Category Archives: Gastroenterology

How Does Remission in Crohn’s Disease Affect the Abnormal Microbiome/Gut Signature?

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T Braun et al. Gastroenterol 2026; 170: 971-984. Open Access! Perturbations of Diet and Gut Signatures Persist During Remission in Crohn’s Disease Despite Effective Immune Suppression

Methods: The authors analyzed diet, ileal transcriptomics, microbiomics, and metabolomics across patients with CD in remission, patients with active CD, and non–inflammatory bowel disease (IBD) controls as the reference for healthy signals.

Key findings:

  • Immune signals: Ileal transcriptomics revealed a significant decrease in genes and pathways associated with adaptive T cells and innate granulocytes during remission, which was even deeper than observed in non-IBD controls.
  • Antimicrobial gene expression: Patients in remission showed an increase in the expression of epithelial antimicrobial pathways and related genes, including DUOX2, along with an increase in genes associated with goblet cells and mucin glycosylation.
  • Microbiome and diet: In patients in remission, there was persistent pathogenic gut microbial composition, metabolic alterations, and less healthy dietary habits, which were characterized by a higher intake of ultraprocessed foods and lower consumption of fiber, folate, vitamin C, and vegetables
Purple = control (n=64), Yellow = CD remission (n=56), Red = CD active disease (n=24). Fecal signals persist during remission and substantially correlate with dietary exposures. (A) Boxplots of Faith’s phylogenetic alpha diversity, our previously defined health index,23 the previously defined Gevers IBD dysbiosis index21, and our IBD-specific index23 between controls, CD patients in remission, and CD with active disease.

Fecal signals persist during remission and substantially correlate with dietary exposures. (A) Boxplots of Faith’s phylogenetic alpha diversity, our previously defined health index,23 the previously defined Gevers IBD dysbiosis index21, and our IBD-specific index23 between controls, CD patients in remission, and CD with active disease.

My take (borrowed from the authors): This study shows that, during remission with advanced therapies, “disturbances in antibacterial epithelial signals, along with unhealthy dietary patterns, altered microbiome, and perturbed metabolome, continue and are partly linked to the risk of flare 6 months later.”

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NSAIDs and IBD Flares (2026)

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AS Mayer,et al. Arthritis Care Res. https://doi.org/10.1002/acr.80067. Open Access! Safety of Prescription Nonsteroidal Anti-inflammatory Drugs in Adults With Inflammatory Bowel Disease: Data From a Large Administrative Claims Cohort.

Methods:

  • “This retrospective cohort study included patients with IBD aged at least 18 years from Optum’s deidentified Clinformatics Data Mart Database (2000–2022). Patients with a new NSAID prescription fill were matched to those without an NSAID fill during the study period…Propensity score-based inverse probability of treatment-weighted Cox proportional hazards models evaluated the association between NSAID exposure and time to IBD-related hospitalization across IBD subtypes.”

Key findings:

Unweighted Kaplan-Meier curve for IBD-related hospitalization in patients
with Crohn disease (B).
Unweighted Kaplan-Meier curve for IBD-related hospitalization in patients
with ulcerative colitis (C).

Discussion:

  • “The use of IPTW [inverse probability of treatment weighting] to balance an extensive number of confounders associated with NSAID use optimizes the assessment of the association of NSAID exposure with IBD-related hospitalization and helps address recent concern of residual confounding in observational studies of NSAID risk in IBD.”
  • Besides the potential risk of an IBD flare, “NSAID use is associated with risk of hospitalization from several non-IBD–related entities such as acute kidney injury and adverse cardiac events…a large prospective multicenter observational study of more than 18,000 admitted patients in England found that NSAIDs were responsible for 29.6% of admissions related to adverse drug reactions, including gastrointestinal bleeding, stroke, and renal impairment.34“

My take: This study shows an association of increased hospitalization in patients with CD but not UC based on NSAID exposure. The absolute risk of this appears low and could be in fact related to residual confounders (despite use of IPTW) as this was not a prospective study. The risk of NSAIDs outside the GI tract are likely more significant for most patients. Nevertheless, there are limited options for pain management and NSAID benefits have to be weighed against other approaches.

Related blog post: Rethinking the Link between NSAIDs and IBD Flares

AGA Clinical Practice Update:  Clostridioides difficile Infection in Inflammatory Bowel Disease

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S Khanna et al. Gastroenterology, 2026 (In press). Open Access! AGA Clinical Practice Update on Management of Clostridioides difficile Infection in Inflammatory Bowel Disease: Expert Review


Best Practice Advice Statements

  1. In patients with IBD who have new or worsening diarrhea, CDI should be excluded, especially among those with colonic involvement, as they are at increased risk of CDI. Clinicians should consider and treat CDI in patients with end ileostomy or ileo-anal pouch anastomosis with worsening diarrhea.
  2. In patients with IBD and suspected CDI, a multistep toxin-based assay should be used for diagnostic evaluation.
  3. In patients with IBD and recent CDI who have been treated successfully with antibiotics, recurrent diarrhea should prompt retesting for CDI.
  4. In patients with IBD who develop an initial episode of CDI, clinicians should preferentially use fidaxomicin or use vancomycin if fidaxomicin is unavailable or cost-prohibitive. Metronidazole should not be used.
  5. Clinicians should strongly consider hospitalization for patients with IBD and CDI who demonstrate features of severe colitis or systemic toxicity (eg, more than 6 bowel movements per day, severe abdominal pain, marked leukocytosis, hemodynamic instability, or other evidence of sepsis).
  6. When selecting an immunosuppressive therapy to treat IBD, no class or mechanism of action has a differential risk of CDI and, therefore, clinicians should choose the therapy that is best to treat the IBD.
  7. In patients with IBD and acute CDI, concurrent treatment of IBD is critical and clinicians should continue therapy with the required immunosuppressive therapies (ie, immunomodulators, biologics, or small molecules). Steroids can also be used if deemed necessary while CDI is treated with antibiotics.
  8. Clinicians should consider endoscopic evaluation for IBD activity and exclusion of concomitant cytomegalovirus infection if symptoms persist 48–72 hours after initiation of treatment for CDI.
  9. Clinicians may consider loperamide in patients with improving inflammation and infection but ongoing diarrhea.
  10. Clinicians should offer microbiome-based therapies (eg, fecal microbiota, live-jslm, fecal microbiota spores, live-brpk, or unapproved fecal microbiota transplantation) to patients with IBD with at least 1 recurrence of CDI to prevent future infection.
  11. In patients with IBD, clinicians should not advise probiotics for primary or secondary prevention of CDI.
  12. In patients with IBD and a history of CDI who are receiving systemic antibiotics, clinicians may consider oral vancomycin prophylaxis as secondary prevention.

Testing Caveats:

  • “Because NAAT (nucleic acid amplification test) alone can detect colonization, positive EIA (enzyme immunoassay) with NAAT confirms diagnosis. Positive NAAT and negative EIA should be interpreted with caution due to low sensitivity of EIA.”

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Reassuring Study of Infants Exposed to Biologics

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L Palomino et al. Clin Gastroenterol Hepatol 2026; 24: 1688-1701. Open Access! Psychomotor Development in Infants Following Maternal Exposure to Biologics: Results From the DUMBO Registry

Methods: DUMBO (NCT03894228) is an ongoing, prospective, multicenter, observational registry study supported by Grupo Español de Trabajo en Enfermedad de Crohn y Colitis Ulcerosa (GETECCU) which includes women with IBD whose pregnancy was known to the investigator before the 28th week of gestation. Psychomotor development of infants was assessed using the Spanish version of the Ages and Stages Questionnaire 3rd edition (ASQ-3) during the first year of life. 

Key findings:

  • Exposure to biologics in utero, had no impact on ASQ-3 scores at month 12.
  • Multivariate analysis revealed that preterm birth (odds ratio, 0.3; 95% confidence interval, 0.1–0.6) and maternal ulcerative colitis (odds ratio, 0.5; 95% confidence interval, 0.3–0.9) were associated with an increased risk of abnormal ASQ-3. 

Discussion Points:

  • “Active maternal inflammation during the periconception period and pregnancy has been associated with low birth weight, preterm delivery, small size for gestational age, spontaneous abortion, and stillbirths.3,4…Active maternal inflammation during the periconception period and pregnancy has been associated with low birth weight, preterm delivery, small size for gestational age, spontaneous abortion, and stillbirths.3,4“
  • “In infants born to mothers with IBD, exposure to biologics would be expected to reduce their exposure to inflammatory cytokines in utero, which could potentially mitigate the impact of maternal inflammation on psychomotor development… our study found no negative impact of biologics exposure on the psychomotor development of infants, either from exposure in utero or during breastfeeding. Furthermore, we observed higher ASQ-3 scores in the personal-social domain at 4 months and in the gross and fine motor domains at 12 months in biologics-exposed vs nonexposed children, possibly reflecting a beneficial effect of treatment in reducing maternal inflammation.”
  • “Data from the PIANO study further supports our findings. Mahadevan et al assessed psychomotor development in 206 children exposed to biologics (both anti-TNF and non-anti-TNF) in utero, and 92 controls, finding higher ASQ-3 scores in the exposed group.”

My take: Biologic exposure does not appear to impair psychomotor development in infants. While this study provides useful information, I am not impressed wtih with the Acronym DUMBO for this registry.

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Yesterday’s Peachtree Road Race Shirt

“Real-World” Impact of Vitamin D for Patients with Inflammatory Bowel Disease

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JA Sninsky et al. Clin Gastroenterol Hepatol 2026; 24: 1666-1674. Open Access! The Real-World Impact of Vitamin D Supplementation on Inflammatory Bowel Disease Clinical Outcomes

Methods: This was a retrospective cohort study of adult patients (n=5021) with IBD seen in the national Veterans Health Administration system from 2000 to 2023. The researchers used 3 different methods to try to determine causality of improved outcomes with supplementation of Vitamin D.

  1. “Difference-in-differences (DiD) approach to compare changes in clinical outcomes before and after vitamin D testing between patients who did and did not receive supplementation”
  2. “The regression discontinuity design leveraged the clinical threshold of 30 ng/mL serum 25-hydroxyvitamin D, comparing outcomes in patients just lower than and just higher than this cutoff, who are assumed to be otherwise similar”
  3. “The inverse probability weighting method adjusted for confounding by weighting patients based on their likelihood (propensity) of receiving vitamin D15“

Key findings:

  • The median 25-hydroxyvitamin D level was 23 ng/mL, and 41% received vitamin D supplementation
  • Vitamin D supplementation was associated with reduction in IBD-related emergency department visits by 2.17% (34.4% relative risk reduction; P = .007), hospitalizations by 2.64% (53.18% relative risk reduction; P = .003), and corticosteroid prescriptions by 1.29% (25.13% relative risk reduction; P = .066)

Discussion:

  • “Collectively, our data strongly suggest that vitamin D supplementation reduces the risk of IBD flare, underscoring its promise as an effective adjunctive therapy in clinical practice.”
  • “Vitamin D deficiency is prevalent among patients with IBD and is strongly linked to poor clinical outcomes, including higher rates of hospitalization and surgery. Patients with IBD are 64% more likely to be vitamin D deficient compared with healthy control subjects.29“
  • “Vitamin D deficiency is prevalent among patients with IBD and is strongly linked to poor clinical outcomes, including higher rates of hospitalization and surgery. Patients with IBD are 64% more likely to be vitamin D deficient compared with healthy control subjects.29“
  • “Although these findings support a strong association between vitamin D deficiency and worse clinical outcomes, they do not address whether supplementation itself mitigates the risk of adverse events, because disease severity confounds this relationship.33 Our study fills this knowledge gap and provides rigorous real-world data to support the effectiveness of vitamin D supplementation.”

My take: There have been large studies (eg. VITAL) study showing that Vitamin D supplementation does not help most people in the general population. In addition, many individuals with IBD who have low Vitamin D levels may see improvement in Vitamin D status by treating the IBD (without Vitamin D supplement). Yet, studies like this one by Sninsky indicate that Vitamin D supplementation is associated with improved outcomes in this retrospective cohort; the study methods likely indicate a causal effect of supplementation; however, a prospective randomized controlled study would be more definitive.

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Here’s Why CYP2C19 Testing May Be Helpful For Refractory Reflux

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Recent pediatric Rome V recommendations suggested the use of CYP2C19 testing in patients with reflux that was not responding to time-limited therapy (link: Rome V Pediatric Upper Gastrointestinal Disorders of Gut-Brain Interaction (Part 1)). The following retrospective study of adults (n=421) at an academic medical center provides a strong rationale.

L Creech et al. Clin Gastroenterol Hepatol 2026; 24: 1550-1557. Open Access! High Prevalence of CYP2C19 Rapid and Ultrarapid Metabolism Among Patients With Gastroesophageal Reflux Disease

Key finding:

  • 44% (n=184) of patients presenting to gastroenterology clinic with gastroesophageal reflux disease who underwent CYP2C19 genotyping were found to be rapid metabolizers (RMs) (38%) or ultrarapid metabolizers (6%)
  • The prevalence of Barrett’s esophagus/erosive esophagitis was higher among ultrarapid metabolizers (24%; n = 5/21) than among normal metabolizers (7%; n = 12/165; odds ratio, 3.5)
  • Among the 184 RMs, 79% (n = 146) had a change in management due to CYP testing results: 65% (n = 120) changed their medication (89 patients were switched to rabeprazole), 22% (n = 41) continued PPI therapy, and 14% (n = 26) increased their PPI dose

Discussion points:

Prevalence of CYP RMs in Other Studies:

  • “Ionovo et al studied over 2 million patients who underwent genetic testing using 23andMe and found that the rate of RMs (∗1/∗17) in the general population was 26.0%, and the rate of URMs (∗17/∗17) was 4.4%.25“
  • “Fricke-Galindo et al analyzed data from 138 studies of over 52,000 healthy volunteers from around the world.26 The highest rates of combined RMs and URMs were reported in the Middle Eastern populations (36%), followed by European (28.6%), African (16.8%), and Asian populations (3.4%).26 The prevalence was 26.7% in the United States.”
  • “Among GI clinical practice guidelines, the 2025 American Society for Gastrointestinal Endoscopy (ASGE) guideline was the first to suggest routine incorporation of CYP testing into the management of patients with GERD.30“
  • “PCABs offer a viable alternative to PPIs in patients who are RMs and should be considered accordingly. PCABs are also not dependent on preprandial dosing and thus are easier for patients to take. However, the cost of PCABs continues to be a limiting factor.”
  • Testing cost: “A typical out-of-pocket price of $250 to $400 and is covered by some insurance.39“
  • Limitations: The study population has a selection bias compared to the general population. Patients referred to a GI clinic are more likely to have treatment-refractory GERD and thus have higher rates of RMs.

My take: In patients with established GERD who are not responding to treatment, CYP testing may be helpful. This is probably true for patients with EoE as well. In patients with GERD who are RMs, options include changing to rabeprazole, higher doses, or possible use of PCABs.

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Low Risk of Solid Organ Transplantation with Celiac Disease

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JB Doyle et al. Clin Gastroenterol Hepatol 2026; Risk of solid organ transplantation in individuals with celiac disease: a nationwide cohort study

Background: “Celiac Disease (CeD) is associated with immune-mediated diseases of the liver, including autoimmune hepatitis, primary biliary cholangitis, primary sclerosing cholangitis. Individuals with CeD are also at increased risk for non-autoimmune diseases of the liver, including metabolic dysfunction-associated fatty liver disease…CeD has also been associated with chronic kidney disease and cardiovascular disease. Multiple studies have demonstrated that individuals with CeD have increased rates of end-stage renal disease than the general population, with particularly strong associations between CeD and
autoimmune nephropathy, diabetic nephropathy, and systemic lupus erythematosus (19-22).
Population-level data also suggests that individuals with CeD have an increased risk of
cardiovascular disease and ischemic heart disease>”

Methods: Population-based matched cohort study in Sweden. We identified individuals with biopsy-proven CeD diagnosed between 2000-2023 using the nationwide histopathology cohort ESPRESSO. We calculated the incidence of solid organ transplantation (liver, heart, kidney, and lung) in CeD patients and estimated the risk relative to the general population. There were  41,277 individuals with CeD and 196,863 age- and sex-matched comparators with a mean follow-up of 12.1 years.

Key findings:

  • There were 85 solid organ transplantations in patients with CeD (17.0 per 100,000 person-years) and 111 in matched comparators (4.6 per 100,000 person-years). This corresponded to an adjusted hazard ratio (HR) of 2.76 
  • The highest relative risk was for liver transplantation: HR 7.26; for kidney HR 1.85. For heart, HR was 2.35 did not reach statistical significance (CI: CI 0.84-6.61)

Discussion:

“Shared genetic susceptibility may explain physiological links between CeD and autoimmune liver disease, especially since we also detected an increase in liver transplantation prior to CeD diagnosis…owever, CeD patients in our analysis had an increased risk of liver transplantation relative to their nonaffected siblings, suggesting that CeD itself may be a risk factor beyond genetic predisposition”

My take: While nearly triple the incidence compared to the general population, the absolute increased risk of needing a solid organ transplant was about 1 in 10,000. For comparison, the risk of dying in a bicycle accident in one’s lifetime is about 1 in 5,000. Nevertheless, it may be worthwhile to screen for CeD in those with end-organ disease. Additionally, checking liver tests periodically in patients with CeD would be reasonable.

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Vonoprazan-Tetracycline: Effective Dual Rescue Regimen for H Pylori

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W Gao et al. Gastroenterol 2026; 170: 1473-1483. Open Access! Vonoprazan-Tetracycline Dual Regimen as Rescue Therapy for Helicobacter pylori Infection: Randomized Controlled Trial

Methods: In this prospective, open-label, randomized controlled trial(n=350), H pylori–positive adults with at least 1 prior eradication failure were allocated 1:1 to VT dual therapy (vonoprazan [20 mg, twice a day] and tetracycline [500 mg, 3 times a day]), or bismuth quadruple therapy (BQT; lansoprazole [30 mg, twice a day], colloidal bismuth [150 mg, 3 times a day], tetracycline [500 mg, 3 times a day], and metronidazole [400 mg, 3 times a day]) for 14 days.

Key findings:

Discussion:

  • “Potent acid suppression broadens the applicability of dual therapy, allowing a single sensitive antibiotic to achieve reliable eradication when gastric pH is maintained at ≥6 with potassium-competitive acid blockers.13–15“
  • “Antibiotic resistance is a major obstacle to the successful eradication of H pylori, particularly in rescue treatment. Surveillance data from the Asia-Pacific region (1990–2022) have shown persistently high resistance rates to metronidazole (52%), levofloxacin (26%), and clarithromycin (22%), whereas resistance to tetracycline and amoxicillin has remained low, both at ∼4%.17“
  • “Although high-dose amoxicillin dual therapy has been well studied and incorporated into guidelines for first-line treatment, the clinical potential of tetracycline-based regimens deserves similar attention.19,20“

Limitations: This was an open-label trial from a single center and did not include antibiotic resistance testing, which may limit generalizability to other regions or clinical settings.

My take (borrowed from authors): Vonoprazan combined with tetracycline is a simplified, penicillin-free rescue regimen, and may offer a practical option for the rescue treatment of H pylori infection. Its eradication rate was comparable to that of traditional tetracycline-metronidazole–based bismuth quadruple therapy, and was associated with fewer adverse events and better adherence. 

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Comparative Safety of Advanced Therapies for Ulcerative Colitis

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D Ahuja et al. Am J Gastroenterol 2026;121:1192–1201. Comparative Safety of Advanced Therapies in Patients With Ulcerative Colitis: An Administrative Claims-Based Study

Methods: Using an administrative claims database (OptumLabs Data Warehouse) with a ‘real-world’ cohort, the authors identified 9,430 patients with UC treated with TNF antagonists (n = 4,111), anti-integrins (n = 3,165), anti-ILs (n = 1,342), JAK inhibitors (n = 701), or sphingosine-1 phosphate receptor modulators (n = 111), followed over median 27 months.

Key findings:

Overall, the risk of serious infections was higher with infliximab than with the other therapies. The incidence of VTE in patients with UC was very low and comparable across all advanced therapies, including JAK inhibitors. Also, the incidence of MACE in patients with UC was
very low and comparable across all advanced therapies, including anti-ILs and JAK inhibitors.

From the discussion: “In a recent network meta-analysis and corresponding clinical guidelines on the management of moderate-to-severe UC, upadacitinib was ranked as having the highest efficacy for induction ofremission compared with all other agents (2,14). However, safety concerns with JAK inhibitors were raised in the pivotal ORAL Surveillance trial (15). In this noninferiority trial, tofacitinib, particularly at higher doses, was associated with a higher risk of serious and opportunistic infections, VTE, and MACE, compared with TNF antagonistsi n patients with rheumatoid arthritis. Following this, the US Food and Drug Administration changed JAK inhibitors’ labeling across all indications, restricting its use in patients with previous failure or intolerance to TNF antagonists…the ORAL Surveillance trial focused on older patients aged 50 years or older with rheumatoid arthritis and at least one cardiovascular risk factor…

[In this study, the] lack of an apparent increase in the risk of JAK inhibitors compared with other medications may be related to superior disease control achieved with JAK inhibitors or reverse causality where patients at high risk of MACE and/or VTE events are not prescribed JAK inhibitors.”

My take: This study provides additional reassurance that newer advanced therapies have similar or better safety than infliximab.

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Don’t Rush to Judge Risankizumab Effectiveness for Ulcerative Colitis

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R Panaccione et al. Clin Gastroenterol Hepatol 2026; 24: 1424-1433. Open Access! Impact of Extended Risankizumab Treatment in Patients With Ulcerative Colitis Who Did Not Respond to Induction Treatment

Methods:

  1. In the AbbVie-funded phase 3 INSPIRE induction study, 209 initial nonresponders to 12 weeks of 1200 mg intravenous (IV) risankizumab induction were rerandomized to receive 12 weeks of additional 1200 mg risankizumab (weeks 12, 16, and 20) or 180 mg or 360 mg subcutaneous [SC] risankizumab (weeks 12 and 20) in a double-blind fashion
  2. Then, the delayed responders continued to receive blinded risankizumab at their assigned dose in the phase 3 COMMAND maintenance study
  • Clinical response per adapted Mayo Score (AMS): decrease from baseline ≥2 points and ≥30% from baseline, plus a decrease in RBS ≥1 or an absolute RBS ≤1
  • Clinical remission per AMS: SFS ≤1 and not greater than baseline, RBS = 0, and endoscopic subscore ≤1 without the evidence of friability

Key findings:

  • Initial nonresponders (1200 mg IV [n = 68], 180 mg SC [n = 71], or 360 mg SC [n = 70]) had week 24 clinical response rates of 50%, 56.3%, and 57.1%, respectively
  • Patients also achieved clinical remission, histologic endoscopic mucosal improvement (8.8%, 12.7%, and 15.7% for both endpoints), endoscopic improvement (17.6%, 18.3%, and 24.3%), and endoscopic remission (1.5%, 8.5%, and 5.7%)

My take: A longer trial of risankizumab is often needed to know with certainty if it will work for ulcerative colitis. More than half of initial nonresponders acquire a clinical response with extended therapy. A similar pattern was noted for risankizumab with Crohn’s disease.

Related blog post: Over 60% of Initial Nonresponders Improve with Extended Risankizumab Therapy for Crohn’s Disease