Imperial College London

COVID-19 clears up rapidly after stool transplant to treat bacterial infection

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faecal microbiota transplant

Researchers suggest that faecal microbiota transplant (FMT) might be worth exploring as a treatment option for coronavirus.

Doctors from Imperial College London and the Medical University of Warsaw have published a letter online in the journal Gut, exploring the use of stool transplants to treat COVID-19 infection, after they used the procedure in two patients for another bacterial infection.

As well as being infected with Clostridioides difficile (a bacterial gut infection), both patients also happened to have COVID-19 infection, the symptoms of which cleared up rapidly after the stool transplant. Furthermore, while SARS-CoV-2 (the virus that causes COVID-19) may be detectable in stool for prolonged periods after the infection, researchers found that the virus was no longer detectable within stool after an apparently shorter period than is typically found.

Stool transplant, or faecal microbiota transplant (FMT) as it is formally known, aims to restore a healthy range of microbes in the gut (the microbiome) to boost the body’s immune response. The researchers describe using the procedure primarily to treat recurrent Clostridioides difficile infection in two people, just before initial symptoms of coexisting COVID-19 appeared.

The first case involved an 80 year old who had pneumonia and sepsis (blood poisoning) on top of recurrent C difficile infection. Symptoms indicative of COVID-19 infection, including fever, were confirmed by a positive swab test. He was given remdesivir and plasma containing antibodies to SARS-CoV2 (‘convalescent plasma’): so far, there’s little evidence that either of these treatments work to any great degree in helping the infection to resolve more quickly. Unexpectedly, two days after the transplant, his COVID-19 symptoms cleared up without further worsening of his pneumonia.

The second case involved a 19-year-old with a form of inflammatory bowel disease (ulcerative colitis) who was being treated with immunosuppressant drugs. He was admitted to hospital because of recurrent C difficile infection. He was treated with antibiotics and given a stool transplant to prevent further recurrence. Fifteen hours later, he developed a suspected COVID-19 infection, which was confirmed by a positive swab test. Subsequently, other than two isolated episodes of fever, his COVID-19 symptoms cleared up.  This second patient was not given any other medication to specifically treat his COVID-19.

The stool samples used for the transplant had been tested for SARS-CoV-2, as were both patients on admission. All the tests came back negative.

Speaking about the cases, Dr Ben Mullish, Department of Metabolism, Digestion and Reproduction, said: “Our main conclusion from these cases is that [stool transplant] appears safe and of comparable efficacy in treating recurrent [C difficile infection] in patients with coexisting COVID-19. A more speculative question is as to whether [it] may impact the clinical course of COVID-19.”

Both patients had risk factors for severe COVID-19 infection, yet both patients experienced only mild disease. Dr Mullish continued “with one possible explanation being that [stool transplant] mitigated more adverse outcomes, potentially through impacting microbiome-immune interactions.” 

These patients represent just two cases, making it hard to draw definitive conclusions on the effectiveness of stool transplant to treat COVID-19 infection. But these findings echo those of two similar published cases, say the authors: “These data lets us speculate that gut microbiome manipulation may merit further exploration as an immunomodulatory strategy in COVID-19."

As such, they plan a clinical trial to find out if stool transplant added to standard COVID-19 treatment might help stop the infection in its tracks.


Rapid resolution of COVID-19 after faecal microbiota transplantation, Gut (2021), doi 10.1136/gutjnl-2021-325010

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Benjamin Coleman

Benjamin Coleman
Department of Surgery & Cancer

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Tel: +44 (0)20 7594 0964
Email: b.coleman@imperial.ac.uk

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