author
Céline Dorival
  • Function : Author
Xavier Duval
  • Function : Author
Philippine Eloy
  • Function : Author
Hélène Esperou
  • Function : Author
Marina Esposito-Farese
  • Function : Author
Manuel Etienne
  • Function : Author
Aline-Marie Florence
  • Function : Author
Alexandre Gaymard
  • Function : Author
Jade Ghosn
  • Function : Author
Tristan Gigante
  • Function : Author
Morgane Gilg
  • Function : Author
François Goehringer
  • Function : Author
Jérémie Guedj
  • Function : Author
Ikram Houas
  • Function : Author
Isabelle Hoffmann
  • Function : Author
Jean-Sébastien Hulot
  • Function : Author
Salma Jaafoura
  • Function : Author
Ouifiya Kafif
  • Function : Author
Antoine Khalil
  • Function : Author
Nadhem Lafhej
  • Function : Author
Cédric Laouénan
  • Function : Author
Samira Laribi
  • Function : Author
Minh Le
  • Function : Author
Quentin Le Hingrat
  • Function : Author
Soizic Le Mestre
  • Function : Author
Sophie Letrou
  • Function : Author
Yves Levy
  • Function : Author
Bruno Lina
  • Function : Author
Guillaume Lingas
  • Function : Author
Denis Malvy
  • Function : Author
France Mentré
  • Function : Author
Hugo Mouquet
  • Function : Author
Nadège Neant
  • Function : Author
Christelle Paul
  • Function : Author
Aurélie Papadopoulos
  • Function : Author
Christelle Paul
  • Function : Author
Ventzislava Petrov-Sanchez
  • Function : Author
Gilles Peytavin
  • Function : Author
Valentine Piquard
  • Function : Author
Olivier Picone
  • Function : Author
Manuel Rosa-Calatrava
  • Function : Author
Bénédicte Rossignol
  • Function : Author
Patrick Rossignol
  • Function : Author
Carine Roy
  • Function : Author
Marion Schneider
  • Function : Author
Richa Su
  • Function : Author
Coralie Tardivon
  • Function : Author
Jean-François Timsit
  • Function : Author
Sarah Tubiana
  • Function : Author
Benoit Visseaux
  • Function : Author
Aurélie Wiedemann
  • Function : Author

Abstract

Background The composition of the digestive microbiota may be associated with outcome and infections in patients admitted to the intensive care unit (ICU). The dominance by opportunistic pathogens (such as Enterococcus ) has been associated with death. However, whether this association remains all throughout the hospitalization are lacking. Methods We performed a single-center observational prospective cohort study in critically ill patients admitted with severe SARS-CoV-2 infection. Oropharyngeal and rectal swabs were collected at admission and then twice weekly until discharge or death. Quantitative cultures for opportunistic pathogens were performed on oropharyngeal and rectal swabs. The composition of the intestinal microbiota was assessed by 16S rDNA sequencing. Oropharyngeal and intestinal concentrations of opportunistic pathogens, intestinal richness and diversity were entered into a multivariable Cox model as time-dependent covariates. The primary outcome was death at day 90. Results From March to September 2020, 95 patients (765 samples) were included. The Simplified Acute Physiology Score 2 ( SAPS 2) at admission was 33 [24; 50] and a Sequential Organ Failure Assessment score (SOFA score) at 6 [4; 8]. Day 90 all-cause mortality was 44.2% (42/95). We observed that the oropharyngeal and rectal concentrations of Enterococcus spp., Staphylococcus aureus and Candida spp. were associated with a higher risk of death. This association remained significant after adjustment for prognostic covariates (age, chronic disease, daily antimicrobial agent use and daily SOFA score). A one-log increase in Enterococcus spp . , S. aureus and Candida spp. in oropharyngeal or rectal swabs was associated with a 17% or greater increase in the risk of death. Conclusion We found that elevated oropharyngeal/intestinal Enterococcus spp. S. aureus and Candida spp. concentrations, assessed by culture, are associated with mortality, independent of age, organ failure, and antibiotic therapy, opening prospects for simple and inexpensive microbiota-based markers for the prognosis of critically ill SARS-CoV-2 patients.
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pasteur-04098000 , version 1 (15-05-2023)

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Juliette Patrier, Khanh Villageois-Tran, Piotr Szychowiak, Stéphane Ruckly, Rémi Gschwind, et al.. Oropharyngeal and intestinal concentrations of opportunistic pathogens are independently associated with death of SARS-CoV-2 critically ill adults. Critical Care, 2022, 26 (1), pp.300. ⟨10.1186/s13054-022-04164-0⟩. ⟨pasteur-04098000⟩
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