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Publications

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

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

PANINI: Pangenome Neighbour Identification for Bacterial Populations

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

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

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

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

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

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

Integrated view of Vibrio cholerae in the Americas

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

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

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