A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers von Quail, Michael A, Smith, Miriam, Coupland, Paul, Otto, Thomas D, Harris, Simon R, Connor, Thomas R, Bertoni, Anna, Swerdlow, Harold P, Gu, Yong

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A structure-based nomenclature for Bacillus thuringiensis and other bacteria-derived pesticidal proteins von Crickmore, Neil, Berry, Colin, Panneerselvam, Suresh, Mishra, Ruchir, Connor, Thomas R., Bonning, Bryony C.

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Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins von Croucher, Nicholas J, Page, Andrew J, Connor, Thomas R, Delaney, Aidan J, Keane, Jacqueline A, Bentley, Stephen D, Parkhill, Julian, Harris, Simon R

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Shedding of SARS-CoV-2 in feces and urine and its potential role in person-to-person transmission and the environment-based spread of COVID-19 von Jones, David L., Baluja, Marcos Quintela, Graham, David W., Corbishley, Alexander, McDonald, James E., Malham, Shelagh K., Hillary, Luke S., Connor, Thomas R., Gaze, William H., Moura, Ines B., Wilcox, Mark H., Farkas, Kata

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Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic von Attwood, Stephen W., Hill, Sarah C., Aanensen, David M., Connor, Thomas R., Pybus, Oliver G.

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Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK von du Plessis, Louis, McCrone, John T, Zarebski, Alexander E, Hill, Verity, Ruis, Christopher, Gutierrez, Bernardo, Raghwani, Jayna, Ashworth, Jordan, Colquhoun, Rachel, Connor, Thomas R, Faria, Nuno R, Jackson, Ben, Loman, Nicholas J, O'Toole, Áine, Nicholls, Samuel M, Parag, Kris V, Scher, Emily, Vasylyeva, Tetyana I, Volz, Erik M, Watts, Alexander, Bogoch, Isaac I, Khan, Kamran, Aanensen, David M, Kraemer, Moritz U G, Rambaut, Andrew, Pybus, Oliver G

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Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health von Holt, Kathryn E, Wertheim, Heiman, Zadoks, Ruth N, Baker, Stephen, Whitehouse, Chris A, Dance, David, Jenney, Adam, Connor, Thomas R, Hsu, Li Yang, Severin, Juliëtte, Brisse, Sylvain, Cao, Hanwei, Wilksch, Jonathan, Gorrie, Claire, Schultz, Mark B, Edwards, David J, Nguyen, Kinh Van, Nguyen, Trung Vu, Dao, Trinh Tuyet, Mensink, Martijn, Minh, Vien Le, Nhu, Nguyen Thi Khanh, Schultsz, Constance, Kuntaman, Kuntaman, Newton, Paul N, Moore, Catrin E, Strugnell, Richard A, Thomson, Nicholas R

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

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Patterns of genome evolution that have accompanied host adaptation in Salmonella von Langridge, Gemma C, Fookes, Maria, Connor, Thomas R, Feltwell, Theresa, Feasey, Nicholas, Parsons, Bryony N, Seth-Smith, Helena M B, Barquist, Lars, Stedman, Anna, Humphrey, Tom, Wigley, Paul, Peters, Sarah E, Maskell, Duncan J, Corander, Jukka, Chabalgoity, Jose A, Barrow, Paul, Parkhill, Julian, Dougan, Gordon, Thomson, Nicholas R

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Evaluating the risk of SARS-CoV-2 reinfection with the Omicron or Delta variant in Wales, UK von Postans, Mark, Pacchiarini, Nicole, Song, Jiao, Cottrell, Simon, Williams, Catie, Beazer, Andrew, Moore, Catherine, Connor, Thomas R, Williams, Christopher

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Evidence for several waves of global transmission in the seventh cholera pandemic von Mutreja, Ankur, Kim, Dong Wook, Thomson, Nicholas R., Connor, Thomas R., Lee, Je Hee, Kariuki, Samuel, Croucher, Nicholas J., Choi, Seon Young, Harris, Simon R., Lebens, Michael, Niyogi, Swapan Kumar, Kim, Eun Jin, Ramamurthy, T., Chun, Jongsik, Wood, James L. N., Clemens, John D., Czerkinsky, Cecil, Nair, G. Balakrish, Holmgren, Jan, Parkhill, Julian, Dougan, Gordon

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Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa von Okoro, Chinyere K, Kingsley, Robert A, Connor, Thomas R, Harris, Simon R, Parry, Christopher M, Al-Mashhadani, Manar N, Kariuki, Samuel, Msefula, Chisomo L, Gordon, Melita A, de Pinna, Elizabeth, Wain, John, Heyderman, Robert S, Obaro, Stephen, Alonso, Pedro L, Mandomando, Inacio, MacLennan, Calman A, Tapia, Milagritos D, Levine, Myron M, Tennant, Sharon M, Parkhill, Julian, Dougan, Gordon

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Detection of recombination events in bacterial genomes from large population samples von Marttinen, Pekka, Hanage, William P., Croucher, Nicholas J., Connor, Thomas R., Harris, Simon R., Bentley, Stephen D., Corander, Jukka

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CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance von Nicholls, Samuel M, Poplawski, Radoslaw, Bull, Matthew J, Underwood, Anthony, Chapman, Michael, Abu-Dahab, Khalil, Taylor, Ben, Colquhoun, Rachel M, Rowe, Will P M, Jackson, Ben, Hill, Verity, O'Toole, Áine, Rey, Sara, Southgate, Joel, Amato, Roberto, Livett, Rich, Gonçalves, Sónia, Harrison, Ewan M, Peacock, Sharon J, Aanensen, David M, Rambaut, Andrew, Connor, Thomas R, Loman, Nicholas J

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Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer von Murchison, Elizabeth P., Schulz-Trieglaff, Ole B., Ning, Zemin, Alexandrov, Ludmil B., Bauer, Markus J., Fu, Beiyuan, Hims, Matthew, Ding, Zhihao, Ivakhno, Sergii, Stewart, Caitlin, Ng, Bee Ling, Wong, Wendy, Aken, Bronwen, White, Simon, Alsop, Amber, Becq, Jennifer, Bignell, Graham R., Cheetham, R. Keira, Cheng, William, Connor, Thomas R., Cox, Anthony J., Feng, Zhi-Ping, Gu, Yong, Grocock, Russell J., Harris, Simon R., Khrebtukova, Irina, Kingsbury, Zoya, Kowarsky, Mark, Kreiss, Alexandre, Luo, Shujun, Marshall, John, McBride, David J., Murray, Lisa, Pearse, Anne-Maree, Raine, Keiran, Rasolonjatovo, Isabelle, Shaw, Richard, Tedder, Philip, Tregidgo, Carolyn, Vilella, Albert J., Wedge, David C., Woods, Gregory M., Gormley, Niall, Humphray, Sean, Schroth, Gary, Smith, Geoffrey, Hall, Kevin, Searle, Stephen M.J., Carter, Nigel P., Papenfuss, Anthony T., Futreal, P. Andrew, Campbell, Peter J., Yang, Fengtang, Bentley, David R., Evers, Dirk J., Stratton, Michael R.

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Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from sub-Saharan Africa von Okoro, Chinyere K, Barquist, Lars, Connor, Thomas R, Harris, Simon R, Clare, Simon, Stevens, Mark P, Arends, Mark J, Hale, Christine, Kane, Leanne, Pickard, Derek J, Hill, Jennifer, Harcourt, Katherine, Parkhill, Julian, Dougan, Gordon, Kingsley, Robert A

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Parallel independent evolution of pathogenicity within the genus Yersinia von Reuter, Sandra, Connor, Thomas R., Barquist, Lars, Walker, Danielle, Feltwell, Theresa, Harris, Simon R., Fookes, Maria, Hall, Miquette E., Petty, Nicola K., Fuchs, Thilo M., Corander, Jukka, Dufour, Muriel, Ringwood, Tamara, Savin, Cyril, Bouchier, Christiane, Martin, Liliane, Miettinen, Minna, Shubin, Mikhail, Riehm, Julia M., Laukkanen-Ninios, Riikka, Sihvonen, Leila M., Siitonen, Anja, Skurnik, Mikael, Falcão, Juliana Pfrimer, Fukushima, Hiroshi, Scholz, Holger C., Prentice, Michael B., Wren, Brendan W., Parkhill, Julian, Carniel, Elisabeth, Achtman, Mark, McNally, Alan, Thomson, Nicholas R.

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Genomic epidemiology reveals geographical clustering of multidrug-resistant Escherichia coli ST131 associated with bacteraemia in Wales von White, Rhys T., Bull, Matthew J., Barker, Clare R., Arnott, Julie M., Wootton, Mandy, Jones, Lim S., Howe, Robin A., Morgan, Mari, Ashcroft, Melinda M., Forde, Brian M., Connor, Thomas R., Beatson, Scott A.

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Genome mining identifies cepacin as a plant-protective metabolite of the biopesticidal bacterium Burkholderia ambifaria von Mullins, Alex J., Murray, James A. H., Bull, Matthew J., Jenner, Matthew, Jones, Cerith, Webster, Gordon, Green, Angharad E., Neill, Daniel R., Connor, Thomas R., Parkhill, Julian, Challis, Gregory L., Mahenthiralingam, Eshwar

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Discovery of the Pseudomonas Polyyne Protegencin by a Phylogeny-Guided Study of Polyyne Biosynthetic Gene Cluster Diversity von Mullins, Alex J, Webster, Gordon, Kim, Hak Joong, Zhao, Jinlian, Petrova, Yoana D, Ramming, Christina E, Jenner, Matthew, Murray, James A H, Connor, Thomas R, Hertweck, Christian, Challis, Gregory L, Mahenthiralingam, Eshwar

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