Differences in gut microbiome linked to risk of death in COVID-19 patients with respiratory failure

In early 2020, Bhakti Patel, MD, a pulmonary and critical care specialist at the University of Chicago Medicine, and Matthew Stutz, MD, who was a critical care fellow at the time, had an idea for a research project. They wanted to study the gut microbiome of patients admitted to the ICU to see if it could help them understand why some patients recover and do well after discharge from the hospital, and others continue to suffer from debilitating complications. Many of the common interventions that physicians use in the ICU, like sedation, antibiotics, putting people on ventilators, or keeping them immobile for long periods of time, can have unintended consequences and cause lasting injuries, even if they ultimately help the patient recover from the initial injury or illness that brought them to the hospital in the first place.

“We were trying to tie together factors that might lend itself to a biologic explanation of why patients get disabled after surviving an ICU stay that goes beyond just the stuff that we do that could have complications,” said Patel, who is an Assistant Professor of Medicine. But, as with so many other projects conceived during this time, Patel said, “And then COVID hit.”

The pandemic upended everything in health care, especially for pulmonary specialists in the ICU. For her part—amidst caring for the crush of patients—Patel worked on an innovative, helmet-based ventilation system that helps prevent critically ill patients from being put on a ventilator. Meanwhile, she and Stutz, who now works at Stroger Hospital in Chicago, pivoted their project to an opportunity to understand the role of the microbiome in severe COVID-19 infections.

The results of this work, published in Nature Communications in November 2022, show that the composition of gut microbiota and the metabolites they produce can predict the trajectory of respiratory function and death in patients with severe COVID-19. This suggests that the gut microbiome has important links to lung health and presents an opportunity to prevent the worst outcomes.

‘There is something else going on’

Patel said one of the most troubling things during the pandemic was seeing patients who were relatively healthy come into the ICU and have completely different outcomes. Some died, some ultimately recovered, and many recovered but were left with lasting complications. “This tells me there is something else going on, and this study shows that there was some interaction between their microbiome health and how they recovered from their infection.”

Between September 2020 and May 2021, nurses collected fecal samples from 71 patients with COVID-19 as they were admitted to the medical ICU at UChicago Medicine; 39 of these patients survived, and 32 later died. To analyze the samples, the physicians turned to scientists at UChicago’s Duchossois Family Institute (DFI), who have extensive, on campus expertise and technical infrastructure to study the composition of the microbial samples, including the metabolites and other chemical compounds that microorganisms in the gut consume and produce.

Eric Pamer, MD, the Donald F. Steiner Professor of Medicine and Director of the DFI, said the careful timing of sample collection is critical, because it enabled Stutz and Patel to make meaningful comparisons between patients who were admitted with similar severities of COVID-19, but went on to either recover from infection or develop progressive respiratory failure. This allowed them to ask whether progression of infection is impacted by the microbiome and the metabolites it produces, specifically in an ICU setting.

“It can be very informative to to investigate groups of patients with similar infections that inexplicably follow different clinical courses, either improving or becoming increasingly compromised” he said. “The study led by the Pulmonary Critical Care team gave us an opportunity to see if there were differences in the microbiomes of patients who recovered or worsened.”

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