1. Introduction

Liver cirrhosis has a multitude of debilitating complications including ascites, bleeding and hepatic encephalopathy (HE). HE is a major neurologic complication of cirrhosis and is estimated to affect between 30 to 70% of patients with cirrhosis [1,2]. It often requires hospitalization, which has a significant economic impact. Studies have shown that the yearly total cost for patients with a primary diagnosis of HE is estimated at USD 620 million in the United States [3]. Cognitive impairment experienced by patients with HE can range from covert (minimal) to overt [2]. Covert HE can be subtle in nature and requires the use of specialized tests for detection. In contrast, overt HE is characterized by behavioral changes, confusion and lethargy [2]. Regardless of type, HE portends a poor prognosis and is associated with increased morbidity [1]. It not only negatively impacts the patient’s quality of life but also places a heavy burden on family and caregivers. Moreover, individuals who experience HE have a high chance of recurrence [1,2].

The exact pathogenesis for the development of HE is yet to be determined. Certain mechanisms have been implicated and have been recognized for years including increased production of neurotoxins, impairment of neurotransmission, systemic inflammation, alteration of the blood–brain barrier and alterations in energy metabolism [4,5]. It is clear that no single entity is solely responsible for HE, and it is a synergistic effect of multiple mechanisms that lead to this illness. In recent years, it has been increasingly recognized that the gut microbiota plays a large role in the development of HE [6,7,8]. This is most evident by the beneficial role of antibiotics in the treatment in HE, which typically decrease the intestinal population of urease-producing microbes [6,7,8]. This suggests that HE is a disease of the gut–liver–brain axis whereby dysregulation in gut microbiota can lead to many downstream effects including bacterial translocation and toxin production subsequently causing systemic and neurological inflammation [6,7,8]. This has led to the evaluation of gut microbiota as a potential therapeutic target, particularly with fecal microbiota transplantation (FMT), and early studies have shown promising results [9].

4. Fecal Microbiota Transplantation in Hepatic Encephalopathy

FMT involves the administration of a solution of a fecal suspension from a donor into the intestinal tract of a recipient. This can be administered in several formulations including enema, via colonoscopy, or in capsular form. This therapy serves to directly change the gut microbiota composition. Previous studies have shown that FMT is effective in conditions associated with dysbiosis particularly recurrent Clostridoides difficile and ulcerative colitis [69,70]. As repeatedly demonstrated, cirrhosis and, in particular, HE is associated with dysbiosis. Reversing dysbiosis and restoring eubiosis can potentially reduce systemic inflammation, preserve gut membrane integrity, prevent bacterial translocation and maintain production of bile acids.

A case report by Kao et al. was the first attempt at treating HE with FMT [71]. Cognition was assessed with the inhibitory control test and the Stroop test, and they showed that the patient’s cognition improved with consecutive FMT until it stabilized by the fourth week after a total of three FMTs. The patient’s cognition reverted to baseline after 14 weeks after withdrawal of FMTs. Interestingly, Lachnospiraceae, which is associated with better cognition, was found to be in reduced quantities in this patient.

The aforementioned results were promising and lead to the first randomized control trial studying the efficacy of FMT in HE, which was conducted by our group. In this study, a single stool specimen was used for the experimental group by identifying a donor with the highest relative abundance of Lachnospiraceae and Ruminococcaceae [72]. A total of 20 cirrhotic patients with recurrent HE (defined as two or more episodes) were enrolled and randomly assigned to the standard of care and to the FMT group. Both groups were to continue their lactulose and rifaximin. Prior to receiving the FMT enema, the experimental group received a five-day treatment of antibiotics to increase the success of donor bacterial colonization. The FMT with antibiotic pretreatment was well tolerated, and the patients were followed for up to 150 days. There was a significant reduction in serious adverse events in the experimental group compared to the control group. Five patients in the control group had a recurrent episode of HE, whereas no patient in the FMT group developed further HE. The psychometric hepatic encephalopathy score (PHES) and EncephalApp Stroop (EAS) were used to assess cognitive ability. These cognitive assessments showed that there was a significant improvement in cognition in the FMT group at day 20 compared to baseline.

A follow-up study was performed to demonstrate the long-term safety of FMT. The study was carried out in a similar fashion to our previous study; however, all participants received proton pump inhibitors in addition to lactulose and rifaximin. The participants were followed for 12 months, and there were significantly fewer hospitalizations and HE episodes in the FMT group compared to the control group [73]. Furthermore, cognition measured by PHES and EAS was found to be significantly better in the experimental group compared to their control counterparts. Similar to the case report by Kao et al., the abundance of the autochthonous organisms Lachnospiraceae and Ruminococcaeae was not statistically different between the two groups despite the FMT donor’s microbiome being rich in these organisms. We concluded that FMT is safe for long-term use; however, this study was limited by a small sample size. This was then followed by a phase 1, randomized, placebo-controlled trial to determine the safety of capsular FMT. The groups were followed for five months after administration of FMT capsules obtained from a single donor with the highest relative abundance of Lachnospiraceae and Ruminococcaceae. Only one serious adverse event was reported in the FMT group as opposed to 11 in the control group, suggesting that FMT capsules are well tolerated and safe [74]. Patients who received FMT capsules had improved cognition when assessed with EAS; however, PHES did not improve. The participants had their microbiomes analyzed, and the FMT group had increases in duodenal Ruminococcaeae and Bifidobacteriaceae and decreases in Streptococcaceae and Veillonellaceae. Moreover, there were reductions in sigmoid and stool populations of Veillonellaceae. As described earlier, Streptococcaceae is an ammionagenic organism and is linked with development of HE. There was a non-significant trend toward fewer hospitalizations in the FMT group. Although the sample size was small, this was one of the first studies to demonstrate that FMT capsules can decrease relative abundance of microorganisms associated with the progression of cirrhosis. A case series published by Mehta et al. performed FMT via colonoscopy in patients with cirrhosis and recurrent HE [75]. Although this retrospective study only had 10 participants, it demonstrated that there was a sustained clinical response in six patients 20 weeks after treatment. These patients showed reductions in arterial ammonia concentration, Child–Pugh score, and model for end-stage liver disease score.

We recently completed a phase 1, double-blind, randomized clinical trial to study the effects of FMT enema on alcohol-use-disorder-related cirrhosis [76]. Although not designed to study FMT on outcomes of HE, this study demonstrated reduced alcohol craving, reduced urinary ethyglucuronide, improved cognition and psychosocial quality of life at day 15 compared to placebo. Moreover, there was a reduction in serum IL-6 and LPS binding protein and increased butyrate/isobutyrate compared to baseline in the FMT group. These metabolic changes are presumed to be due to the increased abundance of Ruminococcaceae in the treatment group. In regard to safety, there was a lower rate of serious adverse events in the FMT group compared to placebo.

Antibiotic resistance is a frequent complication of cirrhosis that leads to poor outcomes. FMT offers a promising therapy that may reduce the population of multidrug resistance organisms. We recently studied this by evaluating the expression of the antibiotic resistance gene (ARG) in patients with decompensated cirrhosis before and after healthy donor capsule and enema FMT [77]. There were 20 patients with cirrhosis in each trial (capsule and enema FMT), and all patients were on rifaximin, lactulose and proton pump inhibitors. ARGs were identified using metagenomics, and changes in ARG abundance were studied within and between groups. Expression of beta-lactamase was decreased post capsule FMT compared to baseline. Beta-lactamase, vancomycin and rifamycin ARGs were significantly lower at 4 weeks post-FMT compared to placebo. A reduction in rifamycin ARG in the interventional group was associated with cognitive improvement. In the enema FMT trial, beta-lactamase and vancomycin ARGs were decreased at day 7 post treatment compared to standard of care, and this reduction in ARGs persisted until day 15. These data suggest that ARG abundance is largely reduced after FMT in decompensated cirrhosis regardless of the route of administration.

7. Future Directions and Challenges

There are several ongoing and future trials studying several aspects of FMT including different routes of administration. The PROFIT trial is an ongoing study designed to assess the effect of FMT delivered directly into the small bowel of patients with cirrhosis [78]. In contrast to previous studies, the patients in this study are not to be pretreated with antibiotics. The idea is that direct instillation of FMT into the jejunum can directly target SIBO. This study is powered to study the feasibility and safety of this technique and not to assess clinical outcome. Preliminary data from this trial were recently presented at the 2020 digital international liver congress [79]. Twenty-one patients with confirmed cirrhosis were included, and 15 patients received FMT and six received placebo. Plasma ammonia was significantly reduced at day 30 compared to baseline. There was also a non-significant increase in plasma ammonia in the placebo group. Ammonia levels in stool were found to be increased in the placebo group but not in the FMT group.

A common criticism of the aforementioned studies is small sample sizes. This is certainly an issue, as small sample sizes can lead to inflated false discovery rate and inflated effect size estimation. Several large studies are ongoing and actively recruiting, one of which we are conducting [80]. This trial includes 100 participants with four groups randomized to oral and/or rectal FMT.

These early studies have shown promising results in treating HE with FMT. Several questions remain answered. One question is safety. Our studies have shown that FMT appears to be well tolerated and safe. A case report by DeFilipp et al. highlights the importance of donor screening to limit transmission of microorganisms [81]. They reported transmission of drug-resistant E. coli in two patients who had undergone FMT obtained from the same donor. Both patients developed bacteremia and one died. Other rare cases of bacteremia and death have been reported suggesting that FMT is not a benign procedure. Careful selection of donor and recipient must be done to minimize the risks. The FDA has updated their protocol on FMT in 2019 mandating that donors be screened for multi-drug-resistant organisms. However, since patients with cirrhosis have compromised intestinal membrane integrity and are immunocompromised, there is potential of transmission of other pathogenic organisms that are not routinely screened for.

The risk to benefit ratio of using FMT to treat chronic liver disease, cirrhosis and hepatic encephalopathy is yet to be established. The benefits are assuredly high, as there is no equivalent alternative therapy available to address the issue of dysbiosis in chronic liver disease. As mentioned previously, the risks include transmission of resistant organisms or other deleterious traits that are not yet measured. Furthermore, patients need to be accepting of this therapy, and it needs to be universally available. For this to occur, certain aspects regarding the implementation of FMT in clinical practice need to be established, particularly regarding the amount of donor material required, optimal route of administration, length and frequency of treatment, and interval between treatments. While FMT has been successful for the treatment of refractory Clostridium difficile, whereby gut microbiota is typically sterilized by antibiotics prior to replacement with a single inoculation of small amount of a donor’s sample, it may not be as simple in chronic liver disease. The dysbiosis in cirrhosis is complex and is not necessarily equivalent amongst patients, which makes its treatment selection challenging. Patients with cirrhosis are routinely treated with antibiotics for HE and spontaneous bacterial peritonitis, which further disturbs the microbiota. Dosing time is likely to be important, and preliminary data from the PROFIT trial, while small in number, have demonstrated this [82]. It is likely that multiple doses are required to achieve a meaningful therapeutic response. As mentioned previously, we have a large clinical trial with 100 participants to address the question of treatment mode of delivery and dose range (0–3, clinicaltrials.gov ID NCT03796598). Our study consists of four groups: dual oral and rectal FMT, oral FMT and rectal placebo, oral placebo and rectal FMT and oral and rectal placebo. Rectal-administered treatment is given once at day 2, and oral administered treatment is given at day 2 and day 30. Participants are then followed for 6 months, and the primary outcome of the study is to determine serious adverse events related to FMT. Secondary outcomes at 6 months include changes in microbial diversity in stool/blood/saliva, changes in intestinal permeability and change in HE status as determined by changes in EAS or PHES. To further assess treatment delivery, the PROFIT trial will be extending their study to recruit 300 more patients over two years to undergo multiple doses using a capsule delivery model in contrast to their previous endoscopically administered treatment. The possibility of long-lasting cure from FMT alone is highly unlikely given the multi-factorial nature of chronic liver disease. The complexity of chronic liver disease and cirrhosis require a multi-faceted treatment approach. It is clear that FMT is not intended to be used as a solo therapy and simply augments the existing armamentarium for treating liver disease.

The need for pre-procedure antibiotics for sterilization has not been studied extensively. Whether antibiotics need to be withheld post-FMT is not clear either, as this may not be feasible in many patients. Multiple routes of administration have been evaluated with many showing successful results; however, the superiority or non-inferiority of one route versus another is unknown. Utilizing FMT in clinical practice will only be possible once we find solutions to these questions.

This entry is adapted from the peer-reviewed paper 10.3390/jcm10020330