A5087112028- Aquaculture disease management and microbiota
- Vibrio bacteria research studies
- Salmonella and Campylobacter epidemiology
- Helicobacter pylori-related gastroenterology studies
- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Invertebrate Immune Response Mechanisms
- Veterinary medicine and infectious diseases
- Mycobacterium research and diagnosis
- COVID-19 diagnosis using AI
- Pancreatic and Hepatic Oncology Research
- Antibiotic Resistance in Bacteria
- Neonatal and Maternal Infections
- Pneumonia and Respiratory Infections
- Tuberculosis Research and Epidemiology
- Streptococcal Infections and Treatments
- Machine Learning in Healthcare
- ATP Synthase and ATPases Research
- Metal Extraction and Bioleaching
- Escherichia coli research studies
- Eosinophilic Esophagitis
- MicroRNA in disease regulation
- Insect symbiosis and bacterial influences
- SARS-CoV-2 detection and testing
- Marine Bivalve and Aquaculture Studies
National University of Singapore
2020-2024
Genome Institute of Singapore
2020
University of Chicago
2020
University of Malaya
2012-2016
University of Hyderabad
2010-2014
National Environmental Engineering Research Institute
2014
Abstract Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, guide public health responses. To investigate global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID estimate impact intensity turnaround times on variant detection in 189 countries. In first two years pandemic, 78% high-income countries sequenced >0.5% their COVID-19 cases, while 42% low- middle-income reached that mark. Around 25%...
The Malaysian giant freshwater prawn, Macrobrachium rosenbergii, is an economically important crustacean worldwide. However, production of this prawn facing a serious threat from Vibriosis disease caused by Vibrio species such as parahaemolyticus. Unfortunately, the mechanisms involved in immune response to bacterial infection are not fully understood. We therefore used high-throughput deep sequencing technology investigate transcriptome and comparative expression profiles hepatopancreas...
ABSTRACT Uropathogenic Escherichia coli (UPEC) causes serious infections in people at risk and has a significant environmental prevalence due to contamination by human animal excreta. In developing countries, UPEC assumes importance certain dwellings because of poor community/personal hygiene exposure contaminated water or soil. We report the complete genome sequence E. strain NA114 from India, with multidrug resistance phenotype capacity produce extended-spectrum beta-lactamase. The...
ABSTRACT The bacterial genus Paracoccus is comprised of metabolically versatile organisms having diverse degradative capabilities and potential industrial environmental applications for bioremediation in particular. We report a de novo -assembled sequence annotation the genome novel isolate denitrificans originally sourced from coal mine tailings India. was capable utilizing N , -dimethylformamide (DMF) as source carbon nitrogen therefore holds mineralization pollutants. biological circuitry...
A decade since the availability of Mycobacterium tuberculosis (Mtb) genome sequence, no promising drug has seen light day. This not only indicates challenges in discovering new drugs but also suggests a gap our current understanding Mtb biology. We attempt to bridge this by carrying out extensive re-annotation and constructing systems level protein interaction map with an objective finding novel target candidates. Towards this, we synergized crowd sourcing social networking methods through...
Being able to link clinical outcomes SARS-CoV-2 virus strains is a critical component of understanding COVID-19. Here, we discuss how current processes hamper sustainable data collection enable meaningful analysis and insights. Following the 'Fast Healthcare Interoperable Resource' (FHIR) implementation guide, introduce an ontology-based standard questionnaire overcome these shortcomings describe patient 'journeys' in coordination with World Health Organization's recommendations. We identify...
The diverse clinical outcomes of colonization by Helicobacter pylori reflect the need to understand genomic rearrangements enabling bacterium adapt host niches and exhibit varied colonization/virulence potential. We describe genome sequences two serial isolates, H. 2017 2018 (the chronological subclones 908), cultured in 2003 from antrum corpus, respectively, an African patient who suffered recrudescent duodenal ulcer disease. When compared with parent strain, 908 (isolated same 1994),...
Group B Streptococcus (GBS; agalactiae) is the most common cause of neonatal meningitis and a rising sepsis in adults. Recently, it has also been shown to foodborne disease. As with many other bacteria, polysaccharide capsule GBS antigenic, enabling its use for strain serotyping. Recent advances DNA sequencing have made sequence-based typing attractive (as implemented several including Escherichia coli, Klebsiella pneumoniae species complex, pyogenes, others). For GBS, existing WGS-based...
Exosomes are extracellular vesicles (EVs) of ~20–200 nm diameter that shuttle DNAs, RNAs, proteins and other biomolecules between cells. The large number present in exosomes demands the frequent use high-throughput analysis. This, turn, requires technical replicates (TRs), biological (BRs) to produce accurate results. As abundance identified varies (Rs), establishing replicate variability predicted for event under study is essential determining Rs required. Although there have been few...
ABSTRACT Helicobacter pylori is a genetically diverse and coevolved pathogen inhabiting human gastric niches leading to spectrum of diseases in susceptible populations. We describe the genome sequence H. 908, which was originally isolated from an African patient living France who suffered with recrudescent duodenal ulcer disease. The strain found be phylogenetically related J99, its comparative analysis revealed several specific features novel insertion-deletion substitution events....
ABSTRACT Salmonella enterica serovar Typhi is a human pathogen that causes typhoid fever predominantly in developing countries. In this article, we describe the whole genome sequence of S. strain CR0044 isolated from carrier Kelantan, Malaysia. These data will further enhance understanding its host persistence and adaptive mechanism.
Among enteric pathogens, Salmonella enterica serovar Typhi is responsible for the largest number of food-borne outbreaks and fatalities. The ability pathogen to cause systemic infection extended durations leads a high cost disease control. Chronic carriers play important roles in evolution Typhi; therefore, identification in-depth characterization isolates from clinical cases carriers, especially those zones endemicity where has not been extensively studied, are necessary. Here, we describe...
The prevalence of different H. pylori genotypes in various geographical regions indicates region-specific adaptations during the course evolution. Complete genomes from countries with high infection burdens, such as India, have not yet been described. Herein we present genome sequences two strains, NAB47 and NAD1, India. In this report, briefly mention sequencing finishing approaches, assembly downstream statistics, important features draft genomes, including their phylogenetic status. We...
ABSTRACT Many of the developing countries Southeast Asian region are significantly affected by endemic typhoid fever, possibly as a result marginal living standards. It is an important public health problem in such Papua New Guinea, which geographically close to some foci endemicity Asia. The severity disease varies different regions, and this may be attributable genetic diversity among native strains. Genome sequence data on strains from needed clearly understand their makeup virulence...
Shrimp aquaculture has been growing rapidly over the last three decades. However, high-density together with environmental degradation led to increased incidence of shrimp infections. Thus, devising and implementing effective strategies predict, diagnose control spread infections shrimps are crucial, also ensure biosecurity sustainability food industry. With recent advancements in biotechnology, more attention given develop novel promising therapeutic tools potential prevent disease...
ABSTRACT Salmonella enterica serovar Typhi is the causative agent of typhoid fever, which causes nearly 21.7 million illnesses and 217,000 deaths globally. Herein, we describe whole-genome sequence strain ST0208, isolated from a sporadic case fever in Kuala Lumpur, Malaysia. The comparative genomics allow an in-depth understanding genetic diversity, its link to pathogenicity evolutionary dynamics, this highly clonal pathogen that endemic
Vibrio parahaemolyticus, an important human pathogen, is associated with gastroenteritis and transmitted through partially cooked seafood. It has become a major concern in the production trade of marine food products. The prevalence potentially virulent pathogenic V. parahaemolyticus raw seafood public health significance. Here we describe genome sequence isolate crustacean origin which was cultured from prawns 2008 Selangor, Malaysia (isolate PCV08-7). next generation sequencing analysis...
Abstract Salmonella Typhi is a human restricted pathogen with significant number of individuals as asymptomatic carriers the bacterium. infection can be effectively controlled if reliable method for identification these developed. In this context, availability whole genomes carrier strains through high- throughput sequencing and further downstream analysis by comparative genomics approaches very promising. Herein we describe genome sequence isolate representing an individual during prolonged...
Being able to link clinical outcomes SARS-CoV-2 virus strains is a critical component of understanding COVID-19. Here we discuss how current processes hamper sustainable data collection enable meaningful analysis and insights. Following 'Fast Healthcare Interoperable Resource' implementation guide, introduce an ontology-based standard questionnaire overcome these shortcomings describe patient "journeys" in coordination with the World Health Organization. We identify steps health acquisition...
Vibrio parahaemolyticus is a Gram-negative halophilic bacterium which found largely in estuarine and coastal waters. The bacteria has been main focus gastro-intestinal infections caused primarily due to the consumption of contaminated seafood. It was shown survive magnesium concentrations as high 300 mM are toxic various other micro-organisms. Several genes V. were studied, among gbpA (N-acetyl glucosamine binding protein) reported cholerae. current study investigates gene expression at...
ABSTRACT The tkt (transketolase) gene is one of the seven fragments used in multilocus sequence typing (MLST) system for Streptococcus agalactiae . We discovered that tkt_134 allele derived from a homologous (which we designate tktX ) not present all S. ; known strains contain match to also much closer identity other non-tkt_134 alleles (i.e., canonical gene) database. Based on these data, has been removed MLST database as September 2021, and types containing have removed. IMPORTANCE...
We report whole-genome sequences of two clinical isolates Mycobacterium tuberculosis isolated from patients in Odisha, India. The sequence analysis revealed that these are an ancestral type and might represent some the "pristine" India have not admixed with other lineages.
ABSTRACT Group B Streptococcus agalactiae (GBS; agalactiae) is the most common cause of neonatal meningitis and a rising sepsis in adults. Recently, it has also been shown to foodborne disease. As with many other bacteria, polysaccharide capsule GBS antigenic, enabling its use for strain serotyping. Recent advances DNA sequencing have made sequence-based typing attractive (as implemented several including Escherichia coli, Klebsiella pneumoniae species complex, pyogenes , others). For GBS,...