Whole genome sequencing reveals high-resolution epidemiological links between clinical and environmental Klebsiella pneumoniae

by Chakkaphan Runcharoen, Danesh Moradigaravand, Beth Blane, Suporn Paksanont, Jeeranan Thammachote, Suthatip Anun, Julian Parkhill, Narisara Chantratita, Sharon J. Peacock
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

Microevolution of Burkholderia pseudomallei during an acute infection

by Direk Limmathurotsakul, Matthew T.G. Holden, Paul Coupland, Erin P. Price, Narisara Chantratita, Vanaporn Wuthiekanun, Premjit Amornchai, Julian Parkhill, Sharon J. Peacock
Published 2018

Whole genome sequencing of ESBL-producing Escherichia coli isolated from patients, farm waste and canals in Thailand

by Chakkaphan Runcharoen, Kathy E. Raven, Sandra Reuter, Teemu Kallonen, Suporn Paksanont, Jeeranan Thammachote, Suthatip Anun, Beth Blane, Julian Parkhill, Sharon J. Peacock, Narisara Chantratita
Published 2018

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

by Susannah J. Salter, Michael J. Cox, Elena M. Turek, Szymon T. Calus, William O. Cookson, Miriam F. Moffatt, Paul Turner, Julian Parkhill, Nicholas J. Loman, Alan W. Walker
Published 2018

’Candidatus Ornithobacterium hominis’: Insights gained from draft genomes obtained from nasopharyngeal swabs

by Susannah J. Salter, Paul Scott, Andrew J. Page, Alan Tracey, Marcus C. de Goffau, Claire Cormie, Bernardo Ochoa-Montaño, Clare L. Ling, Jiraporn Tangmanakit, Paul Turner, Julian Parkhill
Published 2020

Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the env...

by Theodore Gouliouris, Kathy E. Raven, Danesh Moradigaravand, Catherine Ludden, Francesc Coll, Beth Blane, Plamena Naydenova, Carolyne Horner, Nicholas M. Brown, Jukka Corander, Direk Limmathurotsakul, Julian Parkhill, Sharon J. Peacock
Published 2020

Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei

by Claire Chewapreecha, Alison E. Mather, Simon R. Harris, Martin Hunt, Matthew T.G. Holden, Chutima Chaichana, Vanaporn Wuthiekanun, Gordon Dougan, Nicholas P.J. Day, Direk Limmathurotsakul, Julian Parkhill, Sharon J. Peacock
Published 2020

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

Surveillance and Epidemiology of Drug Resistant Infections Consortium (SEDRIC): Supporting the transition from strategy to action [version 1; referees: 2 approved, 1 approved with...

by Sharon J. Peacock, Keiji Fukuda, Direk Limmathurotsakul, Iruka N. Okeke, Nandini Shetty, Rogier van Doorn, Nicholas A. Feasey, Francesca Chiara, Ghada Zoubiane, Tim Jinks, Julian Parkhill, Jean Patel, Stuart W.J. Reid, Alison H. Holmes
Published 2019

Zero tolerance for healthcare-associated MRSA bacteraemia: Is it realistic?

by M. Estée Török, Simon R. Harris, Edward J.P. Cartwright, Kathy E. Raven, Nicholas M. Brown, Michael E.D. Allison, Daniel Greaves, Michael A. Quail, Direk Limmathurotsakul, Matthew T.G. Holden, Julian Parkhill, Sharon J. Peacock
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

Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting

by Steven Y.C. Tong, Matthew T.G. Holden, Emma K. Nickerson, Ben S. Cooper, Claudio U. Koser, Anne Cori, Thibaut Jombart, Simon Cauchemez, Christophe Fraser, Vanaporn Wuthiekanun, Janjira Thaipadungpanit, Maliwan Hongsuwan, Nicholas P. Day, Direk Limmathurotsakul, Julian Parkhill, Sharon J. Peacock
Published 2018

Evolution of the Staphylococcus argenteus ST2250 clone in Northeastern Thailand is linked with the acquisition of livestock-associated staphylococcal genes

by Danesh Moradigaravand, Dorota Jamrozy, Rafal Mostowy, Annaliesa Anderson, Emma K. Nickerson, Janjira Thaipadungpanit, Vanaporn Wuthiekanun, Direk Limmathurotsakul, Sarunporn Tandhavanant, Chanthiwa Wikraiphat, Gumphol Wongsuvan, Nittaya Teerawattanasook, Yaowaruk Jutrakul, Nuttiya Srisurat, Prajuab Chaimanee, T. Eoin West, Beth Blane, Julian Parkhill, Narisara Chantratita, Sharon J. Peacock
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

Co-evolutionary Signals Identify Burkholderia pseudomallei Survival Strategies in a Hostile Environment

by Claire Chewapreecha, Johan Pensar, Supaksorn Chattagul, Maiju Pesonen, Apiwat Sangphukieo, Phumrapee Boonklang, Chotima Potisap, Sirikamon Koosakulnirand, Edward J. Feil, Susanna Dunachie, Narisara Chantratita, Direk Limmathurotsakul, Sharon J. Peacock, Nick P.J. Day, Julian Parkhill, Nicholas R. Thomson, Rasana W. Sermswan, Jukka Corander
Published 2022

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

Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates

by Prasit Palittapongarnpim, Pravech Ajawatanawong, Wasna Viratyosin, Nat Smittipat, Areeya Disratthakit, Surakameth Mahasirimongkol, Hideki Yanai, Norio Yamada, Supalert Nedsuwan, Worarat Imasanguan, Pacharee Kantipong, Boonchai Chaiyasirinroje, Jiraporn Wongyai, Licht Toyo-oka, Jody Phelan, Julian Parkhill, Taane G. Clark, Martin L. Hibberd, Wuthiwat Ruengchai, Panawun Palittapongarnpim, Tada Juthayothin, Sissades Tongsima, Katsushi Tokunaga
Published 2019

Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa

by Chinyere K. Okoro, Robert A. Kingsley, Thomas R. Connor, Simon R. Harris, Christopher M. Parry, Manar N. Al-Mashhadani, Samuel Kariuki, Chisomo L. Msefula, Melita A. Gordon, Elizabeth De Pinna, John Wain, Robert S. Heyderman, Stephen Obaro, Pedro L. Alonso, Inacio Mandomando, Calman A. MacLennan, Milagritos D. Tapia, Myron M. Levine, Sharon M. Tennant, Julian Parkhill, Gordon Dougan
Published 2018