Author

Khalil Abudahab

Wellcome Trust

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 15 Bioinformatics· 2

Signature Assays, Organisms & Methods

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Assay:whole-genome sequencing· 17 Approach:statistical model· 13 Research Focus:variant calling· 12 Organism:human· 8 Research Focus:database / resource· 7 Approach:experimental assay· 4 Organism:bacteria (other)· 3 Research Focus:benchmarking· 1

Frequent Co-Authors

David M. AanenseniD· 17 shared Silvia ArgimóniD· 14 shared Agnettah M Olorosa· 11 shared Celia CarlosiD· 11 shared June M GayetaiD· 11 shared Marietta L LagradaiD· 11 shared Anthony P. UnderwoodiD· 9 shared John M. StellingiD· 8 shared

Activity by Year

2017-2025 · peak 9/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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17 shared papersGenomics

David M. AanensenORCID

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Author profile →

17 papers

Recent·Most cited

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

Genomic Surveillance of Salmonella spp. in the Philippines, 2013-2014

Marietta L Lagrada, Silvia Argimón, Janice B. Borlasa, Jaywardeen P Abad, June M Gayeta, Melissa Masim, Agnettah M Olorosa, Victoria Cohen, Benjamin Jeffrey, Khalil Abudahab, Sonia B. Sia, Charmian M. Hufano, John M. Stelling, Matthew T. G. Holden, David M. Aanensen, , the Philippines Antimicrobial Resistance Surveillance Program

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

bioRxiv · Feb 14, 2022 · PreprintGenomics

Genomic Surveillance of Acinetobacter baumannii in the Philippines, 2013-2014

Jeremiah Chilam, Silvia Argimón, Marilyn T. Limas, Melissa Masim, June M Gayeta, Marietta L Lagrada, Agnettah M Olorosa, Victoria Cohen, Lara Fides T. Hernandez, Benjamin Jeffrey, Khalil Abudahab, Charmian M. Hufano, Sonia B. Sia, Matthew T. G. Holden, John M. Stelling, , Celia Carlos

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

Western Pacific surveillance response journal · Oct 1, 2021Peer-reviewedGenomics

Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch

Silvia Argimón, Sophia David, Anthony P. Underwood, Monica I. Abrudan, Nicole E. Wheeler, Mihir Kekre, Khalil Abudahab, Corin Yeats, Richard Goater, Ben E. W. Taylor, Harry Harste, Dawn Muddyman, Edward J. Feil, Sylvain Brisse, Kathryn E. Holt, , John M. Stelling

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.

Clinical Infectious Diseases · Sep 30, 2021Peer-reviewedGenomics

Clones and Clusters of Antimicrobial-Resistant Klebsiella from Southwestern Nigeria

Ayorinde O. Afolayan, Anderson O. Oaikhena, Aaron Oladipo Aboderin, Olatunde F Olabisi, Adewale A Amupitan, Oyekola V. Abiri, Veronica Olatimbo Ogunleye, Erkison Ewomazino Odih, Abolaji T. Adeyemo, Adeyemi Temitayo Adeyemo, Temitope O Obadare, Monica I. Abrudan, Silvia Argimón, Sophia David, Mihir Kekre, , Carolin Vegvari

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

Clinical Infectious Diseases · Sep 29, 2021Peer-reviewedGenomics

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

Sandra Yamile Saavedra, Johan Fabian Bernal, Efraín Andrés Montilla-Escudero, Stefany Alejandra Arévalo, Diego Prada-Cardozo, María Fernanda Valencia, Jaime Moreno, Andrea Melissa Hidalgo, Ángela Sofía García-Vega, Monica I. Abrudan, Silvia Argimón, Mihir Kekre, Anthony P. Underwood, David M. Aanensen, Carolina Duarte, , Carolin Vegvari

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

Clinical Infectious Diseases · Sep 23, 2021Peer-reviewedGenomics

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

Celia Carlos, Melissa Masim, Marietta L Lagrada, June M Gayeta, Polle Krystle V Macaranas, Sonia B. Sia, Maria Adelina M. Facun, Janziel C. Palarca, Agnettah M Olorosa, Gicell Anne C. Cueno, Monica I. Abrudan, Khalil Abudahab, Silvia Argimón, Mihir Kekre, Anthony P. Underwood, , Carolin Vegvari

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.

Clinical Infectious Diseases · Sep 14, 2021Peer-reviewedGenomics

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

Geetha Nagaraj, Varun Shamanna, Vandana Govindan, Steffimole Rose, Dharmavaram Sravani, K. P. Akshata, Mettingal Ramakrishnan Shincy, VT Venkatesha, Monica I. Abrudan, Silvia Argimón, Mihir Kekre, Anthony P. Underwood, David M. Aanensen, K L Ravikumar, Khalil Abudahab, , Elmer M Herrera

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

Clinical Infectious Diseases · Sep 8, 2021Peer-reviewedGenomics

A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at Pathogenwatch

Silvia Argimón, Corin Yeats, Richard Goater, Khalil Abudahab, Benjamin Taylor, Anthony P. Underwood, Leonor Sánchez-Busó, Vanessa Wong, Zoe A. Dyson, Satheesh Nair, Se Eun Park, Florian Marks, Andrew J. Page, Jacqueline A. Keane, Stephen G. Baker, , David M. Aanensen

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

Nature Communications · May 17, 2021Peer-reviewedGenomics

Genomic Surveillance of Neisseria gonorrhoeae in the Philippines 2013-2014

Manuel C Jamoralin, Silvia Argimón, Marietta L Lagrada, Alfred S. Villamin, Melissa Masim, June M Gayeta, Karis D. Boehme, Agnettah M Olorosa, Sonia B. Sia, Charmian M. Hufano, Victoria Cohen, Lara T. Hernandez, Benjamin Jeffrey, Khalil Abudahab, John Stelling, , Celia Carlos

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.

Western Pacific surveillance response journal · Mar 31, 2021Peer-reviewedGenomics

Genomic Surveillance of Methicillin-Resistant Staphylococcus aureus in the Philippines from 2013-2014

Melissa Masim, Silvia Argimón, Holly Grace Espiritu, Mariane Magbanua, Marietta L Lagrada, Agnettah M Olorosa, Victoria Cohen, June M Gayeta, Benjamin Jeffrey, Khalil Abudahab, Charmian M. Hufano, Sonia B. Sia, Matthew T. G. Holden, John Stelling, David M. Aanensen, , on behalf of the Philippines Antimicrobial Resistance Surveillance Program

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.

Western Pacific surveillance response journal · Mar 31, 2021Peer-reviewedGenomics

MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

Samuel M. Nicholls, Radoslaw Poplawski, Matthew J. Bull, Anthony P. Underwood, Michael Chapman, Khalil Abudahab, Ben E. W. Taylor, Ben Jackson, Sara M. Rey, Roberto Amato, Rich Livett, Sónia Gonçalves, Ewan M. Harrison, Sharon J. Peacock, David M. Aanensen, , Nicholas James Loman

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

bioRxiv · Oct 6, 2020 · PreprintBioinformatics

A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch

Leonor Sánchez-Busó, Corin Yeats, Benjamin Taylor, Richard Goater, Anthony P. Underwood, Khalil Abudahab, Silvia Argimón, Kevin C. Ma, Tatum D. Mortimer, Daniel Golparian, Michelle J. Cole, Yonatan H. Grad, Irene Martin, Brian H. Raphael, William M. Shafer, , David M. Aanensen

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

bioRxiv · Jul 3, 2020 · PreprintGenomics

See and Sequence: Integrating Whole-Genome Sequencing Within the National Antimicrobial Resistance Surveillance Program in the Philippines

Silvia Argimón, Melissa Masim, June M Gayeta, Marietta L Lagrada, Polle Krystle V Macaranas, Victoria Cohen, Marilyn T. Limas, Holly Grace Espiritu, Janziel C. Palarca, Jeremiah Chilam, Manuel C Jamoralin, Alfred S. Villamin, Janice B. Borlasa, Agnettah M Olorosa, Lara Fides T. Hernandez, , on behalf of the Philippines Antimicrobial Resistance Surveillance Program

The paper integrates whole-genome sequencing into the Philippines' antimicrobial resistance surveillance program to better understand and track carbapenem resistance in key bacterial species.

bioRxiv · Mar 19, 2020 · PreprintGenomics

Genomic Surveillance of Pseudomonas aeruginosa in the Philippines from 2013-2014

Jeremiah Chilam, Silvia Argimón, Marilyn T. Limas, Melissa Masim, June M Gayeta, Marietta L Lagrada, Agnettah M Olorosa, Victoria Cohen, Lara T. Hernandez, Benjamin Jeffrey, Khalil Abudahab, Charmian M. Hufano, Sonia B. Sia, Matthew T. G. Holden, John M. Stelling, , on behalf of the Philippines Antimicrobial Resistance Surveillance Program

This study sequenced 176 Pseudomonas aeruginosa isolates from the Philippines to characterize their genomic diversity, antimicrobial resistance mechanisms, and clonal spread.

bioRxiv · Mar 19, 2020 · PreprintGenomics

Phandango: an interactive viewer for bacterial population genomics.

James Hadfield, Nicholas J. Croucher, Richard Goater, Khalil Abudahab, David M. Aanensen, Simon R. Harris

Phandango provides an interactive web tool for exploring large-scale bacterial population genomics datasets by integrating multiple analysis outputs.

Bioinformatics · Sep 23, 2017Peer-reviewedBioinformatics