Publications

Genomic epidemiology of Candida auris introduction and outbreaks in the United Kingdom

Kappel D. et al, (2024)

Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes.

Carey ME. et al, (2023), eLife, 12

Conservation of vaccine antigen sequences encoded by sequenced strains of Streptococcus equi subsp. equi.

Frosth S. et al, (2023), Equine veterinary journal, 55, 92 - 101

Deep clustering of bacterial tree images.

Hayati M. et al, (2022), Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 377

Genomic population structures of microbial pathogens.

Holt KE. et al, (2022), Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 377

Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic

Attwood SW. et al, (2022), Nature Reviews Genetics, 23, 547 - 562

Europe-wide expansion and eradication of multidrug-resistant Neisseria gonorrhoeae lineages: a genomic surveillance study.

Sánchez-Busó L. et al, (2022), The Lancet. Microbe, 3, e452 - e463

Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.

Griffiths EJ. et al, (2022), GigaScience, 11

Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence

Kraemer MUG. et al, (2021), Science, 373, 889 - 895

Genomic Epidemiology of CC30 Methicillin-Resistant Staphylococcus aureus Strains from Argentina Reveals Four Major Clades with Distinctive Genetic Features.

Di Gregorio S. et al, (2021), mSphere, 6, e01297 - e01220

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

du Plessis L. et al, (2021), Science, 371, 708 - 712

Integrated chromosomal and plasmid sequence analyses reveal diverse modes of carbapenemase gene spread among Klebsiella pneumoniae.

David S. et al, (2020), Proceedings of the National Academy of Sciences of the United States of America, 117, 25043 - 25054

Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines.

Argimón S. et al, (2020), Nature communications, 11

Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread

David S. et al, (2019), Nature Microbiology, 4, 1919 - 1929

Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study

Lo SW. et al, (2019), The Lancet Infectious Diseases, 19, 759 - 769

Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection.

McNally A. et al, (2019), mBio, 10, e00644 - e00619

PANINI: Pangenome Neighbour Identification for Bacterial Populations

Abudahab K. et al, (2019), Microbial Genomics, 5

Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris

Rhodes J. et al, (2018), Emerging Microbes & Infections, 7, 1 - 12

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa

Park SE. et al, (2018), Nature Communications, 9

Gene exchange drives the ecological success of a multi-host bacterial pathogen

Richardson EJ. et al, (2018), Nature Ecology & Evolution, 2, 1468 - 1478

Public health surveillance of multidrug-resistant clones of Neisseria gonorrhoeae in Europe: a genomic survey

Harris SR. et al, (2018), The Lancet Infectious Diseases, 18, 758 - 768

Development and worldwide use of non-lethal, and minimal population-level impact, protocols for the isolation of amphibian chytrid fungi

Fisher MC. et al, (2018), Scientific Reports, 8

Recent Asian origin of chytrid fungi causing global amphibian declines

O’Hanlon SJ. et al, (2018), Science, 360, 621 - 627

Phandango: an interactive viewer for bacterial population genomics

Hadfield J. et al, (2018), Bioinformatics, 34, 292 - 293

Genomic epidemiology of Candida auris within the United Kingdom, and the future of whole genome sequencing typing

Rhodes J. et al, (2018), MEDICAL MYCOLOGY, 56, S28 - S28

Integrated view of Vibrio cholerae in the Americas

Domman D. et al, (2017), Science, 358, 789 - 793

Emergence and clonal spread of colistin resistance due to multiple mutational mechanisms in carbapenemase-producing Klebsiella pneumoniae in London

Otter JA. et al, (2017), Scientific Reports, 7

Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination

Mostowy RJ. et al, (2017), Molecular Biology and Evolution, 34, 2537 - 2554

Corrigendum: Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland

Reuter S. et al, (2017), Genome Research, 27, 1622 - 1622

Population genetic structuring of methicillin-resistant Staphylococcus aureus clone EMRSA-15 within UK reflects patient referral patterns.

Donker T. et al, (2017), Microbial genomics, 3

The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens

Bayliss SC. et al, (2017), Frontiers in Microbiology, 8

Occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in the European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE): a prospective, multinational study

Grundmann H. et al, (2017), The Lancet Infectious Diseases, 17, 153 - 163

Species Mash-up

Argimón S. and Aanensen DM., (2016), Nature Reviews Microbiology, 14, 730 - 730

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

Argimón S. et al, (2016), Microbial Genomics, 2

Genomic Analysis and Comparison of Two Gonorrhea Outbreaks

Didelot X. et al, (2016), mBio, 7

Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe

Aanensen DM. et al, (2016), mBio, 7

Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection

Crellen T. et al, (2016), Scientific Reports, 6

Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland

Reuter S. et al, (2016), Genome Research, 26, 263 - 270

The dynamic changes of dominant clones of Staphylococcus aureus causing bloodstream infections in the European region: Results of a second structured survey

Grundmann H. et al, (2014), Eurosurveillance, 19

EpiCollect+: linking smartphones to web applications for complex data collection projects

Aanensen DM. et al, (2014), F1000Research, 3, 199 - 199

OutbreakTools: A new platform for disease outbreak analysis using the R software

Jombart T. et al, (2014), Epidemics, 7, 28 - 34

Dense genomic sampling identifies highways of pneumococcal recombination

Chewapreecha C. et al, (2014), Nature Genetics, 46, 305 - 309

Melioidosis Caused byBurkholderia pseudomalleiin Drinking Water, Thailand, 2012

Limmathurotsakul D. et al, (2014), Emerging Infectious Diseases, 20, 265 - 268

Multilocus Sequence Typing and Further Genetic Characterization of the Enigmatic Pathogen, Staphylococcus hominis

Zhang L. et al, (2013), PLoS ONE, 8, e66496 - e66496

Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

Cheng L. et al, (2013), Molecular Biology and Evolution, 30, 1224 - 1228

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

Holden MTG. et al, (2013), Genome Research, 23, 653 - 664

Genetic Relationships of Vibrio parahaemolyticus Isolates from Clinical, Human Carrier, and Environmental Sources in Thailand, Determined by Multilocus Sequence Analysis

Theethakaew C. et al, (2013), Applied and Environmental Microbiology, 79, 2358 - 2370

Mapping the Global Emergence of Batrachochytrium dendrobatidis, the Amphibian Chytrid Fungus

Olson DH. et al, (2013), PLoS ONE, 8, e56802 - e56802

A Single Multilocus Sequence Typing (MLST) Scheme for Seven Pathogenic Leptospira Species

Boonsilp S. et al, (2013), PLoS Neglected Tropical Diseases, 7, e1954 - e1954

Genetic Characterization of Trichomonas vaginalis Isolates by Use of Multilocus Sequence Typing

Cornelius DC. et al, (2012), Journal of Clinical Microbiology, 50, 3293 - 3300

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Publications