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Iaquinto, G.; Mazzarella, G.; Sellitto, C.; Lucariello, A.; Melina, R.; Iaquinto, S.; De Luca, A.; Rotondi Aufiero, V. Antibiotic Therapy for Active Crohn’s Disease Targeting Pathogens. Encyclopedia. Available online: (accessed on 21 June 2024).
Iaquinto G, Mazzarella G, Sellitto C, Lucariello A, Melina R, Iaquinto S, et al. Antibiotic Therapy for Active Crohn’s Disease Targeting Pathogens. Encyclopedia. Available at: Accessed June 21, 2024.
Iaquinto, Gaetano, Giuseppe Mazzarella, Carmine Sellitto, Angela Lucariello, Raffaele Melina, Salvatore Iaquinto, Antonio De Luca, Vera Rotondi Aufiero. "Antibiotic Therapy for Active Crohn’s Disease Targeting Pathogens" Encyclopedia, (accessed June 21, 2024).
Iaquinto, G., Mazzarella, G., Sellitto, C., Lucariello, A., Melina, R., Iaquinto, S., De Luca, A., & Rotondi Aufiero, V. (2024, February 08). Antibiotic Therapy for Active Crohn’s Disease Targeting Pathogens. In Encyclopedia.
Iaquinto, Gaetano, et al. "Antibiotic Therapy for Active Crohn’s Disease Targeting Pathogens." Encyclopedia. Web. 08 February, 2024.
Antibiotic Therapy for Active Crohn’s Disease Targeting Pathogens

Crohn’s disease (CD) is a multifactorial chronic disorder that involves a combination of factors, including genetics, immune response, and gut microbiota. Therapy includes salicylates, immunosuppressive agents, corticosteroids, and biologic drugs. 

antibiotic therapy Crohn’s disease patients

1. Antibiotic Treatment Targeting Mycobacterium Avium Paratubercolosis  in Active Crohn' s disease Patients

Several meta-analyses have been published concerning long-term antibiotic treatment targeting MAP in patients with active Crohn’s disease (CD) (Table 1).
Table 1. Long-term antibiotic treatment targeting MAP in patients with active CD.
Borgaonkar et al. [1] identified six randomized controlled trials (RCTs) using anti-MAP therapy for 6 to 24 months. Two trials that used corticosteroids in combination with antimicrobial therapy yielded a pooled odds ratio (OR) of 3.37 for maintenance of remission in treatment versus control, which was statistically significant (95% CI: 1.38–8.24; p = 0.013). The subgroup analysis of the other four trials, which did not use corticosteroids to induce remission, yielded a pooled odds ratio of 0.69 (95% CI: 0.39–1.21) for maintenance of remission in treatment versus control, which was not statistically significant (p = 0.25). The pooled OR for maintenance of remission in treatment versus control for all six studies was 1.10 (95% CI: 0.69–1.74) in favor of treatment, which was not statistically significant (p = 0.78). These results suggest that antimicrobial therapy is effective in maintaining remission in patients with CD after a course of corticosteroids combined with anti-MAP therapy.
Feller et al. [2], in a systematic review and meta-analysis of placebo-controlled trials, examined 13 treatment regimens in 865 patients. The average duration of treatment was 6 months. The outcomes were remission in patients with active disease and relapse in patients with inactive disease. The trials using nitroimidazoles showed benefits, with an OR of 3.54, and the OR for the four trials using clofazimine was 2.86. On the contrary, no benefit was found for classic drugs against tuberculosis (OR = 0.58). The results for clarithromycin were mixed (p = 0.005), and in three trials with rifaximin the OR was 2.07. The conclusion of this research was that long-term treatment with nitroimidazoles, clofazimine, or ciprofloxacin appeared to be effective in patients with active CD, while little evidence of benefits was found for clarithromycin and the classical tuberculosis drugs.
Khan et al. [3], in a systematic review including 10 RCTs and 1160 patients, evaluated the effect of antibiotics on remission and relapse of adult patients with active CD. Different kinds of antibiotics were tested, including macrolides, fluoroquinolones, 5-nitroimidazole, and rifaximin, either alone or in combination, for 4 to 16 weeks. There was a statistically significant effect of antibiotics on inducing remission in patients with active CD compared with placebo (OR = 0.85; 95% CI: 0.73–0.99).
Selby et al. [4], in a double-blind, placebo-controlled trial, studied 213 patients with active CD randomized to a 2-year course of daily clarithromycin, rifabutin, and clofazimine or placebo in addition to a 16-week course of prednisolone. The primary endpoint was at least one relapse by 12, 24, or 36 months. Of 122 patients who entered the maintenance phase, 39% who took antibiotics experienced at least one relapse between weeks 16 and 52, compared with 56% who took a placebo (OR = 2.04; p = 0.054). The differences between antibiotics and placebo were not statistically significant. The authors concluded that the study did not support a significant pathogenic role for MAP in most CD patients.
The Graham multicenter MAP US study [5] was the first global randomized trial to assess the efficacy of anti-MAP therapy (RHB-104) for 12 months in active CD patients. The anti-MAP therapy, in addition to standard therapy, demonstrated a clinically meaningful and statistically significant treatment effect in the protocol, in which the primary endpoint was defined as remission (CDAI < 150) at week 26, and the secondary endpoint was early remission at week 16 and durable remission through week 52. The remission rate with or without anti-TNF therapy at 26 weeks was significantly higher than placebo (37% vs. 23%, p = 0.07). At week 16, the remission rate was 42% vs. 29% (p = 0.015).
Agrawal et al. [6], studying a small cohort of pediatric CD patients, concluded that anti-MAP therapy may be more effective than the currently utilized therapies for inducing clinical and endoscopic remission. Although only 47% of patients achieved clinical remission by their first clinical follow-up, 93% of patients achieved remission by the subsequent follow-up appointments after an average of 5 months of treatment (p < 0.001).
Lastly, several case series have also been published concerning long-term antibiotic treatment targeting MAP [7][8]. In the Agrawal case series, CD patients experienced profound remission and required no further treatment for 3–23 years [7]. However, the trials and case series produced conflicting results, and no definitive conclusions could be drawn about the favorable effect of anti-MAP therapy on putative MAP infections in CD patients. Moreover, prophylactic antitubercular therapy was found to accelerate disease progression in patients with CD receiving anti-TNF-α therapy [9].

2. Antibiotic Treatment Targeting Adherent Invasive E. coli  in Patients with Active Crohn’s disease

Most infections due to intracellular bacteria respond poorly to antibiotic treatment [10]. The lack of antibacterial activity is due to inactivation by the low pH of the phagolysosomes in which antimicrobial bacteria live [11]. Like Coxiella burnetii, Tropheryma whipplei, and several other bacteria, AIEC also replicates into macrophage phagolysosomes.
Wiseman et al. [12] first described the effect of pH on the inhibitory activity of chloroquine against E. coli. Recently, hydroxychloroquine (HCQ) was found to enhance antibiotic efficacy and macrophage killing of AIEC due to its alkalizing effect on the pH of phagolysosomes [13]. In a study by Flanagan [14], HCQ showed synergistic effects with doxycycline and ciprofloxacin, which are effective antibiotics against intracellular AIEC. Moreover, both HCQ and vitamin D caused dose-dependent inhibition of intramacrophagic AIEC replication 3 h after infection [14].
Rodhes et al. [15], in a randomized trial investigating the treatment of patients with active CD, evaluated prolonged antibiotic treatment with ciprofloxacin, doxycycline, and HCQ for 4 weeks followed by 20 weeks of doxycycline and HCQ, and compared antibiotics with budesonide treatment. The results, including crossover results, showed remission in 9 out of 24 patients treated with HCQ/antibiotics versus only 1 out of 32 patients treated with budesonide. Overall, the results on the efficacy of antibiotic treatment for AIEC-positive CD patients are still scarce and unimpressive. Further clinical trials will be necessary to assess the efficacy of combinations of antibiotics targeting AIEC.


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  2. Feller, M.; Huwiler, K.; Schoepfer, A.; Shang, A.; Furrer, H.; Egger, M. Long-term antibiotic treatment for Crohn’s disease: Systematic review and me-ta-analysis of placebo-controlled trials. Clin. Infect. Dis. 2010, 50, 473–480.
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