Fecal microbiota transplant

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Fecal microbiota transplant
E coli at 10000x, original.jpg
Escherichia coli at 10,000× magnification
Other namesFecal bacteriotherapy, fecal transfusion, fecal transplant, stool transplant
Specialty Gastroenterology
Fecal microbiota transplant
Clinical data
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Fecal microbiota transplant (FMT), also known as a stool transplant, [2] is the process of transferring fecal bacteria and other microbes from a healthy individual into another individual. FMT is an effective treatment for Clostridioides difficile infection (CDI). [3] [4] [5] For recurrent CDI, FMT is more effective than vancomycin alone, and may improve the outcome after the first index infection. [3] [5] [6]

Contents

Side effects may include a risk of infections, therefore the donor should be screened for pathogens. [7]

With CDI becoming more common, FMT is gaining increasing prominence, with some experts calling for it to become the first-line therapy for CDI. [8] FMT has been used experimentally to treat other gastrointestinal diseases, including colitis, constipation, irritable bowel syndrome, and neurological conditions, such as multiple sclerosis and Parkinson's. [9] [10] In the United States, human feces has been regulated as an experimental drug since 2013. In the United Kingdom, FMT regulation is under the remit of the Medicines and Healthcare products Regulatory Agency. [11]

Medical uses

Clostridioides difficile infection

Scanning electron micrograph of Clostridioides difficile bacteria from a stool sample Clostridium difficile 01.jpg
Scanning electron micrograph of Clostridioides difficile bacteria from a stool sample

Fecal microbiota transplant is approximately 85–90% effective in people with CDI for whom antibiotics have not worked or in whom the disease recurs following antibiotics. [12] [13] Most people with CDI recover with one FMT treatment. [8] [14] [15]

A 2009 study found that fecal microbiota transplant was an effective and simple procedure that was more cost-effective than continued antibiotic administration and reduced the incidence of antibiotic resistance. [16]

Once considered to be a "last resort therapy" by some medical professionals, due to its unusual nature and invasiveness compared with antibiotics, perceived potential risk of infection transmission, and lack of Medicare coverage for donor stool, position statements by specialists in infectious diseases and other societies [14] have been moving toward acceptance of FMT as a standard therapy for relapsing CDI and also Medicare coverage in the United States. [17]

It has been recommended that endoscopic FMT be elevated to first-line treatment for people with deterioration and severe relapsing C. difficile infection. [8]

In November 2022, faecal microbiota transplant (Biomictra) was approved for medical use in Australia, [1] [18] and fecal microbiota, live (Rebyota) was approved for medical use in the United States. [19]

Fecal microbiota spores, live (Vowst) was approved for medical use in the United States in April 2023. [20] [21] It is the first fecal microbiota product that is taken by mouth. [20]

Other conditions

Ulcerative colitis

In May 1988, Australian professor Thomas Borody treated the first ulcerative colitis patient using FMT, which led to longstanding symptom resolution. [22] Following on from that, Justin D. Bennet published the first case report documenting reversal of Bennet's own colitis using FMT. [23] While C. difficile is easily eradicated with a single FMT infusion, this generally appears to not be the case with ulcerative colitis. Published experience of ulcerative colitis treatment with FMT largely shows that multiple and recurrent infusions are required to achieve prolonged remission or cure. [22] [24]

Cancer

Clinical trials are underway to evaluate if FMT from anti-PD-1 immunotherapy donors can promote a therapeutic response in immunotherapy-refractory patients. [25] [26]

Autism

Once linked with naturopathy, [27] there have been serious studies into treating Autism Spectrum Disorder with fecal microbiota transplants. One such study was conducted in Shanghai, China, [28] and an earlier study led by Arizona State University. [29] The Arizona treatment has received a United States Patent (#11,202,808) [30] and the researchers hope for FDA approval. [31]

Adverse effects

Adverse effects were poorly understood as of 2016. [32] They have included bacterial blood infections, fever, SIRS-like syndrome, exacerbation of inflammatory bowel disease in people who also had that condition, and mild GI distress which generally resolve themselves soon after the procedure, including flatulence, diarrhea, irregular bowel movements, abdominal distension/bloating, abdominal pain/tenderness, constipation, cramping, and nausea. [32] [33] There are also concerns that it may spread COVID-19. [34]

A person died in the United States in 2019, after receiving an FMT that contained drug-resistant bacteria, and another person who received the same transplant was also infected. [35] [36] The US Food and Drug Administration (FDA) issued a warning against potentially life-threatening consequences of transplanting material from improperly screened donors. [35]

Technique

There are evidence-based consensus guidelines for the optimal administration of FMT. Such documents outline the FMT procedure, including preparation of material, donor selection and screening, and FMT administration. [11] [14] [37] [38]

The gut microbiota comprises all microorganisms that reside along the gastrointestinal tract, including commensal, symbiotic and pathogenic organisms. FMT is the transfer of fecal material containing bacteria and natural antibacterials from a healthy individual into a diseased recipient. [14]

Donor selection

Preparing for the procedure requires careful selection and screening of the potential donor. Close relatives are often chosen on account of ease of screening; [14] [37] [39] however, in the case of treatment of active C. diff., family members and intimate contacts may be more prone to be carriers themselves. [14] This screening involves medical history questionnaires, screening for various chronic medical diseases (e.g. irritable bowel diseases, Crohn's disease, gastrointestinal cancer, etc.), [37] [40] [41] [42] and laboratory testing for pathogenic gastrointestinal infections (e.g. CMV, C. diff., salmonella, Giardia, GI parasites, etc.). [14] [37] [41]

Specimen preparation

No laboratory standards have been agreed upon, [41] so recommendations vary for size of sample to be prepared, ranging from 30 to 100 grams (1.1 to 3.5 ounces) of fecal material for effective treatment. [13] [37] [39] [42] Fresh stool is used to increase viability of bacteria within the stool [41] [42] and samples are prepared within 6–8 hours. [37] [41] [42] The sample is then diluted with 2.5–5 times the volume of the sample with either normal saline, [37] [41] sterile water, [37] [41] or 4% milk. [14] Some locations mix the sample and the solvent with a mortar and pestle, [42] and others use a blender. [37] [41] [42] There is concern with blender use on account of the introduction of air which may decrease efficacy [9] as well as aerosolization of the feces contaminating the preparation area. [37] [42] The suspension is then strained through a filter and transferred to an administration container. [37] [41] [42] If the suspension is to be used later, it can be frozen after being diluted with 10% glycerol, [37] [41] [42] and used without loss of efficacy compared to the fresh sample. [37] [39] The fecal transplant material is then prepared and administered in a clinical environment to ensure that precautions are taken. [9]

Administration

After being made into suspensions, the fecal material can be given through nasogastric and nasoduodenal tubes, or through a colonoscope or as a retention enema. [14]

Mechanism of action

One hypothesis behind fecal microbiota transplant rests on the concept of bacterial interference, i.e., using harmless bacteria to displace pathogenic organisms, such as by competitive niche exclusion. [43] In the case of CDI, the C. difficile pathogen is identifiable. [44] Recently, in a pilot study of five patients, sterile fecal filtrate was demonstrated to be of comparable efficacy to conventional FMT in the treatment of recurrent CDI. [45] The conclusion from this study was that soluble filtrate components (such as bacteriophages, metabolites, and/or bacterial components, such as enzymes) may be the key mediators of FMT's efficacy, rather than intact bacteria. It has now been demonstrated that the short-chain fatty acid valerate is restored in human fecal samples from CDI patients and a bioreactor model of recurrent CDI by FMT, but not by antibiotic cessation alone; [46] as such, this may be a key mediator of FMT's efficacy. Other studies have identified rapid-onset but well-maintained changes in the gut bacteriophage profile after successful FMT (with colonisation of the recipient with donor bacteriophages), [47] [48] and this is therefore another key area of interest.

In contrast, in the case of other conditions such as ulcerative colitis, no single culprit has yet been identified. [49] However, analysis of gut microbiome and metabolome changes after FMT as treatment for ulcerative colitis has identified some possible candidates of interest. [50]

History

The first use of donor feces as a therapeutic agent for food poisoning and diarrhea was recorded in the Handbook of Emergency Medicine by a Chinese man, Hong Ge, in the 4th century. Twelve hundred years later Ming dynasty physician Li Shizhen used "yellow soup" (aka "golden syrup") which contained fresh, dry or fermented stool to treat abdominal diseases. [51] "Yellow soup" was made of fecal matter and water, which was drunk by the person. [52]

The consumption of "fresh, warm camel feces" has also been recommended by Bedouins as a remedy for bacterial dysentery; its efficacy, probably attributable to the antimicrobial subtilisin produced by Bacillus subtilis, was anecdotally confirmed by German soldiers of the Afrika Korps during World War II. [53] However, this story is likely a myth; independent research was not able to verify any of these claims. [54]

The first use of FMT in western medicine was published in 1958 by Ben Eiseman and colleagues, a team of surgeons from Colorado, who treated four critically ill people with fulminant pseudomembranous colitis (before C. difficile was the known cause) using fecal enemas, which resulted in a rapid return to health. [55] For over two decades, FMT has been provided as a treatment option at the Centre for Digestive Diseases in Five Dock, by Thomas Borody, the modern-day proponent of FMT. In May 1988 their group treated the first ulcerative colitis patient using FMT, which resulted in complete resolution of all signs and symptoms long term. [22] In 1989 they treated a total of 55 patients with constipation, diarrhea, abdominal pain, ulcerative colitis, and Crohn's disease with FMT. After FMT, 20 patients were considered "cured" and a further 9 patients had a reduction in symptoms. [56] Stool transplants are considered about 90 percent effective in those with severe cases of C. difficile colonization, in whom antibiotics have not worked. [12]

The first randomized controlled trial in C. difficile infection was published in January 2013. [3] The study was stopped early due to the effectiveness of FMT, with 81% of patients achieving cure after a single infusion and over 90% achieving a cure after a second infusion.

Since that time various institutions have offered FMT as a therapeutic option for a variety of conditions. [22]

Society and culture

Regulation

Interest in FMT grew in 2012 and 2013, as measured by the number of clinical trials and scientific publications. [57]

In the United States, the FDA announced in February 2013 that it would hold a public meeting entitled "Fecal Microbiota for Transplantation" which was held on May 2–3, 2013. [58] [59] In May 2013 the FDA also announced that it had been regulating human fecal material as a drug. [60] The American Gastroenterological Association (AGA), the American College of Gastroenterology (ACG), the American Society for Gastrointestinal Endoscopy (ASGE), and the North American Society for Pediatric Gastroenterology, Hepatology and Nutrition (NASPGHAN) sought clarification, and the FDA Center for Biologics Evaluation and Research (CBER) stated that FMT falls within the definition of a biological product as defined in the Public Health Service Act and the definition of a drug within the meaning of the Federal Food, Drug, and Cosmetic Act. [61] It argued since FMT is used to prevent, treat, or cure a disease or condition, and intended to affect the structure or any function of the body, "a product for such use" would require an Investigational New Drug (IND) application. [61]

In July 2013, the FDA issued an enforcement policy ("guidance") regarding the IND requirement for using FMT to treat C. difficile infection unresponsive to standard therapies (78 FR 42965, July 18, 2013). [62]

In March 2014, the FDA issued a proposed update (called "draft guidance") that, when finalized, is intended to supersede the July 2013 enforcement policy for FMT to treat C. difficile infections unresponsive to standard therapies. It proposed an interim discretionary enforcement period, if 1) informed consent is used, mentioning investigational aspect and risks, 2) stool donor is known to either the person with the condition or physician, and 3) stool donor and stool are screened and tested under the direction of the physician (79 FR 10814, February 26, 2014). [63] Some doctors and people who want to use FMT have been worried that the proposal, if finalized, would shutter the handful of stool banks which have sprung up, using anonymous donors and ship to providers hundreds of miles away. [57] [64] [65]

As of 2015, FMT for recurrent C. difficile infections can be done without mandatory donor and stool screening, whereas FMT for other indications cannot be performed without an IND. [60]

The FDA has issued three safety alerts regarding the transmission of pathogens. The first safety alert, issued in June 2019, described the transmission of a multidrug resistant organism from a donor stool that resulted in the death of one person. [66] The second safety alert, issued in March 2020, was regarding FMT produced from improperly tested donor stools from a stool bank which resulted in several hospitalizations and two deaths. [67] A safety alert in late March 2020, was due to concerns of transmission of COVID-19 in donor stool. [68]

In November 2022, the AU Therapeutic Goods Administration approved faecal microbiota under the brand name Biomictra, [1] [18] and the US FDA approved a specific C. difficile fecal microbiota treatment under the brand name Rebyota, [19] administered rectally. In April 2023, the FDA approved a live spore capsule that can be taken by mouth, under the brand name Vowst. [20] [69]

Stool banks

In 2012, a team of researchers from the Massachusetts Institute of Technology founded OpenBiome, the first public stool bank in the United States. [70]

Across Europe, numerous stool banks have emerged to serve the increasing demand. While consensus exists, [37] standard operation procedures still differ. Institutions in the Netherlands have published their protocols for managing FMT, [42] and in Denmark institutions manages FMT according to the European Tissue and Cell directive. [41]

Names

Previous terms for the procedure include fecal bacteriotherapy, fecal transfusion, fecal transplant, stool transplant, fecal enema, and human probiotic infusion (HPI). Because the procedure involves the complete restoration of the entire fecal microbiota, not just a single agent or combination of agents, these terms have been replaced by the term fecal microbiota transplantation. [14]

Research

Cultured intestinal bacteria are being studied as an alternative to fecal microbiota transplant. [71] One example is the rectal bacteriotherapy (RBT), developed by Tvede and Helms, containing 12 individually cultured strains of anaerobic and aerobic bacteria originating from healthy human faeces. [72] Research has also been done to identify the most relevant microbes within fecal transplants, which could then be isolated and manufactured via industrial fermentation; such standardized products would be more scalable, would reduce the risk of infections from unwanted microbes, and would improve the scientific study of the approach, since the same substance would be administered each time. [73]

Veterinary use

Elephants, hippos, koalas, and pandas are born with sterile intestines, and to digest vegetation need bacteria which they obtain by eating their mothers' feces, a practice termed coprophagia. Other animals eat dung. [74]

In veterinary medicine fecal microbiota transplant has been known as "transfaunation" and is used to treat ruminating animals, like cows and sheep, by feeding rumen contents of a healthy animal to another individual of the same species in order to colonize its gastrointestinal tract with normal bacteria. [75]

Related Research Articles

<span class="mw-page-title-main">Ulcerative colitis</span> Inflammatory bowel disease that causes ulcers in the colon

Ulcerative colitis (UC) is one of the two types of inflammatory bowel disease (IBD), with the other type being Crohn's disease. It is a long-term condition that results in inflammation and ulcers of the colon and rectum. The primary symptoms of active disease are abdominal pain and diarrhea mixed with blood (hematochezia). Weight loss, fever, and anemia may also occur. Often, symptoms come on slowly and can range from mild to severe. Symptoms typically occur intermittently with periods of no symptoms between flares. Complications may include abnormal dilation of the colon (megacolon), inflammation of the eye, joints, or liver, and colon cancer.

<i>Clostridioides difficile</i> infection Disease caused by C. difficile bacteria

Clostridioides difficile infection, also known as Clostridium difficile infection, is a symptomatic infection due to the spore-forming bacterium Clostridioides difficile. Symptoms include watery diarrhea, fever, nausea, and abdominal pain. It makes up about 20% of cases of antibiotic-associated diarrhea. Antibiotics can contribute to detrimental changes in gut microbiota; specifically, they decrease short-chain fatty acid absorption which results in osmotic, or watery, diarrhea. Complications may include pseudomembranous colitis, toxic megacolon, perforation of the colon, and sepsis.

<span class="mw-page-title-main">Inflammatory bowel disease</span> Medical condition

Inflammatory bowel disease (IBD) is a group of inflammatory conditions of the colon and small intestine, with Crohn's disease and ulcerative colitis (UC) being the principal types. Crohn's disease affects the small intestine and large intestine, as well as the mouth, esophagus, stomach and the anus, whereas UC primarily affects the colon and the rectum.

<span class="mw-page-title-main">Colitis</span> Inflammation of the colon (large intestine)

Colitis is swelling or inflammation of the large intestine (colon). Colitis may be acute and self-limited or long-term. It broadly fits into the category of digestive diseases.

<span class="mw-page-title-main">Stool test</span> Medical examination of fecal matter

A stool test is a medical diagnostic technique that involves the collection and analysis of fecal matter. Microbial analysis (culturing), microscopy and chemical tests are among the tests performed on stool samples.

<span class="mw-page-title-main">Clostridia</span> Class of bacteria

The Clostridia are a highly polyphyletic class of Bacillota, including Clostridium and other similar genera. They are distinguished from the Bacilli by lacking aerobic respiration. They are obligate anaerobes and oxygen is toxic to them. Species of the class Clostridia are often but not always Gram-positive and have the ability to form spores. Studies show they are not a monophyletic group, and their relationships are not entirely certain. Currently, most are placed in a single order called Clostridiales, but this is not a natural group and is likely to be redefined in the future.

<span class="mw-page-title-main">Rifaximin</span> Antibiotic medication

Rifaximin, is a non-absorbable, broad spectrum antibiotic mainly used to treat travelers' diarrhea. It is based on the rifamycin antibiotics family. Since its approval in Italy in 1987, it has been licensed in over more than 30 countries for the treatment of a variety of gastrointestinal diseases like irritable bowel syndrome, and hepatic encephalopathy. It acts by inhibiting RNA synthesis in susceptible bacteria by binding to the RNA polymerase enzyme. This binding blocks translocation, which stops transcription. It is marketed under the brand name Xifaxan by Salix Pharmaceuticals.

Antibiotic-associated diarrhea (AAD) results from an imbalance in the colonic microbiota caused by antibiotics. Microbiotal alteration changes carbohydrate metabolism with decreased short-chain fatty acid absorption and an osmotic diarrhea as a result. Another consequence of antibiotic therapy leading to diarrhea is an overgrowth of potentially pathogenic organisms such as Clostridioides difficile. It is defined as frequent loose and watery stools with no other complications.

Thomas J. Borody is an Australian gastroenterologist.

Dysbiosis is characterized by a disruption to the microbiome resulting in an imbalance in the microbiota, changes in their functional composition and metabolic activities, or a shift in their local distribution. For example, a part of the human microbiota such as the skin flora, gut flora, or vaginal flora, can become deranged (unbalanced), when normally dominating species become underrepresented and species that normally are outcompeted or contained increase to fill the void. Similar to the human gut microbiome, diverse microbes colonize the plant rhizosphere, and dysbiosis in the rhizosphere, can negatively impact plant health. Dysbiosis is most commonly reported as a condition in the gastrointestinal tract or plant rhizosphere.

<span class="mw-page-title-main">Human feces</span> Metabolic waste of the human digestive system

Human feces or faeces, commonly and in medical literature more often called stool, are the solid or semisolid remains of food that could not be digested or absorbed in the small intestine of humans, but has been further broken down by bacteria in the large intestine. It also contains bacteria and a relatively small amount of metabolic waste products such as bacterially altered bilirubin, and the dead epithelial cells from the lining of the gut. It is discharged through the anus during a process called defecation.

<span class="mw-page-title-main">Fidaxomicin</span> Antibiotic

Fidaxomicin, sold under the brand name Dificid among others, is the first member of a class of narrow spectrum macrocyclic antibiotic drugs called tiacumicins. It is a fermentation product obtained from the actinomycete Dactylosporangium aurantiacum subspecies hamdenesis. Fidaxomicin is minimally absorbed into the bloodstream when taken orally, is bactericidal, and selectively eradicates pathogenic Clostridioides difficile with relatively little disruption to the multiple species of bacteria that make up the normal, healthy intestinal microbiota. The maintenance of normal physiological conditions in the colon may reduce the probability of recurrence of Clostridioides difficile infection.

Bacteriotherapy is the purposeful use of bacteria or their products in treating an illness. Forms of bacteriotherapy include the use of probiotics, microorganisms that provide health benefits when consumed; fecal matter transplants (FMT) /intestinal microbiota transplant (IMT), the transfer of gut microorganisms from the fecal matter of healthy donors to recipient patients to restore microbiota; or synbiotics which combine prebiotics, indigestible ingredients that promote growth of beneficial microorganisms, and probiotics. Through these methods, the gut microbiota, the community of 300-500 microorganism species that live in the digestive tract of animals aiding in digestion, energy storage, immune function and protection against pathogens, can be recolonized with favorable bacteria, which in turn has therapeutic effects.

OpenBiome is a nonprofit health research organization based in Massachusetts accelerating research on the human microbiome. They partner with leading researchers, clinicians and innovators to advance and ensure access to novel and affordable microbiome therapeutics.

<i>Clostridioides difficile</i> Species of bacteria

Clostridioides difficile is a bacterium known for causing serious diarrheal infections, and may also cause colon cancer. It is known also as C. difficile, or C. diff, and is a Gram-positive species of spore-forming bacteria. Clostridioides spp. are anaerobic, motile bacteria, ubiquitous in nature and especially prevalent in soil. Its vegetative cells are rod-shaped, pleomorphic, and occur in pairs or short chains. Under the microscope, they appear as long, irregular cells with a bulge at their terminal ends. Under Gram staining, C. difficile cells are Gram-positive and show optimum growth on blood agar at human body temperatures in the absence of oxygen. C. difficile is catalase- and superoxide dismutase-negative, and produces up to three types of toxins: enterotoxin A, cytotoxin B and Clostridioides difficile transferase. Under stress conditions, the bacteria produce spores that are able to tolerate extreme conditions that the active bacteria cannot tolerate.

Serum-derived bovine immunoglobulin/protein isolate (SBI) is a medical food product derived from bovine serum obtained from adult cows in the United States. It is sold under the name EnteraGam.

<span class="mw-page-title-main">Ridinilazole</span> Chemical compound

Ridinilazole is an investigational small molecule antibiotic being evaluated for oral administration to treat Clostridioides difficile infection (CDI). In vitro, it is bactericidal against C. difficile and suppresses bacterial toxin production; the mechanism of action is thought to involve inhibition of cell division. It has properties which are desirable for the treatment of CDI, namely that it is a narrow-spectrum antibiotic which exhibits activity against C. difficile while having little impact on other normal intestinal flora and that it is only minimally absorbed systemically after oral administration. At the time ridinilazole was developed, there were only three antibiotics in use for treating CDI: vancomycin, fidaxomicin, and metronidazole. The recurrence rate of CDI is high, which has spurred research into other treatment options with the aim to reduce the rate of recurrence.

Michael J. Sadowsky is an American microbiologist at the University of Minnesota. He is the director of the BioTechnology Institute and a Professor in the Department of Soil, Water, and Climate. Sadowsky's scientific career spans over 40 years, most of it focused on research studying the nature of bacteria and bacterial genes in ecological settings, with a particular emphasis on soil bacteria that are involved in nitrogen fixation.

Fecal microbiota, sold under the brand name, Rebyota is used for the prevention of recurrence of Clostridioides difficile infection.

Live fecal microbiota spores, sold under the brand name Vowst, is a fecal microbiota product used to prevent the recurrence of Clostridioides difficile infection.

References

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