Global genomic pathogen surveillance to inform vaccine strategies: a decade-long expedition in pneumococcal genomics

by Stephen D. Bentley, Stephanie W. Lo
Published 2021-05-01

A high-resolution view of genome-wide pneumococcal transformation.

by Nicholas J Croucher, Simon R Harris, Lars Barquist, Julian Parkhill, Stephen D Bentley
Published 2012-01-01

Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict.

by Nicholas J Croucher, Rafal Mostowy, Christopher Wymant, Paul Turner, Stephen D Bentley, Christophe Fraser
Published 2016-03-01

Synergistic Activity of Mobile Genetic Element Defences in <i>Streptococcus pneumoniae</i>

by Min Jung Kwun, Marco R. Oggioni, Stephen D. Bentley, Christophe Fraser, Nicholas J. Croucher
Published 2019-09-01

Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions

by Andries J. van Tonder, Andries J. van Tonder, James E. Bray, Keith A. Jolley, Melissa Jansen van Rensburg, Sigríður J. Quirk, Gunnsteinn Haraldsson, Martin C. J. Maiden, Stephen D. Bentley, Stephen D. Bentley, Stephen D. Bentley, Ásgeir Haraldsson, Helga Erlendsdóttir, Karl G. Kristinsson, Angela B. Brueggemann, Angela B. Brueggemann
Published 2019-02-01

RhierBAPS: An R implementation of the population clustering algorithm hierBAPS [version 1; referees: 2 approved]

by Gerry Tonkin-Hill, John A. Lees, Stephen D. Bentley, Simon D.W. Frost, Jukka Corander
Published 2018-07-01

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study [version 1; referees: 1 approved, 2 approved with reservations]

by John A. Lees, Michelle Kendall, Julian Parkhill, Caroline Colijn, Stephen D. Bentley, Simon R. Harris
Published 2018-03-01

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study [version 2; referees: 2 approved, 1 approved with reservations]

by John A. Lees, Michelle Kendall, Julian Parkhill, Caroline Colijn, Stephen D. Bentley, Simon R. Harris
Published 2018-05-01

Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

by John A Lees, Nicholas J Croucher, David Goldblatt, François Nosten, Julian Parkhill, Claudia Turner, Paul Turner, Stephen D Bentley
Published 2017-07-01

The impact of recombination on dN/dS within recently emerged bacterial clones.

by Santiago Castillo-Ramírez, Simon R Harris, Matthew T G Holden, Miao He, Julian Parkhill, Stephen D Bentley, Edward J Feil
Published 2011-07-01

Genomic evolution of Neisseria gonorrhoeae since the preantibiotic era (1928–2013): antimicrobial use/misuse selects for resistance and drives evolution

by Daniel Golparian, Simon R. Harris, Leonor Sánchez-Busó, Steen Hoffmann, William M. Shafer, Stephen D. Bentley, Jörgen S. Jensen, Magnus Unemo
Published 2020-02-01

Selective and genetic constraints on pneumococcal serotype switching.

by Nicholas J Croucher, Lisa Kagedan, Claudette M Thompson, Julian Parkhill, Stephen D Bentley, Jonathan A Finkelstein, Marc Lipsitch, William P Hanage
Published 2015-03-01

A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children.

by Susannah J Salter, Claudia Turner, Wanitda Watthanaworawit, Marcus C de Goffau, Josef Wagner, Julian Parkhill, Stephen D Bentley, David Goldblatt, Francois Nosten, Paul Turner
Published 2017-10-01

High rates of homologous recombination in the mite endosymbiont and opportunistic human pathogen Orientia tsutsugamushi.

by Piengchan Sonthayanon, Sharon J Peacock, Wirongrong Chierakul, Vanaporn Wuthiekanun, Stuart D Blacksell, Mathew T G Holden, Stephen D Bentley, Edward J Feil, Nicholas P J Day
Published 2010-07-01

Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice

by Catriona P. Harkins, Bruno Pichon, Michel Doumith, Julian Parkhill, Henrik Westh, Alexander Tomasz, Herminia de Lencastre, Stephen D. Bentley, Angela M. Kearns, Matthew T. G. Holden
Published 2017-07-01

Genotypic and phenotypic modifications of Neisseria meningitidis after an accidental human passage.

by Hélène Omer, Graham Rose, Keith A Jolley, Eric Frapy, Jean-Ralph Zahar, Martin C J Maiden, Stephen D Bentley, Colin R Tinsley, Xavier Nassif, Emmanuelle Bille
Published 2011-02-01

Genome-wide analysis reveals loci encoding anti-macrophage factors in the human pathogen Burkholderia pseudomallei K96243.

by Andrea J Dowling, Paul A Wilkinson, Matthew T G Holden, Michael A Quail, Stephen D Bentley, Julia Reger, Nicholas R Waterfield, Richard W Titball, Richard H Ffrench-Constant
Published 2010-12-01

Genetic characterisation of Malawian pneumococci prior to the roll-out of the PCV13 vaccine using a high-throughput whole genome sequencing approach.

by Dean B Everett, Jennifer Cornick, Brigitte Denis, Claire Chewapreecha, Nicholas Croucher, Simon Harris, Julian Parkhill, Stephen Gordon, Enitan D Carrol, Neil French, Robert S Heyderman, Stephen D Bentley
Published 2012-01-01

Lineage-specific Virulence Determinants of Haemophilus influenzae Biogroup aegyptius

by Fiona R. Strouts, Peter Power, Nicholas J. Croucher, Nicola Corton, Andries van Tonder, Michael A. Quail, Paul R. Langford, Michael J. Hudson, Julian Parkhill, J. Simon Kroll, Stephen D. Bentley
Published 2012-03-01

Carriage Dynamics of Pneumococcal Serotypes in Naturally Colonized Infants in a Rural African Setting During the First Year of Life

by Chrispin Chaguza, Chrispin Chaguza, Madikay Senghore, Ebrima Bojang, Stephanie W. Lo, Chinelo Ebruke, Rebecca A. Gladstone, Peggy-Estelle Tientcheu, Rowan E. Bancroft, Archibald Worwui, Ebenezer Foster-Nyarko, Fatima Ceesay, Catherine Okoi, Lesley McGee, Keith P. Klugman, Robert F. Breiman, Michael R. Barer, Richard A. Adegbola, Richard A. Adegbola, Martin Antonio, Martin Antonio, Stephen D. Bentley, Stephen D. Bentley, Brenda A. Kwambana-Adams, Brenda A. Kwambana-Adams
Published 2021-01-01