Deep mucosal healing in CD has been reported previously with CD treatments, including infliximab, azathioprine, methotrexate [27], but not seen with 5-aminosalicylates and corticosteroids [28]. In a small sub study conducted by D’Haens et al. (2002) of 19 patients who completed the ACCENT-1 trial, the effect of scheduled (every 8 weeks) versus on demand infliximab treatment on mucosal healing was examined [29]. The median time to relapse was 12 weeks (range 1- > 78 weeks). In the EXTEND trial, which evaluated the efficacy of adalimumab for 52 weeks in moderate-to-severe CD, 27% of patients receiving adalimumab had mucosal healing at week 12 (the primary end point) versus 13% given placebo (p = 0.056). At week 52, rates of mucosal healing were 24% and 0, respectively (p < 0.001) [30]. In a study examining the effects of mucosal healing on long-term outcomes in CD, 64.8% of patients who achieved mucosal healing were in clinical remission at the end of 5 years, whereas only 39.5% of patients who did not achieve mucosal healing attained clinical remission [31]. A pertinent observation from this is that the patients in the trials described above were unable to cease CD therapy without relapsing. There is no long-term follow up data past 2 years.

The treatments described in this case series were individualised to the patient. Most patients (70%) had received AMAT for a period of 3 years to initially induce deep healing, which translated clinically to a remission of their disease. AMAT consisted of a combination of agents effective against MAP, some patients requiring addition of alternate AMAT agents due to occasional adverse effects, generally being arthralgia. The length of treatment was based on observations of Mycobacterium leprae treatment (12–18 months) and that MAP is an even slower growing/reproducing mycobacteria. Several patients received FMT to re-establish a healthy gut microbiome after prolonged antibiotic use. In addition, two patients achieved long-term clinical remission and mucosal healing with FMT alone. This adds further support to an infective aetiology of CD because FMT eradicates pathogens, for example Clostridioides difficile infection, and may have a parallel action in CD. The important observation is that long-term remission here was achieved, not via immune modulating biologics targeting inflammation but rather by the use of antibiotics targeted against MAP and/or FMT targeting dysbiosis of the gut flora. Further optimally designed trials comparing therapy with AMAT and FMT versus current ‘standard of care’ therapy in CD should be conducted. Long-term follow up studies of patients with CD treated with AMAT and/or microbiome modification are also required to confirm our results.

These observations concur with our notion that CD occurs as the result of a primary infection with MAP, or a similar pathogen, and a resulting disruption of the protective mechanisms of the gut microbiome (dysbiosis). We hypothesize that there is a complex interplay, where a predisposition, stemming from innate immune deficiencies (given this particularly is involved in intracellular bacterial infections and perhaps evolved alongside the resident gut flora), that likely arise from certain deficiencies of the gut microbiome. This has been shown to be the case in tuberculosis susceptibility [32]. Genetic factors, such as the NOD2CARD15 mutations contributes to risk of developing disease, as these enable the pathogenesis of CD and also have been shown to confer an increased risk to mycobacterial infections [33, 34]. MAP itself can further disrupt the biodiversity of the microbial environment of the gut [35], leading to excessive and maladaptive immune responses, which current immune suppressive therapy target. MAP behaviour is similar to other mycobacteria, where there are high infectivity rates but low expression/pathogenicity. The rates are in part given to the respective reproductive rates, with MAP having one of the longest known of the Mycobacteria genus. Mycobacterium tuberculosis (MTB) infects a third of the world’s population (~ 3 billion), yet disease presents in 3-5% of individuals (WHO Global tuberculosis report 2015). However, one difference between MAP and the MTB complex is that MAP doesn’t lead to deterioration when immunosuppressives are given, just one of the different characteristics between atypical (avium) mycobacteria and MTB complex. A proposition, based on multiple studies, is that immunosuppressives actually work in CD by their secondary antibiotic action on MAP [36,37,38]. Interestingly, anti-TNF α agents have been shown to reduce Mycobacterial survivability and may be a key reason why they work well with AMAT to accelerate healing [39], especially that of Crohn's fistulae[26]. Though a caveat to this is that they may lead to resistance of MAP, where it resides in tissues [40]. A problem that we have observed in the response using AMAT in patients with a history of biologic use compared to ‘treatment-naïve’ patients [41].

The ability for MAP to influence the gut microbiome has been demonstrated in animal rabbit [35] and cattle [42] models. We propose that the inability to clear MAP from the macrophage and the resulting dysbiosis from viable mycobacteria, leads to granulomas and the relapsing, remitting behaviour observed in CD. Targeting both steps is likely key to higher eradication and recovery rates and a reason as to why efficacy of FMT alone is currently sub-optimal in remission of CD [43]. However, there may be certain circumstances in a minority where recovery of the dysbiosis alone (by FMT only) may be sufficient in clearing/containing MAP, perhaps through restoration of the (innate) immune system functioning. In addition, the dysbiosis of the gut microbiome is a likely reason why dietary intervention plays a key role in the symptoms and treatment of CD [44], by altering (± the activity) of the gut microbiota and so modulating inflammation. Addressing this step after the primary treatment with AMAT may also be critical for long-term remission and requires further evaluation. In addition, sensitivities of MAP to the antibiotic chemotherapy (which are predominately intracellular acting compounds, particularly for Mycobacteria e.g. clofazimine), coupled with the ability to implant healthy commensal microbes will also likely influence the success rates. MAP, like other mycobacteria, has been shown to have the presence of resistant strains to Rifamycin compounds (including Rifampicin and Rifabutin), due to the presence of the rpoB gene. This will influence the response to AMAT [45,46,47].

In addition, further research into the gut dysbiosis, including the role of specific pathogens such as MAP, is required to improve understanding and improving treatment efficacy in CD.

Case series have the benefit of reporting novel clinical outcomes that cannot be established from short-term, expensive RCT research protocols. They in essence highlight principles of a treatment. However, the inherent limitations of case reports including; small sample size, single centre source and clinical nature of the information, resulting in missing data, are recognised and limits the consistency/reproducibility of the results. It is acknowledged that there could be a wide range of possible variables, which could have influenced the outcomes seen. However, this is a precursor highlighting the requirement of larger studies, which will enable multi-variate statistical testing based on a more complete dataset, including negative outcomes, to be utilised. However, given that currently it is thought Crohn’s is incurable with immunosuppressive treatments, alternative lines of causation and treatment should also be investigated in parallel.

A significant limitation of this study is the lack of MAP testing in patients. The unavailability of culturing, cataloguing and diagnostic tests of the microbiome and MAP during this period, has hindered the details and understanding of these results and effects, for which these patients were treated for. Improvements for future research will require better diagnostics for MAP, cataloguing of the gut microbiome before and after therapy, as well as standardised clinical, endoscopic and histological measures in prospective or randomised methods. However, it is likely that standardised treatment regimens may never be achieved. The main factors influencing outcomes are individual responses and immune functioning, use of prior biologics (which appears to make MAP more resistant), and the resistant nature of the organism that is currently seen and understood. This is a pattern reminiscent in Mycobacterium avium and tuberculosis therapy, where Severe-Drug resistant TB (XDR-TB) eradication rate is 35% compared to fully sensitive MTB of 81% (WHO Global Health report). Influencing FMT factors will include implantation success, donor suitability and number of infusions.