Gut microbiome has been analysed using metagenomics approach which combines the power of genomics, bioinformatics, and systems biology, providing new ways to access the microbial world. Gut microbiome evolves from the pre-birth exposure onwards in a child, as a result of its interaction with its environment; and is apparently influenced by various environmental factors all through the life, most important being diet and its composition. Metagenomic analysis of gut microbial communities of a malnourished and a healthy child revealed an abundance of enteric pathogens leading to intestinal inflammation and nutrient malabsorption. The change in diet from vegetarian to non-vegetarian also influences the composition and dynamics of the intestinal microbes. Gut microbiota have been observed to vary with age due to physiological changes in the gastrointestinal tract, modifications in lifestyle, nutritional behavior and weakened functionality of the host immune system. Studies in apparently healthy individuals and patients suffering from intestinal or metabolic disorders revealed differential microbiome compositions, proving that an imbalance of gut microflora leads to dysbiosis which is the major cause of metabolic disorders such as irritable bowel syndrome (IBS), obesity, diarrhea, etc. The investigational studies are trying to assess the relationship between intestinal microbiota dysbiosis and various metabolic diseases. Nutritional interventions in the form of probiotics and prebiotics as investigational new drugs (INDs) are being assessed for correcting dysbiosis in disease states. The current paper focuses on the recent knowledge and databases for the same with pointers to future investigations as the need of the hour studies.

Guillain Barreé syndrome (GBS) is a serious disorder of the peripheral nerves preceded by a recognized acute infectious illness. Campylobacter jejuni has been recognized as an important pathogen precipitating GBS and the structure of C. jejuni lipooligosaccharide (LOS) might have a role in the outcome of infection. The development of GBS and Miller Fisher syndrome has been reported to be due to expression of a GM1 like LOS in class A strains and GQ1b like LOS in class B strains of C. jejuni respectively. Virulence of C. jejuni, subtle differences in the interaction between different strains with the host T lymphocyte receptor and MHC class II and host susceptibility may have a role to play in the development of GBS. A humoral immunopathogenic mechanism for GBS has been envisaged as the disease develops 1 to 3 weeks after C. jejuni infection. Antibodies to C. jejuni may remain elevated for several weeks after acute infection. Host susceptibility factors are also important in the pathogenesis of GBS as this disease occurs within families. Association between the occurrence of GBS and a particular HLA type has been envisaged, but studies to prove it are inconclusive. Despite our increasing understanding of the pathophysiology of GBS, the triggering event leading to the disease is still indeed a great puzzle. This review describes the in-depth association of Campylobacter infections with GBS.

Background and objectives: Bacterial infection of biliary tract may cause severe inflammatory response or sepsis. An immediate bile culture and appropriate antibiotic administration are important to control the biliary tract infection. The objective of the study was to study the microbial profile and antibiotic sensitivity pattern in patients with biliary tract infection. Materials and methods: Fifty suspected cases of biliary tract infection admitted to the Department of Gastroenterology were enrolled. Bile samples from these patients were aseptically collected and sent to the Department of Microbiology. Samples were processed in automated BACTEC or BacT/ALERT system. Further identification and antimicrobial susceptibility testing was done by VITEK-2 system. Results: Of the 50 suspected cases of biliary tract infection, the majority were male patients and in the age group of 51-60 years. Growth was obtained in 22 (44%) bile samples. The organisms obtained were Escherichia coli (40%), Klebsiella spp. (20%), Pseudomonas spp. (16%), and coagulase-negative Staphylococci (8%). All Gram negative isolates were susceptible to tigecycline and colistin. A high susceptibility was seen to amikacin and carbapenems while low susceptibility was seen to others. All the Gram positive organisms were sensitive to vancomycin, teicoplanin and linezolid with low sensitivity to penicillin. Interpretation and conclusion: E. coli is the most common organism isolated from bile. Antimicrobial sensitivity patterns require a revision of empiric antibiotic therapy policy in cholangitis. Early detection and determination of antimicrobial susceptibility pattern is important to reduce the mortality and morbidity associated with bile fluid infections.

Background and Objectives: Chronic hepatitis C (CHC) is a major cause of liver-related morbidity and mortality. Data on the treatment outcomes of CHC with pegylated interferon plus ribavirin (PEG-RBV) in Indian patients are limited. This study aimed to evaluate the efficacy, safety and factors associated with sustained virological response (SVR) in CHC patients treated with PEG-RBV in northern India. Materials and Methods: Consecutive treatment naïve patients with CHC infection treated with PEG-RBV combination therapy between January 2011 and December 2014 were included. Patients with cirrhosis and other contraindications were excluded. Results: Of the total 108 patients enrolled, 102 (94.4%) patients completed the treatment (mean age- 43 ±12.7 years; 62% males). The mean BMI was 23.9 ± 4.2 and mean ALT was 85.7 ± 68 IU/L. HCV viral load >4,00,000 IU/ml was present in 45.4%. The most common genotype was 3 (69.4%; n=75), followed by genotype 1 (26.8%; n=29) and genotype 4 (3.7%; n=4). By intention-to-treat analysis, the overall SVR rate was 94.4% (102/108). In genotype 1 patients it was 86.2% (25/29) and 98.7% (74/75) (p=02) in genotype 3 patients. On multivariate analysis, non-genotype 3 infection predicted lower SVR. Interpretation and Conclusions: SVR rates in CHC patients treated in northern India with PEG-RBV therapy in our study (86.2% for genotype 1 and 98.7% in genotype 3) were better than those reported in western and other Indian studies. Better patient compliance, better monitoring and better management of adverse events lead to superior treatment outcomes.

Background and Objectives: Hepatic dysfunction is known to occur in Plasmodium falciparum malaria with varied incidence in different regions. Recent studies report liver involvement in P. vivax infection also. It is important to know about this entity in order to recognize it early and offer prompt and specific treatment. The present study aimed to assess the incidence, pattern, severity and outcome of hepatic dysfunction in cases of P. falciparum and P. vivax malaria admitted to a tertiary care hospital in northern India. Materials and Methods: This retrospective study included all hospitalized patients diagnosed to have malaria from January 2013 to December 2013. Their clinical and biochemical parameters, complications and outcome were recorded. Results: Of 115 patients included, 85(73.9%) had P. vivax infection and 30 (26.1%) had P. falciparum infection. The mean age was 36.7±16.1 years and male:female ratio was 2.7:1. Hepatic dysfunction was seen in 31.8%(27/85) patients of vivax malaria and 50%(15/30) patients of falciparum malaria (p=0.082). The mean bilirubin, AST and ALT in patients with hepatic dysfunction were 7.7 ±7.3 mg/dL, 97.1 ±103.3 IU/L and 72.3 ±87.8 IU/L respectively. Patients with falciparum malaria had significantly higher levels of mean bilirubin, AST, urea and creatinine. Patients with hepatic dysfunction had higher rate of complications like renal failure, shock, acute respiratory distress syndrome, and mortality. Interpretation and conclusion: Hepatic dysfunction was more common and more severe in patients with P. falciparum malaria compared to P. vivax malaria. Patients with hepatic dysfunction had higher rates of complications and higher mortality.

Background and objectives: Diarrheal diseases are an important cause of morbidity and mortality in children in developing countries. Among diarrheagenic agents, Shigella should be emphasized because of its prevalence and the severity of the associated disease. The present study was done to study the prevalence and antimicrobial susceptibility pattern of Shigella isolates in stool. Materials and methods: Stool samples were collected from cases of dysentery and diarrhea in the laboratory from Jan 2009 to Dec 2013. The specimens were processed and inoculated as per standard protocol. The susceptibility of Shigella serogroups to different antibiotics was done as per the Clinical and Laboratory Standards Institute (CLSI) guidelines. Antibiotic susceptibility between different Shigella serogroups was compared and trends of drug resistance to various antimicrobial agents over a period of five years was seen. Results: Of a total of 6117 samples, Shigella serogroups were isolated in 74 (1.2%) samples. S. flexneri was the most common serogoup identified followed by S. boydii and S. sonnei. Yearwise isolation of Shigella serogroups was 1.58% in 2009 which decreased to 0.38% in 2013. All Shigella serogroups showed higher sensitivity to ciprofloxacin as compared to nalidixic acid, cotrimoxazole and ampicillin. Interpretation and conclusion: There is a significant increase in resistance to several commonly used antimicrobial agents. The rapid increase in ciprofloxacin resistance, especially in S. flexneri, is a major cause of concern. The results suggest reconsideration of the empiric use of these antimicrobial agents for the treatment of shigellosis.

Diarrheal diseases continue to play a major role in the lives of the HIV positive people impacting negatively on the quality of life. Currently only a few studies on intestinal parasites and diarrhea in HIV patients are available from South India. We took up this study to evaluate the prevalence of such infections in HIV patients and to emphasize the importance of stool examination for parasites. A total of 73 stool samples from HIV patients with diarrhea (Jan 2012 – Dec 2012) were processed according to the standard protocol. Of the total 73 cases, 65.75% were with chronic diarrhea and the remaining 34.24% presented with acute diarrhea. Of the 32 (43.83%) intestinal pathogens isolated, 27 (84.37%) were coccidian parasites and the remaining were bacterial agents. Knowledge about the different pattern of pathogens can often guide appropriate therapy to HIV patients. There is an urgent need to interpret the scientific findings into sustainable prevention programs and improve public health policy.

Tuberculosis is a very common condition which at times can present with distinctly atypical findings. In the vast majority of the presenting cases it can pose diagnostic challenge to both the clinician and the radiologist due to its nonspecific clinical manifestations and lack of pathognomonic radiological signs But being a treatable disease utmost care needs to be exercised in establishing this diagnosis. We report a rare radiological finding in a case of small intestinal tuberculosis which confounded the initial diagnosis necessitating pathological proof of tubercular enteroenteric fistula. Following fine needle aspiration cytology, the patient was started on anti-tubercular treatment and conservatively managed. The patient showed significant improvement in clinical symptoms after 3 months and resolution on completion of the treatment.

Mucormycosis is common in immunocompromised patients. Among the various clinical spectrum of mucormycosis gastrointestinal mucormycosis has been documented in about seven percent of cases, more commonly in pediatric population. In large studies (mostly in immunocompromised) the mortality has been documented even up to 100%. Only nine cases have been described so far in immune competent adults globally including ours. We present here a case of successful treatment of ileo-cecal mucormycosis in an immunocompetent middle age man from eastern part of India. This case will enlighten the clinicians and broaden their vision of differential diagnosis while dealing with cases of non- specific pain abdomen. This case also highlights the importance of microbiological studies in addition to conventional biopsy and histopathology alone.

Trichuris trichiura, commonly referred to as a whipworm, has a worldwide distribution, particularly among countries with warm and humid climates. This parasite is carried by nearly one quarter of the world population especially less-developed countries. Poor hygiene is associated with trichuriasis transmission, and children are especially vulnerable because of their high exposure to risk factors. This is especially true in developing countries, where poor sanitary conditions correlate with heavy disease burden and infections. Only patients with heavy parasite burden become symptomatic. The diagnosis is typically confirmed by detection of T. trichiura eggs on examination of a stool sample. This case report deals with a patient with trichuriasis who were diagnosed by detection of the parasite on colonoscopy. Thus colonoscopy might be a useful diagnostic tool, especially in symptomatic patients who are infected by only a few male worms with no eggs in the stool and thus are not diagnosed by conventional methods.