Philip Abraham

An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples

To explore the natural microbial community of any ecosystems by high-resolution molecular approaches including next generation sequencing, it is extremely important to develop a sensitive and reproducible DNA extraction method that facilitate isolation of microbial DNA of sufficient purity and quantity from culturable and uncultured microbial species living in that environment. Proper lysis of heterogeneous community microbial cells without damaging their genomes is a major challenge. In this study, we have developed an improved method for extraction of community DNA from different environmental and human origin samples. We introduced a combination of physical, chemical and mechanical lysis methods for proper lysis of microbial inhabitants. The community microbial DNA was precipitated by using salt and organic solvent. Both the quality and quantity of isolated DNA was compared with the existing methodologies and the supremacy of our method was confirmed. Maximum recovery of genomic DNA in the absence of substantial amount of impurities made the method convenient for nucleic acid extraction. The nucleic acids obtained using this method are suitable for different downstream applications. This improved method has been named as the THSTI method to depict the Institute where the method was developed.

Primary Care Management of Chronic Constipation in Asia: The ANMA Chronic Constipation Tool

Chronic constipation (CC) may impact on quality of life. There is substantial patient dissatisfaction; possible reasons are failure to recognize underlying constipation, inappropriate dietary advice and inadequate treatment. The aim of these practical guidelines intended for primary care physicians, and which are based on Asian perspectives, is to provide an approach to CC that is relevant to the existing health-care infrastructure. Physicians should not rely on infrequent bowel movements to diagnose CC as many patients have one or more bowel movement a day. More commonly, patients present with hard stool, straining, incomplete feeling, bloating and other dyspeptic symptoms. Physicians should consider CC in these situations and when patients are found to use laxative containing supplements. In the absence of alarm features physicians may start with a 2-4 week therapeutic trial of available pharmacological agents including osmotic, stimulant and enterokinetic agents. Where safe to do so, physicians should consider regular (as opposed to on demand dosing), combination treatment and continuous treatment for at least 4 weeks. If patients do not achieve satisfactory response, they should be referred to tertiary centers for physiological evaluation of colonic transit and pelvic floor function. Surgical referral is a last resort, which should be considered only after a thorough physiological and psychological evaluation.

Gut microbiome, gut function, and probiotics: Implications for health

New insights from a rapidly developing field of research have ushered in a new era of understanding of the complexity of host-microbe interactions within the human body. The paradigm shift from culturing to metagenomics has provided an insight into the complex diversity of the microbial species that we harbor, revealing the fact that we are in fact more microbes than human cells. The largest consortium of these microbes resides in the gut and is called the gut microbiota. This new science has expanded the ability to document shifts in microbial populations to an unparalleled degree. It is now understood that signals from the microbiota provide trophic, nutritional, metabolic, and protective effects for the development and maintenance of the host digestive, immune, and neuroendocrine system. Evidence linking changes in the gut microbiota to gastrointestinal and extraintestinal disorders like irritable bowel syndrome, inflammatory bowel disease, obesity, diabetes, and celiac disease have begun to emerge recently. Probiotics act through diverse mechanisms positively affecting the composition and/or function of the commensal microbiota and alter host immunological responses. Well-controlled intervention trials, systematic reviews, and meta-analysis provide convincing evidence for the benefit of probiotics in prevention and treatment of gastrointestinal as well as extraintestinal disorders.

Acute renal tubular injury with acute hepatitis A infection: Is it just a coincidence?

SUMMARY:  Acute renal failure has rarely been reported in association with acute hepatitis A infection. The commonest form of renal injury in such patients has been found to be acute tubular necrosis. We report two cases of hepatitis A infection in which acute renal failure occurred very early in the course of the illness and had a clinical presentation and recovery pattern suggestive of acute tubular necrosis. In both patients, the clinical course of renal dysfunction was almost parallel to the course of hepatic dysfunction. Patient 1 needed dialysis, whereas patient 2 did not need dialysis and had a very rapid recovery from renal function in spite of having more severe azotaemia. Patient 2 was administered acetylcysteine in high doses for suspected fulminant hepatic failure. A potential benefit of a high dose of acetylcysteine in recovery of renal function from acute tubular necrosis is postulated.

Gastric bacterial Flora in patients Harbouring Helicobacter pylori with or without chronic dyspepsia: analysis with matrix-assisted laser desorption ionization time-of-flight mass spectroscopy

BackgroundThe gastric microbiota has recently been implicated in the causation of organic/structural gastroduodenal diseases (gastric and duodenal ulcers, gastric cancer) in patients with Helicobacter pylori (H. pylori) infection. We aimed to ascertain, in patients harbouring H. pylori, the role of the gastric microbiota in the causation of symptoms (chronic dyspepsia) in the absence of organic disease.MethodsSeventy-four gastric biopsy samples obtained at endoscopy from patients with (n = 21) or without (n = 53) chronic dyspepsia, and that tested positive by the bedside rapid urease test for H. pylori infection, were cultured for detection of H. pylori and non-H. pylori organisms. The cultured organisms were identified by matrix-assisted laser desorption ionization time-of-flight mass spectroscopy (MALDI-TOF MS).ResultsA total of 106 non-H. pylori isolates were obtained from 74 patients’ samples. This included 33 isolates (median 2, range 1–2 per patient) from dyspeptic and 73 (median 2, range 1–2 per patient) from non-dyspeptic patients. These were identified from the Bruker Biotyper 2 database as Staphylococcus spp., Streptococcus spp., Lactobacillus spp., Micrococcus spp., Enterococcus spp., Pseudomonas spp., Escherichia spp., Klebsiella spp. and Bacillus spp., Staphylococcus and Lactobacillus were identified significantly more commonly in dyspeptics and Streptococcus, Pseudomonas, Escherichia coli and Klebsiella pneumoniae in non-dyspeptics. All identified organisms belonged to the phyla Firmicutes and Proteobacteria.ConclusionsThere is a qualitative difference in the gastric microbial spectrum between patients harbouring H. pylori with and without chronic dyspepsia. Whether these organisms have an independent role in the development or prevention of dyspepsia or act in concurrence with H. pylori needs study.

Comparison of Mycobacterium tuberculosis culture using liquid culture medium and Lowenstein Jensen medium in abdominal tuberculosis

BackgroundTraditionally, the Lowenstein Jensen (LJ) medium has been used for culturing Mycobacterium tuberculosis. In abdominal tuberculosis (TB), the reported yield from tissue culture is between 20% and 60%. Liquid cultures are reported to give a higher yield but there is little data available in abdominal TB.AimTo compare the yield of TB culture with BACTEC 460TB liquid medium and LJ medium for patients with suspected abdominal TB and determine cost effectiveness.MethodsThis prospective study was done in consecutive cases with clinical, radiological, endoscopic/surgical, and histological suspicion of abdominal TB. Tissue biopsies obtained at colonoscopy or surgery were processed and plated on LJ medium as well as the BACTEC 460TB system. NAP (ρ-nitro-α-acetylamino-β-hydroxy-propiophenone) differentiation was carried out to determine species. The cost of each method and cost per yield were calculated.ResultsOf the 29 cases, 22 cases (76%) were positive on BACTEC 460TB culture while 14 (48%) were positive on LJ medium giving a 64% increment in yield. However, the culture of one patient grew on LJ medium, where the BACTEC 460TB was negative. The additional cost of BACTEC 460TB is Rs. 460 and LJ is Rs. 40.ConclusionsSamples from patients with abdominal TB should be processed on both liquid and LJ medium. For high yield, the use of a liquid culture medium system is essential.

Rate of recurrence in Indian patients presenting with acute pancreatitis and identification of chronicity on follow up: Possible risk factors for progression

BackgroundTo study the profile and long-term outcome of Indian patients presenting with acute pancreatitis and the possible risk factors for progression.MethodsConsecutive patients with acute or recurrent acute pancreatitis seen in our department during July 2013 to December 2014 were included. Details of past episodes were collected and patients were followed up till March 2015.ResultsIn the 97 patients included (mean age 47.2 [SD 16.9] years; 74 men), gallstones (37 [38.1%]) and alcohol (19 [19.6%]) were the major identified etiologies; the idiopathic (31 [32%]) group constituted a third of patients. Recurrences were more common with idiopathic etiology (14 patients out of 30 had recurrences [46.7%]) as compared to alcoholic (5 out of 19 [26.3%]) and biliary (4 out of 37 [10.8%]) pancreatitis and with mild index episode. Following the episode of acute pancreatitis, identification of chronic pancreatitis was more common with alcoholic (6 out of 18 [33%]) and idiopathic (9 out of 30 [30%]) etiology as compared to other etiologies. Longer duration of follow up, but not number of recurrent episodes, was associated with identification of chronicity in patients presenting as acute pancreatitis.ConclusionsOut of 97 patients with acute pancreatitis, 27 (27.8%) developed recurrences with risk factors being idiopathic etiology and mild index episode. Eighteen of 97 (18.6%) patients had evidence of chronic pancreatitis on follow up, risk factors being the alcoholic and idiopathic varieties, and longer duration of follow up.

Response to Treatment of Helicobacter pylori-associated Dyspepsia: Eradication of Helicobacter pylori or Correction of Gastric or Intestinal Dysbiosis?

c 2018 The Korean Society of Neurogastroenterology and Motility J Neurogastroenterol Motil, Vol. 24 No. 3 July, 2018 www.jnmjournal.org TO THE EDITOR: We have a special interest in the findings reported by Kim et al. that the symptom response following treatment for Helicobacter pylori in functional dyspepsia (FD) depends on the type of antibiotic used (metronidazole better than clarithromycin), the duration of therapy (10-14 days better than 7 days), and the presence or absence of concomitant irritable bowel syndrome (IBS). The authors speculate that the symptom relief could also be due to correction of accompanying intestinal dysbiosis. Some years ago, we showed that patients with non-ulcer dyspepsia (now termed FD) had altered colonic motility, irrespective of the subtype (ulcer type––now termed epigastric pain syndrome, or dysmotility type––now termed postprandial distress syndrome). We suggested that the dysmotility in these patients is a diffuse phenomenon although the presenting symptom may be localized. Recent literature accepts that there is an overlap between FD and IBS. We had also reported then that short courses of metronidazole give symptom relief in IBS. Thus, the authors’ observation that patients with FD respond better to anti-H. pylori treatment regimens incorporating metronidazole and in the presence of IBS, is not surprising. We recently reported that the gastric microbiota in patients infected with H. pylori differs between those with and without FD, and the intricate networking between H. pylori and the concomitant gastric microbiota. There has been speculation that the relief of symptoms after H. pylori treatment could also be due to eradication of coexisting bacteria in the stomach. The issue is thus more complex than it seems. In FD, does metronidazole provide relief by affecting H. pylori, the concomitant gastric microbiota, or the intestinal microbiota? Since intestinal microbiota may have a role in IBS pathogenesis, is relief of FD symptoms partially affected by relief of IBS symptoms, the two conditions known to overlap?

Drug resistance in intestinal tuberculosis: A reason to worry?: Drug resistance in intestinal tuberculosis

Emergence of drug resistance in intestinal tuberculosis (ITB) makes the treatment of this condition challenging. While there is growing evidence of multiple and extensive drug resistance in pulmonary and glandular tuberculosis (TB), literature regarding susceptibility and resistance patterns in ITB is scarce. The aim of the current paper was to study the prevalence of drug resistance in patients with ITB.

Imaging of the small intestine in Crohn’s disease: Joint position statement of the Indian Society of Gastroenterology and Indian Radiological and Imaging Association

The Indian Society of Gastroenterology (ISG) Task Force on Inflammatory Bowel Disease and the Indian Radiological and Imaging Association (IRIA) developed combined ISG-IRIA evidence-based best-practice guidelines for imaging of the small intestine in patients with suspected or known Crohn’s disease. These 29 position statements, developed through a modified Delphi process, are intended to serve as reference for teaching, clinical practice, and research.