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Publications

Geographical distribution, disease association and diversity of Klebsiella pneumoniae K/L and O antigens in India: roadmap for vaccine development.

Shamanna V. et al, (2024), Microb Genom, 10

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), Nat Rev Genet, 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 Vet J

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

PYBUS O. et al, (2021), Science

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

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

DU PLESSIS L., (2020), Science

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

David S. et al, (2020), Proc Natl Acad Sci U S A, 117, 25043 - 25054

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

Argimón S. et al, (2020), Nat Commun, 11

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

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

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

(2019), Emerging Microbes and Infections

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

(2019), mBio

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

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

Park SE. et al, (2018), Nat Commun, 9

PANINI: Pangenome Neighbour Identification for Bacterial Populations.

Abudahab K. et al, (2018), Microbial genomics

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

Richardson EJ. et al, (2018), Nat Ecol Evol, 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

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