Varun Shamanna

Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi

Mykrobe k-mer panel genotypes Salmonella Typhi lineages, antimicrobial resistance (AMR) markers and plasmids from Illumina or nanopore reads, matching mapping-based lineage calls for 99.8% of genomes.

Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae

This paper reclassifies SHV β-lactamase alleles in K. pneumoniae genomes based on mutations, improving genotype-phenotype understanding and updating the Kleborate tool.

Geographical distribution, disease association and diversity of Klebsiella pneumoniae KL and O antigens in India: roadmap for vaccine development

This study analyzes K. pneumoniae serotypes in India, identifying prevalent types and their geographical and resistance associations, suggesting vaccine strategies to cover >85% of strains.

Large retrospective WGS study describes three major sequence types of S. aureus in India and reveals two novel multi-drug resistant sub-lineages of S. aureus Clonal Complex 22

The paper uses WGS to analyze 508 S. aureus isolates from India, identifying three major clones and two novel MRSA sub-lineages of CC22, with evidence of global transmission.

Circulation of third-generation cephalosporin resistant Salmonella Typhi in Mumbai, India

The paper reports the persistent circulation of third-generation cephalosporin-resistant Salmonella Typhi in Mumbai, India, linked to an IncX3 plasmid carrying resistance genes.

Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch

The paper introduces Pathogenwatch, a web tool for genomic surveillance of Klebsiella, showing it identifies drug-resistant clones and vaccine candidate O-types in genomes from low- and middle-income countries.

Clones and Clusters of Antimicrobial-Resistant Klebsiella from Southwestern Nigeria

This study uses whole genome sequencing to analyze antimicrobial-resistant Klebsiella isolates from Nigeria, identifying known and novel lineages, including multidrug-resistant ESBL producers.

Complexity of genomic epidemiology of carbapenem-resistant Klebsiella pneumoniae isolates in Colombia urges the reinforcement of whole genome sequencing based surveillance programs

This study analyzes CRKP isolates in Colombia using WGS, identifying high-risk clones and carbapenemase genes, emphasizing the need for WGS-based surveillance.

Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines

Whole genome sequencing identified three previously unrecognized Klebsiella pneumoniae outbreaks in neonatal intensive care units in the Philippines, revealing an epidemic plasmid associated with carbapenem resistance.

High-Resolution Genomic Profiling of Carbapenem-Resistant Klebsiella pneumoniae Isolates: A Multicentric Retrospective Indian Study

This study characterizes the genomic diversity of carbapenem-resistant Klebsiella pneumoniae isolates from India, identifying high-risk clones and resistance mechanisms.

Molecular dissection of Carbapenem-resistant Acinetobacter baumannii circulating in Indian hospitals usingWhole Genome Sequencing

The paper uses whole genome sequencing to analyze carbapenem-resistant Acinetobacter baumannii isolates from Indian hospitals, identifying novel sequence types and clonal complexes associated with carbapenemase resistance.