Next generation sequencing and microbiome's taxonomical characterization of frozen soil of north western Himalayas of Jammu and Kashmir, India

BACKGROUND: Traditionally, microbial genome sequencing has been restrained to the species grown in pure culture. The development of culture-independent techniques over the last decade allows scientists to sequence microbial communities directly from environmental samples. Metagenomics is the study of complex genome by the isolation of DNA of the whole community. Next generation sequencing (NGS) of metagenomic DNA gives information about the microbial and taxonomical characterization of a particular niche. The objective of the present research is to study the microbial and taxonomical characterization of the metagenomic DNA, isolated from the frozen soil sample of a glacier in the north western Himalayas through NGS. RESULTS: The glacier community comprised of 16 phyla with the representation of members belonging to Proteobacteria and Acidobacteria. The number of genes annotated through the Kyoto Encyclopedia of Genes and Genomes (KEGG), GO, Pfam, Clusters of Orthologous Groups of proteins (COGs), and FIG databases were generated by COGNIZER. The annotation of genes assigned in each group from the metagenomics data through COG database and the number of genes annotated in different pathways through KEGG database were reported. CONCLUSION: Results indicate that the glacier soil taken in the present study, harbors taxonomically and metabolically diverse communities. The major bacterial group present in the niche is Proteobacteria followed by Acidobacteria, and Actinobacteria, etc. Different genes were annotated through COG and KEGG databases that integrate genomic, chemical, and systemic functional information.

Prevalence of hepatitis B and hepatitis C in patients of chronic kidney disease

Background: Patients of CKD are highly exposed to HBV and HCV because of multiple blood transfusions and exposure to contaminated equipments. Infections by HBV and HCV are significant cause of morbidity in CKD patients by causing liver damage and membranoproliferative GN. Present study was done to observe the prevalence of HBV and HCV in patients of CKD and to compare the prevalence of these infections in patients who were on maintenance haemodialysis and who were not on maintenance hemodialysis.Methods: This study had been conducted on 140 patients. Patients were diagnosed as having CKD on basis of Cockcroft-gault equation as per KDOQI guidelines. Stage 3, 4 or 5 patients were included for the study whereas patients with stage 1 or 2 were excluded. These 140 cases were divided into 2 groups, Group I included 70 cases who were on maintenance hemodialysis and Group II included 70 patients who were not on maintenance hemodialysis. The prevalence of HBV and HCV in the two groups was observed. Diagnosis of HBV was made by detection of HBsAg (one step immunoassay) and diagnosis of HCV was made by detection of antibodies to Hepatitis C(enzyme linked immunoassay). Prevalence data of NCDC was used for comparison with general population.Results: In Group I, 15 (21%) patients were positive for HCV and 9 (12.9%) were positive for HBV which is significantly higher compared to Group II patients in which 6 (8.6%) and 2 (2.9%) were positive respectively. Overall out of 140 patients,21(15%) were positive for HCV and 11(7.9%) were positive for HBV, which is significantly higher compared to data of NCDC for general population in which prevalence of HCV and HBV is 1% and 4% respectivelyConclusions: Prevalence of HBV and HCV was significantly higher in patients of CKD than the general population, which was further higher in patients who were on maintenance hemodialysis and have received multiple blood transfusions, emphasizing the need to implement the methods to limit the spread of HBV and HCV.

Efficacy of sequential therapy versus standard triple therapy versus quinolone-based triple therapy for eradication of Helicobacter pylori infection

Background: Helicobacter pylori colonization is a risk factor for Adenocarcinomas of the distal (noncardia) stomach. The presence of Helicobacter pylori is strongly associated with primary gastric lymphoma. The urea breath test, the stool antigen test, and biopsy-based tests can all be used to assess the success of treatment. Helicobacter pylori is susceptible to a wide range of antibiotics in vitro, monotherapy is not usually successful, probably because of inadequate antibiotic delivery to the colonization niche. Current regimens consist of a PPI or H2 blocker, bismuth citrate and two or three antimicrobial agents given for 7-14 days. Research on optimizing drug combinations to increase efficacy continues. Efficacy of Sequential Therapy versus Standard Triple Therapy versus Quinolone-based Triple Therapy for eradication of Helicobacter pylori infection is done in this study.Methods: This study had been conducted on 150 patients divided into three groups randomly 50 Patients each and were treated with Sequential, Standard and Quinolone based triple therapy respectively. Patients were followed up no sooner than four weeks of completing therapy by rapid urease test to confirm eradication.Results: There was no significant difference with regards to presence of GERD, Gastric Ulcers, Duodenal Ulcers (p value>0.05) except for presence of erosive gastritis which was significantly higher in patients in quinolone group (p value<0.05). The eradication rate was 90%, 86%, 82% in Sequential therapy group, Triple therapy group and Fluroquinolone group respectively. However, there was no statistically significant difference in eradication rates in these groups (p value>0.05).Conclusions: Sequential therapy group had better eradication rates (90%) as compared to standard triple therapy group (86%) and fluroquinolone therapy group (82%) but results were not statistically significant when all three groups were compared together.