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2. Index

Author

Rodger, Gillian M

Published
2018

3. Appendix

Author

Rodger, Gillian M

Published
2018

4. Notes

Author

Rodger, Gillian M

Published
2018

13. Contents

Author

Rodger, Gillian M

Published
2018

20. A crowd of BashTheBug volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates

Author

Fowler, Philip W, Wright, Carla, Spiers, Helen, Zhu, Tingting, Baeten, Elisabeth ML, Hoosdally, Sarah W, Cruz, Ana L Gibertoni, Roohi, Aysha, Kouchaki, Samaneh, Walker, Timothy M, Peto, Timothy EA, Miller, Grant, Lintott, Chris, Clifton, David, Crook, Derrick W, Walker, A Sarah, Barilar, Ivan, Battaglia, Simone, Borroni, Emanuele, Brandao, Angela Pires, Brankin, Alice, Cabibbe, Andrea Maurizio, Carter, Joshua, Cirillo, Daniela Maria, Claxton, Pauline, Clifton, David A, Cohen, Ted, Coronel, Jorge, Earle, Sarah G, Escuyer, Vincent, Ferrazoli, Lucilaine, Gao, George F, Gardy, Jennifer, Gharbia, Saheer, Ghisi, Kelen Teixeira, Ghodousi, Arash, Cruz, Ana Luıza Gibertoni, Grazian, Clara, Guthrie, Jennifer L, He, Wencong, Hoffmann, Harald, Hoosdally, Sarah J, Hunt, Martin, Iqbal, Zamin, Ismail, Nazir Ahmed, Jarrett, Lisa, Joseph, Lavania, Jou, Ruwen, Kambli, Priti, Knaggs, Jeff, Koch, Anastasia, Kohlerschmidt, Donna, Lachapelle, Alexander S, Lalvani, Ajit, Lapierre, Simon Grandjean, Laurenson, Ian F, Letcher, Brice, Lin, Wan-Hsuan, Liu, Chunfa, Liu, Dongxin, Malone, Kerri M, Mandal, Ayan, Matias, Daniela, Meintjes, Graeme, Mendes, Flavia Freitas, Merker, Matthias, Mihalic, Marina, Millard, James, Miotto, Paolo, Mistry, Nerges, Moore, David, Dreyer, Viola, Chetty, Darren, Musser, Kimberlee A, Ngcamu, Dumisani, Nhung, Hoang Ngoc, Grandjean, Louis, Nilgiriwala, Kayzad Soli, Nimmo, Camus, Okozi, Nana, Oliveira, Rosangela Siqueira, Omar, Shaheed Vally, Paton, Nicholas, Pinhata, Juliana Maira Watanabe, Plesnik, Sara, Puyen, Zully M, Rabodoarivelo, Marie Sylvianne, Rakotosamimanana, Niaina, Rancoita, Paola MV, Rathod, Priti, Robinson, Esther, Rodger, Gillian, Rodrigues, Camilla, Rodwell, Timothy C, and Santos-Lazaro, David

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Clinical Sciences, Emerging Infectious Diseases, Infectious Diseases, Prevention, Antimicrobial Resistance, 5.1 Pharmaceuticals, Development of treatments and therapeutic interventions, Infection, Good Health and Well Being, Antitubercular Agents, Humans, Microbial Sensitivity Tests, Mycobacterium tuberculosis, Tuberculosis, Volunteers, Zooniverse Volunteer Community, CRyPTIC Consortium, M. tuberculosis, antibiotics, citizen science, clinical microbiology, infectious disease, microbiology, tuberculosis, Biochemistry and Cell Biology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Tuberculosis is a respiratory disease that is treatable with antibiotics. An increasing prevalence of resistance means that to ensure a good treatment outcome it is desirable to test the susceptibility of each infection to different antibiotics. Conventionally, this is done by culturing a clinical sample and then exposing aliquots to a panel of antibiotics, each being present at a pre-determined concentration, thereby determining if the sample isresistant or susceptible to each sample. The minimum inhibitory concentration (MIC) of a drug is the lowestconcentration that inhibits growth and is a more useful quantity but requires each sample to be tested at a range ofconcentrations for each drug. Using 96-well broth micro dilution plates with each well containing a lyophilised pre-determined amount of an antibiotic is a convenient and cost-effective way to measure the MICs of several drugs at once for a clinical sample. Although accurate, this is still an expensive and slow process that requires highly-skilled and experienced laboratory scientists. Here we show that, through the BashTheBug project hosted on the Zooniverse citizen science platform, a crowd of volunteers can reproducibly and accurately determine the MICs for 13 drugs and that simply taking the median or mode of 11-17 independent classifications is sufficient. There is therefore a potential role for crowds to support (but not supplant) the role of experts in antibiotic susceptibility testing.

Published
2022

21. The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis

Author

Walker, Timothy M, Miotto, Paolo, Köser, Claudio U, Fowler, Philip W, Knaggs, Jeff, Iqbal, Zamin, Hunt, Martin, Chindelevitch, Leonid, Farhat, Maha R, Cirillo, Daniela Maria, Comas, Iñaki, Posey, James, Omar, Shaheed V, Peto, Timothy EA, Suresh, Anita, Uplekar, Swapna, Laurent, Sacha, Colman, Rebecca E, Nathanson, Carl-Michael, Zignol, Matteo, Walker, Ann Sarah, Crook, Derrick W, Ismail, Nazir, Rodwell, Timothy C, Consortium, the SeqTreat Consortium CRyPTIC, Walker, A Sarah, Steyn, Adrie JC, Lalvani, Ajit, Baulard, Alain, Christoffels, Alan, Mendoza-Ticona, Alberto, Trovato, Alberto, Skrahina, Alena, Lachapelle, Alexander S, Brankin, Alice, Piatek, Amy, Cruz, Ana Gibertoni, Koch, Anastasia, Cabibbe, Andrea Maurizio, Spitaleri, Andrea, Brandao, Angela P, Chaiprasert, Angkana, Barbova, Anna, Van Rie, Annelies, Ghodousi, Arash, Bainomugisa, Arnold, Mandal, Ayan, Roohi, Aysha, Javid, Babak, Zhu, Baoli, Letcher, Brice, Rodrigues, Camilla, Nimmo, Camus, NATHANSON, Carl-Michael, Duncan, Carla, Coulter, Christopher, Utpatel, Christian, Liu, Chunfa, Grazian, Clara, Kong, Clare, Wilson, Daniel J, Matias, Daniela, Jorgensen, Danielle, Zimenkov, Danila, Chetty, Darren, Moore, David AJ, Clifton, David A, van Soolingen, Dick, Liu, Dongxin, Kohlerschmidt, Donna, Barreira, Draurio, Ngcamu, Dumisani, Lazaro, Elias David Santos, Kelly, Ellis, Borroni, Emanuele, Roycroft, Emma, Andre, Emmanuel, Böttger, Erik C, Robinson, Esther, Menardo, Fabrizio, Mendes, Flavia F, Jamieson, Frances B, Coll, Francesc, Gao, George Fu, Kasule, George W, Rossolini, Gian Maria, Rodger, Gillian, Smith, E Grace, Meintjes, Graeme, Thwaites, Guy, Hoffmann, Harald, Albert, Heidi, Cox, Helen, Laurenson, Ian F, and Arandjelovic, Irena

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Microbiology, Clinical Sciences, Tuberculosis, Infectious Diseases, Rare Diseases, Antimicrobial Resistance, Orphan Drug, Development of treatments and therapeutic interventions, 5.1 Pharmaceuticals, Infection, Good Health and Well Being, Antitubercular Agents, Drug Resistance, Ethambutol, Microbial Sensitivity Tests, Mutation, Mycobacterium tuberculosis, World Health Organization, CRyPTIC Consortium, Seq&Treat Consortium, Immunology, Medical microbiology
Abstract

BackgroundMolecular diagnostics are considered the most promising route to achieving rapid, universal drug susceptibility testing for Mycobacterium tuberculosiscomplex (MTBC). We aimed to generate a WHO endorsed catalogue of mutations to serve as a global standard for interpreting molecular information for drug resistance prediction.MethodsA candidate gene approach was used to identify mutations as associated with resistance, or consistent with susceptibility, for 13 WHO endorsed anti-tuberculosis drugs. 38,215 MTBC isolates with paired whole-genome sequencing and phenotypic drug susceptibility testing data were amassed from 45 countries. For each mutation, a contingency table of binary phenotypes and presence or absence of the mutation computed positive predictive value, and Fisher's exact tests generated odds ratios and Benjamini-Hochberg corrected p-values. Mutations were graded as Associated with Resistance if present in at least 5 isolates, if the odds ratio was >1 with a statistically significant corrected p-value, and if the lower bound of the 95% confidence interval on the positive predictive value for phenotypic resistance was >25%. A series of expert rules were applied for final confidence grading of each mutation.Findings15,667 associations were computed for 13,211 unique mutations linked to one or more drugs. 1,149/15,667 (7·3%) mutations were classified as associated with phenotypic resistance and 107/15,667 (0·7%) were deemed consistent with susceptibility. For rifampicin, isoniazid, ethambutol, fluoroquinolones, and streptomycin, the mutations' pooled sensitivity was >80%. Specificity was over 95% for all drugs except ethionamide (91·4%), moxifloxacin (91·6%) and ethambutol (93·3%). Only two resistance mutations were classified for bedaquiline, delamanid, clofazimine, and linezolid as prevalence of phenotypic resistance was low for these drugs.InterpretationThis first WHO endorsed catalogue of molecular targets for MTBC drug susceptibility testing provides a global standard for resistance interpretation. Its existence should encourage the implementation of molecular diagnostics by National Tuberculosis Programmes.FundingUNITAID, Wellcome, MRC, BMGF.

Published
2022

22. Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19

Author

Ahern, David J, Ai, Zhichao, Ainsworth, Mark, Allan, Chris, Allcock, Alice, Angus, Brian, Ansari, M Azim, Arancibia-Cárcamo, Carolina, Aschenbrenner, Dominik, Attar, Moustafa, Baillie, J Kenneth, Barnes, Eleanor, Bashford-Rogers, Rachael, Bashyal, Archana, Beer, Sally, Berridge, Georgina, Beveridge, Amy, Bibi, Sagida, Bicanic, Tihana, Blackwell, Luke, Bowness, Paul, Brent, Andrew, Brown, Andrew, Broxholme, John, Buck, David, Burnham, Katie, Byrne, Helen, Camara, Susana, Ferreira, Ivan Candido, Charles, Philip, Chen, Wentao, Chen, Yi-Ling, Chong, Amanda, Clutterbuck, Elizabeth, Coles, Mark, Conlon, Christopher, Cornall, Richard, Cribbs, Adam, Curion, Fabiola, Davenport, Emma, Davidson, Neil, Davis, Simon, Dendrou, Calliope, Dequaire, Julie, Dib, Lea, Docker, James, Dold, Christina, Dong, Tao, Downes, Damien, Drakesmith, Hal, Dunachie, Susanna, Duncan, David, Eijsbouts, Chris, Esnouf, Robert, Espinosa, Alexis, Etherington, Rachel, Fairfax, Benjamin, Fairhead, Rory, Fang, Hai, Fassih, Shayan, Felle, Sally, Fernandez Mendoza, Maria, Ferreira, Ricardo, Fischer, Roman, Foord, Thomas, Forrow, Aden, Frater, John, Fries, Anastasia, Gallardo Sanchez, Veronica, Garner, Lucy, Geeves, Clementine, Georgiou, Dominique, Godfrey, Leila, Golubchik, Tanya, Gomez Vazquez, Maria, Green, Angie, Harper, Hong, Harrington, Heather, Heilig, Raphael, Hester, Svenja, Hill, Jennifer, Hinds, Charles, Hird, Clare, Ho, Ling-Pei, Hoekzema, Renee, Hollis, Benjamin, Hughes, Jim, Hutton, Paula, Jackson-Wood, Matthew, Jainarayanan, Ashwin, James-Bott, Anna, Jansen, Kathrin, Jeffery, Katie, Jones, Elizabeth, Jostins, Luke, Kerr, Georgina, Kim, David, Klenerman, Paul, Knight, Julian, Kumar, Vinod, Kumar Sharma, Piyush, Kurupati, Prathiba, Kwok, Andrew, Lee, Angela, Linder, Aline, Lockett, Teresa, Lonie, Lorne, Lopopolo, Maria, Lukoseviciute, Martyna, Luo, Jian, Marinou, Spyridoula, Marsden, Brian, Martinez, Jose, Matthews, Philippa, Mazurczyk, Michalina, McGowan, Simon, McKechnie, Stuart, Mead, Adam, Mentzer, Alexander, Mi, Yuxin, Monaco, Claudia, Montadon, Ruddy, Napolitani, Giorgio, Nassiri, Isar, Novak, Alex, O'Brien, Darragh, O'Connor, Daniel, O'Donnell, Denise, Ogg, Graham, Overend, Lauren, Park, Inhye, Pavord, Ian, Peng, Yanchun, Penkava, Frank, Pereira Pinho, Mariana, Perez, Elena, Pollard, Andrew, Powrie, Fiona, Psaila, Bethan, Quan, T Phuong, Repapi, Emmanouela, Revale, Santiago, Silva-Reyes, Laura, Richard, Jean-Baptiste, Rich-Griffin, Charlotte, Ritter, Thomas, Rollier, Christine, Rowland, Matthew, Ruehle, Fabian, Salio, Mariolina, Sansom, Stephen Nicholas, Sanches Peres, Raphael, Santos Delgado, Alberto, Sauka-Spengler, Tatjana, Schwessinger, Ron, Scozzafava, Giuseppe, Screaton, Gavin, Seigal, Anna, Semple, Malcolm, Sergeant, Martin, Simoglou Karali, Christina, Sims, David, Skelly, Donal, Slawinski, Hubert, Sobrinodiaz, Alberto, Sousos, Nikolaos, Stafford, Lizzie, Stockdale, Lisa, Strickland, Marie, Sumray, Otto, Sun, Bo, Taylor, Chelsea, Taylor, Stephen, Taylor, Adan, Thongjuea, Supat, Thraves, Hannah, Todd, John, Tomic, Adriana, Tong, Orion, Trebes, Amy, Trzupek, Dominik, Tucci, Felicia Anna, Turtle, Lance, Udalova, Irina, Uhlig, Holm, van Grinsven, Erinke, Vendrell, Iolanda, Verheul, Marije, Voda, Alexandru, Wang, Guanlin, Wang, Lihui, Wang, Dapeng, Watkinson, Peter, Watson, Robert, Weinberger, Michael, Whalley, Justin, Witty, Lorna, Wray, Katherine, Xue, Luzheng, Yuen Yeung, Hing, Yin, Zixi, Young, Rebecca, Youngs, Jonathan, Zhang, Ping, Zurke, Yasemin-Xiomara, Banning, Adrian, Antonopoulos, Alexios, Bajaj, Amrita, Kelion, Andrew, Deshpande, Aparna, Kardos, Attila, Hudson, Benjamin, Koo, Bon-Kwon, Shirodaria, Cheerag, Xie, Cheng, Kotanidis, Christos, Mahon, Ciara, Berry, Colin, Adlam, David, Newby, David, Connolly, Derek, Scaletta, Diane, Alexander, Donna, Nicol, Ed, McAlindon, Elisa, Oikonomou, Evangelos, Pugliese, Francesca, Pontone, Gianluca, Benedetti, Giulia, He, Guo-Wei, West, Henry, Kondo, Hidekazu, Benedek, Imre, Das, Intrajeet, Deanfield, John, Graby, John, Greenwood, John, Rodrigues, Jonathan, Ge, Junbo, Channon, Keith, Fabritz, Larissa, Fan, Li-Juan, Kingham, Lucy, Guglielmo, Marco, Lyasheva, Maria, Schmitt, Matthias, Beer, Meinrad, Anderson, Michelle, Desai, Milind, Marwan, Mohamed, Takahashi, Naohiko, Mehta, Nehal, Dai, Neng, Screaton, Nicholas, Sabharwal, Nikant, Maurovich-Horvat, Pál, Rao, Praveen, Kotronias, Rafail, Kharbanda, Rajesh, Preston, Rebecca, Wood, Richard, Blankstein, Ron, Rajani, Ronak, Mirsadraee, Saeed, Munir, Shahzad, Thomas, Sheena, Neubauer, Stefan, Klömpken, Steffen, Petersen, Steffen, Achenbach, Stephan, Anthony, Susan, Mak, Sze, Mittal, Tarun, Benedek, Theodora, Sharma, Vinoda, Lin, Wen-Hua, Kotanidis, Christos P, Rodrigues, Jonathan C L, O’Connor, Daniel, Siddique, Muhammad, Lockstone, Helen, Oikonomou, Evangelos K, Badi, Ileana, Lumley, Sheila F, Constantinides, Bede, Sanderson, Nicholas, Rodger, Gillian, Chau, Kevin K, Lodge, Archie, Tsakok, Maria, Gleeson, Fergus, Indrajeet, Das, Hudson, Benjamin J, Srivastava, Vivek, Farid, Shakil, Krasopoulos, George, Sayeed, Rana, Newby, David E, Channon, Keith M, and Antoniades, Charalambos

Published
2022
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24. Author Correction: The plasmidome associated with Gram-negative bloodstream infections: a large-scale observational study using complete plasmid assemblies

Author

Lipworth, Samuel, primary, Matlock, William, additional, Shaw, Liam, additional, Vihta, Karina-Doris, additional, Rodger, Gillian, additional, Chau, Kevin, additional, Barker, Leanne, additional, George, Sophie, additional, Kavanagh, James, additional, Davies, Timothy, additional, Vaughan, Alison, additional, Andersson, Monique, additional, Jeffery, Katie, additional, Oakley, Sarah, additional, Morgan, Marcus, additional, Hopkins, Susan, additional, Peto, Timothy, additional, Crook, Derrick, additional, Walker, A. Sarah, additional, and Stoesser, Nicole, additional

Published
2024
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25. COVID-19: Rapid antigen detection for SARS-CoV-2 by lateral flow assay: A national systematic evaluation of sensitivity and specificity for mass-testing

Author

Affron, Dominic, Afrough, Babak, Agasu, Anita, Ainsworth, Mark, Allanson, Alison, Allen, Katherine, Allen, Collette, Archer, Lorraine, Ashbridge, Natasha, Aurfan, Iman, Avery, Miriam, Badenoch, Ellena, Bagga, Priya, Balaji, Rishab, Baldwin, Ella, Barraclough, Sophie, Beane, Carol, Bell, John, Benford, Tracy, Bird, Susan, Bishop, Marina, Bloss, Angela, Body, Richard, Boulton, Rosie, Bown, Abbie, Bratten, Carla, Bridgeman, Chris, Britton, Dominic, Brooks, Tim, Broughton-Smith, Margaret, Brown, Pauline, Buck, Beverley, Butcher, Elaine, Byrne, Wendy, Calderon, Gloria, Campbell, Siobhan, Carr, Olivia, Carter, Penny, Carter, Daniel, Cathrall, Megan, Catton, Matthew, Chadwick, Jim, Chapman, David, Chau, Kevin K., Chaudary, Tanzina, Chidavaenzi, Shaolin, Chilcott, Samatha, Choi, Bea, Claasen, Hannah, Clark, Simon, Clarke, Richard, Clarke, Dawn, Clayton, Richard, Collins, Kayleigh, Colston, Rima, Connolly, James, Cook, Eloïse, Corcoran, Marie, Corley, Ben, Costello, Laura, Coulson, Caroline, Crook, Ant, Crook, Derrick W., D'Arcangelo, Silvia, Darby, Mary-Anne, Davis, John, de Koning, Rosaline, Derbyshire, Pauline, Devall, Pam, Dolman, Mark, Draper, Natalie, Driver, Mark, Dyas, Sarah, Eaton, Emily, Edwards, Joy, Elderfield, Ruth, Ellis, Kate, Ellis, Graham, Elwell, Sue, Evans, Rachel, Evans, Becky, Evans, Marion, Evans, Ranoromanana, Eyre, David, Fahey, Codie, Fenech, Vanessa, Field, Janet, Field, Alice, Foord, Tom, Fowler, Tom, French, Mollie, Fuchs, Hannah, Gan, Jasmine, Gernon, Joseph, Ghadiali, Geeta, Ghuman, Narindar, Gibbons, Kerry, Gill, Gurvinder, Gilmour, Kate, Goel, Anika, Gordon, Sally, Graham, Tillie, Grassam-Rowe, Alexander, Green, David, Gronert, Anna, Gumsley-Read, Tegan, Hall, Claire, Hallis, Bassam, Hammond, Sally, Hammond, Peter, Hanney, Beth, Hardy, Victoria, Harker, Gabriella, Harris, Andrew, Havinden-Williams, May, Hazell, Elena, Henry, Joanne, Hicklin, Kim, Hollier, Kelly, Holloway, Ben, Hoosdally, Sarah J., Hopkins, Susan, Hughes, Lucy, Hurdowar, Steve, Hurford, Sally-Anne, Jackman, Joanne, Jackson, Harriet, Johns, Ruth, Johnston, Susan, Jones, Juliet, Kanyowa, Tinashe, Keating-Fedders, Katie, Kempson, Sharon, Khan, Iftikhar, Khulusi, Beinn, Knight, Thomas, Krishna, Anuradha, Lahert, Patrick, Lampshire, Zoe, Lasserson, Daniel, Lee, Kirsten, Lee, Lennard Y.W., Legard, Arabella, Leggio, Cristina, Liu, Justin, Lockett, Teresa, Logue, Christopher, Lucas, Vanessa, Lumley, Sheila F., Maripuri, Vindhya, Markham, Des, Marshall, Emma, Matthews, Philippa C., Mckee, Sarah, McKee, Deborah F., McLeod, Neil, McNulty, Antoinette, Mellor, Freddie, Michel, Rachel, Mighiu, Alex, Miller, Julie, Mirza, Zarina, Mistry, Heena, Mitchell, Jane, Moeser, Mika Erik, Moore, Sophie, Muthuswamy, Akhila, Myers, Daniel, Nanson, Gemma, Newbury, Mike, Nicol, Scott, Nuttall, Harry, Nwanaforo, Jewel Jones, Oliver, Louise, Osbourne, Wendy, Osbourne, Jake, Otter, Ashley, Owen, Jodie, Panchalingam, Sulaksan, Papoulidis, Dimitris, Pavon, Juan Dobaldo, Peace, Arro, Pearson, Karen, Peck, Liam, Pegg, Ashley, Pegler, Suzannah, Permain, Helen, Perumal, Prem, Peto, Leon, Peto, Tim E.A., Pham, Thanh, Pickford, Hayleah L., Pinkerton, Mark, Platton, Michelle, Price, Ashley, Protheroe, Emily, Purnell, Hellen, Rawden, Lottie, Read, Sara, Reynard, Charles, Ridge, Susan, Ritter, Tom G., Robinson, James, Robinson, Patrick, Rodger, Gillian, Rowe, Cathy, Rowell, Bertie, Rowlands, Alexandra, Sampson, Sarah, Saunders, Kathryn, Sayers, Rachel, Sears, Jackie, Sedgewick, Richard, Seeney, Laura, Selassie, Amanda, Shail, Lloyd, Shallcross, Jane, Sheppard, Lucy, Sherkat, Anna, Siddiqui, Shelha, Sienkiewicz, Alex, Sinha, Lavanya, Smith, Jennifer, Smith, Ella, Stanton, Emma, Starkey, Thomas, Stawiarski, Aleksander, Sterry, Amelia, Stevens, Joe, Stockbridge, Mark, Stoesser, Nicole, Sukumaran, Anila, Sweed, Angela, Tatar, Sami, Thomas, Hema, Tibbins, Carly, Tiley, Sian, Timmins, Julie, Tomas-Smith, Cara, Topping, Oliver, Turek, Elena, Neibler, Toi, Trigg-Hogarth, Kate, Truelove, Elizabeth, Turnbull, Chris, Tyrrell, David, Vaughan, Alison, Vertannes, John, Vipond, Richard, Wagstaff, Linda, Waldron, Joanne, Walker, Philip, Walker, Ann Sarah, Walters, Mary, Wang, Jenny Y, Watson, Ellie, Webberley, Kate, Webster, Kimerbley, Westland, Grace, Wickens, Ian, Willcocks, Jane, Willis, Herika, Wilson, Stephen, Wilson, Barbara, Woodhead, Louise, Wright, Deborah, Xavier, Bindhu, Yelnoorkar, Fiona, Zeidan, Lisa, Zinyama, Rangeni, and Peto, Tim

Published
2021
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27. Performance characteristics of five immunoassays for SARS-CoV-2: a head-to-head benchmark comparison

Author

Ainsworth, Mark, Andersson, Monique, Auckland, Kathryn, Baillie, J Kenneth, Barnes, Eleanor, Beer, Sally, Beveridge, Amy, Bibi, Sagida, Blackwell, Luke, Borak, Martyna, Bown, Abbie, Brooks, Tim, Burgess-Brown, Nicola A, Camara, Susana, Catton, Matthew, Chau, Kevin K., Christott, Thomas, Clutterbuck, Elizabeth, Coker, Jesse, Cornall, Richard J, Cox, Stuart, Crawford-Jones, David, Crook, Derrick W, D'Arcangelo, Silvia, Dejnirattsai, Wanwisa, Dequaire, Julie M M, Dimitriadis, Stavros, Dingle, Kate E, Doherty, George, Dold, Christina, Dong, Tao, Dunachie, Susanna J, Ebner, Daniel, Emmenegger, Marc, Espinosa, Alexis, Eyre, David W, Fairhead, Rory, Fassih, Shayan, Feehily, Conor, Felle, Sally, Fernandez-Cid, Alejandra, Fernandez Mendoza, Maria, Foord, Thomas H, Fordwoh, Thomas, Fox McKee, Deborah, Frater, John, Gallardo Sanchez, Veronica, Gent, Nick, Georgiou, Dominique, Groves, Christopher J, Hallis, Bassam, Hammond, Peter M, Hatch, Stephanie B., Harvala, Heli J, Hill, Jennifer, Hoosdally, Sarah J, Horsington, Bryn, Howarth, Alison, James, Tim, Jeffery, Katie, Jones, Elizabeth, Justice, Anita, Karpe, Fredrik, Kavanagh, James, Kim, David S, Kirton, Richard, Klenerman, Paul, Knight, Julian C, Koukouflis, Leonidas, Kwok, Andrew, Leuschner, Ullrich, Levin, Robert, Linder, Aline, Lockett, Teresa, Lumley, Sheila F, Marinou, Spyridoula, Marsden, Brian D, Martinez, Jose, Martins Ferreira, Lucas, Mason, Lara, Matthews, Philippa C, Mentzer, Alexander J, Mobbs, Alexander, Mongkolsapaya, Juthathip, Morrow, Jordan, Mukhopadhyay, Shubhashish M M, Neville, Matthew J, Oakley, Sarah, Oliveira, Marta, Otter, Ashley, Paddon, Kevin, Pascoe, Jordan, Peng, Yanchun, Perez, Elena, Perumal, Prem K, Peto, Timothy E A, Pickford, Hayleah, Ploeg, Rutger J, Pollard, Andrew J, Richardson, Anastasia, Ritter, Thomas G, Roberts, David J, Rodger, Gillian, Rollier, Christine S, Rowe, Cathy, Rudkin, Justine K, Screaton, Gavin, Semple, Malcolm G, Sienkiewicz, Alex, Silva-Reyes, Laura, Skelly, Donal T, Sobrino Diaz, Alberto, Stafford, Lizzie, Stockdale, Lisa, Stoesser, Nicole, Street, Teresa, Stuart, David I, Sweed, Angela, Taylor, Adan, Thraves, Hannah, Tsang, Hoi P, Verheul, Marije K, Vipond, Richard, Walker, Timothy M, Wareing, Susan, Warren, Yolanda, Wells, Charlie, Wilson, Clare, Withycombe, Kate, and Young, Rebecca K

Published
2020
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32. The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies.

Author

Lipworth, Samuel, Matlock, Willam, Shaw, Liam, Vihta, Karina-Doris, Rodger, Gillian, Chau, Kevin, Barker, Leanne, George, Sophie, Kavanagh, James, Davies, Timothy, Vaughan, Alison, Andersson, Monique, Jeffery, Katie, Oakley, Sarah, Morgan, Marcus, Hopkins, Susan, Peto, Timothy, Crook, Derrick, Walker, A. Sarah, and Stoesser, Nicole

Subjects
GRAM-negative bacteria, DRUG resistance in microorganisms, SCIENTIFIC observation, PLASMIDS, DISEASE resistance of plants
Abstract

Plasmids carry genes conferring antimicrobial resistance and other clinically important traits, and contribute to the rapid dissemination of such genes. Previous studies using complete plasmid assemblies, which are essential for reliable inference, have been small and/or limited to plasmids carrying antimicrobial resistance genes (ARGs). In this study, we sequenced 1,880 complete plasmids from 738 isolates from bloodstream infections in Oxfordshire, UK. The bacteria had been originally isolated in 2009 (194 isolates) and 2018 (368 isolates), plus a stratified selection from intervening years (176 isolates). We demonstrate that plasmids are largely, but not entirely, constrained to a single host species, although there is substantial overlap between species of plasmid gene-repertoire. Most ARGs are carried by a relatively small number of plasmid groups with biological features that are predictable. Plasmids carrying ARGs (including those encoding carbapenemases) share a putative 'backbone' of core genes with those carrying no such genes. These findings suggest that future surveillance should, in addition to tracking plasmids currently associated with clinically important genes, focus on identifying and monitoring the dissemination of high-risk plasmid groups with the potential to rapidly acquire and disseminate these genes. Plasmids carry antimicrobial resistance genes and contribute to the rapid dissemination of resistance. Here, the authors sequence 1,880 complete plasmids from 738 isolates from bloodstream infections, shedding light on the links between plasmid types, bacterial hosts and antimicrobial resistance. [ABSTRACT FROM AUTHOR]

Published
2024
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34. Bedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis

Author

Sonnenkalb, Lindsay, primary, Carter, Joshua James, additional, Spitaleri, Andrea, additional, Iqbal, Zamin, additional, Hunt, Martin, additional, Malone, Kerri Marie, additional, Utpatel, Christian, additional, Cirillo, Daniela Maria, additional, Rodrigues, Camilla, additional, Nilgiriwala, Kayzad Soli, additional, Fowler, Philip William, additional, Merker, Matthias, additional, Niemann, Stefan, additional, Barilar, Ivan, additional, Battaglia, Simone, additional, Borroni, Emanuele, additional, Brandao, Angela Pires, additional, Brankin, Alice, additional, Cabibbe, Andrea Maurizio, additional, Carter, Joshua, additional, Claxton, Pauline, additional, Clifton, David A, additional, Cohen, Ted, additional, Coronel, Jorge, additional, Crook, Derrick W, additional, Dreyer, Viola, additional, Earle, Sarah G, additional, Escuyer, Vincent, additional, Ferrazoli, Lucilaine, additional, Fowler, Philip W, additional, Fu Gao, George, additional, Gardy, Jennifer, additional, Gharbia, Saheer, additional, Ghisi, Kelen Teixeira, additional, Ghodousi, Arash, additional, Gibertoni Cruz, Ana Luíza, additional, Grandjean, Louis, additional, Grazian, Clara, additional, Groenheit, Ramona, additional, Guthrie, Jennifer L, additional, He, Wencong, additional, Hoffmann, Harald, additional, Hoosdally, Sarah J, additional, Ismail, Nazir Ahmed, additional, Jarrett, Lisa, additional, Joseph, Lavania, additional, Jou, Ruwen, additional, Kambli, Priti, additional, Khot, Rukhsar, additional, Knaggs, Jeff, additional, Koch, Anastasia, additional, Kohlerschmidt, Donna, additional, Kouchaki, Samaneh, additional, Lachapelle, Alexander S, additional, Lalvani, Ajit, additional, Grandjean Lapierre, Simon, additional, Laurenson, Ian F, additional, Letcher, Brice, additional, Lin, Wan-Hsuan, additional, Liu, Chunfa, additional, Liu, Dongxin, additional, Malone, Kerri M, additional, Mandal, Ayan, additional, Mansjö, Mikael, additional, Matias, Daniela, additional, Meintjes, Graeme, additional, de Freitas Mendes, Flávia, additional, Mihalic, Marina, additional, Millard, James, additional, Miotto, Paolo, additional, Mistry, Nerges, additional, Moore, David, additional, Musser, Kimberlee A, additional, Ngcamu, Dumisani, additional, Hoang, Ngoc Nhung, additional, Nimmo, Camus, additional, Okozi, Nana, additional, Oliveira, Rosangela Siqueira, additional, Omar, Shaheed Vally, additional, Paton, Nicholas, additional, Peto, Timothy EA, additional, Watanabe Pinhata, Juliana Maira, additional, Plesnik, Sara, additional, Puyen, Zully M, additional, Rabodoarivelo, Marie Sylvianne, additional, Rakotosamimanana, Niaina, additional, Rancoita, Paola MV, additional, Rathod, Priti, additional, Rodger, Gillian, additional, Rodwell, Timothy C, additional, Roohi, Eaysha, additional, Santos-Lazaro, David, additional, Shah, Sanchi, additional, Kohl, Thomas Andreas, additional, Smith, Grace, additional, Solano, Walter, additional, Supply, Philip, additional, Surve, Utkarsha, additional, Tahseen, Sabira, additional, Thuong, Nguyen Thuy Thuong, additional, Thwaites, Guy, additional, Todt, Katharina, additional, Trovato, Alberto, additional, Van Rie, Annelies, additional, Vijay, Srinivasan, additional, Walker, Timothy M, additional, Walker, Sarah A, additional, Warren, Robin, additional, Werngren, Jim, additional, Wijkander, Maria, additional, Wilkinson, Robert J, additional, Wilson, Daniel J, additional, Wintringer, Penelope, additional, Yu, Xin Xiao, additional, Yang, Yang, additional, Zhao, Yanlin, additional, Yao, Shen-Yuan, additional, and Zhu, Baoli, additional

Published
2023
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35. Evaluation of Fourier Transform Infrared spectroscopy (IR Biotyper) as a complement to Whole genome sequencing (WGS) to characterise Enterobacter cloacae, Citrobacter freundii and Klebsiella pneumoniae isolates recovered from hospital sinks

Author

Aranega Bou, Paz, primary, Cornbill, Charlotte, additional, Rodger, Gillian, additional, Bird, Matthew, additional, Moore, Ginny, additional, Roohi, Aysha, additional, Hopkins, Katie L, additional, Hopkins, Susan, additional, Ribeca, Paolo, additional, Stoesser, Nicole, additional, and Lipworth, Sam I, additional

Published
2023
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37. Genomic Sequencing from Sputum for Tuberculosis Disease Diagnosis, Lineage Determination, and Drug Susceptibility Prediction

Author

Nilgiriwala, Kayzad, primary, Rabodoarivelo, Marie-Sylvianne, additional, Hall, Michael B., additional, Patel, Grishma, additional, Mandal, Ayan, additional, Mishra, Shefali, additional, Andrianomanana, Fanantenana Randria, additional, Dingle, Kate, additional, Rodger, Gillian, additional, George, Sophie, additional, Crook, Derrick W., additional, Hoosdally, Sarah, additional, Mistry, Nerges, additional, Rakotosamimanana, Niaina, additional, Iqbal, Zamin, additional, Grandjean Lapierre, Simon, additional, and Walker, Timothy M., additional

Published
2023
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40. Genomic Sequencing from Sputum for Tuberculosis Disease Diagnosis, Lineage Determination and Drug Susceptibility Prediction

Author

Nilgiriwala, Kayzad, primary, Rabodoarivelo, Marie-Sylvianne, additional, Hall, Michael B., additional, Patel, Grishma, additional, Mandal, Ayan, additional, Mishra, Shefali, additional, Andrianomanana, Fanantenana Randria, additional, Dingle, Kate, additional, Rodger, Gillian, additional, George, Sophie, additional, Crook, Derrick W., additional, Hoosdally, Sarah, additional, Mistry, Nerges, additional, Rakotosamimanana, Niaina, additional, Iqbal, Zamin, additional, Lapierre, Simon Grandjean, additional, and Walker, Timothy M., additional

Published
2022
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41. Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19

Author

Kotanidis, Christos P, primary, Xie, Cheng, additional, Alexander, Donna, additional, Rodrigues, Jonathan C L, additional, Burnham, Katie, additional, Mentzer, Alexander, additional, O’Connor, Daniel, additional, Knight, Julian, additional, Siddique, Muhammad, additional, Lockstone, Helen, additional, Thomas, Sheena, additional, Kotronias, Rafail, additional, Oikonomou, Evangelos K, additional, Badi, Ileana, additional, Lyasheva, Maria, additional, Shirodaria, Cheerag, additional, Lumley, Sheila F, additional, Constantinides, Bede, additional, Sanderson, Nicholas, additional, Rodger, Gillian, additional, Chau, Kevin K, additional, Lodge, Archie, additional, Tsakok, Maria, additional, Gleeson, Fergus, additional, Adlam, David, additional, Rao, Praveen, additional, Indrajeet, Das, additional, Deshpande, Aparna, additional, Bajaj, Amrita, additional, Hudson, Benjamin J, additional, Srivastava, Vivek, additional, Farid, Shakil, additional, Krasopoulos, George, additional, Sayeed, Rana, additional, Ho, Ling-Pei, additional, Neubauer, Stefan, additional, Newby, David E, additional, Channon, Keith M, additional, Deanfield, John, additional, Antoniades, Charalambos, additional, Ahern, David J, additional, Ai, Zhichao, additional, Ainsworth, Mark, additional, Allan, Chris, additional, Allcock, Alice, additional, Angus, Brian, additional, Ansari, M Azim, additional, Arancibia-Cárcamo, Carolina, additional, Aschenbrenner, Dominik, additional, Attar, Moustafa, additional, Baillie, J Kenneth, additional, Barnes, Eleanor, additional, Bashford-Rogers, Rachael, additional, Bashyal, Archana, additional, Beer, Sally, additional, Berridge, Georgina, additional, Beveridge, Amy, additional, Bibi, Sagida, additional, Bicanic, Tihana, additional, Blackwell, Luke, additional, Bowness, Paul, additional, Brent, Andrew, additional, Brown, Andrew, additional, Broxholme, John, additional, Buck, David, additional, Byrne, Helen, additional, Camara, Susana, additional, Ferreira, Ivan Candido, additional, Charles, Philip, additional, Chen, Wentao, additional, Chen, Yi-Ling, additional, Chong, Amanda, additional, Clutterbuck, Elizabeth, additional, Coles, Mark, additional, Conlon, Christopher, additional, Cornall, Richard, additional, Cribbs, Adam, additional, Curion, Fabiola, additional, Davenport, Emma, additional, Davidson, Neil, additional, Davis, Simon, additional, Dendrou, Calliope, additional, Dequaire, Julie, additional, Dib, Lea, additional, Docker, James, additional, Dold, Christina, additional, Dong, Tao, additional, Downes, Damien, additional, Drakesmith, Hal, additional, Dunachie, Susanna, additional, Duncan, David, additional, Eijsbouts, Chris, additional, Esnouf, Robert, additional, Espinosa, Alexis, additional, Etherington, Rachel, additional, Fairfax, Benjamin, additional, Fairhead, Rory, additional, Fang, Hai, additional, Fassih, Shayan, additional, Felle, Sally, additional, Fernandez Mendoza, Maria, additional, Ferreira, Ricardo, additional, Fischer, Roman, additional, Foord, Thomas, additional, Forrow, Aden, additional, Frater, John, additional, Fries, Anastasia, additional, Gallardo Sanchez, Veronica, additional, Garner, Lucy, additional, Geeves, Clementine, additional, Georgiou, Dominique, additional, Godfrey, Leila, additional, Golubchik, Tanya, additional, Gomez Vazquez, Maria, additional, Green, Angie, additional, Harper, Hong, additional, Harrington, Heather, additional, Heilig, Raphael, additional, Hester, Svenja, additional, Hill, Jennifer, additional, Hinds, Charles, additional, Hird, Clare, additional, Hoekzema, Renee, additional, Hollis, Benjamin, additional, Hughes, Jim, additional, Hutton, Paula, additional, Jackson-Wood, Matthew, additional, Jainarayanan, Ashwin, additional, James-Bott, Anna, additional, Jansen, Kathrin, additional, Jeffery, Katie, additional, Jones, Elizabeth, additional, Jostins, Luke, additional, Kerr, Georgina, additional, Kim, David, additional, Klenerman, Paul, additional, Kumar, Vinod, additional, Kumar Sharma, Piyush, additional, Kurupati, Prathiba, additional, Kwok, Andrew, additional, Lee, Angela, additional, Linder, Aline, additional, Lockett, Teresa, additional, Lonie, Lorne, additional, Lopopolo, Maria, additional, Lukoseviciute, Martyna, additional, Luo, Jian, additional, Marinou, Spyridoula, additional, Marsden, Brian, additional, Martinez, Jose, additional, Matthews, Philippa, additional, Mazurczyk, Michalina, additional, McGowan, Simon, additional, McKechnie, Stuart, additional, Mead, Adam, additional, Mi, Yuxin, additional, Monaco, Claudia, additional, Montadon, Ruddy, additional, Napolitani, Giorgio, additional, Nassiri, Isar, additional, Novak, Alex, additional, O'Brien, Darragh, additional, O'Connor, Daniel, additional, O'Donnell, Denise, additional, Ogg, Graham, additional, Overend, Lauren, additional, Park, Inhye, additional, Pavord, Ian, additional, Peng, Yanchun, additional, Penkava, Frank, additional, Pereira Pinho, Mariana, additional, Perez, Elena, additional, Pollard, Andrew, additional, Powrie, Fiona, additional, Psaila, Bethan, additional, Quan, T Phuong, additional, Repapi, Emmanouela, additional, Revale, Santiago, additional, Silva-Reyes, Laura, additional, Richard, Jean-Baptiste, additional, Rich-Griffin, Charlotte, additional, Ritter, Thomas, additional, Rollier, Christine, additional, Rowland, Matthew, additional, Ruehle, Fabian, additional, Salio, Mariolina, additional, Sansom, Stephen Nicholas, additional, Sanches Peres, Raphael, additional, Santos Delgado, Alberto, additional, Sauka-Spengler, Tatjana, additional, Schwessinger, Ron, additional, Scozzafava, Giuseppe, additional, Screaton, Gavin, additional, Seigal, Anna, additional, Semple, Malcolm, additional, Sergeant, Martin, additional, Simoglou Karali, Christina, additional, Sims, David, additional, Skelly, Donal, additional, Slawinski, Hubert, additional, Sobrinodiaz, Alberto, additional, Sousos, Nikolaos, additional, Stafford, Lizzie, additional, Stockdale, Lisa, additional, Strickland, Marie, additional, Sumray, Otto, additional, Sun, Bo, additional, Taylor, Chelsea, additional, Taylor, Stephen, additional, Taylor, Adan, additional, Thongjuea, Supat, additional, Thraves, Hannah, additional, Todd, John, additional, Tomic, Adriana, additional, Tong, Orion, additional, Trebes, Amy, additional, Trzupek, Dominik, additional, Tucci, Felicia Anna, additional, Turtle, Lance, additional, Udalova, Irina, additional, Uhlig, Holm, additional, van Grinsven, Erinke, additional, Vendrell, Iolanda, additional, Verheul, Marije, additional, Voda, Alexandru, additional, Wang, Guanlin, additional, Wang, Lihui, additional, Wang, Dapeng, additional, Watkinson, Peter, additional, Watson, Robert, additional, Weinberger, Michael, additional, Whalley, Justin, additional, Witty, Lorna, additional, Wray, Katherine, additional, Xue, Luzheng, additional, Yuen Yeung, Hing, additional, Yin, Zixi, additional, Young, Rebecca, additional, Youngs, Jonathan, additional, Zhang, Ping, additional, Zurke, Yasemin-Xiomara, additional, Banning, Adrian, additional, Antonopoulos, Alexios, additional, Kelion, Andrew, additional, Kardos, Attila, additional, Hudson, Benjamin, additional, Koo, Bon-Kwon, additional, Kotanidis, Christos, additional, Mahon, Ciara, additional, Berry, Colin, additional, Newby, David, additional, Connolly, Derek, additional, Scaletta, Diane, additional, Nicol, Ed, additional, McAlindon, Elisa, additional, Oikonomou, Evangelos, additional, Pugliese, Francesca, additional, Pontone, Gianluca, additional, Benedetti, Giulia, additional, He, Guo-Wei, additional, West, Henry, additional, Kondo, Hidekazu, additional, Benedek, Imre, additional, Das, Intrajeet, additional, Graby, John, additional, Greenwood, John, additional, Rodrigues, Jonathan, additional, Ge, Junbo, additional, Channon, Keith, additional, Fabritz, Larissa, additional, Fan, Li-Juan, additional, Kingham, Lucy, additional, Guglielmo, Marco, additional, Schmitt, Matthias, additional, Beer, Meinrad, additional, Anderson, Michelle, additional, Desai, Milind, additional, Marwan, Mohamed, additional, Takahashi, Naohiko, additional, Mehta, Nehal, additional, Dai, Neng, additional, Screaton, Nicholas, additional, Sabharwal, Nikant, additional, Maurovich-Horvat, Pál, additional, Kharbanda, Rajesh, additional, Preston, Rebecca, additional, Wood, Richard, additional, Blankstein, Ron, additional, Rajani, Ronak, additional, Mirsadraee, Saeed, additional, Munir, Shahzad, additional, Klömpken, Steffen, additional, Petersen, Steffen, additional, Achenbach, Stephan, additional, Anthony, Susan, additional, Mak, Sze, additional, Mittal, Tarun, additional, Benedek, Theodora, additional, Sharma, Vinoda, additional, and Lin, Wen-Hua, additional

Published
2022
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42. A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics

Author

Brankin, Alice, Malone, Kerri, Barilar, Ivan, Battaglia, Simone, Borroni, Emanuele, Pires Brandao, Angela, Cabibbe, Andrea Maurizio, Carter, Joshua, Chetty, Darren, Cirillo, Daniela María, Claxton, Pauline, Clifton, David, Cohen, Ted, Coronel, Jorge, Crook, Derrick, Dreyer, Viola, Earle, Sarah, Escuyer, Vincent, Ferrazoli, Lucilaine, Gāo, George Fú, Gardy, Jennifer, Gharbia, Saheer, Teixeira Ghisi, Kelen, Ghodousi, Arash, Gibertoni Cruz, Ana Lúıza, Grandjean, Louis, Grazian, Clara, Groenheit, Ramona, Guthrie, Jennifer, He, Wencong, Hoffmann, Harald, J., Sarah, Hunt, Martin, Ismail, Nazir Ahmed, Jarrett, Lisa, Joseph, Lavania, Jou, Ruwen, Kambli, Priti, Khot, Rukhsar, Knaggs, Jeff, Koch, Anastasia, Kohlerschmidt, Donna, Kouchaki, Samaneh, Lachapelle, Alexander, Lalvani, Ajit, Grandjean Lapierre, Simon, Laurenson, Ian, Letcher, Brice, Lin, Wan-Hsuan, Liu, Chunfa, Liu, Dongxin, Mandal, Ayan, Mansjö, Mikael, Matias, Daniela, Meintjes, Graeme, de Freitas Mendes, Flávia, Merker, Matthias, Mihalic, Marina, Millard, James, Miotto, Paolo, Mistry, Nerges, Moore, David, Musser, Kimberlee A., Ngcamu, Dumisani, Ngoc Nhung, Hoang, Niemann, Stefan, Soli Nilgiriwala, Kayzad, Nimmo, Camus, O'Donnell, Max, Okozi, Nana, Siqueira Oliveira, Rosangela, Omar, Shaheed Vally, Paton, Nicholas, Peto, Timothy Ea, Watanabe Pinhata, Juliana Maira, Plesnik, Sara, Puyen, Zully, Rabodoarivelo, Marie, Rakotosamimanana, Niaina, Rancoita, Paola, Rathod, Priti, Robinson, Esther, Rodger, Gillian, Rodrigues, Camilla, Rodwell, Timothy, Roohi, Aysha, Santos-Lazaro, David, Shah, Sanchi, Kohl, Thomas Andreas, Smith, Grace, Solano, Walter, Spitaleri, Andrea, Supply, Philip, Steyn, Adrie, Surve, Utkarsha, Tahseen, Sabira, Thuong, Nguyen, Thwaites, Guy, Todt, Katharina, Trovato, Alberto, Utpatel, Christian, van Rie, Annelies, Vijay, Srinivasan, Walker, Timothy, Walker, A. Sarah, Warren, Robin M., Werngren, Jim, Wijkander, Maria, Wilkinson, Robert, Wilson, Daniel, Wintringer, Penelope, Xiao, Yu-Xin, Yang, Yang, Zhao, Yanlin, Yao, Shen-Yuan, Zhu, Baoli, Fowler, Philip, Iqbal, Zamin, Consortium, The CRyPTIC, University of Oxford, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Forschungszentrum Borstel - Research Center Borstel, IRCCS San Raffaele Scientific Institute [Milan, Italie], Casa de Oswaldo Cruz [Rio de Janeiro] (COC), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Instituto Adolfo Lutz [São Paulo, Brazil], Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Africa Health Research Institute [Durban/Mtubatuba] (AHRI), University of Edinburgh, Yale School of Public Health (YSPH), Universidad Peruana de Ciencias Aplicadas (Lima) (UPC), Wadsworth Center, New York State Department of Health [Albany], Chinese Center for Disease Control and Prevention, Bill & Melinda Gates Foundation [Seattle], UK Health Security Agency [London] (UKHSA), Universita Vita Salute San Raffaele = Vita-Salute San Raffaele University [Milan, Italie] (UniSR), University College of London [London] (UCL), University of New South Wales [Sydney] (UNSW), Public Health Agency of Sweden, University of British Columbia [Vancouver], Public Health Ontario - Santé publique Ontario, Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim, National Institute for Communicable Diseases [Johannesburg] (NICD), Taipei Medical University, PD Hinduja Hospital & Research Institute, Mumbai, University of Cape Town, University of Surrey (UNIS), Imperial College London, Université de Montréal (UdeM), PRA Health sciences [Mumbai], London School of Hygiene and Tropical Medicine (LSHTM), Oxford University Clinical Research Unit [Ho Chi Minh City] (OUCRU), German Centre for Infection Research - partner site Hamburg-Lübeck-Borstel-Riems (DZIF), Columbia University Irving Medical Center (CUIMC), National University of Singapore (NUS), Socios En Salud [Lima, Peru], Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP), Foundation for Innovative New Diagnostics (FIND), University of California [San Diego] (UC San Diego), University of California (UC), Universidad Peruana Cayetano Heredia (UPCH), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), National TB control Program [Islamabad, Pakistan], University of Antwerp (UA), Stellenbosch University, Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, Department of Medicine, University of Cape Town, The Francis Crick Institute [London], Shanghai Jiao Tong University School of Medicine, Chinese Academy of Sciences [Beijing] (CAS), and Wellcome Trust (200205/Z/15/Z)Bill and Melinda Gates Foundation (OPP1133541)National Institute for Health Research Oxford Biomedical Research CentreNational Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial ResistanceWellcome Trust (203919/Z/16/Z)National Mega Project on Major Infectious Disease Prevention (2018ZX10103001)H2020 Marie Skłodowska-Curie Actions (EIPOD3)Unitaid (2019-32-FIND MDR)FAPESP (17/16082-7)FAPESP (2012/51756-5)National Natural Science Foundation of China (81991534)Beijing Municipal Science and Technology Commission (Z201100005520041)Wellcome Trust International Intermediate Fellowship (206724/Z/17/Z)Wellcome TrustSouth African Medical Research Councilthe Rhodes Trust and Stanford Medical Scientist Training Program (T32 GM007365)National Institute for Health Research (NIHR) Health Protection Research Unit in Respiratory Infections at Imperial College LondonFonds de Recherche en Santé du QuébecWellcome Trust (203583/Z/16/Z)Research Foundation Flanders (G0F8316N)Wellcome Trust (98316)Wellcome Trust (214321/Z/18/Z)Wellcome Trust (203135/Z/16/Z)National Research Foundation South Africa (64787)Wellcome Trust (201470/Z/16/Z)National Institute of Allergy and Infectious Diseases (1R01AI146338)GOSH (1R01AI146338)GOSH/ICH Biomedical Research CentreOxford Medical Research Council Doctoral Training Partnership (NDM Prize Studentship)Nuffield Department of Clinical MedicineSir Henry Dale Fellowship (101237/Z/13/B)The Robertson FoundationNIHRWellcome Trust (214560/Z/18/Z)Rhodes TrustWellcome Trust (FC0010218)UK Research and Innovation (FC0010218)Cancer Research UK (FC0010218)National Institutes of HealthCenters for Disease Control and PreventionUSAIDBill and Melinda Gates FoundationWellcome Trust (203141/Z/16/Z)NIHR Oxford Biomedical Research Centre (BRC BRC-1215-20008)Deutsches Zentrum für InfektionsforschungPublic Health ScotlandCenters for Disease Control and Prevention (U60OE000103)Division of Intramural Research, National Institute of Allergy and Infectious Diseases (AI-117312)

Subjects
General Immunology and Microbiology, General Neuroscience, Extensively Drug-Resistant Tuberculosis, Antitubercular Agents, Microbial Sensitivity Tests, Mycobacterium tuberculosis, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, General Biochemistry, Genetics and Molecular Biology, Phenotype, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Drug Resistance, Multiple, Bacterial, Mutation, Tuberculosis, Multidrug-Resistant, Humans, Rifampin, General Agricultural and Biological Sciences
Abstract

The Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC) presents here a data compendium of 12,289 Mycobacterium tuberculosis global clinical isolates, all of which have undergone whole-genome sequencing and have had their minimum inhibitory concentrations to 13 antitubercular drugs measured in a single assay. It is the largest matched phenotypic and genotypic dataset for M. tuberculosis to date. Here, we provide a summary detailing the breadth of data collected, along with a description of how the isolates were selected, collected, and uniformly processed in CRyPTIC partner laboratories across 23 countries. The compendium contains 6,814 isolates resistant to at least 1 drug, including 2,129 samples that fully satisfy the clinical definitions of rifampicin resistant (RR), multidrug resistant (MDR), pre-extensively drug resistant (pre-XDR), or extensively drug resistant (XDR). The data are enriched for rare resistance-associated variants, and the current limits of genotypic prediction of resistance status (sensitive/resistant) are presented by using a genetic mutation catalogue, along with the presence of suspected resistance-conferring mutations for isolates resistant to the newly introduced drugs bedaquiline, clofazimine, delamanid, and linezolid. Finally, a case study of rifampicin monoresistance demonstrates how this compendium could be used to advance our genetic understanding of rare resistance phenotypes. The data compendium is fully open source and it is hoped that it will facilitate and inspire future research for years to come.

Published
2022

44. The mobilome associated with Gram-negative bloodstream infections: A large-scale observational hybrid sequencing based study

Author

Lipworth, Samuel, primary, Matlock, Willam, additional, Shaw, Liam, additional, Vihta, Karina-Doris, additional, Rodger, Gillian, additional, Chau, Kevin, additional, Barker, Leanne, additional, George, Sophie, additional, Kavanagh, James, additional, Davies, Timothy, additional, Vaughan, Alison, additional, Andersson, Monique, additional, Jeffery, Katie, additional, Oakley, Sarah, additional, Morgan, Marcus, additional, Hopkins, Susan, additional, Peto, Timothy, additional, Crook, Derrick, additional, Walker, A. Sarah, additional, and Stoesser, Nicole, additional

Published
2022
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45. Rapid turnaround multiplex sequencing of SARS-CoV-2: comparing tiling amplicon protocol performance

Author

Constantinides, Bede, primary, Webster, Hermione, additional, Gentry, Jessica, additional, Bastable, Jasmine, additional, Dunn, Laura, additional, Oakley, Sarah, additional, Swann, Jeremy, additional, Sanderson, Nicholas D, additional, Fowler, Philip W, additional, Ma, Geoffrey, additional, Rodger, Gillian, additional, Barrett, Lucinda, additional, Jeffery, Katie JM, additional, Peto, Timothy EA JM, additional, Stoesser, Nicole, additional, Street, Teresa L, additional, and Crook, Derrick W, additional

Published
2022
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47. Epidemiological data and genome sequencing reveals that nosocomial transmission of SARS-CoV-2 is underestimated and mostly mediated by a small number of highly infectious individuals

Author

Lumley, Sheila F, primary, Constantinides, Bede, additional, Sanderson, Nicholas, additional, Rodger, Gillian, additional, Street, Teresa L, additional, Swann, Jeremy, additional, Chau, Kevin K, additional, O'Donnell, Denise, additional, Warren, Fiona, additional, Hoosdally, Sarah, additional, O'Donnell, Anne-Marie, additional, Walker, Timothy M, additional, Stoesser, Nicole E, additional, Butcher, Lisa, additional, Peto, Tim EA, additional, Crook, Derrick W, additional, Jeffery, Katie, additional, Matthews, Philippa C, additional, and Eyre, David W, additional

Published
2021
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48. COVID-19: Rapid antigen detection for SARS-CoV-2 by lateral flow assay: A national systematic evaluation of sensitivity and specificity for mass-testing

Author

Peto, Tim, primary, Affron, Dominic, additional, Afrough, Babak, additional, Agasu, Anita, additional, Ainsworth, Mark, additional, Allanson, Alison, additional, Allen, Katherine, additional, Allen, Collette, additional, Archer, Lorraine, additional, Ashbridge, Natasha, additional, Aurfan, Iman, additional, Avery, Miriam, additional, Badenoch, Ellena, additional, Bagga, Priya, additional, Balaji, Rishab, additional, Baldwin, Ella, additional, Barraclough, Sophie, additional, Beane, Carol, additional, Bell, John, additional, Benford, Tracy, additional, Bird, Susan, additional, Bishop, Marina, additional, Bloss, Angela, additional, Body, Richard, additional, Boulton, Rosie, additional, Bown, Abbie, additional, Bratten, Carla, additional, Bridgeman, Chris, additional, Britton, Dominic, additional, Brooks, Tim, additional, Broughton-Smith, Margaret, additional, Brown, Pauline, additional, Buck, Beverley, additional, Butcher, Elaine, additional, Byrne, Wendy, additional, Calderon, Gloria, additional, Campbell, Siobhan, additional, Carr, Olivia, additional, Carter, Penny, additional, Carter, Daniel, additional, Cathrall, Megan, additional, Catton, Matthew, additional, Chadwick, Jim, additional, Chapman, David, additional, Chau, Kevin K., additional, Chaudary, Tanzina, additional, Chidavaenzi, Shaolin, additional, Chilcott, Samatha, additional, Choi, Bea, additional, Claasen, Hannah, additional, Clark, Simon, additional, Clarke, Richard, additional, Clarke, Dawn, additional, Clayton, Richard, additional, Collins, Kayleigh, additional, Colston, Rima, additional, Connolly, James, additional, Cook, Eloïse, additional, Corcoran, Marie, additional, Corley, Ben, additional, Costello, Laura, additional, Coulson, Caroline, additional, Crook, Ant, additional, Crook, Derrick W., additional, D'Arcangelo, Silvia, additional, Darby, Mary-Anne, additional, Davis, John, additional, de Koning, Rosaline, additional, Derbyshire, Pauline, additional, Devall, Pam, additional, Dolman, Mark, additional, Draper, Natalie, additional, Driver, Mark, additional, Dyas, Sarah, additional, Eaton, Emily, additional, Edwards, Joy, additional, Elderfield, Ruth, additional, Ellis, Kate, additional, Ellis, Graham, additional, Elwell, Sue, additional, Evans, Rachel, additional, Evans, Becky, additional, Evans, Marion, additional, Evans, Ranoromanana, additional, Eyre, David, additional, Fahey, Codie, additional, Fenech, Vanessa, additional, Field, Janet, additional, Field, Alice, additional, Foord, Tom, additional, Fowler, Tom, additional, French, Mollie, additional, Fuchs, Hannah, additional, Gan, Jasmine, additional, Gernon, Joseph, additional, Ghadiali, Geeta, additional, Ghuman, Narindar, additional, Gibbons, Kerry, additional, Gill, Gurvinder, additional, Gilmour, Kate, additional, Goel, Anika, additional, Gordon, Sally, additional, Graham, Tillie, additional, Grassam-Rowe, Alexander, additional, Green, David, additional, Gronert, Anna, additional, Gumsley-Read, Tegan, additional, Hall, Claire, additional, Hallis, Bassam, additional, Hammond, Sally, additional, Hammond, Peter, additional, Hanney, Beth, additional, Hardy, Victoria, additional, Harker, Gabriella, additional, Harris, Andrew, additional, Havinden-Williams, May, additional, Hazell, Elena, additional, Henry, Joanne, additional, Hicklin, Kim, additional, Hollier, Kelly, additional, Holloway, Ben, additional, Hoosdally, Sarah J., additional, Hopkins, Susan, additional, Hughes, Lucy, additional, Hurdowar, Steve, additional, Hurford, Sally-Anne, additional, Jackman, Joanne, additional, Jackson, Harriet, additional, Johns, Ruth, additional, Johnston, Susan, additional, Jones, Juliet, additional, Kanyowa, Tinashe, additional, Keating-Fedders, Katie, additional, Kempson, Sharon, additional, Khan, Iftikhar, additional, Khulusi, Beinn, additional, Knight, Thomas, additional, Krishna, Anuradha, additional, Lahert, Patrick, additional, Lampshire, Zoe, additional, Lasserson, Daniel, additional, Lee, Kirsten, additional, Lee, Lennard Y.W., additional, Legard, Arabella, additional, Leggio, Cristina, additional, Liu, Justin, additional, Lockett, Teresa, additional, Logue, Christopher, additional, Lucas, Vanessa, additional, Lumley, Sheila F., additional, Maripuri, Vindhya, additional, Markham, Des, additional, Marshall, Emma, additional, Matthews, Philippa C., additional, Mckee, Sarah, additional, McKee, Deborah F., additional, McLeod, Neil, additional, McNulty, Antoinette, additional, Mellor, Freddie, additional, Michel, Rachel, additional, Mighiu, Alex, additional, Miller, Julie, additional, Mirza, Zarina, additional, Mistry, Heena, additional, Mitchell, Jane, additional, Moeser, Mika Erik, additional, Moore, Sophie, additional, Muthuswamy, Akhila, additional, Myers, Daniel, additional, Nanson, Gemma, additional, Newbury, Mike, additional, Nicol, Scott, additional, Nuttall, Harry, additional, Nwanaforo, Jewel Jones, additional, Oliver, Louise, additional, Osbourne, Wendy, additional, Osbourne, Jake, additional, Otter, Ashley, additional, Owen, Jodie, additional, Panchalingam, Sulaksan, additional, Papoulidis, Dimitris, additional, Pavon, Juan Dobaldo, additional, Peace, Arro, additional, Pearson, Karen, additional, Peck, Liam, additional, Pegg, Ashley, additional, Pegler, Suzannah, additional, Permain, Helen, additional, Perumal, Prem, additional, Peto, Leon, additional, Peto, Tim E.A., additional, Pham, Thanh, additional, Pickford, Hayleah L., additional, Pinkerton, Mark, additional, Platton, Michelle, additional, Price, Ashley, additional, Protheroe, Emily, additional, Purnell, Hellen, additional, Rawden, Lottie, additional, Read, Sara, additional, Reynard, Charles, additional, Ridge, Susan, additional, Ritter, Tom G., additional, Robinson, James, additional, Robinson, Patrick, additional, Rodger, Gillian, additional, Rowe, Cathy, additional, Rowell, Bertie, additional, Rowlands, Alexandra, additional, Sampson, Sarah, additional, Saunders, Kathryn, additional, Sayers, Rachel, additional, Sears, Jackie, additional, Sedgewick, Richard, additional, Seeney, Laura, additional, Selassie, Amanda, additional, Shail, Lloyd, additional, Shallcross, Jane, additional, Sheppard, Lucy, additional, Sherkat, Anna, additional, Siddiqui, Shelha, additional, Sienkiewicz, Alex, additional, Sinha, Lavanya, additional, Smith, Jennifer, additional, Smith, Ella, additional, Stanton, Emma, additional, Starkey, Thomas, additional, Stawiarski, Aleksander, additional, Sterry, Amelia, additional, Stevens, Joe, additional, Stockbridge, Mark, additional, Stoesser, Nicole, additional, Sukumaran, Anila, additional, Sweed, Angela, additional, Tatar, Sami, additional, Thomas, Hema, additional, Tibbins, Carly, additional, Tiley, Sian, additional, Timmins, Julie, additional, Tomas-Smith, Cara, additional, Topping, Oliver, additional, Turek, Elena, additional, Neibler, Toi, additional, Trigg-Hogarth, Kate, additional, Truelove, Elizabeth, additional, Turnbull, Chris, additional, Tyrrell, David, additional, Vaughan, Alison, additional, Vertannes, John, additional, Vipond, Richard, additional, Wagstaff, Linda, additional, Waldron, Joanne, additional, Walker, Philip, additional, Walker, Ann Sarah, additional, Walters, Mary, additional, Wang, Jenny Y, additional, Watson, Ellie, additional, Webberley, Kate, additional, Webster, Kimerbley, additional, Westland, Grace, additional, Wickens, Ian, additional, Willcocks, Jane, additional, Willis, Herika, additional, Wilson, Stephen, additional, Wilson, Barbara, additional, Woodhead, Louise, additional, Wright, Deborah, additional, Xavier, Bindhu, additional, Yelnoorkar, Fiona, additional, Zeidan, Lisa, additional, and Zinyama, Rangeni, additional

Published
2021
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49. The Duration, Dynamics, and Determinants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antibody Responses in Individual Healthcare Workers

Author

Lumley, Sheila F, Wei, Jia, O’Donnell, Denise, Stoesser, Nicole E, Matthews, Philippa C, Howarth, Alison, Hatch, Stephanie B, Marsden, Brian D, Cox, Stuart, James, Tim, Peck, Liam J, Ritter, Thomas G, de Toledo, Zoe, Cornall, Richard J, Jones, E Yvonne, Stuart, David I, Screaton, Gavin, Ebner, Daniel, Hoosdally, Sarah, Crook, Derrick W, Conlon, Christopher P, Pouwels, Koen B, Walker, A Sarah, Peto, Tim E A, Walker, Timothy M, Jeffery, Katie, Eyre, David W, Abbott, Molly, Abhari, Roxanna, Abuelgasim, Hibatullah, Ahmed-Firani, Tariq, Alhussni, Ahmed, Argles, Isobel, Ashworth, Rebecca, Back, Francesca, Black, Susannah, Brennan, Isabelle, Cansdale, Lottie, Chakravorty, Triya, Choudhury, Zahra, Clay, Helen, Conway-Jones, Rebecca, Curtis, Aisling, Cutteridge, Joseph, Danbury, Hannah, Davies, Hettie, Denly, Lucy, Dequaire, Julie, Dimitrov, Stoyan, Dunlop, Ella, Dunn, Polly, East, Cameron, Eastwood, Ben, Edwardes, Chantal, Evans, Meirian, Fields, Charlotte, Flaherty, Sarah, Foord, Thomas, Freer, Rosie, Fuchs, Hannah, Grassam-Rowe, Alexander, Greenan-Barrett, Lewis, Gunnell, James, Harries, Callum, Harris, Edward, Hatton, Elizabeth, Hennessy, Conor, Holland, Christian, Holloway, Ben, Howgego, Gregory, Barnham, Isaac Jarratt, Johnson, Síle, Johnson, Thomas, Johnstone, Daniela, Jurdon, Rebecca, Kelly, Gabriella, Kerneis, Sven, Khulusi, Beinn, Killen, Annabel, Kourdov, Stefan, Kumarendran, Mary, Laurenson-Schafer, Hannah, Lawrence, Ruby, Lee, Charlotte, Livingstone, Angus, Lynch, Rosie, Madsen, Tara, Manji, Ali, Marsh, James, Mason, Chris, Mccance, Angus, Mcgivern, Euan, Mckinlay, Ailsa, Mighiu, Alexandra, Millar, Lancelot, Mohamed, Yethrib, Motohashi, Kenzo, Myat, San, Nezhentsev, Andrey, O’Byrne, Katherine, Okuwoga, Temitope, Oliver, Madeleine, Pattenden, Saxon, Perera, Vimukthi, Petit, Yva, Pickles, Florence, Pikoula, Maria, Randhawa, Govind, Ravi, Krupa, Reed, Lara, Rigler, Caitlin, Robinson, Charlotte, Rothwell, Evie, Santos-Paulo, Stephanie, Savva, Constantinos, Scharmeli, Alice, Scott, Samuel, Shabir, Zamin, Sharma, Ishta, Sheehan, Remarez, Shibu, Afrah, Somanathan, Arun, Sussmes, Samuel, Sweeney, Owen, Swift, Emily, Tadikamalla, Gayatri, Tamblyn, Morwenna, Taylor, Adan, Naudé, Rebecca Te Water, Thomas, Sarah, Thompson, Connor, Till, Lottie, Toward, Ross, Virgo, Charis, Vorley, Imogen, Waite, Seren, Ward, Harry, Ward, Jocelyn, Watson, Adam, Watson, Lily, Wedlich, Matthew, Wilkins, Laura, Wilson, Jack, Wilson, Joseph, Wong, William, Young, Rebecca, Doherty, George, Kavanagh, James, Chau, Kevin K, Fowler, Philip W, Swann, Jeremy, Volk, Denis, Yang-Turner, Fan, Skelly, Donal, Karpe, Fredrik, Neville, Matt J, Ferreira, Lucas Martins, Christott, Thomas, Rodger, Gillian, Pickford, Hayleah, Cameron, Sarah, Tamblin-Hopper, Phoebe, Amini, Ali, Andersson, Monique, Anson, Karen, Aston, Lisa, Axten, David, Barot, Simran, Bellinger, Trisha, Bialek, Adrian, Bodo, Noemi, Brent, Andrew, Campbell, Mark, Cox, Vanessa, Cronin, Tammy, Davies, Timothy, Deales, Alessio, Downs, Louise, Drennan, Philip, Dudareva, Maria, Gates, Laura, Gates, Michelle, Georgiou, Dominique, Gergely, Bernadett, Holland, Louise, Jones, Nicola, Jones, Sarah, Kerr, Sharon, Lawson, Elaine, Looms, Stacy, Luciw, Michael, Martins, Diva, Mcknight, Mary, Mentzer, Alexander, Millard, Rebecca, Mitchell, Tracey, Morgan, Lisa, Morrow, Jordan, Mortimore, Emma, Mullins, Harriet, Nevard, Heather, O’Donnell, Anne-Marie, Patel, Kaisha, Peto, Leon, Philips, Jane, Ponting, Jessica, Ray, Roshni, Robles, Maria, Rughani, Sonam, Sande, Nellia, Shaw, Robert, Simons, Emma-Jane, Sims, Elizabeth, Smit, Kyla, Smith, Lucianne, Szczurkowska, Justyna, Thompson, Zoe, Turford, Rachel, Vilca, Kim, Vogt, Alexander, Warren, Fiona, Warren, Laura, Wharton, Vicki, Whitty, Alison, Woodley, Heather, Wozniak, Barbara, Young, Bernadette, Justice, Anita, Jesuthasan, Gerald, Wareing, Susan, Fadzillah, Nurul Huda Mohamad, Cann, Kathryn, Kirton, Richard, Sutton, Claire, Salvagno, Claudia, D’Amato, Gabriella, Pill, Gemma, Butcher, Lisa, Rylance-Knight, Lydia, Tabirao, Merline, Moroney, Ruth, Wright, Sarah, and Group, Oxford University Hospitals Staff Testing

Subjects
0301 basic medicine, Microbiology (medical), Adult, medicine.medical_specialty, Health Personnel, Population, Antibodies, Viral, Immunoglobulin G, Serology, 03 medical and health sciences, 0302 clinical medicine, Seroepidemiologic Studies, Internal medicine, Correspondence, Credible interval, Major Article, Seroprevalence, Medicine, Humans, 030212 general & internal medicine, education, Survival analysis, Antibody, education.field_of_study, biology, business.industry, SARS-CoV-2, COVID-19, Bayes Theorem, Waning, Titer, 030104 developmental biology, Infectious Diseases, AcademicSubjects/MED00290, Reinfection, Antibody Formation, biology.protein, Longitudinal, business
Abstract

Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulin G (IgG) antibody measurements can be used to estimate the proportion of a population exposed or infected and may be informative about the risk of future infection. Previous estimates of the duration of antibody responses vary. Methods We present 6 months of data from a longitudinal seroprevalence study of 3276 UK healthcare workers (HCWs). Serial measurements of SARS-CoV-2 anti-nucleocapsid and anti-spike IgG were obtained. Interval censored survival analysis was used to investigate the duration of detectable responses. Additionally, Bayesian mixed linear models were used to investigate anti-nucleocapsid waning. Results Anti-spike IgG levels remained stably detected after a positive result, for example, in 94% (95% credibility interval [CrI] 91–96%) of HCWs at 180 days. Anti-nucleocapsid IgG levels rose to a peak at 24 (95% CrI 19–31) days post first polymerase chain reaction (PCR)-positive test, before beginning to fall. Considering 452 anti-nucleocapsid seropositive HCWs over a median of 121 days from their maximum positive IgG titer, the mean estimated antibody half-life was 85 (95% CrI 81–90) days. Higher maximum observed anti-nucleocapsid titers were associated with longer estimated antibody half-lives. Increasing age, Asian ethnicity, and prior self-reported symptoms were independently associated with higher maximum anti-nucleocapsid levels and increasing age and a positive PCR test undertaken for symptoms with longer anti-nucleocapsid half-lives. Conclusions SARS-CoV-2 anti-nucleocapsid antibodies wane within months and fall faster in younger adults and those without symptoms. However, anti-spike IgG remains stably detected. Ongoing longitudinal studies are required to track the long-term duration of antibody levels and their association with immunity to SARS-CoV-2 reinfection.

Published
2021

50. Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae

Author

Shaw, Liam P., Chau, Kevin K., Kavanagh, James, AbuOun, Manal, Stubberfield, Emma, Gweon, H. Soon, Barker, Leanne, Rodger, Gillian, Bowes, Mike J., Hubbard, Alasdair T.M., Pickford, Hayleah, Swann, Jeremy, Gilson, Daniel, Smith, Richard P., Hoosdally, Sarah J., Sebra, Robert, Brett, Howard, Peto, Tim E.A., Bailey, Mark J., Crook, Derrick W., Read, Daniel S., Anjum, Muna F., Walker, A. Sarah, Stoesser, Nicole, Shaw, Liam P., Chau, Kevin K., Kavanagh, James, AbuOun, Manal, Stubberfield, Emma, Gweon, H. Soon, Barker, Leanne, Rodger, Gillian, Bowes, Mike J., Hubbard, Alasdair T.M., Pickford, Hayleah, Swann, Jeremy, Gilson, Daniel, Smith, Richard P., Hoosdally, Sarah J., Sebra, Robert, Brett, Howard, Peto, Tim E.A., Bailey, Mark J., Crook, Derrick W., Read, Daniel S., Anjum, Muna F., Walker, A. Sarah, and Stoesser, Nicole

Abstract

Escherichia coli and other Enterobacteriaceae are diverse species with “open” pangenomes, where genes move intra- and interspecies via horizontal gene transfer. However, most analyses focus on clinical isolates. The pangenome dynamics of natural populations remain understudied, despite their suggested role as reservoirs for antimicrobial resistance (AMR) genes. Here, we analyze near-complete genomes for 827 Enterobacteriaceae (553 Escherichia and 274 non-Escherichia spp.) with 2292 circularized plasmids in total, collected from 19 locations (livestock farms and wastewater treatment works in the United Kingdom) within a 30-km radius at three time points over a year. We find different dynamics for chromosomal and plasmid-borne genes. Plasmids have a higher burden of AMR genes and insertion sequences, and AMR-gene-carrying plasmids show evidence of being under stronger selective pressure. Environmental niche and local geography both play a role in shaping plasmid dynamics. Our results highlight the importance of local strategies for controlling the spread of AMR.

Published
2021

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