Profile of Helicobacter pylori cagA &vacA genotypes and its association with the spectrum of gastroduodenal disease.

PURPOSE: Globally, H. pylori virulence factors cagA and vacA genotypes and its variation is leading to the austere form of the gastroduodenal disease. Our objectives were to detect H. pylori in dyspeptic patients from biopsy samples with the validation of the various existing diagnostic tools and to screen the cagA, vacA genotypes profile from biopsy specimens and how it impacts in progression of gastroduodenal disease in southern India. METHODS: 374 patients who attended endoscopy unit at Kasturba Hospital, Manipal with their consent obtained their biopsies. H. pylori were detected by HPE, Culture, RUT and PCR and its virulence gene were patterned with PCR. RESULTS: The positive rate of H. pylori by HPE, RUT, Culture and PCR were 51.33%, 47.1%, 32.4% and 50.3% respectively and comparison by Bayesian LCMs analysis showed PCR is superior among them. The frequency of H. pylori virulence gene viz cagPAI (cagA) were 80.9%, and vacA alleles-s1m1 (42%), s1m2 (33%) and s2m2 (25%) genotypes by PCR respectively. Four combinations of cagA/vacA genotypes were noted, majority of strains harboured cagA+/vacA s1m1 genotypes (42.6%), interestingly this hyper-virulent strain more frequently seen in severe gastroduodenal disease whereas cagPAI negative strains as well as cagA-/vacA s2m2 combinations (19.1%) are seen most commonly in functional dyspepsia cases and depicted significant association by Chi-square test. CONCLUSIONS: This study validates and compares the existing diagnostic methods for detecting H. pylori in biopsies. Also, it reveals some pattern of virulence gene combination will play a vital role in disease progression.

Prevalence of low bone mineral density in inflammatory bowel disease and factors associated with it.

BACKGROUND: Patients with inflammatory bowel disease (IBD) have numerous risk factors for low bone mineral density (BMD). We aimed to study the prevalence of low BMD in IBD and the factors associated with it. METHODS: BMD was measured by radial quantitative ultrasound, and clinical and biochemical characteristics were compared in prospectively enrolled patients and healthy age and gender-matched controls. Chi-square test, t test for independent samples, analysis of variance (ANOVA), Mann-Whitney U test and Kruskal-Wallis H tests were used as appropriate for univariate analysis to compare the characteristics between patients with and without abnormal BMD. Binary logistic regression analysis was done to determine the factors associated with low BMD in IBD patients. RESULTS: One hundred and six patients (Crohn's disease [CD] = 35, ulcerative colitis [UC] = 71) and 55 controls were included. Low BMD was equally prevalent in CD, UC and controls (42.9%, 36.6%, 36.4% respectively, p = 0.791). Serum calcium and vitamin D were significantly lower in IBD patients compared to controls (p < 0.001 and p = 0.003, respectively) but not between patients with low and normal BMD. Older age (Odds ratio [OR] = 66.12 [9.299-470.243], p < 0.001), late onset of disease (OR = 4.795 [1.067-21.543], p = 0.041) and absence of steroid usage (OR = 0.272 [0.089-0.832], p = 0.022) were significantly associated with low BMD. CONCLUSIONS: The prevalence of low BMD in patients with IBD was similar to controls and this was associated with increasing age, late onset of disease, and absence of steroid usage. Judicious use of steroids can help preserve bone health in IBD.

High primary resistance to metronidazole and levofloxacin, and a moderate resistance to clarithromycin in Helicobacter pylori isolated from Karnataka patients.

BACKGROUND: Due to increased prevalence of H. pylori antimicrobial resistance worldwide and more importantly the resistance patterns vary between different geographical regions, it is important to survey local H. pylori antibiotic resistance profile to provide physicians with more informed drug choices to better treat H. pylori infection. To our knowledge, this is the first study to examine the prevalence of antimicrobial resistance of H. pylori in Karnataka state of South India. RESULTS: A total of 113 H. pylori strains were isolated from gastric biopsies and tested: 81.4% were resistant to metronidazole, 54.9% were resistant to levofloxacin, 20.4% were resistant to clarithromycin, 5.3% were resistant to tetracycline and 7.1% were resistant to amoxicillin. Multidrug resistance was detected in 59.3% of total isolated strains, among which 86.6% were resistant to at least both metronidazole and levofloxacin. In this study, 38 out of 113 H. pylori strains had been whole-genome sequenced. Based on the draft genomes, RdxA and/or FrxA inactivation mutations were found to present in 75% of metronidazole-resistant strains. Clarithromycin-resistant strains had mainly A2143G and G2224A mutations in the 23 rRNA gene. While 87.1% levofloxacin-resistant strains had amino acid substitution mutations occurring predominantly at N87 and D91 in GyrA, novel mutations in the same protein including an insertion of five amino acid residues (QDNSV), immediately after the start codon, and a substitution mutation at R295 were identified. CONCLUSION: High primary resistance to metronidazole and levofloxacin, and a modest occurrence of clarithromycin resistance were revealed in H. pylori strains isolated from Karnataka patients. Therefore metronidazole-, levofloxacin- and clarithromycin-based triple therapies are not suitable as first-line treatment in Karnataka. Both amoxicillin and tetracycline can still be used to eradicate H. pylori infection in this region. We also revealed novel mutations in GyrA protein that possibly contribute to H. pylori resistance in levofloxacin, which merit further investigations.

Helicobacter pylori in Dyspepsia: Phenotypic and Genotypic Methods of Diagnosis.

BACKGROUND: Helicobacter pylori affects almost half of the world's population and therefore is one of the most frequent and persistent bacterial infections worldwide. H. pylori is associated with chronic gastritis, ulcer disease (gastric and duodenal), mucosa-associated lymphoid tissue lymphoma, and gastric cancer. Several diagnostic methods exist to detect infection and the option of one method or another depends on various genes, such as availability, advantages and disadvantages of each method, monetary value, and the age of patients. MATERIALS AND METHODS: Patients with complaints of abdominal pain, discomfort, acidity, and loss of appetite were chosen for endoscopy, detailed history was contained, and a physical examination was conducted before endoscopy. Biopsies (antrum + body) were received from each patient and subjected to rapid urease test (RUT), histopathological examination (HPE), polymerase chain reaction (PCR), and culture. RESULTS: Of the total 223 biopsy specimens obtained from dyspeptic patients, 122 (54.7%) were positive for H. pylori for HPE, 109 (48.9%) by RUT, 65 (29.1%) by culture, and 117 (52.5%) by PCR. The specificity and sensitivity were as follows: RUT (99% and 88.5%), phosphoglucosamine mutase PCR assay (100% and 95.9%), and culture (100% and 53.3%), respectively. CONCLUSION: In this study, we compared the various diagnostic methods used to identify H. pylori infection indicating that, in comparison with histology as gold standard for detection of H. pylori infection, culture and PCR showed 100% specificity whereas RUT and PCR showed 99% and 100% sensitivity, respectively.

Intraindividual somatic variations in MTHFR gene polymorphisms in relation to colon cancer.

AIM: MTHFR mediates the one carbon metabolism pathway. Two common genetic variants, C677T and A1298C, of MTHFR are associated with number of human diseases, including cancer, as well as being involved in the modulation of therapy outcome to antifolate drugs. To understand the distribution pattern of SNPs among different tissues of an individual, we examined MTHFR polymorphisms in normal and colon cancer tissues and compared the genotype frequencies in peripheral blood samples. MATERIALS & METHODS: DNA was isolated from tumor tissue and matched normal tissues from 155 colon cancer patients. These samples as well as DNA from blood samples of the control group (n = 294) were analyzed for MTHFR polymorphisms by PCR-RFLP and confirmed by a direct DNA sequencing method. RESULTS: Our data suggest that the allele and genotype frequencies of C677T and A1298C were significantly different between tumor tissues and both types of normal tissues. We have established that MTHFR variants that exist in tumor and matched normal tissues of colon cancer patients differ suggesting somatic variation in MTHFR polymorphisms among different tissues of an individual. The MTHFR A1298C polymorphism was associated with risk of colon cancer. CONCLUSION: Different MTHFR variants may exist in different tissues to maintain physiological functions and may have implications for disease susceptibility and pharmacogenomics based therapies. Original submitted 21 January 2013; Revision submitted 3 January 2014.

Synchronous colorectal neoplasms in ulcerative pancolitis of 6 years duration: pathological and molecular heterogeneity.

Colorectal cancer (CRC) complicating ulcerative colitis (UC) accounts for about 1% of all cases of CRC. Such tumours develop from pre-existing foci of dysplasia in patients with extensive and long-standing UC. We report a case of UC-associated synchronous CRC and foci of high-grade dysplasia with an additional malignant focus in the appendix in a female patient after only 6 years of pancolitis who did not have other risk factors for the development of complications. The multiplicity and the timings of the early changes noted suggest that long-standing inflammation in UC randomly damages multiple genes in epithelial cells known to contribute to colorectal carcinogenesis. Current findings also support a molecular and pathological heterogeneity during multiclonal origin of synchronous tumours whereby differences occur at various sites that were absent during the initial stages of the disease.