AMRgen is an R package that links antimicrobial resistance genotypes to phenotypes through data harmonization, analysis, and visualization, using surveillance data from priority pathogens.

bioRxiv · May 4, 2026 · PreprintMicrobiology

amr.watch - monitoring antimicrobial resistance trends from global genomics data

Sophia David, Julio Diaz Caballero, Natacha Couto, Khalil Abudahab, Nabil-Fareed Alikhan, Corin Yeats, Anthony P. Underwood, Alison Molloy, Diana Connor, Heather M. Shane, Philip Ashton, Hajo Grundmann, Matthew T. G. Holden, Edward J. Feil, Sonia B. Sia, , David M. Aanensen

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

PLOS Global Public Health · Nov 24, 2025Peer-reviewedGenomics

Monitoring of vaccine targets and interventions using global genome data: vaccines.watch

Sophia David, Khalil Abudahab, Natacha Couto, Wa Ode Dwi Daningrat, Corin Yeats, Alison Molloy, Philip Ashton, Nabil-Fareed Alikhan, David M. Aanensen

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.

bioRxiv · Jun 13, 2025 · PreprintGenomics

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

Varun Shamanna, Srikanth Srinivas, Natacha Couto, Geetha Nagaraj, Shyama Prasad Sajankila, Harshitha Gangaiah Krishnappa, Kavitha Arakalgud Kumar, David M. Aanensen, Ravikumar Kadahalli Lingegowda

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.

Microbial Genomics · Jul 22, 2024Peer-reviewedGenomics

Convergence and global epidemiology of Klebsiella pneumoniae plasmids harbouring the iuc3 virulence locus.

Marjorie J. Gibbon, Natacha Couto, Keira Cozens, Samia Habib, Lauren A. Cowley, David M. Aanensen, Jukka Corander, Harry A. Thorpe, Marit Andrea Klokkhammer Hetland, Davide Sassera, Cristina Merla, Marta Corbella, Carolina Ferrari, Katy Turner, Kwanrawee Sirikancha, , Edward J. Feil

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

bioRxiv · Jan 5, 2024 · PreprintGenomics

DEN-IM: Dengue Virus identification from shotgun and targeted metagenomics

Catarina Inês Mendes, Erley Lizarazo, Miguel P. Machado, Diogo Nuno Silva, Adriana Tami, Mário Ramirez, Natacha Couto, John W. A. Rossen, João André Carriço

DEN-IM is a workflow for analyzing DENV sequencing data from shotgun and targeted metagenomics, enabling CDS inference, serotype/genotype identification, and phylogenetic tree generation.

bioRxiv · May 6, 2019 · PreprintBioinformatics