Fecal Microbiota Transplantation Could Be the Answer to the Global Threat of Antimicrobial Resistance


Scientists hypothesize that fecal microbiota transplant restores the recipient’s gut microbiota to an environment that mimics the healthy donor’s microbiota

Although fairly harmless for individuals whose gut microbiome is in good shape, the bacterial spore Clostridium difficile (C. diff) can spell trouble for patients on antibiotics.1,2 However, new research suggests that an effective treatment for C. diff could also be effective in other resistant bacterial infections.

Antimicrobial Resistance (AMR) occurs when bacteria change over time and no longer respond to medicines. Genetic mutation in bacteria can lead to antibiotic resistance

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Antibiotics can compromise the microbiome of the colon, allowing unruly bacteria to take over the colon. C. diff is one such example. Once it takes over, massive overgrowth ensues and C. diff releases toxins into the colon. The toxins inflame the colon, leading to difficult-to-cure loose stools, severe diarrhea, fever, and abdominal pain.1 Fecal microbiota transplant (FMT) has helped many patients overcome C. diff, and some researchers believe it may be able to treat other resistant bacterial infections, as well.

The journal Genome Medicine has published a study that shows FMT to be beneficial for treating multi-drug resistant bacteria (MDR). Treating patients with recurrent C. diff infection, researchers studied the growth of other known multi-drug resistant bacteria and antibiotic-resistant genes (ARG) in the colon before and after treatment with FMT.2

Some of the multi drug resistant bacteria included in the study were as follows:2

  • Extended-spectrum beta–lactamase (ESBL)-producing Enterobacterales
  • Enterobacterales and Acinetobacter species that are resistant to both fluroquinolones and aminoglycoside or produce carbapenemases
  • Pseudomonas aeruginosa that produces carbapenemase or is resistant to at least 3 of the following antibiotic classes: fluoroquinolones, aminoglycosides, ceftazidime or piperacillin, and carbapenems
  • Enterococcus faecium that are resistant to both penicillin and vancomycin
  • Methicillin-Resistant Staphylococcus aureus (MRSA)

Analysis of MDR was completed after FMT for 87 patients. At 3 weeks, the researchers observed a reduction of 11.5% in the colonization rate of MDR bacteria.2 They also observed a reduced load of antibiotic-resistant genes, although the assortment of resistance genes remained higher than compared to the feces of healthy donors. In the long-term arm of the study, 22 patients seemed to retain the microbiome that FMT had introduced from the donor 1 to 3 years later.2

Based on these results, scientists hypothesize that FMT restores the recipient’s gut microbiota to an environment that mimics the healthy donor’s microbiota. FMT decreases or eliminates undesirable pathogens, although the conversion is not immediately seen and can take months to years to develop.2

Although more studies are needed, researchers recommend larger randomized controlled trials and improved genetic testing of antibiotic resistant genes that definitively link those genes to specific species. Registries to log data from local, national, and international sites would also benefit in collecting and analyzing infection risk in different patient populations and tracking MDR outcomes.

About the Author

Jennifer A. Kuivinen, BSPharm, CIP, is a pharmacist at Meijer Pharmacy in Petoskey, Michigan.


1. Clostridium Difficile (C.Diff). Yale Medicine. Accessed March 15, 2024. https://www.yalemedicine.org/conditions/c-diff-infection

2. Nooij S, Vendrik KEW, Zwittink RD, et al. Long‑term beneficial effect of faecal

microbiota transplantation on colonization of multidrug‑resistant bacteria and resistome abundance in patients with recurrent Clostridioides difficile infection. Genome Medicine. 2024; 16:37. doi:10.1186/s13073-024-013606-7

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