Real-Time Polymerase Chain Reaction-Based Detection and Quantification of Hepatitis B Virus DNA.

Hepatitis B virus (HBV) is a significant cause of liver disease worldwide. It can lead to acute or chronic infections, making individuals highly susceptible to fatal cirrhosis and liver cancer. Accurate detection and quantification of HBV DNA in the blood are essential for diagnosing and monitoring HBV infection.

Foodborne Pathogenic Vibrios: Antimicrobial Resistance.

Foodborne illness caused by pathogenic Vibrios is generally associated with the consumption of raw or undercooked seafood. Fish and other seafood can be contaminated with Vibrio species, natural inhabitants of the marine, estuarine, and freshwater environment. Pathogenic Vibrios of major public health concerns are , , and .

Integrated genomic view of SARS-CoV-2 in India.

India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest of the world followed by seeding of local transmission triggered further outbreaks in India. We used ARTIC protocol-based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred.

Molecular insights into the genome dynamics and interactions between core and acquired genomes of .

Bacterial species are hosts to horizontally acquired mobile genetic elements (MGEs), which encode virulence, toxin, antimicrobial resistance, and other metabolic functions. The bipartite genome of harbors sporadic and conserved MGEs that contribute in the disease development and survival of the pathogens. For a comprehensive understanding of dynamics of MGEs in the bacterial genome, we engineered the genome of and examined in vitro and in vivo stability of genomic islands (GIs), integrative conjugative elements (ICEs), and prophages.

Conversion of a -Mediated Non-toxigenic O1 Strain to a Toxigenic Strain Using Chitin-Induced Transformation.

Toxigenic strains, including strains in serogroups O1 and O139 associated with the clinical disease cholera, are ubiquitous in aquatic reservoirs, including fresh, estuarine, and marine environments. Humans acquire cholera by consuming water and/or food contaminated with the microorganism. The genome of toxigenic harbors a cholera-toxin producing prophage (CT-prophage) encoding genes that promote expression of cholera toxin.

Genomic plasticity associated with antimicrobial resistance in .

The Bay of Bengal is known as the epicenter for seeding several devastating cholera outbreaks across the globe. , the etiological agent of cholera, has extraordinary competency to acquire exogenous DNA by horizontal gene transfer (HGT) and adapt them into its genome for structuring metabolic processes, developing drug resistance, and colonizing the human intestine. Antimicrobial resistance (AMR) in has become a global concern.

Molecular Insights into Antimicrobial Resistance Traits of Commensal Human Gut Microbiota.

Antimicrobial resistance (AMR) among bacterial species that resides in complex ecosystems is a natural phenomenon. Indiscriminate use of antimicrobials in healthcare, livestock, and agriculture provides an evolutionary advantage to the resistant variants to dominate the ecosystem. Ascendency of resistant variants threatens the efficacy of most, if not all, of the antimicrobial drugs commonly used to prevent and/or cure microbial infections.

Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas.

The diversity and basic functional attributes of the gut microbiome of healthy Indians is not well understood. This study investigated the gut microbiome of three Indian communities: individuals residing in rural and urban (n = 49) sea level Ballabhgarh areas and in rural high altitude areas of Leh, Ladakh in North India (n = 35). Our study revealed that the gut microbiome of Indian communities is dominated by Firmicutes followed by Bacteroidetes, Actinobateria and Proteobacteria.

Novel Genetic Tool to Study the Stability of Genomic Islands.

Background: Genomic islands (GIs) are discrete segments of mobile DNA with defined boundaries according to recent patents, acquired in the bacterial genome from another organism by horizontal gene transfer during the course of evolution. GIs contribute significantly to virulence, disease development, antimicrobial resistance and metabolic process.

Objective: The present study focuses on the development of a vector based genetic tool carrying selectable and counter-selectable markers, in order to flag the GIs in the bacterial chromosome and monitor their stability under in vitro and in vivo conditions.

Complete Genome Sequence of Isolated from the Gut of a Healthy Indian Subject.

, a rod-shaped nonmotile obligate anaerobe, is the most abundant actinobacterium in the gastrointestinal tract of healthy humans. An altered abundance of may be linked with several health disorders, including irritable bowel syndrome. In the present study, we report the complete genome sequence of strain indica.

Complete Genome Sequence of Isolated from the Gut of a Healthy Indian Adult.

is the most abundant (~4%) member of the phylum found in the colon of healthy humans. It is a strict anaerobe and plays an important role in intestinal homeostasis. Here, we report the complete genome sequence of strain Indica.

Gastric microbiome of Indian patients with Helicobacter pylori infection, and their interaction networks.

The gastric microbiome is suspected to have a role in the causation of diseases by Helicobacter pylori. Reports on their relative abundance vis-à-vis H. pylori are available from various ethnic and geographic groups, but little is known about their interaction patterns.

Molecular Insights into Antimicrobial Resistance Traits of Multidrug Resistant Enteric Pathogens isolated from India.

Emergence of antimicrobial resistant Gram-negative bacteria has created a serious global health crisis and threatens the effectiveness of most, if not all, antibiotics commonly used to prevent and treat bacterial infections. There is a dearth of detailed studies on the prevalence of antimicrobial resistance (AMR) patterns in India. Here, we have isolated and examined AMR patterns of 654 enteric pathogens and investigated complete genome sequences of isolates from six representative genera, which in aggregate encode resistance against 22 antibiotics representing nine distinct drug classes.

Whole-Genome Sequence of a Strain Isolated from the Gut of a Healthy Indian Adult Subject.

has been previously reported in the gut of ruminating animals. Its role as an animal probiotic is being investigated, specifically from the perspective of enhancing animal productivity. Herein, we report the draft genome sequence of strain indica isolated from the stool sample of a healthy Indian subject.

Whole-Genome Sequence of Strain Indica, Isolated from the Gut of a Healthy Indian Adult.

, a Gram-positive rod-shaped anaerobic bacterium, inhabits the human gastrointestinal tract and contributes significantly to oligosaccharide production, amino acid metabolism, and protection against intestinal inflammation. Here, we report the whole-genome sequence of , which was isolated from the gastrointestinal tract of a healthy Indian adult.

Draft Genome Sequence of Isolated from the Gut of a Healthy Indian Adult.

, a Gram-negative anaerobic rod-shaped bacterium, is frequently associated with the human gastrointestinal tract and influences host physiology, immunity, and metabolic pathways. In the present study, we report the draft genome sequence of isolated from the gut of a healthy Indian adult.

Rugose atypical Vibrio cholerae O1 El Tor responsible for 2009 cholera outbreak in India.

Vibrio cholerae causes cholera outbreaks in endemic regions where the water quality and sanitation facilities remain poor. Apart from biotype and serotype changes, V. cholerae undergoes phase variation, which results in the generation of two morphologically different variants termed smooth and rugose.

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.

Effect of LexA on Chromosomal Integration of CTXϕ in Vibrio cholerae.

Unlabelled: The genesis of toxigenic Vibrio cholerae involves acquisition of CTXϕ, a single-stranded DNA (ssDNA) filamentous phage that encodes cholera toxin (CT). The phage exploits host-encoded tyrosine recombinases (XerC and XerD) for chromosomal integration and lysogenic conversion. The replicative genome of CTXϕ produces ssDNA by rolling-circle replication, which may be used either for virion production or for integration into host chromosome.

Genetic and mutational characterization of the small alarmone synthetase gene relV of Vibrio cholerae.

In Vibrio cholerae, the causative agent of cholera, products of three genes, relA, spoT and relV, govern nutritional stress related stringent response (SR). SR in bacteria is critically regulated by two intracellular small molecules, guanosine 3'-diphosphate 5'-triphosphate (pppGpp) and guanosine 3',5'-bis(diphosphate) (ppGpp), collectively called (p)ppGpp or alarmone. Evolution of relV is unique in V.

Mutational analysis of the (p)ppGpp synthetase activity of the Rel enzyme of Mycobacterium tuberculosis.

Rel(Mtb), a GTP pyrophosphokinase encoded by the Mycobacterium tuberculosis (Mtb) genome, catalyzes synthesis of (p)ppGpp from ATP and GDP(GTP) and its hydrolysis to GDP(GTP) and pyrophosphate to mediate stringent response, which helps bacteria to survive during nutrient limitation. Like other members of Rel_Spo homologs, Rel(Mtb) has four distinct domains: HD, Rel_Spo (RSD), TGS and ACT. The N-terminal HD and RSD are responsible for (p)ppGpp hydrolysis and synthesis, respectively.

Functional characterization of the stringent response regulatory gene dksA of Vibrio cholerae and its role in modulation of virulence phenotypes.

In bacteria, nutrient deprivation evokes the stringent response, which is mediated by the small intracellular signaling molecule ppGpp. In Gram negatives, the RelA enzyme synthesizes and SpoT hydrolyzes ppGpp, although the latter protein also has weak synthetase activity. DksA, a recently identified RNA polymerase binding transcription factor, acts as a coregulator along with ppGpp for controlling the stringent response.

Stringent response in Vibrio cholerae: genetic analysis of spoT gene function and identification of a novel (p)ppGpp synthetase gene.

RelA and SpoT of Gram-negative organisms critically regulate cellular levels of (p)ppGpp. Here, we have dissected the spoT gene function of the cholera pathogen Vibrio cholerae by extensive genetic analysis. Unlike Escherichia coli, V.