Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia

Lucie Bernard-Raichon, Mericien Venzon, Jon Klein, Jordan E. Axelrad, Chenzhen Zhang, Alexis P. Sullivan, Grant A. Hussey, Arnau Casanovas-Massana, Maria G. Noval, Ana M. Valero-Jimenez, Juan Gago, Gregory Putzel, Alejandro Pironti, Evan Wilder, Lorna E. Thorpe, Dan R. Littman, Meike Dittmann, Kenneth A. Stapleford, Bo Shopsin, Victor J. Torres, Albert I. Ko, Akiko Iwasaki, Ken Cadwell () and Jonas Schluter ()
Additional contact information
Lucie Bernard-Raichon: New York University Grossman School of Medicine
Mericien Venzon: New York University Grossman School of Medicine
Jon Klein: Yale School of Medicine
Jordan E. Axelrad: New York University Grossman School of Medicine
Chenzhen Zhang: New York University Grossman School of Medicine
Alexis P. Sullivan: New York University Grossman School of Medicine
Grant A. Hussey: New York University Grossman School of Medicine
Arnau Casanovas-Massana: Yale School of Public Health
Maria G. Noval: New York University Grossman School of Medicine
Ana M. Valero-Jimenez: New York University Grossman School of Medicine
Juan Gago: New York University Grossman School of Medicine
Gregory Putzel: New York University Grossman School of Medicine
Alejandro Pironti: New York University Grossman School of Medicine
Evan Wilder: New York University Grossman School of Medicine
Lorna E. Thorpe: New York University Grossman School of Medicine
Dan R. Littman: New York University Grossman School of Medicine
Meike Dittmann: New York University Grossman School of Medicine
Kenneth A. Stapleford: New York University Grossman School of Medicine
Bo Shopsin: New York University Grossman School of Medicine
Victor J. Torres: New York University Grossman School of Medicine
Albert I. Ko: Yale School of Public Health
Akiko Iwasaki: Yale School of Medicine
Ken Cadwell: New York University Grossman School of Medicine
Jonas Schluter: New York University Grossman School of Medicine

Nature Communications, 2022, vol. 13, issue 1, 1-13

Abstract: Abstract Although microbial populations in the gut microbiome are associated with COVID-19 severity, a causal impact on patient health has not been established. Here we provide evidence that gut microbiome dysbiosis is associated with translocation of bacteria into the blood during COVID-19, causing life-threatening secondary infections. We first demonstrate SARS-CoV-2 infection induces gut microbiome dysbiosis in mice, which correlated with alterations to Paneth cells and goblet cells, and markers of barrier permeability. Samples collected from 96 COVID-19 patients at two different clinical sites also revealed substantial gut microbiome dysbiosis, including blooms of opportunistic pathogenic bacterial genera known to include antimicrobial-resistant species. Analysis of blood culture results testing for secondary microbial bloodstream infections with paired microbiome data indicates that bacteria may translocate from the gut into the systemic circulation of COVID-19 patients. These results are consistent with a direct role for gut microbiome dysbiosis in enabling dangerous secondary infections during COVID-19.

Date: 2022
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DOI: 10.1038/s41467-022-33395-6

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