Varun Shamanna
A5073869172- Antibiotic Resistance in Bacteria
- Bacterial Identification and Susceptibility Testing
- Genomics and Phylogenetic Studies
- Vibrio bacteria research studies
- Salmonella and Campylobacter epidemiology
- Bacteriophages and microbial interactions
- Bacterial biofilms and quorum sensing
- Antimicrobial Resistance in Staphylococcus
- Pneumonia and Respiratory Infections
- Antibiotics Pharmacokinetics and Efficacy
- Tuberculosis Research and Epidemiology
- Plant Pathogenic Bacteria Studies
- Hepatitis B Virus Studies
- Mycobacterium research and diagnosis
- Hepatitis Viruses Studies and Epidemiology
- SARS-CoV-2 and COVID-19 Research
- Plant Pathogens and Fungal Diseases
- Botanical Studies and Applications
- Platelet Disorders and Treatments
- Brucella: diagnosis, epidemiology, treatment
- SARS-CoV-2 detection and testing
- Healthcare Systems and Reforms
- Health Systems, Economic Evaluations, Quality of Life
- Bacillus and Francisella bacterial research
- Global Health and Surgery
Central Laboratory For Agricultural Expert Systems
2024
Kempegowda Institute of Medical Sciences
2021-2024
Institute of Epidemiology, Disease Control and Research
2023
Nitte University
2023
University of Peradeniya
2023
Universiti Malaysia Kelantan
2023
Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini"
2023
International Centre for Diarrhoeal Disease Research
2023
Mohammed V University
2022
Bangalore Medical College and Research Institute
2022
Abstract Background Klebsiella species, including the notable pathogen K. pneumoniae, are increasingly associated with antimicrobial resistance (AMR). Genome-based surveillance can inform interventions aimed at controlling AMR. However, its widespread implementation requires tools to streamline bioinformatic analyses and public health reporting. Methods We developed web application Pathogenwatch, which implements analytics tailored species for integration visualization of genomic...
Abstract Background Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a threat to public health in India because of its high dissemination, mortality, and limited treatment options. Its genomic variability reflected the diversity sequence types, virulence factors, antimicrobial resistance (AMR) mechanisms. This study aims characterize clonal relationships genetic mechanisms CRKP isolates India. Materials Methods We characterized 344 retrospective K. clinical collected from 8 centers...
Abstract Background Klebsiella pneumoniae is a World Health Organization high-priority antibiotic-resistant pathogen. However, little known about lineages circulating in Nigeria. Methods We performed whole-genome sequencing (WGS) of 141 isolated between 2016 and 2018 from clinical specimens at 3 antimicrobial-resistance (AMR) sentinel surveillance tertiary hospitals southwestern conducted silico multilocus sequence typing; AMR gene, virulence plasmid, K O loci profiling; as well phylogenetic...
Abstract Background Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an emerging public health problem. This study explores the specifics of CRKP epidemiology in Colombia based on whole genome sequencing (WGS) National Reference Laboratory at Instituto Nacional de Salud (INS)’s 2013–2017 sample collection. Methods A total 425 isolates from 21 departments were analyzed by HiSeq-X10®Illumina high-throughput sequencing. Bioinformatic analysis was performed, primarily using pipelines...
Abstract Antimicrobial resistance (AMR) is considered a global threat, and novel drug discovery needs to be complemented with systematic standardized epidemiological surveillance. Surveillance data are currently generated using phenotypic characterization. However, due poor scalability, this approach does little for true investigations. There strong case whole-genome sequencing (WGS) enhance the data. To establish AMR surveillance WGS, we developed laboratory implementation that applied...
We report the persistent circulation of third-generation cephalosporin resistant Salmonella Typhi in Mumbai, linked to acquisition and maintenance a previously characterized IncX3 plasmid carrying ESBL gene blaSHV-12 fluoroquinolone resistance qnrB7 genetic context triple mutant also associated with resistance.
Klebsiella pneumoniae is a critically important pathogen in the Philippines. Isolates are commonly resistant to at least 2 classes of antibiotics, yet mechanisms and spread its resistance not well studied.A retrospective sequencing survey was performed on carbapenem-, extended spectrum beta-lactam-, cephalosporin-resistant isolated 20 antimicrobial (AMR) surveillance sentinel sites from 2015 through 2017. We characterized 259 isolates using biochemical methods, susceptibility testing,...
Abstract Klebsiella pneumoniae poses a significant healthcare challenge due to its multidrug resistance and diverse serotype landscape. This study aimed explore the diversity of 1072 K. association with geographical distribution, disease severity antimicrobial/virulence patterns in India. Whole-genome sequencing was performed on Illumina platform, genomic analysis carried out using Kleborate tool. KL64 (n=264/1072, 26%), KL51 (249/1072, 24%), KL2 (n=88/1072, 8%), O1/O2v1 (n=471/1072, 44%),...
Abstract Performing whole genome sequencing (WGS) for the surveillance of antimicrobial resistance offers ability to determine not only antimicrobials which rates are increasing, but also evolutionary mechanisms and transmission routes responsible increase at local, national, global scales. To derive WGS-based outputs, a series processes required, beginning with sample metadata collection, followed by nucleic acid extraction, library preparation, sequencing, analysis. Throughout this pathway...
Abstract Advanced genomics and sequencing technologies are increasingly becoming critical for global health applications such as pathogen antimicrobial resistance (AMR) surveillance. Limited resources challenge capacity development in low- middle-income countries (LMICs), with few having facilities adequately trained staff. Training research public experts who directly involved the establishment of offers an effective, but limited, solution to a growing need. Instead, training them impart...
poses a significant healthcare challenge due to its multidrug resistance and diverse serotype landscape. This study aimed explore the diversity of 1072
In this Supplement, we detail outputs of the National Institute for Health Research Global Unit on Genomic Surveillance Antimicrobial Resistance project, covering practical implementation whole-genome sequencing across our consortium, which consists laboratories in Colombia, India, Nigeria, and Philippines.
The administration and governance of grant funding across global health organizations presents enormous challenges. Meeting these challenges is crucial to ensuring that funds are used in the most effective way improve outcomes, line with United Nations' Sustainable Development Goal 3, "Ensure healthy lives promote well-being for all at ages." Good Financial Grant Practice (GFGP) Standard (ARS 1651) world's first and, currently, only international standard financial management funding....
Abstract The Global Typhoid Genomics Consortium was established to bring together the typhoid research community aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data inform public health action. This analysis, which marks twenty-one years since publication of first genome, represents largest genome sequence collection date (n=13,000), provides a detailed overview global genotype antimicrobial resistance (AMR) distribution temporal trends, generated using open analysis...
To provide an insight into the Whole-genome sequencing (WGS) data of MRSA strains circulating in a teaching hospital north India.An exploratory study was conducted which fifty non-repetitive isolates obtained from pus samples inpatients July 2018 to February 2019 were subjected preliminary identification (ID) and antibiotic susceptibility testing (AST) at our centre. These later sent Central Research Laboratory, India for further using VITEK-2 compact system followed by WGS. Only eighteen...
is a major pathogen in India causing community and nosocomial infections, but little known about its molecular epidemiology mechanisms of resistance hospital settings. Here, we use whole-genome sequencing (WGS) to characterize 478
ABSTRACT Objectives Carbapenem-resistant Acinetobacter baumannii (CRAB) has acquired worldwide recognition as a serious nosocomial infection. It poses concern to hospitalized patients because of the limited therapeutic options available. Thus, we investigated molecular epidemiology and antibiotic resistance profiles A. isolates in India. Materials Methods We characterized 306 retrospective clinical collected from 18 centers across 10 states 1 Union Territory India between 2015 2019....
Performing whole genome sequencing (WGS) for the surveillance of antimicrobial resistance (AMR) offers ability to determine not only antimicrobials which rates are increasing, but also evolutionary mechanisms and transmission routes responsible increase at local, national, global scales. To derive WGS-based outputs, a series processes required, beginning with sample metadata collection, followed by nucleic acid extraction, library preparation, sequencing, analysis. Throughout this pathway...
Background Typhoid fever results from systemic infection with Salmonella enterica serovar Typhi (Typhi) and causes 10 million illnesses annually. Disease control relies on prevention (water, sanitation, hygiene interventions or vaccination) effective antimicrobial treatment. Antimicrobial resistant (AMR) lineages have emerged become established in many parts of the world. Knowledge local pathogen populations informed by genomic surveillance, including (defined GenoTyphi scheme) AMR...
There is a lack of whole-genome sequencing (WGS) data on multidrug-resistant (MDR) bacteria from the Uttarakhand region India. The aim this study was to generate WGS carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates recovered patients in Uttarakhand's tertiary care centre.A cross-sectional included 29 MDR K. test obtained various clinical samples submitted bacteriology laboratory for culture and sensitivity testing July 2018 August 2019. After preliminary identification antibiotic...
Abstract Interpreting phenotypes of bla SHV alleles in Klebsiella pneumoniae genomes is complex. While all strains are expected to carry a chromosomal copy conferring resistance ampicillin, they may also mutations or additional plasmid-borne that have extended-spectrum β-lactamase (ESBL) activity and/or inhibitor (BLI) activity. In addition, the role individual mutations/amino acid changes not completely documented understood. This has led confusion literature and antimicrobial (AMR) gene...