Two-phase importance sampling for inference about transmission trees

by Elina Numminen, Claire Chewapreecha, Jukka Sirén, Claudia Turner, Paul Turner, Stephen D. Bentley, Jukka Corander
Published 2018

Improved detection of nasopharyngeal cocolonization by multiple pneumococcal serotypes by use of latex agglutination or molecular serotyping by microarray

by Paul Turner, Jason Hinds, Claudia Turner, Auscharee Jankhot, Katherine Gould, Stephen D. Bentley, François Nosten, David Goldblatt
Published 2018

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 2018

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 2018

Genomic identification of a novel co-trimoxazole resistance genotype and its prevalence amongst Streptococcus pneumoniae in Malawi

by Jennifer E. Cornick, Simon R. Harris, Christopher M. Parry, Michael J. Moore, Chikondi Jassi, Arox Kamng'ona, Benard Kulohoma, Robert S. Heyderman, Stephen D. Bentley, Dean B. Everett
Published 2018

Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes

by Claire Chewapreecha, Pekka Marttinen, Nicholas J. Croucher, Susannah J. Salter, Simon R. Harris, Alison E. Mather, William P. Hanage, David Goldblatt, Francois H. Nosten, Claudia Turner, Paul Turner, Stephen D. Bentley, Julian Parkhill
Published 2018

Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

by Marcin J. Skwark, Nicholas J. Croucher, Santeri Puranen, Claire Chewapreecha, Maiju Pesonen, Ying Ying Xu, Paul Turner, Simon R. Harris, Stephen B. Beres, James M. Musser, Julian Parkhill, Stephen D. Bentley, Erik Aurell, Jukka Corander
Published 2018

Evolution of MRSA during hospital transmission and intercontinental spread

by Simon R. Harris, Edward J. Feil, Matthew T.G. Holden, Michael A. Quail, Emma K. Nickerson, Narisara Chantratita, Susana Gardete, Ana Tavares, Nick Day, Jodi A. Lindsay, Jonathan D. Edgeworth, Hermínia De Lencastre, Julian Parkhill, Sharon J. Peacock, Stephen D. Bentley
Published 2018

Dense genomic sampling identifies highways of pneumococcal recombination

by Claire Chewapreecha, Simon R. Harris, Nicholas J. Croucher, Claudia Turner, Pekka Marttinen, Lu Cheng, Alberto Pessia, David M. Aanensen, Alison E. Mather, Andrew J. Page, Susannah J. Salter, David Harris, Francois Nosten, David Goldblatt, Jukka Corander, Julian Parkhill, Paul Turner, Stephen D. Bentley
Published 2018

Early signals of vaccine-driven perturbation seen in pneumococcal carriage population genomic data

by Chrispin Chaguza, Ellen Heinsbroek, Rebecca A. Gladstone, Terence Tafatatha, Maaike Alaerts, Chikondi Peno, Jennifer E. Cornick, Patrick Musicha, Naor Bar-Zeev, Arox Kamng'Ona, Aras Kadioglu, Lesley McGee, William P. Hanage, Robert F. Breiman, Robert S. Heyderman, Neil French, Dean B. Everett, Stephen D. Bentley
Published 2020

Evidence for soft selective sweeps in the evolution of pneumococcal multidrug resistance and vaccine escape

by Nicholas J. Croucher, Claire Chewapreecha, William P. Hanage, Simon R. Harris, Lesley McGee, Mark Van Der Linden, Jae Hoon Song, Kwan Soo Ko, Herminia De Lencastre, Claudia Turner, Fan Yang, Raquel Sa-Leao, Bernard Beall, Keith P. Klugman, Julian Parkhill, Paul Turner, Stephen D. Bentley
Published 2018

Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages

by Markus Hilty, Daniel Wüthrich, Susannah J. Salter, Hansjürg Engel, Samuel Campbell, Raquel Sá-Leão, Hermínia De Lencastre, Peter Hermans, Ewa Sadowy, Paul Turner, Claire Chewapreecha, Mathew Diggle, Gerd Pluschke, Lesley McGee, Özgen Köseoʇlu Eser, Donald E. Low, Heidi Smith-Vaughan, Andrea Endimiani, Marianne Kü Ffer, Mélanie Dupasquier, Emmanuel Beaudoing, Johann Weber, Rémy Bruggmann, William P. Hanage, Julian Parkhill, Lucy J. Hathaway, Kathrin Mü Hlemann, Stephen D. Bentley
Published 2018

Complete genomes of two clinical Staphylococcus aureus strains: Evidence for the evolution of virulence and drug resistance

by Matthew T.G. Holden, Edward J. Feil, Jodi A. Lindsay, Sharon J. Peacock, Nicholas P.J. Day, Mark C. Enright, Tim J. Foster, Catrin E. Moore, Laurence Hurst, Rebecca Atkin, Andrew Barron, Nathalie Bason, Stephen D. Bentley, Carol Chillingworth, Tracey Chillingworth, Carol Churcher, Louise Clark, Craig Corton, Ann Cronin, Jon Doggett, Linda Dowd, Theresa Feltwell, Zahra Hance, Barbara Harris, Heidi Hauser, Simon Holroyd, Kay Jagels, Keith D. James, Nicola Lennard, Alexandra Line, Rebecca Mayes, Sharon Moule, Karen Mungall, Douglas Ormond, Michael A. Quail, Ester Rabbinowitsch, Kim Rutherford, Mandy Sanders, Sarah Sharp, Mark Simmonds, Kim Stevens, Sally Whitehead, Bart G. Barrell, Brian G. Spratt, Julian Parkhill
Published 2018

Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei

by Matthew T.G. Holden, Richard W. Titball, Sharon J. Peacock, Ana M. Cerdeño-Tárraga, Timothy Atkins, Lisa C. Crossman, Tyrone Pitt, Carol Churcher, Karen Mungall, Stephen D. Bentley, Mohammed Sebaihia, Nicholas R. Thomson, Mathalie Bason, Ifor R. Beacham, Karen Brooks, Katherine A. Brown, Nat F. Brown, Greg L. Challis, Inna Cherevach, Tracy Chillingworth, Ann Cronin, Ben Crossett, Paul Davis, David DeShazer, Theresa Feltwell, Audrey Fraser, Zahra Hance, Heidi Hauser, Simon Holroyd, Kay Jagels, Karen E. Keith, Mark Maddison, Sharon Moule, Claire Price, Michael A. Quail, Ester Rabbinowitsch, Kim Rutherford, Mandy Sanders, Mark Simmonds, Sirirurg Songsivilai, Kim Stevens, Sarinna Tumapa, Monkgol Vesaratchavest, Sally Whitehead, Corin Yeats, Bart G. Barrell, Petra C.F. Oyston, Julian Parkhill
Published 2018