Whole Genome Sequence Analysis of a Large Isoniazid-Resistant Tuberculosis Outbreak in London: A Retrospective Observational Study. by Nicola Casali, Agnieszka Broda, Simon R Harris, Julian Parkhill, Timothy Brown, Francis Drobniewski

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Patent human infections with the whipworm, Trichuris trichiura, are not associated with alterations in the faecal microbiota. by Philip Cooper, Alan W Walker, Jorge Reyes, Martha Chico, Susannah J Salter, Maritza Vaca, Julian Parkhill

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Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila. by Sophia David, Leonor Sánchez-Busó, Simon R Harris, Pekka Marttinen, Christophe Rusniok, Carmen Buchrieser, Timothy G Harrison, Julian Parkhill

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Genomic Analysis of Companion Rabbit Staphylococcus aureus. by Mark A Holmes, Ewan M Harrison, Elizabeth A Fisher, Elizabeth M Graham, Julian Parkhill, Geoffrey Foster, Gavin K Paterson

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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

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Transposon insertion sequencing reveals novel hypermutator genes in Acinetobacter baumannii by Francesca L. Short, Ram Maharjan, Liping Li, Nusrat Afrin, Natasha Delgado, Christine J. Boinett, Julian Parkhill, Amy K. Cain, Ian T. Paulsen

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Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis. by Kristine B Arnvig, Iñaki Comas, Nicholas R Thomson, Joanna Houghton, Helena I Boshoff, Nicholas J Croucher, Graham Rose, Timothy T Perkins, Julian Parkhill, Gordon Dougan, Douglas B Young

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The mutational landscape of Staphylococcus aureus during colonisation by Francesc Coll, Beth Blane, Katherine L. Bellis, Marta Matuszewska, Toska Wonfor, Dorota Jamrozy, Michelle S. Toleman, Joan A. Geoghegan, Julian Parkhill, Ruth C. Massey, Sharon J. Peacock, Ewan M. Harrison

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Incidence and characterisation of methicillin-resistant Staphylococcus aureus (MRSA) from nasal colonisation in participants attending a cattle veterinary conference in the UK. by Gavin K Paterson, Ewan M Harrison, Emily F Craven, Andreas Petersen, Anders Rhod Larsen, Matthew J Ellington, M Estée Török, Sharon J Peacock, Julian Parkhill, Ruth N Zadoks, Mark A Holmes

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Cell envelope polysaccharide modifications alter the surface properties and interactions of Mycobacterium abscessus with innate immune cells in a morphotype-dependent manner by Elena Lian, Juan M. Belardinelli, Kavita De, Arun Prasad Pandurangan, Shiva K. Angala, Zuzana Palčeková, Anna E. Grzegorzewicz, Josephine M. Bryant, Tom L. Blundell, Julian Parkhill, R. Andres Floto, William H. Wheat, Mary Jackson

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Whole Genome Sequencing Shows a Low Proportion of Tuberculosis Disease Is Attributable to Known Close Contacts in Rural Malawi. by Judith R Glynn, José Afonso Guerra-Assunção, Rein M G J Houben, Lifted Sichali, Themba Mzembe, Lorrain K Mwaungulu, J Nimrod Mwaungulu, Ruth McNerney, Palwasha Khan, Julian Parkhill, Amelia C Crampin, Taane G Clark

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The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing. by Nicholas A Kennedy, Alan W Walker, Susan H Berry, Sylvia H Duncan, Freda M Farquarson, Petra Louis, John M Thomson, UK IBD Genetics Consortium, Jack Satsangi, Harry J Flint, Julian Parkhill, Charlie W Lees, Georgina L Hold

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The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex. by Stephen D Bentley, Iñaki Comas, Josephine M Bryant, Danielle Walker, Noel H Smith, Simon R Harris, Scott Thurston, Sebastien Gagneux, Jonathan Wood, Martin Antonio, Michael A Quail, Florian Gehre, Richard A Adegbola, Julian Parkhill, Bouke C de Jong

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The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water. by Abhilasha Karkey, Thibaut Jombart, Alan W Walker, Corinne N Thompson, Andres Torres, Sabina Dongol, Nga Tran Vu Thieu, Duy Pham Thanh, Dung Tran Thi Ngoc, Phat Voong Vinh, Andrew C Singer, Julian Parkhill, Guy Thwaites, Buddha Basnyat, Neil Ferguson, Stephen Baker

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Emergence of the Asian 1 genotype of dengue virus serotype 2 in viet nam: in vivo fitness advantage and lineage replacement in South-East Asia. by Thi Ty Hang Vu, Edward C Holmes, Veasna Duong, Thien Quy Nguyen, Tinh Hien Tran, Michael Quail, Carol Churcher, Julian Parkhill, Jane Cardosa, Jeremy Farrar, Bridget Wills, Niall J Lennon, Bruce W Birren, Philippe Buchy, Matthew R Henn, Cameron P Simmons

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Defining the estimated core genome of bacterial populations using a Bayesian decision model. by Andries J van Tonder, Shilan Mistry, James E Bray, Dorothea M C Hill, Alison J Cody, Chris L Farmer, Keith P Klugman, Anne von Gottberg, Stephen D Bentley, Julian Parkhill, Keith A Jolley, Martin C J Maiden, Angela B Brueggemann

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Rapid emergence of multidrug resistant, H58-lineage Salmonella typhi in Blantyre, Malawi. by Nicholas A Feasey, Katherine Gaskell, Vanessa Wong, Chisomo Msefula, George Selemani, Save Kumwenda, Theresa J Allain, Jane Mallewa, Neil Kennedy, Aisleen Bennett, Joram O Nyirongo, Patience A Nyondo, Madalitso D Zulu, Julian Parkhill, Gordon Dougan, Melita A Gordon, Robert S Heyderman

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Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. by Trevor D Lawley, Simon Clare, Alan W Walker, Mark D Stares, Thomas R Connor, Claire Raisen, David Goulding, Roland Rad, Fernanda Schreiber, Cordelia Brandt, Laura J Deakin, Derek J Pickard, Sylvia H Duncan, Harry J Flint, Taane G Clark, Julian Parkhill, Gordon Dougan

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Whole genome sequencing identifies zoonotic transmission of MRSA isolates with the novel mecA homologue mecC by Ewan M. Harrison, Gavin K. Paterson, Matthew T.G. Holden, Jesper Larsen, Marc Stegger, Anders Rhod Larsen, Andreas Petersen, Robert L. Skov, Judit Marta Christensen, Anne Bak Zeuthen, Ole Heltberg, Simon R. Harris, Ruth N. Zadoks, Julian Parkhill, Sharon J. Peacock, Mark A. Holmes

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Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing. by Taane G Clark, Kim Mallard, Francesc Coll, Mark Preston, Samuel Assefa, David Harris, Sam Ogwang, Francis Mumbowa, Bruce Kirenga, Denise M O'Sullivan, Alphonse Okwera, Kathleen D Eisenach, Moses Joloba, Stephen D Bentley, Jerrold J Ellner, Julian Parkhill, Edward C Jones-López, Ruth McNerney

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