Swapna Uplekar
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View article: Targeted next-generation sequencing for drug-resistant tuberculosis diagnosis: implementation considerations for bacterial load, regimen selection and diagnostic algorithm placement
Targeted next-generation sequencing for drug-resistant tuberculosis diagnosis: implementation considerations for bacterial load, regimen selection and diagnostic algorithm placement Open
Introduction Early and accurate diagnosis of drug-resistant tuberculosis (DR-TB) is essential for improving treatment outcomes. Phenotypic drug susceptibility testing (pDST) is comprehensive but slow, while rapid molecular assays provide r…
View article: Cost-effectiveness of Targeted Next-Generation Sequencing for Tuberculosis Drug-resistance Testing as an Alternative to the Standard of Care in South Africa
Cost-effectiveness of Targeted Next-Generation Sequencing for Tuberculosis Drug-resistance Testing as an Alternative to the Standard of Care in South Africa Open
Background South Africa faces emerging resistance to tuberculosis drugs like bedaquiline. Phenotypic drug-susceptibility testing (DST), the current reference standard for bedaquiline DST, has long turnaround times. Targeted next-generation…
View article: Comparative assessment of line probe assays and targeted next-generation sequencing in drug-resistant tuberculosis diagnosis
Comparative assessment of line probe assays and targeted next-generation sequencing in drug-resistant tuberculosis diagnosis Open
View article: Cost-effectiveness of Targeted Next Generation Sequencing for TB drug-resistance testing as an alternative to the standard of care in South Africa
Cost-effectiveness of Targeted Next Generation Sequencing for TB drug-resistance testing as an alternative to the standard of care in South Africa Open
Background South Africa faces emerging resistance to key TB drugs, including bedaquiline. Phenotypic drug susceptibility testing (pDST), the current reference standard for bedaquiline DST, while accurate has long turnaround times. Targeted…
View article: Evaluating culture-free targeted next-generation sequencing for diagnosing drug-resistant tuberculosis: a multicentre clinical study of two end-to-end commercial workflows
Evaluating culture-free targeted next-generation sequencing for diagnosing drug-resistant tuberculosis: a multicentre clinical study of two end-to-end commercial workflows Open
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View article: Investing in health preparedness, response and resilience: a genomics costing tool focused on next generation sequencing
Investing in health preparedness, response and resilience: a genomics costing tool focused on next generation sequencing Open
The world has seen unprecedented gains in the global genomic surveillance capacities for pathogens with pandemic and epidemic potential within the last 4 years. To strengthen and sustain the gains made, WHO is working with countries and pa…
View article: Antimalarial drug resistance profiling of Plasmodium falciparum infections in India using Ion Torrent deep sequencing
Antimalarial drug resistance profiling of Plasmodium falciparum infections in India using Ion Torrent deep sequencing Open
Introduction Tracking the emergence and spread of antimalarial drug resistance is critical for supporting progress towards the control and eventual elimination of malaria in South Asia, especially India. Plasmodium falciparum has evolved r…
View article: Ten simple rules for the sharing of bacterial genotype—Phenotype data on antimicrobial resistance
Ten simple rules for the sharing of bacterial genotype—Phenotype data on antimicrobial resistance Open
The increasing availability of high-throughput sequencing (frequently termed next-generation sequencing (NGS)) data has created opportunities to gain deeper insights into the mechanisms of a number of diseases and is already impacting many…
View article: Antimalarial Drug Resistance Profiling of<i>Plasmodium falciparum</i>Infections in India Using Next-Generation Sequencing
Antimalarial Drug Resistance Profiling of<i>Plasmodium falciparum</i>Infections in India Using Next-Generation Sequencing Open
Background Tracking the emergence and spread of antimalarial drug resistance has become critical to sustaining progress towards the control and eventual elimination of malaria in South Asia, especially India. Methods An amplicon sequencing…
View article: In silico evaluation of WHO-endorsed molecular methods to detect drug resistant tuberculosis
In silico evaluation of WHO-endorsed molecular methods to detect drug resistant tuberculosis Open
View article: In silico evaluation of WHO-endorsed molecular methods to detect drug resistant tuberculosis
In silico evaluation of WHO-endorsed molecular methods to detect drug resistant tuberculosis Open
Universal drug susceptibility testing (DST) for tuberculosis is a major goal of the END TB strategy. PCR-based molecular diagnostic tests have been instrumental in increasing DST globally and several assays have now been endorsed by the Wo…
View article: The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis
The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis Open
View article: Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance
Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance Open
View article: The 2021 WHO Catalogue of <i>Mycobacterium Tuberculosis</i> Complex Mutations Associated with Drug Resistance: A New Global Standard for Molecular Diagnostics
The 2021 WHO Catalogue of <i>Mycobacterium Tuberculosis</i> Complex Mutations Associated with Drug Resistance: A New Global Standard for Molecular Diagnostics Open
View article: Application of Targeted Next-Generation Sequencing Assay on a Portable Sequencing Platform for Culture-Free Detection of Drug-Resistant Tuberculosis from Clinical Samples
Application of Targeted Next-Generation Sequencing Assay on a Portable Sequencing Platform for Culture-Free Detection of Drug-Resistant Tuberculosis from Clinical Samples Open
Targeted next-generation sequencing (tNGS) has emerged as a comprehensive alternative to existing methods for drug susceptibility testing (DST) of Mycobacterium tuberculosis from patient sputum samples for clinical diagnosis of drug-resist…
View article: Characterizing Antibody Responses to Plasmodium vivax and Plasmodium falciparum Antigens in India Using Genome-Scale Protein Microarrays
Characterizing Antibody Responses to Plasmodium vivax and Plasmodium falciparum Antigens in India Using Genome-Scale Protein Microarrays Open
Understanding naturally acquired immune responses to Plasmodium in India is key to improving malaria surveillance and diagnostic tools. Here we describe serological profiling of immune responses at three sites in India by probing protein m…
View article: A Method for Amplicon Deep Sequencing of Drug Resistance Genes in Plasmodium falciparum Clinical Isolates from India
A Method for Amplicon Deep Sequencing of Drug Resistance Genes in Plasmodium falciparum Clinical Isolates from India Open
A major challenge to global malaria control and elimination is early detection and containment of emerging drug resistance. Next-generation sequencing (NGS) methods provide the resolution, scalability, and sensitivity required for high-thr…
View article: Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis strain 18b
Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis strain 18b Open
View article: Additional file 9: Dataset S1. of Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis strain 18b
Additional file 9: Dataset S1. of Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis strain 18b Open
Occurrence of the 66 unique 18b SNPs in the SRA. (XLSX 2826 kb)
View article: Additional file 10: Dataset S2. of Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis strain 18b
Additional file 10: Dataset S2. of Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis strain 18b Open
Differential gene expression analysis results of SS18b (2 weeks STR depletion, 4 weeks STR depletion and re-addition of STR). (XLSX 2308 kb)
View article: Population Genetics, Evolutionary Genomics, and Genome-Wide Studies of Malaria: A View Across the International Centers of Excellence for Malaria Research
Population Genetics, Evolutionary Genomics, and Genome-Wide Studies of Malaria: A View Across the International Centers of Excellence for Malaria Research Open
The study of the three protagonists in malaria-the Plasmodium parasite, the Anopheles mosquito, and the human host-is key to developing methods to control and eventually eliminate the disease. Genomic technologies, including the recent dev…