Last reviewed: 24 Oct 2020
Last updated: 06 May 2020
06 May 2020

FDA warns of the potential risk of pathogenic bacteria transmission associated with fecal microbiota transplantation

The Food and Drug Administration (FDA) is warning healthcare providers to consider the potential risk of pathogenic bacteria transmission associated with fecal microbiota transplant (FMT) products, which may result in serious adverse reactions.

The agency has been made aware of six reports of infections caused by enteropathogenic Escherichia coli (EPEC) and Shiga toxin-producing Escherichia coli (STEC) that have occurred following investigational use of FMT. It suspects these infections were due to transmission of pathogenic organisms from FMT products supplied by a stool bank company based in the US. Two of these patients died; however, it is unknown whether STEC infection contributed to these deaths.

The FDA previously issued a safety alert in June 2019 warning that FMT may transmit multidrug-resistant organisms, leading to serious or life-threatening infections, particularly in patients who are immunocompromised. This followed two cases of immunocompromised adults who received FMT and developed invasive infections caused by extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli. One of the patients died.[74]

FMT is currently recommended as an option by the Infectious Diseases Society of America/Society for Healthcare Epidemiology of America guidelines for patients with at least two recurrences and where antibiotic therapy has failed.[2]

See Management: approach

See Management: treatment algorithm

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History and exam

Other diagnostic factors

  • fever
  • abdominal tenderness
  • nausea and vomiting
  • abdominal distension
  • symptoms of shock

Risk factors

  • antibiotic exposure
  • advanced age
  • hospitalization or residence in a nursing home
  • history of Clostridium difficile-associated disease
  • use of acid-suppressing drugs
  • inflammatory bowel disease
  • solid organ transplant recipients
  • hematopoietic stem cell transplant recipients
  • chronic kidney disease
  • HIV infection
  • immunosuppressive agents or chemotherapy
  • gastrointestinal surgery
  • vitamin D deficiency

Diagnostic investigations

1st investigations to order

  • CBC
  • stool guaiac (fecal occult blood test)
  • stool polymerase chain reaction (PCR)
  • stool immunoassay for glutamate dehydrogenase
  • stool immunoassay for toxins A and B
  • abdominal x-ray
More 1st investigations to order

Investigations to consider

  • cell culture cytotoxicity neutralization assay
  • CT abdomen
  • sigmoidoscopy or colonoscopy
More investigations to consider

Emerging tests

  • stool lactoferrin or calprotectin
More emerging tests

Treatment algorithm


Clinical Associate Professor of Medicine

Alabama Infectious Diseases Center




AH declares that he has no competing interests.

Peer reviewersVIEW ALL

Department of Epidemiology

Division of General Medicine and Epidemiology

UNC at Chapel Hill

Chapel Hill



JA declares that he has no competing interests.

Consultant Gastroenterologist

Department of Gastroenterology

John Radcliffe Hospital




SK declares that he has no competing interests.

Clinical Reader and Consultant Gastroenterologist

Norfolk and Norwich University Hospital




IB declares that he has no competing interests.

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