Mihir Kekre

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.

Detection of simple and complex de novo mutations without, with, or with multiple reference sequences

The paper introduces Corticall, a graph-based method to detect de novo mutations using short-read and long-read data, validated on Plasmodium falciparum crosses.

Development of copy number assays for detection and surveillance of piperaquine resistance associated plasmepsin 2/3 copy number variation in Plasmodium falciparum

The paper develops and validates PCR assays to detect plasmepsin 2/3 and pfmdr1 copy number variations in Plasmodium falciparum field isolates, finding increasing plasmepsin 2/3 duplications and loss of pfmdr1 mutations in Cambodia.

Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification

This paper develops a method to sequence Plasmodium falciparum genomes from dried blood spots using selective whole genome amplification, achieving high concordance with venous blood samples.

Genomic epidemiology of the current wave of artemisinin resistant malaria

This study identifies kelch13 mutations associated with artemisinin resistance in Southeast Asia and finds low frequency of these mutations in Africa, suggesting different evolutionary pressures.