Geographical distribution, disease association and diversity of Klebsiella pneumoniae K/L and O antigens in India: roadmap for vaccine development
Journal article
Shamanna V. et al, (2024), Microbial Genomics, 10
Genomic epidemiology of Candida auris introduction and outbreaks in the United Kingdom
Preprint
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.
Journal article
Carey ME. et al, (2023), eLife, 12
Conservation of vaccine antigen sequences encoded by sequenced strains of Streptococcus equi subsp. equi.
Journal article
Frosth S. et al, (2023), Equine veterinary journal, 55, 92 - 101
Deep clustering of bacterial tree images.
Journal article
Hayati M. et al, (2022), Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 377
Genomic population structures of microbial pathogens.
Journal article
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
Journal article
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.
Journal article
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.
Journal article
Griffiths EJ. et al, (2022), GigaScience, 11
Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence
Journal article
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.
Journal article
Di Gregorio S. et al, (2021), mSphere, 6, e01297 - e01220
Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK
Journal article
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.
Journal article
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.
Journal article
Argimón S. et al, (2020), Nature communications, 11
Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread
Journal article
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
Journal article
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.
Journal article
McNally A. et al, (2019), mBio, 10, e00644 - e00619
PANINI: Pangenome Neighbour Identification for Bacterial Populations
Journal article
Abudahab K. et al, (2019), Microbial Genomics, 5
Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris
Journal article
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
Journal article
Park SE. et al, (2018), Nature Communications, 9
Gene exchange drives the ecological success of a multi-host bacterial pathogen
Journal article
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
Journal article
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
Journal article
Fisher MC. et al, (2018), Scientific Reports, 8
Recent Asian origin of chytrid fungi causing global amphibian declines
Journal article
O’Hanlon SJ. et al, (2018), Science, 360, 621 - 627
Phandango: an interactive viewer for bacterial population genomics
Journal article
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
Conference paper
Rhodes J. et al, (2018), MEDICAL MYCOLOGY, 56, S28 - S28
Integrated view of Vibrio cholerae in the Americas
Journal article
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
Journal article
Otter JA. et al, (2017), Scientific Reports, 7
Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination
Journal article
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
Journal article
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.
Journal article
Donker T. et al, (2017), Microbial genomics, 3
The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens
Journal article
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
Journal article
Grundmann H. et al, (2017), The Lancet Infectious Diseases, 17, 153 - 163
Species Mash-up
Journal article
Argimón S. and Aanensen DM., (2016), Nature Reviews Microbiology, 14, 730 - 730
Microreact: visualizing and sharing data for genomic epidemiology and phylogeography
Journal article
Argimón S. et al, (2016), Microbial Genomics, 2
Genomic Analysis and Comparison of Two Gonorrhea Outbreaks
Journal article
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
Journal article
Aanensen DM. et al, (2016), mBio, 7
Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection
Journal article
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
Journal article
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
Journal article
Grundmann H. et al, (2014), Eurosurveillance, 19
EpiCollect+: linking smartphones to web applications for complex data collection projects
Journal article
Aanensen DM. et al, (2014), F1000Research, 3, 199 - 199
OutbreakTools: A new platform for disease outbreak analysis using the R software
Journal article
Jombart T. et al, (2014), Epidemics, 7, 28 - 34
Dense genomic sampling identifies highways of pneumococcal recombination
Journal article
Chewapreecha C. et al, (2014), Nature Genetics, 46, 305 - 309
Melioidosis Caused byBurkholderia pseudomalleiin Drinking Water, Thailand, 2012
Journal article
Limmathurotsakul D. et al, (2014), Emerging Infectious Diseases, 20, 265 - 268
Multilocus Sequence Typing and Further Genetic Characterization of the Enigmatic Pathogen, Staphylococcus hominis
Journal article
Zhang L. et al, (2013), PLoS ONE, 8, e66496 - e66496
Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software
Journal article
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
Journal article
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
Journal article
Theethakaew C. et al, (2013), Applied and Environmental Microbiology, 79, 2358 - 2370
Mapping the Global Emergence of Batrachochytrium dendrobatidis, the Amphibian Chytrid Fungus
Journal article
Olson DH. et al, (2013), PLoS ONE, 8, e56802 - e56802
A Single Multilocus Sequence Typing (MLST) Scheme for Seven Pathogenic Leptospira Species
Journal article
Boonsilp S. et al, (2013), PLoS Neglected Tropical Diseases, 7, e1954 - e1954