Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus by Andrew J. Page, Jacqueline A. Keane

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Scalable neighbour search and alignment with uvaia by Leonardo de Oliveira Martins, Alison E. Mather, Andrew J. Page

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Stability of the Encoding Plasmids and Surface Expression of CS6 Differs in Enterotoxigenic Escherichia coli (ETEC) Encoding Different Heat-Stable (ST) Enterotoxins (STh and STp). by Joshua Tobias, Astrid Von Mentzer, Patricia Loayza Frykberg, Martin Aslett, Andrew J Page, Åsa Sjöling, Ann-Mari Svennerholm

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AlbaTraDIS: Comparative analysis of large datasets from parallel transposon mutagenesis experiments. by Andrew J Page, Sarah Bastkowski, Muhammad Yasir, A Keith Turner, Thanh Le Viet, George M Savva, Mark A Webber, Ian G Charles

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Long-read sequencing for identification of insertion sites in large transposon mutant libraries by Muhammad Yasir, A. Keith Turner, Martin Lott, Steven Rudder, David Baker, Sarah Bastkowski, Andrew J. Page, Mark A. Webber, Ian G. Charles

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Long-read-sequenced reference genomes of the seven major lineages of enterotoxigenic Escherichia coli (ETEC) circulating in modern time by Astrid von Mentzer, Grace A. Blackwell, Derek Pickard, Christine J. Boinett, Enrique Joffré, Andrew J. Page, Ann-Mari Svennerholm, Gordon Dougan, Åsa Sjöling

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Genome-Wide Analysis of Innate Susceptibility Mechanisms of <i>Escherichia coli</i> to Colistin by Muhammad Yasir, A. Keith Turner, Sarah Bastkowski, Martin Lott, Emma R. Holden, Andrea Telatin, Andrew J. Page, Mark A. Webber, Ian G. Charles

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Phylogenetic Analysis of Klebsiella pneumoniae from Hospitalized Children, Pakistan by Hasan Ejaz, Nancy Wang, Jonathan J. Wilksch, Andrew J. Page, Hanwei Cao, Shruti Gujaran, Jacqueline A. Keane, Trevor Lithgow, Ikram ul-Haq, Gordon Dougan, Richard A. Strugnell, Eva Heinz

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Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine by Suheir Ereqat, Nabil-Fareed Alikhan, Amer Al-Jawabreh, Michaela Matthews, Ahmed Al-Jawabreh, Leonardo de Oliveira Martins, Alexander J. Trotter, Mai Al-Kaila, Andrew J. Page, Mark J. Pallen, Abedelmajeed Nasereddin

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An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid by Vanessa K. Wong, Stephen Baker, Thomas R. Connor, Derek Pickard, Andrew J. Page, Jayshree Dave, Niamh Murphy, Richard Holliman, Armine Sefton, Michael Millar, Zoe A. Dyson, Gordon Dougan, Kathryn E. Holt, International Typhoid Consortium

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Genomic surveillance of SARS-CoV-2 in COVID-19 vaccinated healthcare workers in Lebanon by Habib AlKalamouni, Farouk F. Abou Hassan, Mirna Bou Hamdan, Andrew J. Page, Martin Lott, Michaela Matthews, Nada Ghosn, Alissar Rady, Rami Mahfouz, George F. Araj, Ghassan Dbaibo, Hassan Zaraket, Nada M. Melhem, Ghassan M. Matar

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Hybrid metagenome assemblies link carbohydrate structure with function in the human gut microbiome by Anuradha Ravi, Perla Troncoso-Rey, Jennifer Ahn-Jarvis, Kendall R. Corbin, Suzanne Harris, Hannah Harris, Alp Aydin, Gemma L. Kay, Thanh Le Viet, Rachel Gilroy, Mark J. Pallen, Andrew J. Page, Justin O’Grady, Frederick J. Warren

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Emergence of an Extensively Drug-Resistant <italic toggle="yes">Salmonella enterica</italic> Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinol... by Elizabeth J. Klemm, Sadia Shakoor, Andrew J. Page, Farah Naz Qamar, Kim Judge, Dania K. Saeed, Vanessa K. Wong, Timothy J. Dallman, Satheesh Nair, Stephen Baker, Ghazala Shaheen, Shahida Qureshi, Mohammad Tahir Yousafzai, Muhammad Khalid Saleem, Zahra Hasan, Gordon Dougan, Rumina Hasan

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Dynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England by Oliver Eales, Leonardo de Oliveira Martins, Andrew J. Page, Haowei Wang, Barbara Bodinier, David Tang, David Haw, Jakob Jonnerby, Christina Atchison, Deborah Ashby, Wendy Barclay, Graham Taylor, Graham Cooke, Helen Ward, Ara Darzi, Steven Riley, Paul Elliott, Christl A. Donnelly, Marc Chadeau-Hyam

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Breakthrough SARS-CoV-2 infections in double and triple vaccinated adults and single dose vaccine effectiveness among children in Autumn 2021 in England: REACT-1 study by Marc Chadeau-Hyam, Oliver Eales, Barbara Bodinier, Haowei Wang, David Haw, Matthew Whitaker, Joshua Elliott, Caroline E. Walters, Jakob Jonnerby, Christina Atchison, Peter J. Diggle, Andrew J. Page, Deborah Ashby, Wendy Barclay, Graham Taylor, Graham Cooke, Helen Ward, Ara Darzi, Christl A. Donnelly, Paul Elliott

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Omicron SARS-CoV-2 epidemic in England during February 2022: A series of cross-sectional community surveys by Marc Chadeau-Hyam, David Tang, Oliver Eales, Barbara Bodinier, Haowei Wang, Jakob Jonnerby, Matthew Whitaker, Joshua Elliott, David Haw, Caroline E. Walters, Christina Atchison, Peter J. Diggle, Andrew J. Page, Deborah Ashby, Wendy Barclay, Graham Taylor, Graham Cooke, Helen Ward, Ara Darzi, Christl A. Donnelly, Paul Elliott

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Clinical Performance of Direct RT-PCR Testing of Raw Saliva for Detection of SARS-CoV-2 in Symptomatic and Asymptomatic Individuals by Rosa Castillo-Bravo, Noel Lucca, Linyi Lai, Killian Marlborough, Galina Brychkova, Maryam Shideh Sakhteh, Charlie Lonergan, Justin O’Grady, Nabil-Fareed Alikhan, Alexander J. Trotter, Andrew J. Page, Breda Smyth, Peter C. McKeown, Jelena D. M. Feenstra, Camilla Ulekleiv, Oceane Sorel, Manoj Gandhi, Charles Spillane

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SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2 by Oliver Eales, Andrew J. Page, Leonardo de Oliveira Martins, Haowei Wang, Barbara Bodinier, David Haw, Jakob Jonnerby, Christina Atchison, The COVID-19 Genomics UK (COG-UK) Consortium, Deborah Ashby, Wendy Barclay, Graham Taylor, Graham Cooke, Helen Ward, Ara Darzi, Steven Riley, Marc Chadeau-Hyam, Christl A. Donnelly, Paul Elliott

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Dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England by Paul Elliott, Oliver Eales, Barbara Bodinier, David Tang, Haowei Wang, Jakob Jonnerby, David Haw, Joshua Elliott, Matthew Whitaker, Caroline E. Walters, Christina Atchison, Peter J. Diggle, Andrew J. Page, Alexander J. Trotter, Deborah Ashby, Wendy Barclay, Graham Taylor, Helen Ward, Ara Darzi, Graham S. Cooke, Marc Chadeau-Hyam, Christl A. Donnelly

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A Phylogenetic and Phenotypic Analysis of Salmonella enterica Serovar Weltevreden, an Emerging Agent of Diarrheal Disease in Tropical Regions. by Carine Makendi, Andrew J Page, Brendan W Wren, Tu Le Thi Phuong, Simon Clare, Christine Hale, David Goulding, Elizabeth J Klemm, Derek Pickard, Chinyere Okoro, Martin Hunt, Corinne N Thompson, Nguyen Phu Huong Lan, Nhu Tran Do Hoang, Guy E Thwaites, Simon Le Hello, Anne Brisabois, François-Xavier Weill, Stephen Baker, Gordon Dougan

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