Sophia David

The paper develops a rules-based classifier to predict ciprofloxacin resistance in Klebsiella pneumoniae from genotype data and demonstrates its global distribution association with quinolone consumption.

This paper identifies PgaR as a positive regulator of the pgaABCD operon in Klebsiella pneumoniae, showing that genetic variation in this region leads to loss or hyper-production of PNAG, with distinct fitness consequences.

The paper proposes the Life Identification Number (LIN) system as a stable, multilevel strain taxonomy for bacterial pathogens based on core genome MLST to improve epidemiological tracking and nomenclature consistency.

This study identifies how personalized gut microbiotas influence the competitiveness of antibiotic-resistant pathogens through carbohydrate competition and specific genetic mutations.

The paper shows that pilin cyclisation and pilus formation are robust to amino acid substitutions, but electrostatic changes impair conjugation efficiency.

amr.watch provides an interactive platform to analyze and visualize AMR trends from global WGS data, enabling ongoing situational awareness for research and policy.

The paper evaluates MrkA expression variability in Klebsiella pneumoniae and shows that anti-MrkA mAb efficacy depends on antigen abundance.

vaccines.watch is an interactive platform that uses global genome data to monitor vaccine targets and interventions, enabling analysis of vaccine target diversity and genomic landscape gaps.

The paper determines the cryo-EM structure of TraT proteins from plasmids and reveals their evolutionary history, showing independent acquisition by different plasmid backbones.

This study evaluates ONT-only assemblies for genomic surveillance of Klebsiella pneumoniae, showing reliable MLST, K type, and AMR detection but challenges in cluster detection.

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.

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

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

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.

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

The paper introduces mSWEEP, a method for high-resolution bacterial lineage quantification from plate sweeps, showing improved accuracy in detecting and estimating abundances of bacterial lineages.