David M. Aanensen

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.

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 a mobile resistance island driving carbapenem resistance in Enterobacter hormaechei and Klebsiella pneumoniae in a Nigerian ICU, highlighting the role of horizontal gene transfer in AMR spread.

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

This study uses whole genome sequencing to identify Enterobacter hormaechei as the most common bloodstream pathogen in Nigerian hospitals, revealing its diversity and potential outbreaks.

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 introduces TyphiNET, a dashboard for exploring Typhi genomics data to support public health decisions on antimicrobial resistance and vaccine implementation.

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.

hAMRonization standardizes AMR gene detection outputs from multiple tools into a unified format for easier analysis and integration.

This study uses genomic data to trace the introduction and transmission of Candida auris in the UK between 2014 and 2019, identifying at least three introductions and multiple transmission events.

The paper characterizes iuc3-carrying plasmids in Klebsiella pneumoniae isolates, identifying convergent plasmids with resistance and virulence genes and highlighting their global epidemiology.

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.

This study characterizes the genetic diversity and carbapenem resistance mechanisms in Acinetobacter baumannii isolates from Nigerian hospitals using whole-genome sequencing, revealing high prevalence of blaNDM-1 and transposon-mediated dissemination of resistance genes.

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.

This study uses whole genome sequencing to characterize Salmonella isolates from the Philippines, revealing AMR patterns and population structure compared to traditional methods.

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

This study uses whole-genome sequencing to analyze carbapenem-resistant Acinetobacter baumannii isolates in the Philippines, identifying resistance mechanisms and transmission patterns.

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 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.

The paper reconstructs the evolutionary histories of antibiotic-resistant pneumococcal lineages PMEN3 and PMEN9, showing how interspecies recombination contributes to antibiotic resistance and serotype switching.

The paper introduces Pathogenwatch, a tool for genomic surveillance of Salmonella Typhi, enabling AMR prediction and population-level risk assessment through global data sharing.

The paper sequenced N. gonorrhoeae isolates from the Philippines to assess antimicrobial resistance and genetic diversity, finding high resistance to penicillin, ciprofloxacin, and tetracycline and genetic diversity within global lineage A.

The paper sequenced S. aureus isolates from the Philippines to analyze MRSA clones and resistance patterns, finding a limited number of genetic clones and high concordance between phenotypic and genotypic resistance.

MAJORA enables decentralized sequencing and integration of SARS-CoV-2 genomic data and metadata across the COG-UK network, supporting rapid genomic surveillance.

This paper introduces a community-driven genomic resource for Neisseria gonorrhoeae that predicts antimicrobial resistance and supports public health surveillance.