Microbiome and metabolome in inflammatory bowel disease.

Inflammatory bowel disease (IBD) is a chronic gastrointestinal disease of unknown etiology, involving complex interactions between the gut microbiome and host immune response. The microbial dysbiosis is well documented in IBD and significantly influences the host metabolic pathways. Thus, a metabolomic fingerprint resulting from the influence of gut dysbiosis in IBD could aid in assessing the disease activity. PubMed, Medline, Science Direct, and Web of Science were searched for studies exploring the association between microbiome and metabolome in IBD patients in the last 5 years. Additionally, references of cited original articles and reviews were further assessed for relevant work. We provide a literature overview of the recent metabolomic studies performed on patients with IBD. The findings report alterations in the metabolite levels of these patients. We also discuss the gut dysbiosis observed in IBD and its influence on host metabolic pathways such as lipids, amino acids, short-chain fatty acids, and others. IBD, being a chronic idiopathic disease, requires routine monitoring. The available non-invasive markers have their limitations. The metabolite changes account for both dysbiosis and its influence on the host's immune response and metabolism. A metabolome approach would thus facilitate the identification of surrogate metabolite markers reflecting the disease activity.

Emerging inflammatory bowel disease demographics, phenotype, and treatment in South Asia, South-East Asia, and Middle East: Preliminary findings from the Inflammatory Bowel Disease-Emerging Nations' Consortium.

BACKGROUND AND AIM: Inflammatory bowel disease (IBD) is emerging in the newly industrialized countries of South Asia, South-East Asia, and the Middle East, yet epidemiological data are scarce. METHODS: We performed a cross-sectional study of IBD demographics, disease phenotype, and treatment across 38 centers in 15 countries of South Asia, South-East Asia, and Middle East. Intergroup comparisons included gross national income (GNI) per capita. RESULTS: Among 10 400 patients, ulcerative colitis (UC) was twice as common as Crohn's disease (CD), with a male predominance (UC 6678, CD 3495, IBD unclassified 227, and 58% male). Peak age of onset was in the third decade, with a low proportion of elderly-onset IBD (5% age > 60). Familial IBD was rare (5%). The extent of UC was predominantly distal (proctitis/left sided 67%), with most being treated with mesalamine (94%), steroids (54%), or immunomodulators (31%). Ileocolic CD (43%) was the commonest, with low rates of perianal disease (8%) and only 6% smokers. Diagnostic delay for CD was common (median 12 months; interquartile range 5-30). Treatment of CD included mesalamine, steroids, and immunomodulators (61%, 51%, and 56%, respectively), but a fifth received empirical antitubercular therapy. Treatment with biologics was uncommon (4% UC and 13% CD), which increased in countries with higher GNI per capita. Surgery rates were 0.1 (UC) and 2 (CD) per 100 patients per year. CONCLUSIONS: The IBD-ENC cohort provides insight into IBD in South-East Asia and the Middle East, but is not yet population based. UC is twice as common as CD, familial disease is uncommon, and rates of surgery are low. Biologic use correlates with per capita GNI.

Optimization of infliximab therapy in inflammatory bowel disease using a dashboard approach-an Indian experience.

PURPOSE: Infliximab (IFX) therapy in inflammatory bowel disease (IBD) is associated with loss of response in half the patients, due to complex pharmacokinetic and immunological factors. Dashboard's Bayesian algorithms use information from model and individual multivariate determinants of IFX concentration and can predict dose and dosing interval. AIM: To compare measured IFX concentrations in our laboratory with values predicted by iDose dashboard system and report its efficacy in managing patients not responding to conventional dosing schedule. METHOD: Clinical history, demographic details, and laboratory findings such as albumin and C-reactive protein (CRP) data of IBD patients (n = 30; median age 23 years (IQR: 14.25 - 33.5)) referred for IFX drug monitoring in our laboratory from November 2017 to November 2019 were entered in iDose software. The IFX concentration predicted by iDose based on this information was compared with that measured in our laboratory. In addition, a prospective dashboard-guided dosing was prescribed in 11 of these 30 patients not responding to conventional dosing and was followed to assess their clinical outcome. RESULT: IFX monitoring in our 30 patients had shown therapeutic concentration in 12, supratherapeutic in 2 and subtherapeutic concentration in 16 patients. The iDose predicted concentration showed concordance in 21 of these 30 patients. Of 11 patients managed with iDose-assisted prospective dosing, 8 achieved clinical remission, 2 showed partial response, and one developed antibodies. CONCLUSION: Retrospective data analysis showed concordance between laboratory measured and iDose-predicted IFX level in 70% of patients. iDose-assisted management achieved clinical remission and cost reduction.

Infliximab-induced tuberculosis in patients with UC: Experience from India-a country with high prevalence of tuberculosis.

BACKGROUND AND AIM: Tuberculosis (TB) is a well-recognized iatrogenic adverse event following administration of biologic therapy given for a variety of clinical indications. There is paucity of data on the development of TB following the use of biologics from countries with a high prevalence of TB. The aim of this study was to determine the risk of development of TB following biological therapy in a country, which is highly endemic for TB. METHODS: The article retrospectively analyse data from three referral inflammatory bowel disease centers to evaluate the risk of development of TB following biological therapy for patients with ulcerative colitis. RESULTS: Of the 79 patients with ulcerative colitis treated with infliximab, seven (8.8%) developed TB at a median interval of 8 weeks after the first exposure despite screening for latent TB. Three of the seven (42%) patients developed disseminated disease, whereas pulmonary disease was documented in four patients (57%). All patients were successfully treated with anti-tuberculous drugs for a period of 6-13 months. In contrast to data from the West, none of the patients in our study had a fatal outcome. None of the patients required a colectomy after a median follow up of 2 years following cessation of the infliximab therapy. CONCLUSIONS: These data suggest that despite the significantly higher prevalence, the outcome of TB after infliximab therapy is quite sanguine in the Indian subcontinent.

Nucleoside diphosphate-linked moiety X-type motif 15 C415T variant as a predictor for thiopurine-induced toxicity in Indian patients.

BACKGROUND AND AIM: Interindividual variation seen in the thiopurine metabolism is attributed to the genetic variant in thiopurine methyltransferase (TPMT) gene leading to myelosuppression. In Asians, the thiopurine-induced toxicity is not completely explained by TPMT variants. Literature indicates that a newer genetic variant in nucleoside diphosphate-linked moiety X-type motif 15 (NUDT15) gene is associated with thiopurine intolerance. We aimed to determine the risk allele frequency of NUDT15 genetic variant and its association with thiopurine-induced toxicity in Indian patients. METHODS: In this pilot study, 69 patients on thiopurine therapy were analyzed. The frequencies of thiopurine-induced leukopenia were recorded. NUDT15 (C415T) and TPMT (*2, *3A, *3B, and *3C) genotyping was performed using amplification refractory mutation system-polymerase chain reaction and restriction fragment length polymorphism technique. Results were validated by DNA sequencing. RESULTS: The NUDT15 CC, CT, and TT genotypes were found to be 86.9%, 11.5%, and 1.5%, respectively, whereas TPMT genetic variants were absent. Of 60 patients without NUDT15 variant, none developed leukopenia, whereas of nine patients with NUDT15 variant, six developed leukopenia (P-value < 0.0001). The mean thiopurine dose of 1.01 and 0.73 mg/kg/day for patients with wild and mutant NUDT15 alleles, respectively, was statistically significant (P < 0.01). The sensitivity and specificity for NUDT15 variant were 100% and 95.2%, respectively. CONCLUSIONS: The NUDT15 risk allele frequency was 7.2%. There are 6/69 (8.7%) patients who developed leukopenia and harbored NUDT15 variant, thus showing a strong association for thiopurine-induced toxicity. Hence, NUDT15 genotyping may be considered before thiopurine therapy in Indian patients.

Rare biliary cystic tumors: a case series of biliary cystadenomas and cystadenocarcinoma.

Cystic lesions of the liver are common and a major proportion is formed by parasitic cysts and simple cysts. Biliary cystic tumors (BCTs), namely biliary cystadenoma (BCA) and biliary cystadenocarcinoma (BCAC), are rare tumors which usually arise from the intrahepatic biliary tree. BCAs have malignant potential and are difficult to differentiate from BCAC pre-operatively on radiological imaging. Here we have presented 4 patients with BCTs and reviewed the literature pertaining to them.The data of four patients with BCA/BCAC diagnosed and treated at our institute were retrieved from our database and records were reviewed for age, sex, history, imaging, surgery, pathology and follow-up. Mean age of the patients was 53.5 years (range 30-71 years). Two male and two female patients presented with abdominal pain, of which one male patient had pancreatitis at diagnosis. Characteristic features were seen on pre-operative imaging (cystic lesions with internal septations) and biliary communication was identified in the patient with pancreatitis. Three patients were diagnosed with a BCA on final histology, while one patient had a BCAC. Following surgical resection, all the patients are asymptomatic and disease free with a mean follow-up of 24 months (range 10-40 months). In conclusion, BCTs should be suspected in the presence of a well-encapsulated, cystic hepatic lesion with internal septations. Although pre-operative distinction between BCA and BCAC is difficult, the lesion, whenever possible, should be completely resected as long-term outcomes are good, especially with BCA.

Single use versus reuse of endoscopy biopsy forceps: A survey of patient preference.

BACKGROUND: Although there are no confirmatory data on this, we suspect that most endoscopy centres in India reuse single-use ('disposable') endoscopic biopsy forceps due to the cost of these forceps and the perceived low risk of infection transmission on reuse. Low-cost single-use biopsy forceps are now available in India, bringing into question the justification for such a practice. We aimed to determine the type of forceps (single-use or reused) patients would prefer during endoscopy for themselves, whether this is dependent on cost, and what cost would be acceptable to them. METHODS: Among patients (conveniently selected from indoor or outdoor) reporting for endoscopy at the division of gastroenterology at a private tertiary-level hospital, we distributed an information sheet about the survey 30-45 minutes before the procedure. After they completed reading the sheet, an endoscopy nurse and/or doctor explained the study. The patient then completed a questionnaire of multiple choices with tick boxes. RESULTS: Of 151 patients approached, 4 declined to participate. Of 147 patients surveyed (age range 16-83 years; 82 men), 127 (86.4%) preferred single-use forceps, 16 (10.9%) preferred reused forceps, and 4 (2.7%) could not decide and left the decision to the physician. When informed that single-use forceps may be available for about ₹1000 (approximately US$ 15), 131 patients (89.1%) preferred these forceps, 11 (7.4%) preferred reused forceps, and 5 (3.4%) could not decide. Forty-four patients (33.1%) stated that an acceptable cost for a forceps for them would be ₹500 (approximately US$ 8), for 65 patients (48.9%) patients it was ₹1000, and for 24 (18.1%) it was ₹1500. CONCLUSION: About 90% of patients in this survey preferred single-use forceps; a cost of ₹1000 for single-use forceps was acceptable to over two-thirds of them.

Evidence for presence of mismatch repair gene expression positive Lynch syndrome cases in India.

Lynch syndrome (LS), the most common form of familial CRC predisposition that causes tumor onset at a young age, is characterized by the presence of microsatellite instability (MSI) in tumors due to germline inactivation of mismatch repair (MMR) system. Two MMR genes namely MLH1 and MSH2 account for majority of LS cases while MSH6 and PMS2 may account for a minor proportion. In order to identify MMR genes causing LS in India, we analyzed MSI and determined expression status of the four MMR genes in forty eight suspected LS patient colorectal tumor samples. Though a majority exhibited MSI, only 58% exhibited loss of MMR expression, a significantly low proportion compared to reports from other populations. PCR-DNA sequencing and MLPA-based mutation and exonic deletion/duplication screening respectively, revealed genetic lesions in samples with and without MMR gene expression. Interestingly, tumor samples with and without MMR expression exhibited significant differences with respect to histological (mucin content) and molecular (instability exhibited by mononucleotide microsatellites) features. The study has revealed for the first time a significant proportion of LS tumors not exhibiting loss of MMR expression.

Therapeutic drug monitoring in inflammatory bowel disease: A practical approach.

The global burden of inflammatory bowel diseases (IBD) is estimated at 4.9 million and the global prevalence exceeds 0.3%. Multiple newer therapeutic agents have broadened the options for the therapy of IBD in the last three decades. Thiopurines, however, have retained their place as maintenance therapy in IBD, especially in resource-constrained setting. But thiopurines have narrow therapeutic range, often needing discontinuation due to side effects or lack of efficacy. Biologic agents revolutionized the treatment of IBD, but the efficacy is lost in 50% of patient after one year. These outcomes are often due to inadequate drug concentrations that may lead to the development of antibodies as well as pharmacodynamic failure. Therapeutic drug monitoring (TDM) was proposed to reduce loss of response and to optimize the therapy in patients on thiopurine and biologic therapy. TDM is based on exposure-response relationship, suggesting a positive correlation between elevated serum anti-TNF concentrations and favorable therapeutic outcomes. TDM has multiple facets. This article discusses the benefits, evidence and limitations of TDM. The practical use of TDM in clinical practice is highlighted. Newer developments in the field and their relevance in practice are discussed.

Renal dysfunction in routine proton-pump inhibitor use may be linked to comorbidities: A real-world observational study.

INTRODUCTION: The use of proton-pump inhibitors (PPI) is linked with infrequent but serious adverse events, including acute kidney injury, chronic kidney disease (CKD) and progression of CKD. Data on renal safety in routine use of PPI are more relevant to clinical practice. We studied whether such use of PPI is associated with renal dysfunction. METHODS: Patients taking PPI for at least six weeks had serum creatinine tested pre (n = 200) and post (n = 180) recruitment. These patients were then advised to follow-up: those taking PPI for at least 90 days in the next six months (n = 77) and at least another 90 days in the following six months (n = 50), had serum creatinine tested at such follow-up. Renal dysfunction was defined as any increase in serum creatinine level above baseline. RESULTS: The 200 patients recruited had mean age 39.6 (SD 9.2) years. Ninety-eight (49%) patients had a history of previous PPI use (median six months; interquartile range [IQR] 3-24). Only 20 (11.1%) patients at six weeks, 11 (14.3%) at six months and six (12%) at one year had increase in creatinine level; a majority of them had less than 0.3 mg/dL increase. Ten of these 20 (six weeks), five of 11 (six months) and five of six (one year) had other risk factors for renal dysfunction. No patient developed CKD during the study period. CONCLUSIONS: Mild and non-progressive increase in serum creatinine occurred in 10% to 15% of patients on routine PPI use. A majority of them had other risk factors. Small sample size and short follow-up duration are a few limitations of this study.

Tofacitinib use in ulcerative colitis: An expert consensus for day-to-day clinical practice.

Rising number of inflammatory bowel disease (IBD) cases in developing countries necessitate clear guidance for clinicians for the appropriate use of advanced therapies. An expert consensus document was generated to guide the usage of tofacitinib, a Janus kinase inhibitor, in ulcerative colitis. Tofacitinib is a useful agent for the induction and maintenance of remission in ulcerative colitis. It can be used in the setting of biological failure or even steroid-dependent and thiopurine refractory disease. Typically, the induction dose is 10 mg BD orally. Usually, clinical response is evident within eight weeks of therapy. In those with clinical response, the dose can be reduced from 10 mg BD to 5 mg BD. Tofacitinib should be avoided or used cautiously in the elderly, patients with cardiovascular co-morbidity, uncontrolled cardiac risk factors, previous thrombotic episodes and those at high risk for venous thrombosis or previous malignancy. Baseline evaluation should include testing for and management of hepatitis B infection and latent tuberculosis. Where feasible, it is prudent to ensure complete adult vaccination, including Herpes zoster, before starting tofacitinib. The use of tofacitinib may be associated with an increased risk of infections such as herpes zoster and tuberculosis reactivation. Maternal exposure to tofacitinib should be avoided during pre-conception, pregnancy, and lactation. There is emerging evidence of tofacitinib in acute severe colitis, although the exact positioning (first-line with steroids or second-line) is uncertain.

Time to incorporate preemptive NUDT15 testing before starting thiopurines in inflammatory bowel disease in Asia and beyond: a review.

INTRODUCTION: Thiopurine toxicity is related to genetic polymorphism. Thiopurine methyltransferase (TPMT) variants do not explain thiopurine toxicity in more than half of patients. Asians, despite the low prevalence of TPMT variants, are more susceptible to thiopurine toxicity. Since 2014, studies from many Asian countries have shown a strong association between nucleoside diphosphate-linked moiety X-type motif (NUDT) 15 polymorphism and thiopurine-induced myelotoxicity. AREAS COVERED: An English language literature search was performed for TPMT and NUDT15 genetic variants in inflammatory bowel disease and other diseases. This article discusses the merits of preemptive NUDT15 and TPMT testing in Asian and non-Asian IBD populations. EXPERT OPINION: The NUDT polymorphism occurs in up to 27% of the Asian and Hispanic population. Hematological toxicity occurs in up to one-third of patients with this genetic variant. Given this, preemptive testing for NUDT15 variant is worthwhile and is probably more cost-effective than TPMT testing in these groups. Prevalence of NUDT15 variants is low in non-Finnish European population, but NUDT15 variants have been linked to myelotoxicity along with TPMT genetic variants. NUDT15 preemptive testing should be considered in the migrant Asian population in Europe and North America and in Caucasian populations who develop myelotoxicity.

The treatment of patients with inflammatory bowel diseases (ulcerative colitis andCrohn's disease) is based on the severity of the disease. They may need drugs called 'thiopurines' if the disease is not controlled by initial therapy. These drugs have side effects which are related to genetic variations. These side effects can be potentially prevented by testing for these genetic variants prior to starting these drugs. These tests include thiopurine methyltransferase (TPMT) genotype testing and nucleoside diphosphate-linked moiety X-typemotif (NUDT) 15 genotype testing. By doing these tests before starting the drugs, the dose can be modified to prevent side effects on the bone marrow and other tissues.

Personalized Dosing of Infliximab in Patients With Inflammatory Bowel Disease Using a Bayesian Approach: A Next Step in Therapeutic Drug Monitoring.

Although biological agents have revolutionized the management of inflammatory bowel diseases (IBDs), a significant proportion of patients show primary non-response or develop secondary loss of response. Therapeutic drug monitoring (TDM) is advocated to maintain the efficacy of biologic agents. Reactive TDM can rationalize the management of primary non-response and secondary loss of response and has shown to be more cost-effective compared with empiric dose escalation. Proactive TDM is shown to increase clinical remission and the durability of the response to a biologic agent. However, the efficacy of proactive and reactive TDM has been questioned in recent studies and meta-analyses. Hence, we need a different approach to TDM, which addresses inflammatory burden, the individual patient, and disease factors. Bayesian approaches, which use population pharmacokinetic models, enable clinicians to make better use of TDM for dose adjustment. With rapid improvement in computer technology, these Bayesian model-based software packages are now available for clinical use. Bayesian dashboard systems allow clinicians to apply model-based dosing to understand an individual's pharmacokinetics and achieve a target serum drug concentration. The model is updated using previously measured drug concentrations and relevant patient factors, such as body weight, C-reactive protein, and serum albumin concentration, to maintain effective drug concentrations in the serum. Initial studies have found utility for the Bayesian approach in induction and maintenance, in adult and pediatric patients, in clinical trials, and in real-life situations for patients with IBD treated with infliximab. This needs confirmation in larger studies. This article reviews the Bayesian approach to therapeutic drug monitoring in IBD.

A prospective study of inflammatory bowel disease phenotypes in extremes of age and comparison with adults.

BACKGROUND AND AIMS: Pediatric and elderly inflammatory bowel disease (IBD) are less explored, often in retrospective studies. The pediatric group has a more extensive and aggressive disease phenotype requiring aggressive treatments, whereas the elderly group may have less aggressive diseases. METHODS: We prospectively compared disease characteristics of a single center cohort of IBD patients (pediatric age ≤ 16 years; adults 17 to 59 years; and elderly ≥ 60 years) seen between September 2018 and November 2019 with at least six months of follow-up. RESULTS: Total 266 IBD patients (137 males) included 47 pediatric, 175 adults and 44 elderly patients. Among ulcerative colitis (UC) patients, pancolitis was more common in the pediatric group (p = 0.018), while the elderly group had more indolent behaviors and infrequent extraintestinal manifestations (p = 0.005). Among patients with Crohn's disease (CD), the pediatric group had more often colonic diseases (p = 0.02) and the elderly, ileal diseases (p = 0.04). The disease behavior was similar in the three age groups. Perianal disease was least common in elderly CD patients (p = 0.03). There was no treatment difference among different age groups in UC. In CD, pediatric patients needed biologics more frequently (p = 0.005), while elderly CD patients less frequently required steroids, biologics, immunosuppressants and surgery (p < 0.05). CONCLUSIONS: We noted differences compared to western literature such as colonic location in pediatric CD and ileal location in elderly CD. Perianal disease was less frequent in the elderly CD group. There was no difference in treatment in the three age groups in UC, while there were no inter-age-group disease behavioral differences for UC and CD.

Self-reported food intolerances in an Indian population: Need for individualization rather than a universal low-FODMAP diet.

Background and Aim: Low-fermentable oligo-, di-, and monosaccharides and polyol (FODMAP) diets have been recommended for individuals with food intolerance and irritable bowel syndrome (IBS). Individual food intolerances may, however, not correspond to the FODMAP content alone. Methods: We conducted a survey on self-reported intolerance to articles of food commonly identified as high FODMAP in 400 healthy Indian subjects (median age 40 years; 69% men) and 204 consecutive consenting patients with IBS (median age 36 years; 58% men). Results: One-hundred seventy-nine (44.8%) healthy subjects and 147 (72.1%) patients with IBS reported some food intolerance (P < 0.00001); the latter reported intolerance to all items (except nuts) more frequently than healthy subjects. The prevalence, however, varied from 2.5 to 32%. Milk intolerance was reported equally commonly by healthy subjects and patients (23% vs 29.9%). Twenty-three (11.3%) patients and no healthy subjects reported wheat sensitivity. The IBS diarrhea subgroup reported intolerance to milk, pulses, capsicum, cauliflower, leafy vegetables, and dry fruits more frequently than the constipation subgroup. Conclusion: From among a list of high-FODMAP items, individuals' intolerance varied widely, suggesting that individuals should be the final judge in deciding their elimination diets rather than devise them based on the FODMAP content alone. As in the West, food intolerance was reported more commonly by patients with IBS, especially those with diarrhea, than by healthy individuals. Also noteworthy is the low prevalence of milk intolerance in a subcontinent labeled as high in lactose intolerance. Unlike in the West, wheat intolerance was not reported by any healthy individual.

Low prevalence of primary sclerosing cholangitis in patients with inflammatory bowel disease in India.

BACKGROUND/AIMS: Primary sclerosing cholangitis (PSC) represents the most common hepatobiliary extraintestinal manifestation of inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD). Limited data exist on PSC in patients with IBD from India. We aimed to assess the prevalence and disease spectrum of PSC in Indian patients with IBD. METHODS: Database of IBD patients at 5 tertiary care IBD centers in India were analyzed retrospectively. Data were extracted and the prevalence of PSC-IBD was calculated. RESULTS: Forty-eight patients out of 12,216 patients with IBD (9,231 UC, 2,939 CD, and 46 IBD unclassified) were identified to have PSC, resulting in a prevalence of 0.39%. The UC to CD ratio was 7:1. Male sex and pancolitis (UC) or colonic CD were more commonly associated with PSC-IBD. The diagnosis of IBD preceded the diagnosis of PSC in most of the patients. Majority of the patients were symptomatic for liver disease at diagnosis. Eight patients (16.66%) developed cirrhosis, 5 patients (10.41%), all UC, developed malignancies (3 colorectal cancer [6.25%] and 2 cholangiocarcinoma [4.16%]), and 3 patients died (2 decompensated liver disease [4.16%] and 1 cholangiocarcinoma [2.08%]) on follow-up. None of the patients mandated surgical therapy for IBD. CONCLUSIONS: Concomitant PSC in patients with IBD is uncommon in India and is associated with lower rates of development of malignancies.