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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

Deep clustering of bacterial tree images.

Hayati M. et al, (2022), Philos Trans R Soc Lond B Biol Sci, 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), 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

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

Frosth S. et al, (2022), Equine veterinary journal

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

Kraemer MUG. et al, (2021), Science (New York, N.Y.), 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 (New York, N.Y.), 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

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

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

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

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

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