Year Item Type Full Text

Bibliographic data only

Evolutionary dynamics of Clostridium difficile over short and long time scales. (2010) He, Miao; Sebaihia, Mohammed; Lawley, Trevor D; Stabler, Richard A; Dawson, Lisa F; Martin, Melissa J; Holt, Kathryn E; Seth-Smith, Helena MB; Quail, Michael A; Rance, Richard; Brooks, Karen; Churcher, Carol; Harris, David; Bentley, Stephen D; Burrows, Christine; Clark, Louise; Corton, Craig; Murray, Vicky; Rose, Graham; Thurston, Scott; van Tonder, Andries; Walker, Danielle; Wren, Brendan W; Dougan, Gordon; Parkhill, Julian

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. (2008) Holt, Kathryn E; Parkhill, Julian; Mazzoni, Camila J; Roumagnac, Philippe; Weill, François-Xavier; Goodhead, Ian; Rance, Richard; Baker, Stephen; Maskell, Duncan J; Wain, John; Dolecek, Christiane; Achtman, Mark; Dougan, Gordon

Tracking the establishment of local endemic populations of an emergent enteric pathogen. (2013) Holt, Kathryn E; Thieu Nga, Tran Vu; Thanh, Duy Pham; Vinh, Ha; Kim, Dong Wook; Vu Tra, My Phan; Campbell, James I; Hoang, Nguyen Van Minh; Vinh, Nguyen Thanh; Minh, Pham Van; Thuy, Cao Thu; Nga, Tran Thi Thu; Thompson, Corinne; Dung, Tran Thi Ngoc; Nhu, Nguyen Thi Khanh; Vinh, Phat Voong; Tuyet, Pham Thi Ngoc; Phuc, Hoang Le; Lien, Nguyen Thi Nam; Phu, Bui Duc; Ai, Nguyen Thi Thuy; Tien, Nguyen Manh; Dong, Nguyen; Parry, Christopher M; Hien, Tran Tinh; Farrar, Jeremy J; Parkhill, Julian; Dougan, Gordon; Thomson, Nicholas R; Baker, Stephen

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. (2015) 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

Global phylogeography and evolutionary history of Shigella dysenteriae type 1. (2016) Njamkepo, Elisabeth; Fawal, Nizar; Tran-Dien, Alicia; Hawkey, Jane; Strockbine, Nancy; Jenkins, Claire; Talukder, Kaisar A; Bercion, Raymond; Kuleshov, Konstantin; Kolínská, Renáta; Russell, Julie E; Kaftyreva, Lidia; Accou-Demartin, Marie; Karas, Andreas; Vandenberg, Olivier; Mather, Alison E; Mason, Carl J; Page, Andrew J; Ramamurthy, Thandavarayan; Bizet, Chantal; Gamian, Andrzej; Carle, Isabelle; Sow, Amy Gassama; Bouchier, Christiane; Wester, Astrid Louise; Lejay-Collin, Monique; Fonkoua, Marie-Christine; Le Hello, Simon; Blaser, Martin J; Jernberg, Cecilia; Ruckly, Corinne; Mérens, Audrey; Page, Anne-Laure; Aslett, Martin; Roggentin, Peter; Fruth, Angelika; Denamur, Erick; Venkatesan, Malabi; Bercovier, Hervé; Bodhidatta, Ladaporn; Chiou, Chien-Shun; Clermont, Dominique; Colonna, Bianca; Egorova, Svetlana; Pazhani, Gururaja P; Ezernitchi, Analia V; Guigon, Ghislaine; Harris, Simon R; Izumiya, Hidemasa; Korzeniowska-Kowal, Agnieszka; Lutyńska, Anna; Gouali, Malika; Grimont, Francine; Langendorf, Céline; Marejková, Monika; Peterson, Lorea AM; Perez-Perez, Guillermo; Ngandjio, Antoinette; Podkolzin, Alexander; Souche, Erika; Makarova, Mariia; Shipulin, German A; Ye, Changyun; Žemličková, Helena; Herpay, Mária; Grimont, Patrick AD; Parkhill, Julian; Sansonetti, Philippe; Holt, Kathryn E; Brisse, Sylvain; Thomson, Nicholas R; Weill, François-Xavier

Inducible colistin resistance via a disrupted plasmid-borne mcr-1 gene in a 2008 Vietnamese Shigella sonnei isolate. (2016) Pham Thanh, Duy; Thanh Tuyen, Ha; Nguyen Thi Nguyen, To; Chung The, Hao; Wick, Ryan R; Thwaites, Guy E; Baker, Stephen; Holt, Kathryn E

The genomic signatures of Shigella evolution, adaptation and geographical spread. (2016) The, Hao Chung; Thanh, Duy Pham; Holt, Kathryn E; Thomson, Nicholas R; Baker, Stephen

Genomic history of the seventh pandemic of cholera in Africa. (2017) Weill, François-Xavier; Domman, Daryl; Njamkepo, Elisabeth; Tarr, Cheryl; Rauzier, Jean; Fawal, Nizar; Keddy, Karen H; Salje, Henrik; Moore, Sandra; Mukhopadhyay, Asish K; Bercion, Raymond; Luquero, Francisco J; Ngandjio, Antoinette; Dosso, Mireille; Monakhova, Elena; Garin, Benoit; Bouchier, Christiane; Pazzani, Carlo; Mutreja, Ankur; Grunow, Roland; Sidikou, Fati; Bonte, Laurence; Breurec, Sébastien; Damian, Maria; Njanpop-Lafourcade, Berthe-Marie; Sapriel, Guillaume; Page, Anne-Laure; Hamze, Monzer; Henkens, Myriam; Chowdhury, Goutam; Mengel, Martin; Koeck, Jean-Louis; Fournier, Jean-Michel; Dougan, Gordon; Grimont, Patrick AD; Parkhill, Julian; Holt, Kathryn E; Piarroux, Renaud; Ramamurthy, Thandavarayan; Quilici, Marie-Laure; Thomson, Nicholas R

Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events. (2015) Wong, Vanessa K; Baker, Stephen; Pickard, Derek J; Parkhill, Julian; Page, Andrew J; Feasey, Nicholas A; Kingsley, Robert A; Thomson, Nicholas R; Keane, Jacqueline A; Weill, François-Xavier; Edwards, David J; Hawkey, Jane; Harris, Simon R; Mather, Alison E; Cain, Amy K; Hadfield, James; Hart, Peter J; Thieu, Nga Tran Vu; Klemm, Elizabeth J; Glinos, Dafni A; Breiman, Robert F; Watson, Conall H; Kariuki, Samuel; Gordon, Melita A; Heyderman, Robert S; Okoro, Chinyere; Jacobs, Jan; Lunguya, Octavie; Edmunds, W John; Msefula, Chisomo; Chabalgoity, Jose A; Kama, Mike; Jenkins, Kylie; Dutta, Shanta; Marks, Florian; Campos, Josefina; Thompson, Corinne; Obaro, Stephen; MacLennan, Calman A; Dolecek, Christiane; Keddy, Karen H; Smith, Anthony M; Parry, Christopher M; Karkey, Abhilasha; Mulholland, E Kim; Campbell, James I; Dongol, Sabina; Basnyat, Buddha; Dufour, Muriel; Bandaranayake, Don; Naseri, Take Toleafoa; Singh, Shalini Pravin; Hatta, Mochammad; Newton, Paul; Onsare, Robert S; Isaia, Lupeoletalalei; Dance, David; Davong, Viengmon; Thwaites, Guy; Wijedoru, Lalith; Crump, John A; De Pinna, Elizabeth; Nair, Satheesh; Nilles, Eric J; Thanh, Duy Pham; Turner, Paul; Soeng, Sona; Valcanis, Mary; Powling, Joan; Dimovski, Karolina; Hogg, Geoff; Farrar, Jeremy; Holt, Kathryn E; Dougan, Gordon

Public

Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch. (2021) Argimón, Silvia; David, Sophia; Underwood, Anthony; Abrudan, Monica; Wheeler, Nicole E; Kekre, Mihir; Abudahab, Khalil; Yeats, Corin A; Goater, Richard; Taylor, Ben; Harste, Harry; Muddyman, Dawn; Feil, Edward J; Brisse, Sylvain; Holt, Kathryn; Donado-Godoy, Pilar; Ravikumar, KL; Okeke, Iruka N; Carlos, Celia; Aanensen, David M; NIHR Global Health Research Unit on Genomic Surveillance of Anti

A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch. (2021) Argimón, Silvia; Yeats, Corin A; Goater, Richard J; Abudahab, Khalil; Taylor, Benjamin; Underwood, Anthony; Sánchez-Busó, Leonor; Wong, Vanessa K; Dyson, Zoe A; Nair, Satheesh; Park, Se Eun; Marks, Florian; Page, Andrew J; Keane, Jacqueline A; Baker, Stephen; Holt, Kathryn E; Dougan, Gordon; Aanensen, David M

Making microbial genomics work for clinical and public health microbiology. (2022) Azarian, Taj; Sherry, Norelle L; Baker, Kate; Holt, Kathryn E; Okeke, Iruka N

Convergent adaptation in the dominant global hospital clone ST239 of methicillin-resistant Staphylococcus aureus. (2015) Baines, Sarah L; Holt, Kathryn E; Schultz, Mark B; Seemann, Torsten; Howden, Brian O; Jensen, Slade O; van Hal, Sebastiaan J; Coombs, Geoffrey W; Firth, Neville; Powell, David R; Stinear, Timothy P; Howden, Benjamin P

Navigating the future of bacterial molecular epidemiology. (2010) Baker, Stephen; Hanage, William P; Holt, Kathryn E

Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission. (2011) Baker, Stephen; Holt, Kathryn E; Clements, Archie CA; Karkey, Abhilasha; Arjyal, Amit; Boni, Maciej F; Dongol, Sabina; Hammond, Naomi; Koirala, Samir; Duy, Pham Thanh; Nga, Tran Vu Thieu; Campbell, James I; Dolecek, Christiane; Basnyat, Buddha; Dougan, Gordon; Farrar, Jeremy J

A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi. (2007) Baker, Stephen; Holt, Kathryn; Whitehead, Sally; Goodhead, Ian; Perkins, Tim; Stocker, Bruce; Hardy, Jonathan; Dougan, Gordon

Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens. (2018) Baker, Stephen; Thomson, Nicholas; Weill, François-Xavier; Holt, Kathryn E

Multidrug-resistant Salmonella enterica serotype Typhi, Gulf of Guinea Region, Africa. (2015) Baltazar, Murielle; Ngandjio, Antoinette; Holt, Kathryn Elizabeth; Lepillet, Elodie; Pardos de la Gandara, Maria; Collard, Jean-Marc; Bercion, Raymond; Nzouankeu, Ariane; Le Hello, Simon; Dougan, Gordon; Fonkoua, Marie-Christine; Weill, François-Xavier

Species interactions constrain adaptation and preserve ecological stability in an experimental microbial community. (2022) Barber, Jake N; Nicholson, Luke C; Woods, Laura C; Judd, Louise M; Sezmis, Aysha L; Hawkey, Jane; Holt, Kathryn E; McDonald, Michael J

Properties of genes encoding transfer RNAs as integration sites for genomic islands and prophages in<i>Klebsiella pneumoniae</i>. (2020) Berríos-Pastén, Camilo; Acevedo, Rodolfo; Arros, Patricio; Varas, Macarena A; Wyres, Kelly L; Lam, Margaret MC; Holt, Kathryn E; Lagos, Rosalba; Marcoleta, Andrés E

Variants of AbGRI3 carrying the armA gene in extensively antibiotic-resistant Acinetobacter baumannii from Singapore. (2017) Blackwell, Grace A; Holt, Kathryn E; Bentley, Stephen D; Hsu, Li Yang; Hall, Ruth M

Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii. (2019) Boinett, Christine J; Cain, Amy K; Hawkey, Jane; Do Hoang, Nhu Tran; Khanh, Nhu Nguyen Thi; Thanh, Duy Pham; Dordel, Janina; Campbell, James I; Lan, Nguyen Phu Huong; Mayho, Matthew; Langridge, Gemma C; Hadfield, James; Chau, Nguyen Van Vinh; Thwaites, Guy E; Parkhill, Julian; Thomson, Nicholas R; Holt, Kathryn E; Baker, Stephen

Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: Antimicrobial resistance and implications for vaccine policy. (2018) Britto, Carl D; Dyson, Zoe A; Duchene, Sebastian; Carter, Michael J; Gurung, Meeru; Kelly, Dominic F; Murdoch, David R; Ansari, Imran; Thorson, Stephen; Shrestha, Shrijana; Adhikari, Neelam; Dougan, Gordon; Holt, Kathryn E; Pollard, Andrew J

Persistent circulation of a fluoroquinolone-resistant Salmonella enterica Typhi clone in the Indian subcontinent. (2020) Britto, Carl D; Dyson, Zoe A; Mathias, Sitarah; Bosco, Ashish; Dougan, Gordon; Jose, Sanju; Nagaraj, Savitha; Holt, Kathryn E; Pollard, Andrew J

Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation. (2018) Brynildsrud, Ola B; Pepperell, Caitlin S; Suffys, Philip; Grandjean, Louis; Monteserin, Johana; Debech, Nadia; Bohlin, Jon; Alfsnes, Kristian; Pettersson, John O-H; Kirkeleite, Ingerid; Fandinho, Fatima; da Silva, Marcia Aparecida; Perdigao, Joao; Portugal, Isabel; Viveiros, Miguel; Clark, Taane; Caws, Maxine; Dunstan, Sarah; Thai, Phan Vuong Khac; Lopez, Beatriz; Ritacco, Viviana; Kitchen, Andrew; Brown, Tyler S; van Soolingen, Dick; O'Neill, Mary B; Holt, Kathryn E; Feil, Edward J; Mathema, Barun; Balloux, Francois; Eldholm, Vegard

Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin. (2018) Cain, Amy K; Boinett, Christine J; Barquist, Lars; Dordel, Janina; Fookes, Maria; Mayho, Matthew; Ellington, Matthew J; Goulding, David; Pickard, Derek; Wick, Ryan R; Holt, Kathryn E; Parkhill, Julian; Thomson, Nicholas R

Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization. (2023) Carey, Megan E; Dyson, Zoe A; Argimón, Silvia; Cerdeira, Louise; Yeats, Corin; Aanensen, David; Mboowa, Gerald; Baker, Stephen; Tessema, Sofonias K; Smith, Anthony M; Okeke, Iruka N; Holt, Kathryn E

Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes. (2023) Carey, Megan E; Dyson, Zoe A; Ingle, Danielle J; Amir, Afreenish; Aworh, Mabel K; Chattaway, Marie Anne; Chew, Ka Lip; Crump, John A; Feasey, Nicholas A; Howden, Benjamin P; Keddy, Karen H; Maes, Mailis; Parry, Christopher M; Van Puyvelde, Sandra; Webb, Hattie E; Afolayan, Ayorinde Oluwatobiloba; Alexander, Anna P; Anandan, Shalini; Andrews, Jason R; Ashton, Philip M; Basnyat, Buddha; Bavdekar, Ashish; Bogoch, Isaac I; Clemens, John D; da Silva, Kesia Esther; De, Anuradha; de Ligt, Joep; Diaz Guevara, Paula Lucia; Dolecek, Christiane; Dutta, Shanta; Ehlers, Marthie M; Francois Watkins, Louise; Garrett, Denise O; Godbole, Gauri; Gordon, Melita A; Greenhill, Andrew R; Griffin, Chelsey; Gupta, Madhu; Hendriksen, Rene S; Heyderman, Robert S; Hooda, Yogesh; Hormazabal, Juan Carlos; Ikhimiukor, Odion O; Iqbal, Junaid; Jacob, Jobin John; Jenkins, Claire; Jinka, Dasaratha Ramaiah; John, Jacob; Kang, Gagandeep; Kanteh, Abdoulie; Kapil, Arti; Karkey, Abhilasha; Kariuki, Samuel; Kingsley, Robert A; Koshy, Roshine Mary; Lauer, AC; Levine, Myron M; Lingegowda, Ravikumar Kadahalli; Luby, Stephen P; Mackenzie, Grant Austin; Mashe, Tapfumanei; Msefula, Chisomo; Mutreja, Ankur; Nagaraj, Geetha; Nagaraj, Savitha; Nair, Satheesh; Naseri, Take K; Nimarota-Brown, Susana; Njamkepo, Elisabeth; Okeke, Iruka N; Perumal, Sulochana Putli Bai; Pollard, Andrew J; Pragasam, Agila Kumari; Qadri, Firdausi; Qamar, Farah N; Rahman, Sadia Isfat Ara; Rambocus, Savitra Devi; Rasko, David A; Ray, Pallab; Robins-Browne, Roy; Rongsen-Chandola, Temsunaro; Rutanga, Jean Pierre; Saha, Samir K; Saha, Senjuti; Saigal, Karnika; Sajib, Mohammad Saiful Islam; Seidman, Jessica C; Shakya, Jivan; Shamanna, Varun; Shastri, Jayanthi; Shrestha, Rajeev; Sia, Sonia; Sikorski, Michael J; Singh, Ashita; Smith, Anthony M; Tagg, Kaitlin A; Tamrakar, Dipesh; Tanmoy, Arif Mohammed; Thomas, Maria; Thomas, Mathew S; Thomsen, Robert; Thomson, Nicholas R; Tupua, Siaosi; Vaidya, Krista; Valcanis, Mary; Veeraraghavan, Balaji; Weill, François-Xavier; Wright, Jackie; Dougan, Gordon; Argimón, Silvia; Keane, Jacqueline A; Aanensen, David M; Baker, Stephen; Holt, Kathryn E; Global Typhoid Genomics Consortium Group Authorship

A bioinformatic strategy for the detection, classification and analysis of bacterial autotransporters. (2012) Celik, Nermin; Webb, Chaille T; Leyton, Denisse L; Holt, Kathryn E; Heinz, Eva; Gorrell, Rebecca; Kwok, Terry; Naderer, Thomas; Strugnell, Richard A; Speed, Terence P; Teasdale, Rohan D; Likić, Vladimir A; Lithgow, Trevor

Small IncQ1 and Col-Like Plasmids Harboring blaKPC-2 and Non-Tn4401 Elements (NTEKPC-IId) in High-Risk Lineages of Klebsiella pneumoniae CG258. (2019) Cerdeira, Louise T; Lam, Margaret MC; Wyres, Kelly L; Wick, Ryan R; Judd, Louise M; Lopes, Ralf; Ribas, Rosineide M; Morais, Marcia M; Holt, Kathryn E; Lincopan, Nilton

Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei. (2019) Chung The, Hao; Boinett, Christine; Pham Thanh, Duy; Jenkins, Claire; Weill, Francois-Xavier; Howden, Benjamin P; Valcanis, Mary; De Lappe, Niall; Cormican, Martin; Wangchuk, Sonam; Bodhidatta, Ladaporn; Mason, Carl J; Nguyen, To Nguyen Thi; Ha Thanh, Tuyen; Voong, Vinh Phat; Duong, Vu Thuy; Nguyen, Phu Huong Lan; Turner, Paul; Wick, Ryan; Ceyssens, Pieter-Jan; Thwaites, Guy; Holt, Kathryn E; Thomson, Nicholas R; Rabaa, Maia A; Baker, Stephen

South Asia as a Reservoir for the Global Spread of Ciprofloxacin-Resistant Shigella sonnei: A Cross-Sectional Study. (2016) Chung The, Hao; Rabaa, Maia A; Pham Thanh, Duy; De Lappe, Niall; Cormican, Martin; Valcanis, Mary; Howden, Benjamin P; Wangchuk, Sonam; Bodhidatta, Ladaporn; Mason, Carl J; Nguyen Thi Nguyen, To; Vu Thuy, Duong; Thompson, Corinne N; Phu Huong Lan, Nguyen; Voong Vinh, Phat; Ha Thanh, Tuyen; Turner, Paul; Sar, Poda; Thwaites, Guy; Thomson, Nicholas R; Holt, Kathryn E; Baker, Stephen

Introduction and establishment of fluoroquinolone-resistant Shigella sonnei into Bhutan. (2015) Chung The, Hao; Rabaa, Maia A; Thanh, Duy Pham; Ruekit, Sirigade; Wangchuk, Sonam; Dorji, Tshering; Tshering, Kinzang Pem; Nguyen, To Nguyen Thi; Vinh, Phat Voong; Thanh, Tuyen Ha; Minh, Chau Nguyen Ngoc; Turner, Paul; Sar, Poda; Thwaites, Guy; Holt, Kathryn E; Thomson, Nicholas R; Bodhidatta, Ladaporn; Jeffries Mason, Carl; Baker, Stephen

Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. (2013) Comas, Iñaki; Coscolla, Mireia; Luo, Tao; Borrell, Sonia; Holt, Kathryn E; Kato-Maeda, Midori; Parkhill, Julian; Malla, Bijaya; Berg, Stefan; Thwaites, Guy; Yeboah-Manu, Dorothy; Bothamley, Graham; Mei, Jian; Wei, Lanhai; Bentley, Stephen; Harris, Simon R; Niemann, Stefan; Diel, Roland; Aseffa, Abraham; Gao, Qian; Young, Douglas; Gagneux, Sebastien

A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex. (2024) Cooper, Helena B; Vezina, Ben; Hawkey, Jane; Passet, Virginie; López-Fernández, Sebastián; Monk, Jonathan M; Brisse, Sylvain; Holt, Kathryn E; Wyres, Kelly L

wMel Wolbachia genome remains stable after 7 years in Australian Aedes aegypti field populations. (2021) Dainty, Kimberley R; Hawkey, Jane; Judd, Louise M; Pacidônio, Etiene C; Duyvestyn, Johanna M; Gonçalves, Daniela S; Lin, Silk Yu; O'Donnell, Tanya B; O'Neill, Scott L; Simmons, Cameron P; Holt, Kathryn E; Flores, Heather A

The STRATAA study protocol: a programme to assess the burden of enteric fever in Bangladesh, Malawi and Nepal using prospective population census, passive surveillance, serological studies and healthcare utilisation surveys. (2017) Darton, Thomas C; Meiring, James E; Tonks, Susan; Khan, Md Arifuzzaman; Khanam, Farhana; Shakya, Mila; Thindwa, Deus; Baker, Stephen; Basnyat, Buddha; Clemens, John D; Dougan, Gordon; Dolecek, Christiane; Dunstan, Sarah J; Gordon, Melita A; Heyderman, Robert S; Holt, Kathryn E; Pitzer, Virginia E; Qadri, Firdausi; Zaman, K; Pollard, Andrew J; STRATAA Study Consortium

Act now against new NHS competition regulations: an open letter to the BMA and the Academy of Medical Royal Colleges calls on them to make a joint public statement of opposition to the amended section 75 regulations. (2013) Davis, Jacky; Banks, Ian; Wrigley, David; Peedell, Clive; Pollock, Alyson; McPherson, Klim; McKee, Martin; Irving, William L; Crome, Peter; Greenhalgh, Trisha; Holland, Walter; Evans, David; Maryon-Davis, Alan; Smyth, Alan; Fleming, Peter; Coleman, Michel; Sharp, Deborah J; Whincup, Peter; Logan, Stuart; Cook, Derek; Moore, Robert; Rawaf, Salman; McEewen, J; West, Robert; Yudkin, John S; Clarke, Aileen; Finer, Nick; Domizio, Paola; Bambra, Clare; Jones, Anna; Feder, Gene; Scott-Samuel, Alex; Irvine, Louise; Sharma, Ajay; Fitchett, Mike; Boomla, Kambiz; Folb, Jonathan; Paul, Ashish; McCoy, David; Tallis, Ray; Burgess-Allen, Jilla; Edwards, Mark; Tomlinson, Jonathon; Colvin, Deborah; Gore, Jonathan; Brown, Kirsten; Mitchel, Sarah; Lau, Alice; Sayer, Mel; Clark, Leon; Silverman, Ruth; Marmot, Saul; Rainbow, Daniel; Carter, Lucy; Mann, Nick; Fielding, Richard; Logan, Jane; Tebboth, Louise; Arnold, Natasha; Stobbart, Kate; Cabot, Kate; Finer, Sarah; Edwards, Martin; Davies, David; Buttivant, Helen; Kraemer, Sebastian; Newell, Jo; Griffiths, Alun; Fitzgerald, Richard; Macgibbon, Robert; Lee, Alan; Macklon, AF; Hobson, Esther; Jenner, David; Jacobson, Bobbie; Timmis, Alison; Salim, Asad; Evans-Jones, John; Caan, Woody; Awsare, Ninaad; Pride, Neil; Suckling, Ruth; Bratty, Catherine; Rossiter, Brian; Hawkins, David; Currie, Jonny; Camilleri-Ferrante, Corinne; Fluxman, Jonathan; Bhatti, Osman; Anson, James; Etherington, Robert; Lawrence, David; Fell, Henry; Clarke, Edward; Ormerod, Julian; Ormerod, Oliver; Ireland, Maggie; Duncan, John AT; Chandy, Rajiv; Mindell, Jennifer; Mullen, Paul; Bennett-Richards, Phillip; Hirst, Julie; Murphy, E; Martin, P; Lowes, Simon; Fleming, Peter; Grunewald, Richard; Reeve, Joanne; Schweiger, Martin; Coates, Jonathan; Farrelly, George; Chamberlain, MA; Lewis, Geoffrey; Young, Jane; Scott, Brian; Gibbs, John; Landers, Aileen; Deveson, Pete; Ingrams, Grant; Leigh, Martha; Gawler, Jeff; Ford, Amy; Nixon, Jonathan; McCartney, Margaret; Bareford, David; Singh, Surinder; Lockwood, Kate; Cripwell, Michael; Ehrhardt, Peter; Bell, David; Wortley, Pam; Tomlinson, Laurie; Hotchkiss, Julie; Ford, Steven; Turner, Gill; Reissman, Gerard; Lewis, David; Johnstone, Chris; Tomson, Mike; Torabi, Payam; Bell, David; Tomson, D; Tulloch, Alex; Johnston, Sally; Dickinson, Jane; McElderry, Elisabeth; Ross, Wendy; Holt, Kim; Logan, Mary; Klonin, Hilary; Jenner, David; Danby, Jude; Goodger, V; Puntis, John; Dickson, Harriet; Gould, Derek A; Livingstone, Anna; Lefevre, Dianne; Kendall, Bryony; Singh, G; Hall, Peter; Darling, Jonathan; Hamlyn, Adrian N; Patel, Anita; Erskine, Jonathan; Fisher, Brian; Hughes, Richard; Highton, Clare; Venning, Helen; Singer, Ron; Brearey, Steve; Sikorski, Jim; Paintin, David; Feehally, John; Savage, Wendy; Freud, Kathy McAdam; Holt, Victoria J; Gill, Alison; Waterston, Tony; Souza, Richard de; Hopkinson, Nicholas; Beadsworth, Mike; Franks, Andrea; Daley, Helen; Cullinan, Paul; Basarab, Adriana; Folb, Jonathan; Gurling, Hugh; Zinkin, Pam; Kirwin, Simon; Buhrs, Ernst; Brown, Raymond; West, Andrew; Marlowe, Gary; Fellows, Griffith; Main, John; Applebee, Jackie; Koperski, M; Jones, Phil; Macfarlane, Alison; Beer, Naomi; Mason, Rebecca; West, Robert; Eisner, Maggie; Smailes, Alison; Timms, Philip; Knight, David; Jones, Coral; Wesby, Barbara; Lyttelton, Laura; Morrison, Richard; Bossano, David; Walker, Jonathan; Davies, Gerry; Godfrey, Peter; Wolfe, Ingrid; Nsutebu, Emmanuel; Stevenson, Nicola; Cheeroth, Sheila; Miller, Jo; Johnson, Guy; Noor, R; Hall, Alyson; Bostock, David; Michael, Benedict; Sharvill, John; Macpherson, Jamie; Lewis, David; Ma, Richard; Middleton, John; Jeffreys, Anne; Cole, Jim; Boswell, John P; Bury, Bob; Mitchison, Sally; Kinmonth, Ann-Louise; Young, Gail; Maclennan, Iain; Munday, Pat

On the origin of Mycobacterium ulcerans, the causative agent of Buruli ulcer. (2012) Doig, Kenneth D; Holt, Kathryn E; Fyfe, Janet AM; Lavender, Caroline J; Eddyani, Miriam; Portaels, Françoise; Yeboah-Manu, Dorothy; Pluschke, Gerd; Seemann, Torsten; Stinear, Timothy P

Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods. (2018) Duchene, Sebastian; Duchene, David A; Geoghegan, Jemma L; Dyson, Zoe A; Hawkey, Jane; Holt, Kathryn E

Genome-scale rates of evolutionary change in bacteria. (2016) Duchêne, Sebastian; Holt, Kathryn E; Weill, François-Xavier; Le Hello, Simon; Hawkey, Jane; Edwards, David J; Fourment, Mathieu; Holmes, Edward C

Cross-validation to select Bayesian hierarchical models in phylogenetics. (2016) Duchêne, Sebastián; Duchêne, David A; Di Giallonardo, Francesca; Eden, John-Sebastian; Geoghegan, Jemma L; Holt, Kathryn E; Ho, Simon YW; Holmes, Edward C

Pathogen diversity and antimicrobial resistance transmission of Salmonella enterica serovars Typhi and Paratyphi A in Bangladesh, Nepal, and Malawi: a genomic epidemiological study. (2024) Dyson, Zoe A; Ashton, Philip M; Khanam, Farhana; Chunga Chirambo, Angeziwa; Shakya, Mila; Meiring, James E; Tonks, Susan; Karkey, Abhilasha; Msefula, Chisomo; Clemens, John D; Dunstan, Sarah J; Baker, Stephen; Dougan, Gordon; Pitzer, Virginia E; Basnyat, Buddha; Qadri, Firdausi; Heyderman, Robert S; Gordon, Melita A; Pollard, Andrew J; Holt, Kathryn E; STRATAA Study Group

The TyphiNET data visualisation dashboard: unlocking Salmonella Typhi genomics data to support public health. (2025) Dyson, Zoe A; Cerdeira, Louise; Sharma, Vandana; Carey, Megan E; Holt, Kathryn E; Aanensen, David M; Abbas, Ali H; Fayad, Antoine Abou; Afolayan, Ayorinde O; Ahmed, Niyaz; Ahmed, Irshad; Amir, Afreenish; Andleeb, Saadia; Argimón, Silvia; Aseffa, Abraham; Ashton, Philip M; Aworh, Mabel K; Bavdekar, Ashish R; Chattaway, Marie A; Chew, Ka Lip; Crump, John A; Darton, Thomas C; Diaz, Paula L; Dolecek, Christiane; Feasey, Nicholas A; Greenhill, Andrew R; Gupta, Madhu; Hatta, Mochammad; Hendriksen, Rene S; Heyderman, Robert S; Ikhimiukor, Odion O; Ikram, Aamer; Ingle, Danielle J; Kapil, Arti; Keane, Jacqueline A; Keddy, Karen H; Kingsley, Robert A; Levine, Myron M; MacLennan, Calman A; Maes, Mailis; Mahindroo, Jaspreet; Mashe, Tapfumanei; Morita, Masatomo; Mylona, Elli; Nagaraj, Geetha; Nair, Satheesh; Naseri, Take K; Njamkepo, Elisabeth; Octavia, Sophie; Okeke, Iruka N; Owusu, Michael; de la Gandara, Maria Pardos; Pollard, Andrew J; Rahman, Sadia IA; Rahman, Saikt; Rasko, David A; Redwan, Elrashdy M; Rokney, Assaf; Rupali, Priscilla; Rutanga, Jean Pierre; Shakya, Jivan; Saha, Senjuti; Sikorski, Michael J; Smith, Anthony M; Tagg, Kaitlin A; Taneja, Neelam; Tamrakar, Dipesh; Turner, Paul; Ussher, James E; Van Puyvelde, Sandra; Vandelannoote, Koen; Weill, François-Xavier; Wong, Vanessa K; Wright, Jackie

Five Years of GenoTyphi: Updates to the Global Salmonella Typhi Genotyping Framework. (2021) Dyson, Zoe A; Holt, Kathryn E

Whole Genome Sequence Analysis of Salmonella Typhi Isolated in Thailand before and after the Introduction of a National Immunization Program. (2016) Dyson, Zoe A; Thanh, Duy Pham; Bodhidatta, Ladaporn; Mason, Carl Jeffries; Srijan, Apichai; Rabaa, Maia A; Vinh, Phat Voong; Thanh, Tuyen Ha; Thwaites, Guy E; Baker, Stephen; Holt, Kathryn E

Whole genome sequence analysis of Salmonella Typhi in Papua New Guinea reveals an established population of genotype 2.1.7 sensitive to antimicrobials. (2022) Dyson, Zoe Anne; Malau, Elisheba; Horwood, Paul F; Ford, Rebecca; Siba, Valentine; Yoannes, Mition; Pomat, William; Passey, Megan; Judd, Louise M; Ingle, Danielle J; Williamson, Deborah A; Dougan, Gordon; Greenhill, Andrew R; Holt, Kathryn E

SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments. (2021) Edwards, David J; Duchene, Sebastián; Pope, Bernard; Holt, Kathryn E

SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments. (2020) Edwards, David J; Duchêne, Sebastián; Pope, Bernard; Holt, Kathryn E

The diversity of Klebsiella pneumoniae surface polysaccharides. (2016) Follador, Rainer; Heinz, Eva; Wyres, Kelly L; Ellington, Matthew J; Kowarik, Michael; Holt, Kathryn E; Thomson, Nicholas R

Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae. (2023) Foster-Nyarko, Ebenezer; Cottingham, Hugh; Wick, Ryan R; Judd, Louise M; Lam, Margaret MC; Wyres, Kelly L; Stanton, Thomas D; Tsang, Kara K; David, Sophia; Aanensen, David M; Brisse, Sylvain; Holt, Kathryn E

Corrigendum: 'Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae'. (2023) Foster-Nyarko, Ebenezer; Cottingham, Hugh; Wick, Ryan R; Judd, Louise M; Lam, Margaret MC; Wyres, Kelly L; Stanton, Thomas D; Tsang, Kara K; David, Sophia; Aanensen, David M; Brisse, Sylvain; Holt, Kathryn E

A nationwide genomic study of clinical Klebsiella pneumoniae in Norway 2001-15: introduction and spread of ESBLs facilitated by clonal groups CG15 and CG307. (2021) Fostervold, Aasmund; Hetland, Marit AK; Bakksjø, Ragna; Bernhoff, Eva; Holt, Kathryn E; Samuelsen, Ørjan; Simonsen, Gunnar Skov; Sundsfjord, Arnfinn; Wyres, Kelly L; Löhr, Iren Høyland; Norwegian Study Group on Klebsiella pneumoniae

Detection of plasmid contigs in draft genome assemblies using customized Kraken databases. (2021) Gomi, Ryota; Wyres, Kelly L; Holt, Kathryn E

Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients. (2017) Gorrie, Claire L; Mirceta, Mirjana; Wick, Ryan R; Edwards, David J; Thomson, Nicholas R; Strugnell, Richard A; Pratt, Nigel F; Garlick, Jill S; Watson, Kerri M; Pilcher, David V; McGloughlin, Steve A; Spelman, Denis W; Jenney, Adam WJ; Holt, Kathryn E

Antimicrobial-Resistant Klebsiella pneumoniae Carriage and Infection in Specialized Geriatric Care Wards Linked to Acquisition in the Referring Hospital. (2018) Gorrie, Claire L; Mirceta, Mirjana; Wick, Ryan R; Judd, Louise M; Wyres, Kelly L; Thomson, Nicholas R; Strugnell, Richard A; Pratt, Nigel F; Garlick, Jill S; Watson, Kerrie M; Hunter, Peter C; McGloughlin, Steve A; Spelman, Denis W; Jenney, Adam WJ; Holt, Kathryn E

Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen. (2022) Gorrie, Claire L; Mirčeta, Mirjana; Wick, Ryan R; Judd, Louise M; Lam, Margaret MC; Gomi, Ryota; Abbott, Iain J; Thomson, Nicholas R; Strugnell, Richard A; Pratt, Nigel F; Garlick, Jill S; Watson, Kerrie M; Hunter, Peter C; Pilcher, David V; McGloughlin, Steve A; Spelman, Denis W; Wyres, Kelly L; Jenney, Adam WJ; Holt, Kathryn E

Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1. (2015) Hamidian, Mohammad; Hawkey, Jane; Holt, Kathryn E; Hall, Ruth M

Evolution of a clade of Acinetobacter baumannii global clone 1, lineage 1 via acquisition of carbapenem- and aminoglycoside-resistance genes and dispersion of ISAba1. (2018) Hamidian, Mohammad; Hawkey, Jane; Wick, Ryan; Holt, Kathryn E; Hall, Ruth M

A GC1 Acinetobacter baumannii isolate carrying AbaR3 and the aminoglycoside resistance transposon TnaphA6 in a conjugative plasmid. (2014) Hamidian, Mohammad; Holt, Kathryn E; Pickard, Derek; Dougan, Gordon; Hall, Ruth M

A small Acinetobacter plasmid carrying the tet39 tetracycline resistance determinant. (2016) Hamidian, Mohammad; Holt, Kathryn E; Pickard, Derek; Hall, Ruth M

Insights from the revised complete genome sequences of Acinetobacter baumannii strains AB307-0294 and ACICU belonging to global clones 1 and 2. (2019) Hamidian, Mohammad; Wick, Ryan R; Hartstein, Rebecca M; Judd, Louise M; Holt, Kathryn E; Hall, Ruth M

Complete Genome Sequence of A388, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 1 Isolate from Greece. (2019) Hamidian, Mohammad; Wick, Ryan R; Judd, Louise M; Holt, Kathryn E; Hall, Ruth M

Identification of a marker for two lineages within the GC1 clone of Acinetobacter baumannii. (2014) Hamidian, Mohammad; Wynn, Matthew; Holt, Kathryn E; Pickard, Derek; Dougan, Gordon; Hall, Ruth M

Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection. (2018) Hawkey, Jane; Ascher, David B; Judd, Louise M; Wick, Ryan R; Kostoulias, Xenia; Cleland, Heather; Spelman, Denis W; Padiglione, Alex; Peleg, Anton Y; Holt, Kathryn E

Linear plasmids in Klebsiella and other Enterobacteriaceae. (2022) Hawkey, Jane; Cottingham, Hugh; Tokolyi, Alex; Wick, Ryan R; Judd, Louise M; Cerdeira, Louise; de Oliveira Garcia, Doroti; Wyres, Kelly L; Holt, Kathryn E

Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198. (2019) Hawkey, Jane; Le Hello, Simon; Doublet, Benoît; Granier, Sophie A; Hendriksen, Rene S; Fricke, W Florian; Ceyssens, Pieter-Jan; Gomart, Camille; Billman-Jacobe, Helen; Holt, Kathryn E; Weill, François-Xavier

Impact of insertion sequences on convergent evolution of Shigella species. (2020) Hawkey, Jane; Monk, Jonathan M; Billman-Jacobe, Helen; Palsson, Bernhard; Holt, Kathryn E

Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei. (2021) Hawkey, Jane; Paranagama, Kalani; Baker, Kate S; Bengtsson, Rebecca J; Weill, François-Xavier; Thomson, Nicholas R; Baker, Stephen; Cerdeira, Louise; Iqbal, Zamin; Hunt, Martin; Ingle, Danielle J; Dallman, Timothy J; Jenkins, Claire; Williamson, Deborah A; Holt, Kathryn E

A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality. (2022) Hawkey, Jane; Vezina, Ben; Monk, Jonathan M; Judd, Louise M; Harshegyi, Taylor; López-Fernández, Sebastián; Rodrigues, Carla; Brisse, Sylvain; Holt, Kathryn E; Wyres, Kelly L

ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting. (2022) Hawkey, Jane; Wyres, Kelly L; Judd, Louise M; Harshegyi, Taylor; Blakeway, Luke; Wick, Ryan R; Jenney, Adam WJ; Holt, Kathryn E

Addressing parachute research and removing barriers for LMIC researchers in Microbial Genomics. (2021) Heinz, Eva; Holt, Kathryn E; Meehan, Conor J; Sheppard, Samuel K

Within-patient and global evolutionary dynamics of Klebsiella pneumoniae ST17. (2023) Hetland, Marit AK; Hawkey, Jane; Bernhoff, Eva; Bakksjø, Ragna-Johanne; Kaspersen, Håkon; Rettedal, Siren I; Sundsfjord, Arnfinn; Holt, Kathryn E; Löhr, Iren H picture_as_pdf

Draft Genome Sequences for Ten Salmonella enterica Serovar Typhimurium Phage Type 135 Variants. (2013) Hogg, Geoff; Dimovski, Karolina; Hiley, Lester; Holt, Kathryn E

Genomic population structures of microbial pathogens. (2022) Holt, Kathryn E; Aanensen, David M; Achtman, Mark

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. (2012) Holt, Kathryn E; Baker, Stephen; Weill, François-Xavier; Holmes, Edward C; Kitchen, Andrew; Yu, Jun; Sangal, Vartul; Brown, Derek J; Coia, John E; Kim, Dong Wook; Choi, Seon Young; Kim, Su Hee; da Silveira, Wanderley D; Pickard, Derek J; Farrar, Jeremy J; Parkhill, Julian; Dougan, Gordon; Thomson, Nicholas R

Temporal fluctuation of multidrug resistant salmonella typhi haplotypes in the mekong river delta region of Vietnam. (2011) Holt, Kathryn E; Dolecek, Christiane; Chau, Tran Thuy; Duy, Pham Thanh; La, Tran Thi Phi; Hoang, Nguyen Van Minh; Nga, Tran Vu Thieu; Campbell, James I; Manh, Bui Huu; Vinh Chau, Nguyen Van; Hien, Tran Tinh; Farrar, Jeremy; Dougan, Gordon; Baker, Stephen

Genome Sequence of Acinetobacter baumannii Strain A1, an Early Example of Antibiotic-Resistant Global Clone 1. (2015) Holt, Kathryn E; Hamidian, Mohammad; Kenyon, Johanna J; Wynn, Matthew T; Hawkey, Jane; Pickard, Derek; Hall, Ruth M

Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales. (2019) Holt, Kathryn E; Lassalle, Florent; Wyres, Kelly L; Wick, Ryan; Mostowy, Rafal J

Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales. (2020) Holt, Kathryn E; Lassalle, Florent; Wyres, Kelly L; Wick, Ryan; Mostowy, Rafał J

Correction to: Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales. (2022) Holt, Kathryn E; Lassalle, Florent; Wyres, Kelly L; Wick, Ryan; Mostowy, Rafał J

Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam. (2018) Holt, Kathryn E; McAdam, Paul; Thai, Phan Vuong Khac; Thuong, Nguyen Thuy Thuong; Ha, Dang Thi Minh; Lan, Nguyen Ngoc; Lan, Nguyen Huu; Nhu, Nguyen Thi Quynh; Hai, Hoang Thanh; Ha, Vu Thi Ngoc; Thwaites, Guy; Edwards, David J; Nath, Artika P; Pham, Kym; Ascher, David B; Farrar, Jeremy; Khor, Chiea Chuen; Teo, Yik Ying; Inouye, Michael; Caws, Maxine; Dunstan, Sarah J

ModuleFinder and CoReg: alternative tools for linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants. (2006) Holt, Kathryn E; Millar, A Harvey; Whelan, James

Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA. (2009) Holt, Kathryn E; Teo, Yik Y; Li, Heng; Nair, Satheesh; Dougan, Gordon; Wain, John; Parkhill, Julian

Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi. (2009) Holt, Kathryn E; Thomson, Nicholas R; Wain, John; Langridge, Gemma C; Hasan, Rumina; Bhutta, Zulfiqar A; Quail, Michael A; Norbertczak, Halina; Walker, Danielle; Simmonds, Mark; White, Brian; Bason, Nathalie; Mungall, Karen; Dougan, Gordon; Parkhill, Julian

Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1. (2016) Holt, Kathryn; Kenyon, Johanna J; Hamidian, Mohammad; Schultz, Mark B; Pickard, Derek J; Dougan, Gordon; Hall, Ruth

Genomic insights to control the emergence of vancomycin-resistant enterococci. (2013) Howden, Benjamin P; Holt, Kathryn E; Lam, Margaret MC; Seemann, Torsten; Ballard, Susan; Coombs, Geoffrey W; Tong, Steven YC; Grayson, M Lindsay; Johnson, Paul DR; Stinear, Timothy P

Neonatal genetics of gene expression reveal potential origins of autoimmune and allergic disease risk. (2020) Huang, Qin Qin; Tang, Howard HF; Teo, Shu Mei; Mok, Danny; Ritchie, Scott C; Nath, Artika P; Brozynska, Marta; Salim, Agus; Bakshi, Andrew; Holt, Barbara J; Khor, Chiea Chuen; Sly, Peter D; Holt, Patrick G; Holt, Kathryn E; Inouye, Michael

Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in Australia. (2019) Ingle, Danielle J; Easton, Marion; Valcanis, Mary; Seemann, Torsten; Kwong, Jason C; Stephens, Nicola; Carter, Glen P; Gonçalves da Silva, Anders; Adamopoulos, James; Baines, Sarah L; Holt, Kathryn E; Chow, Eric PF; Fairley, Christopher K; Chen, Marcus Y; Kirk, Martyn D; Howden, Benjamin P; Williamson, Deborah A

Dynamics of antimicrobial resistance in intestinal Escherichia coli from children in community settings in South Asia and sub-Saharan Africa. (2018) Ingle, Danielle J; Levine, Myron M; Kotloff, Karen L; Holt, Kathryn E; Robins-Browne, Roy M

Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers. (2019) Ingle, Danielle J; Nair, Satheesh; Hartman, Hassan; Ashton, Philip M; Dyson, Zoe A; Day, Martin; Freedman, Joanne; Chattaway, Marie A; Holt, Kathryn E; Dallman, Timothy J

In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages. (2016) Ingle, Danielle J; Valcanis, Mary; Kuzevski, Alex; Tauschek, Marija; Inouye, Michael; Stinear, Tim; Levine, Myron M; Robins-Browne, Roy M; Holt, Kathryn E

Short read sequence typing (SRST): multi-locus sequence types from short reads. (2012) Inouye, Michael; Conway, Thomas C; Zobel, Justin; Holt, Kathryn E

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. (2014) Inouye, Michael; Dashnow, Harriet; Raven, Lesley-Ann; Schultz, Mark B; Pope, Bernard J; Tomita, Takehiro; Zobel, Justin; Holt, Kathryn E

Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa. (2016) International Typhoid Consortium; Wong, Vanessa K; Holt, Kathryn E; Okoro, Chinyere; Baker, Stephen; Pickard, Derek J; Marks, Florian; Page, Andrew J; Olanipekun, Grace; Munir, Huda; Alter, Roxanne; Fey, Paul D; Feasey, Nicholas A; Weill, Francois-Xavier; Le Hello, Simon; Hart, Peter J; Kariuki, Samuel; Breiman, Robert F; Gordon, Melita A; Heyderman, Robert S; Jacobs, Jan; Lunguya, Octavie; Msefula, Chisomo; MacLennan, Calman A; Keddy, Karen H; Smith, Anthony M; Onsare, Robert S; De Pinna, Elizabeth; Nair, Satheesh; Amos, Ben; Dougan, Gordon; Obaro, Stephen

A Salmonella Typhimurium-Typhi genomic chimera: a model to study Vi polysaccharide capsule function in vivo. (2011) Jansen, Angela M; Hall, Lindsay J; Clare, Simon; Goulding, David; Holt, Kathryn E; Grant, Andrew J; Mastroeni, Piero; Dougan, Gordon; Kingsley, Robert A

Multicentre stepped-wedge cluster randomised controlled trial of an antimicrobial stewardship programme in residential aged care: protocol for the START trial. (2021) Jokanovic, Natali; Haines, Terry; Cheng, Allen C; Holt, Kathryn E; Hilmer, Sarah N; Jeon, Yun-Hee; Stewardson, Andrew J; Stuart, Rhonda L; Spelman, Tim; Peel, Trisha N; Peleg, Anton Y; START Trial Group

Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya. (2021) Kariuki, Samuel; Dyson, Zoe A; Mbae, Cecilia; Ngetich, Ronald; Kavai, Susan M; Wairimu, Celestine; Anyona, Stephen; Gitau, Naomi; Onsare, Robert Sanaya; Ongandi, Beatrice; Duchene, Sebastian; Ali, Mohamed; Clemens, John David; Holt, Kathryn E; Dougan, Gordon

The burden and characteristics of enteric fever at a healthcare facility in a densely populated area of Kathmandu. (2010) Karkey, Abhilasha; Arjyal, Amit; Anders, Katherine L; Boni, Maciej F; Dongol, Sabina; Koirala, Samir; My, Phan Vu Tra; Nga, Tran Vu Thieu; Clements, Archie CA; Holt, Kathryn E; Duy, Pham Thanh; Day, Jeremy N; Campbell, James I; Dougan, Gordon; Dolecek, Christiane; Farrar, Jeremy; Basnyat, Buddha; Baker, Stephen

Empirical ways to identify novel Bedaquiline resistance mutations in AtpE. (2019) Karmakar, Malancha; Rodrigues, Carlos HM; Holt, Kathryn E; Dunstan, Sarah J; Denholm, Justin; Ascher, David B

The impact of genomics on precision public health: beyond the pandemic. (2021) Khoury, Muin J; Holt, Kathryn E

Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar. (2013) Kingsley, Robert A; Kay, Sally; Connor, Thomas; Barquist, Lars; Sait, Leanne; Holt, Kathryn E; Sivaraman, Karthi; Wileman, Thomas; Goulding, David; Clare, Simon; Hale, Christine; Seshasayee, Aswin; Harris, Simon; Thomson, Nicholas R; Gardner, Paul; Rabsch, Wolfgang; Wigley, Paul; Humphrey, Tom; Parkhill, Julian; Dougan, Gordon

Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex. (2022) Lam, Margaret MC; Wick, Ryan R; Judd, Louise M; Holt, Kathryn E; Wyres, Kelly L

A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. (2021) Lam, Margaret MC; Wick, Ryan R; Watts, Stephen C; Cerdeira, Louise T; Wyres, Kelly L; Holt, Kathryn E

Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations. (2018) Lam, Margaret MC; Wick, Ryan R; Wyres, Kelly L; Gorrie, Claire L; Judd, Louise M; Jenney, Adam WJ; Brisse, Sylvain; Holt, Kathryn E

Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination. (2018) Lam, Margaret MC; Wyres, Kelly L; Duchêne, Sebastian; Wick, Ryan R; Judd, Louise M; Gan, Yunn-Hwen; Hoh, Chu-Han; Archuleta, Sophia; Molton, James S; Kalimuddin, Shirin; Koh, Tse Hsien; Passet, Virginie; Brisse, Sylvain; Holt, Kathryn E

Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae. (2018) Lam, Margaret MC; Wyres, Kelly L; Judd, Louise M; Wick, Ryan R; Jenney, Adam; Brisse, Sylvain; Holt, Kathryn E

Convergence of virulence and MDR in a single plasmid vector in MDR Klebsiella pneumoniae ST15. (2019) Lam, Margaret MC; Wyres, Kelly L; Wick, Ryan R; Judd, Louise M; Fostervold, Aasmund; Holt, Kathryn E; Löhr, Iren Høyland

Genomic epidemiology and temperature dependency of hypermucoviscous Klebsiella pneumoniae in Japan. (2022) Le, Mi Nguyen-Tra; Kayama, Shizuo; Wyres, Kelly L; Yu, Liansheng; Hisatsune, Junzo; Suzuki, Masato; Yahara, Koji; Terachi, Tsuneko; Sawa, Kana; Takahashi, Shin; Okuhara, Toshihiko; Kohama, Kunihiko; Holt, Kathryn E; Mizutani, Tetsu; Ohge, Hiroki; Sugai, Motoyuki

Differential host susceptibility and bacterial virulence factors driving Klebsiella liver abscess in an ethnically diverse population. (2016) Lee, I Russel; Molton, James S; Wyres, Kelly L; Gorrie, Claire; Wong, Jocelyn; Hoh, Chu Han; Teo, Jeanette; Kalimuddin, Shirin; Lye, David C; Archuleta, Sophia; Holt, Kathryn E; Gan, Yunn-Hwen

Direct Nanopore Sequencing of mRNA Reveals Landscape of Transcript Isoforms in Apicomplexan Parasites. (2021) Lee, V Vern; Judd, Louise M; Jex, Aaron R; Holt, Kathryn E; Tonkin, Christopher J; Ralph, Stuart A

Mercury methylation by metabolically versatile and cosmopolitan marine bacteria. (2021) Lin, Heyu; Ascher, David B; Myung, Yoochan; Lamborg, Carl H; Hallam, Steven J; Gionfriddo, Caitlin M; Holt, Kathryn E; Moreau, John W

Detection of Klebsiella pneumoniae human gut carriage: a comparison of culture, qPCR, and whole metagenomic sequencing methods. (2022) Lindstedt, Kenneth; Buczek, Dorota; Pedersen, Torunn; Hjerde, Erik; Raffelsberger, Niclas; Suzuki, Yutaka; Brisse, Sylvain; Holt, Kathryn; Samuelsen, Ørjan; Sundsfjord, Arnfinn

Rapid Whole Genome Sequencing of Serotype K1 Hypervirulent Klebsiella pneumoniae from an Undocumented Chinese Migrant. (2021) Macleod, CK; Khokhar, FA; Warne, B; Wick, R; Butcher, R; Cassimon, B; Hayden, P; Holt, K; Török, ME picture_as_pdf

A novel genetic variant of Streptococcus pneumoniae serotype 11A discovered in Fiji. (2018) Manna, S; Ortika, BD; Dunne, EM; Holt, KE; Kama, M; Russell, FM; Hinds, J; Satzke, C

Burden of enteric fever at three urban sites in Africa and Asia: a multicentre population-based study. (2021) Meiring, James E; Shakya, Mila; Khanam, Farhana; Voysey, Merryn; Phillips, Maile T; Tonks, Susan; Thindwa, Deus; Darton, Thomas C; Dongol, Sabina; Karkey, Abilasha; Zaman, K; Baker, Stephen; Dolecek, Christiane; Dunstan, Sarah J; Dougan, Gordon; Holt, Kathryn E; Heyderman, Robert S; Qadri, Firdausi; Pitzer, Virginia E; Basnyat, Buddha; Gordon, Melita A; Clemens, John; Pollard, Andrew J; STRATAA Study Group

Using zebrafish to study the evolution and pathogenesis of Shigella. (2025) Miles, SL

Genomic diversity and antimicrobial resistance in clinical Klebsiella pneumoniae isolates from tertiary hospitals in Southern Ghana. (2024) Mills, Richael O; Dadzie, Isaac; Le-Viet, Thanh; Baker, David J; Addy, Humphrey PK; Akwetey, Samuel A; Donkoh, Irene E; Quansah, Elvis; Semanshia, Prince S; Morgan, Jennifer; Mensah, Abraham; Adade, Nana E; Ampah, Emmanuel O; Owusu, Emmanuel; Mwintige, Philimon; Amoako, Eric O; Spadar, Anton; Holt, Kathryn E; Foster-Nyarko, Ebenezer

Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating. (2018) Mostowy, Rafał J; Holt, Kathryn E

Correcting index databases improves metagenomic studies. (2019) Méric, Guillaume; Wick, Ryan R; Watts, Stephen C; Holt, Kathryn E; Inouye, Michael

The sensitivity of real-time PCR amplification targeting invasive Salmonella serovars in biological specimens. (2010) Nga, Tran Vu Thieu; Karkey, Abhilasha; Dongol, Sabina; Thuy, Hang Nguyen; Dunstan, Sarah; Holt, Kathryn; Tu, Le Thi Phuong; Campbell, James I; Chau, Tran Thuy; Chau, Nguyen Van Vinh; Arjyal, Amit; Koirala, Samir; Basnyat, Buddha; Dolecek, Christiane; Farrar, Jeremy; Baker, Stephen

Carbapenem and amikacin resistance on a large conjugative Acinetobacter baumannii plasmid. (2015) Nigro, Steven J; Holt, Kathryn E; Pickard, Derek; Hall, Ruth M

Complete Genome Sequence of WM99c, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 2 (GC2) Strain Representing an Australian GC2 Lineage. (2018) Nigro, Steven J; Wick, Ryan; Holt, Kathryn E; Hall, Ruth M

Maternal colonization and early-onset neonatal bacterial sepsis in the Gambia, West Africa: a genomic analysis of vertical transmission. (2023) Okomo, Uduak A; Darboe, Saffiatou; Bah, Saikou Y; Ayorinde, Abigail; Jarju, Sheikh; Sesay, Abdul Karim; Kebbeh, Ngange; Gai, Abdou; Dibbasey, Tida; Grey-Johnson, Mary; Le Doare, Kirsty; Holt, Kathryn E; Lawn, Joy E; Kampmann, Beate

Investigation of sequential outbreaks of Burkholderia cepacia and multidrug-resistant extended spectrum β-lactamase producing Klebsiella species in a West African tertiary hospital neonatal unit: a retrospective genomic analysis. (2020) Okomo, Uduak; Senghore, Madikay; Darboe, Saffiatou; Bojang, Ebrima; Zaman, Syed MA; Hossain, Mohammad Jahangir; Nwakanma, Davis; Le Doare, Kirsty; Holt, Kathryn E; Hos, Nina Judith; Lawn, Joy E; Bentley, Stephen D; Kampmann, Beate

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa. (2018) Park, Se Eun; Pham, Duy Thanh; Boinett, Christine; Wong, Vanessa K; Pak, Gi Deok; Panzner, Ursula; Espinoza, Ligia Maria Cruz; von Kalckreuth, Vera; Im, Justin; Schütt-Gerowitt, Heidi; Crump, John A; Breiman, Robert F; Adu-Sarkodie, Yaw; Owusu-Dabo, Ellis; Rakotozandrindrainy, Raphaël; Soura, Abdramane Bassiahi; Aseffa, Abraham; Gasmelseed, Nagla; Keddy, Karen H; May, Jürgen; Sow, Amy Gassama; Aaby, Peter; Biggs, Holly M; Hertz, Julian T; Montgomery, Joel M; Cosmas, Leonard; Olack, Beatrice; Fields, Barry; Sarpong, Nimako; Razafindrabe, Tsiriniaina Jean Luco; Raminosoa, Tiana Mirana; Kabore, Leon Parfait; Sampo, Emmanuel; Teferi, Mekonnen; Yeshitela, Biruk; El Tayeb, Muna Ahmed; Sooka, Arvinda; Meyer, Christian G; Krumkamp, Ralf; Dekker, Denise Myriam; Jaeger, Anna; Poppert, Sven; Tall, Adama; Niang, Aissatou; Bjerregaard-Andersen, Morten; Løfberg, Sandra Valborg; Seo, Hye Jin; Jeon, Hyon Jin; Deerin, Jessica Fung; Park, Jinkyung; Konings, Frank; Ali, Mohammad; Clemens, John D; Hughes, Peter; Sendagala, Juliet Nsimire; Vudriko, Tobias; Downing, Robert; Ikumapayi, Usman N; Mackenzie, Grant A; Obaro, Stephen; Argimon, Silvia; Aanensen, David M; Page, Andrew; Keane, Jacqueline A; Duchene, Sebastian; Dyson, Zoe; Holt, Kathryn E; Dougan, Gordon; Marks, Florian; Baker, Stephen

Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain. (2017) Perrin, Amandine; Larsonneur, Elise; Nicholson, Ainsley C; Edwards, David J; Gundlach, Kristin M; Whitney, Anne M; Gulvik, Christopher A; Bell, Melissa E; Rendueles, Olaya; Cury, Jean; Hugon, Perrine; Clermont, Dominique; Enouf, Vincent; Loparev, Vladimir; Juieng, Phalasy; Monson, Timothy; Warshauer, David; Elbadawi, Lina I; Walters, Maroya Spalding; Crist, Matthew B; Noble-Wang, Judith; Borlaug, Gwen; Rocha, Eduardo PC; Criscuolo, Alexis; Touchon, Marie; Davis, Jeffrey P; Holt, Kathryn E; McQuiston, John R; Brisse, Sylvain

A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure. (2016) Pham Thanh, Duy; Karkey, Abhilasha; Dongol, Sabina; Ho Thi, Nhan; Thompson, Corinne N; Rabaa, Maia A; Arjyal, Amit; Holt, Kathryn E; Wong, Vanessa; Tran Vu Thieu, Nga; Voong Vinh, Phat; Ha Thanh, Tuyen; Pradhan, Ashish; Shrestha, Saroj Kumar; Gajurel, Damoder; Pickard, Derek; Parry, Christopher M; Dougan, Gordon; Wolbers, Marcel; Dolecek, Christiane; Thwaites, Guy E; Basnyat, Buddha; Baker, Stephen

The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia. (2016) Pham Thanh, Duy; Thompson, Corinne N; Rabaa, Maia A; Sona, Soeng; Sopheary, Sun; Kumar, Varun; Moore, Catrin; Tran Vu Thieu, Nga; Wijedoru, Lalith; Holt, Kathryn E; Wong, Vanessa; Pickard, Derek; Thwaites, Guy E; Day, Nicholas; Dougan, Gordon; Turner, Paul; Parry, Christopher M; Baker, Stephen

Identification of Salmonella enterica serovar Typhi genotypes by use of rapid multiplex ligation-dependent probe amplification. (2013) Pham Thanh, Duy; Tran Vu Thieu, Nga; Tran Thuy, Chau; Lodén, Martin; Tuin, Kiki; Campbell, James I; Van Minh Hoang, Nguyen; Voong Vinh, Phat; Farrar, Jeremy J; Holt, Kathryn E; Dougan, Gordon; Baker, Stephen

A Bayesian approach for estimating typhoid fever incidence from large-scale facility-based passive surveillance data. (2021) Phillips, Maile T; Meiring, James E; Voysey, Merryn; Warren, Joshua L; Baker, Stephen; Basnyat, Buddha; Clemens, John D; Dolecek, Christiane; Dunstan, Sarah J; Dougan, Gordon; Gordon, Melita A; Thindwa, Deus; Heyderman, Robert S; Holt, Kathryn E; Qadri, Firdausi; Pollard, Andrew J; Pitzer, Virginia E; STRATAA Study Group

A Shigella sonnei clone with extensive drug resistance associated with waterborne outbreaks in China. (2022) Qiu, Shaofu; Liu, Kangkang; Yang, Chaojie; Xiang, Ying; Min, Kaiyuan; Zhu, Kunpeng; Liu, Hongbo; Du, Xinying; Yang, Mingjuan; Wang, Ligui; Sun, Yong; Zhou, Haijian; Mahe, Muti; Zhao, Jiayong; Li, Shijun; Yu, Deshan; Hawkey, Jane; Holt, Kathryn E; Baker, Stephen; Yang, Juntao; Xu, Xuebin; Song, Hongbin

Gastrointestinal carriage of Klebsiella pneumoniae in a general adult population: a cross-sectional study of risk factors and bacterial genomic diversity. (2021) Raffelsberger, Niclas; Hetland, Marit Andrea Klokkhammer; Svendsen, Kristian; Småbrekke, Lars; Löhr, Iren Høyland; Andreassen, Lotte Leonore Eivindsdatter; Brisse, Sylvain; Holt, Kathryn E; Sundsfjord, Arnfinn; Samuelsen, Ørjan; Gravningen, Kirsten

Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016. (2020) Rahman, Sadia Isfat Ara; Dyson, Zoe A; Klemm, Elizabeth J; Khanam, Farhana; Holt, Kathryn E; Chowdhury, Emran Kabir; Dougan, Gordon; Qadri, Firdausi

The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns. (2020) Repetti, Sonja I; Jackson, Christopher J; Judd, Louise M; Wick, Ryan R; Holt, Kathryn E; Verbruggen, Heroen

A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets. (2016) Ritchie, Scott C; Watts, Stephen; Fearnley, Liam G; Holt, Kathryn E; Abraham, Gad; Inouye, Michael

Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing? (2016) Robins-Browne, Roy M; Holt, Kathryn E; Ingle, Danielle J; Hocking, Dianna M; Yang, Ji; Tauschek, Marija

Repeated local emergence of carbapenem-resistant Acinetobacter baumannii in a single hospital ward. (2016) Schultz, Mark B; Pham Thanh, Duy; Tran Do Hoan, Nhu; Wick, Ryan R; Ingle, Danielle J; Hawkey, Jane; Edwards, David J; Kenyon, Johanna J; Phu Huong Lan, Nguyen; Campbell, James I; Thwaites, Guy; Thi Khanh Nhu, Nguyen; Hall, Ruth M; Fournier-Level, Alexandre; Baker, Stephen; Holt, Kathryn E

A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A. (2010) Song, Yajun; Roumagnac, Philippe; Weill, François-Xavier; Wain, John; Dolecek, Christiane; Mazzoni, Camila J; Holt, Kathryn E; Achtman, Mark

Epidemiology and genomic analysis of Klebsiella oxytoca from a single hospital network in Australia. (2022) Stewart, James; Judd, Louise M; Jenney, Adam; Holt, Kathryn E; Wyres, Kelly L; Hawkey, Jane

Adaptive change inferred from genomic population analysis of the ST93 epidemic clone of community-associated methicillin-resistant Staphylococcus aureus. (2014) Stinear, Timothy P; Holt, Kathryn E; Chua, Kyra; Stepnell, Justin; Tuck, Kellie L; Coombs, Geoffrey; Harrison, Paul Francis; Seemann, Torsten; Howden, Benjamin P

Abstract. (2018) Tang, Howard HF; Teo, Shu Mei; Belgrave, Danielle CM; Evans, Michael D; Jackson, Daniel J; Brozynska, Marta; Kusel, Merci MH; Johnston, Sebastian L; Gern, James E; Lemanske, Robert F; Simpson, Angela; Custovic, Adnan; Sly, Peter D; Holt, Patrick G; Holt, Kathryn E; Inouye, Michael

Trajectories of childhood immune development and respiratory health relevant to asthma and allergy. (2018) Tang, Howard Hf; Teo, Shu Mei; Belgrave, Danielle Cm; Evans, Michael D; Jackson, Daniel J; Brozynska, Marta; Kusel, Merci Mh; Johnston, Sebastian L; Gern, James E; Lemanske, Robert F; Simpson, Angela; Custovic, Adnan; Sly, Peter D; Holt, Patrick G; Holt, Kathryn E; Inouye, Michael

Airway Microbiota Dynamics Uncover a Critical Window for Interplay of Pathogenic Bacteria and Allergy in Childhood Respiratory Disease. (2018) Teo, Shu Mei; Tang, Howard HF; Mok, Danny; Judd, Louise M; Watts, Stephen C; Pham, Kym; Holt, Barbara J; Kusel, Merci; Serralha, Michael; Troy, Niamh; Bochkov, Yury A; Grindle, Kristine; Lemanske, Robert F; Johnston, Sebastian L; Gern, James E; Sly, Peter D; Holt, Patrick G; Holt, Kathryn E; Inouye, Michael

Shigella sonnei. (2020) Torraca, Vincenzo; Holt, Kathryn; Mostowy, Serge

Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae. (2024) Tsang, Kara K; Lam, Margaret MC; Wick, Ryan R; Wyres, Kelly L; Bachman, Michael; Baker, Stephen; Barry, Katherine; Brisse, Sylvain; Campino, Susana; Chiaverini, Alexandra; Cirillo, Daniela Maria; Clark, Taane; Corander, Jukka; Corbella, Marta; Cornacchia, Alessandra; Cuénod, Aline; D'Alterio, Nicola; Di Marco, Federico; Donado-Godoy, Pilar; Egli, Adrian; Farzana, Refath; Feil, Edward J; Fostervold, Aasmund; Gorrie, Claire L; Hassan, Brekhna; Hetland, Marit Andrea Klokkhammer; Hoa, Le Nguyen Minh; Hoi, Le Thi; Howden, Benjamin; Ikhimiukor, Odion O; Jenney, Adam WJ; Kaspersen, Håkon; Khokhar, Fahad; Leangapichart, Thongpan; Ligowska-Marzęta, Małgorzata; Löhr, Iren Høyland; Long, Scott W; Mathers, Amy J; McArthur, Andrew G; Nagaraj, Geetha; Oaikhena, Anderson O; Okeke, Iruka N; Perdigão, João; Parikh, Hardik; Pham, My H; Pomilio, Francesco; Raffelsberger, Niclas; Rakotondrasoa, Andriniaina; Kumar, KL Ravi; Roberts, Leah W; Rodrigues, Carla; Samuelsen, Ørjan; Sands, Kirsty; Sassera, Davide; Seth-Smith, Helena; Shamanna, Varun; Sherry, Norelle L; Sia, Sonia; Spadar, Anton; Stoesser, Nicole; Sunde, Marianne; Sundsfjord, Arnfinn; Thach, Pham Ngoc; Thomson, Nicholas R; Thorpe, Harry A; Torok, M Estée; Trang, Van Dinh; Trung, Nguyen Vu; Vornhagen, Jay; Walsh, Timothy; Warne, Ben; Wilson, Hayley; Wright, Gerard D; Holt, Kathryn E; KlebNET-Gsp Amr Genotype-Phenotype Group

Transmission of Klebsiella strains and plasmids within and between grey-headed flying fox colonies. (2022) Vezina, Ben; Judd, Louise M; McDougall, Fiona K; Boardman, Wayne SJ; Power, Michelle L; Hawkey, Jane; Brisse, Sylvain; Monk, Jonathan M; Holt, Kathryn E; Wyres, Kelly L

Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae. (2021) Viehweger, Adrian; Blumenscheit, Christian; Lippmann, Norman; Wyres, Kelly L; Brandt, Christian; Hans, Jörg B; Hölzer, Martin; Irber, Luiz; Gatermann, Sören; Lübbert, Christoph; Pletz, Mathias W; Holt, Kathryn E; König, Brigitte

Klebsiella pneumoniae with capsule type K64 is overrepresented among invasive disease in Vietnam. (2021) Vu Thi Ngoc, Bich; Brisse, Sylvain; Dao Tuyet, Trinh; Vu Tien Viet, Dung; Holt, Kathryn E; Nguyen Vu, Trung; Tran Thi Kieu, Huong; Nguyen Thi Ngoc, Diep; van Doorn, H Rogier; Wertheim, Heiman FL

An outpatient, ambulant-design, controlled human infection model using escalating doses of Salmonella Typhi challenge delivered in sodium bicarbonate solution. (2014) Waddington, Claire S; Darton, Thomas C; Jones, Claire; Haworth, Kathryn; Peters, Anna; John, Tessa; Thompson, Ben AV; Kerridge, Simon A; Kingsley, Robert A; Zhou, Liqing; Holt, Kathryn E; Yu, Ly-Mee; Lockhart, Stephen; Farrar, Jeremy J; Sztein, Marcelo B; Dougan, Gordon; Angus, Brian; Levine, Myron M; Pollard, Andrew J

Elucidation of pathways driving asthma pathogenesis: development of a systems-level analytic strategy. (2014) Walker, Michael L; Holt, Kathryn E; Anderson, Gary P; Teo, Shu Mei; Sly, Peter D; Holt, Patrick G; Inouye, Michael

GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure. (2020) Wan, Yu; Wick, Ryan R; Zobel, Justin; Ingle, Danielle J; Inouye, Michael; Holt, Kathryn E

GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene Associations Controlled for Population Structure. (2020) Wan, Yu; Wick, Ryan R; Zobel, Justin; Ingle, Danielle J; Inouye, Michael; Holt, Kathryn E

hicap: In Silico Serotyping of the Haemophilus influenzae Capsule Locus. (2019) Watts, Stephen C; Holt, Kathryn E

Genomic Diversity and Antimicrobial Resistance of Haemophilus Colonizing the Airways of Young Children with Cystic Fibrosis. (2021) Watts, Stephen C; Judd, Louise M; Carzino, Rosemary; Ranganathan, Sarath; Holt, Kathryn E

FastSpar: rapid and scalable correlation estimation for compositional data. (2018) Watts, Stephen C; Ritchie, Scott C; Inouye, Michael; Holt, Kathryn E

Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes. (2018) Wick, Ryan R; Heinz, Eva; Holt, Kathryn E; Wyres, Kelly L

Benchmarking of long-read assemblers for prokaryote whole genome sequencing. (2019) Wick, Ryan R; Holt, Kathryn E

Polypolish: Short-read polishing of long-read bacterial genome assemblies. (2022) Wick, Ryan R; Holt, Kathryn E

Trycycler: consensus long-read assemblies for bacterial genomes. (2021) Wick, Ryan R; Judd, Louise M; Cerdeira, Louise T; Hawkey, Jane; Méric, Guillaume; Vezina, Ben; Wyres, Kelly L; Holt, Kathryn E

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. (2017) Wick, Ryan R; Judd, Louise M; Gorrie, Claire L; Holt, Kathryn E

Completing bacterial genome assemblies with multiplex MinION sequencing. (2017) Wick, Ryan R; Judd, Louise M; Gorrie, Claire L; Holt, Kathryn E

Completing bacterial genome assemblies with multiplex MinION sequencing. (2017) Wick, Ryan R; Judd, Louise M; Gorrie, Claire L; Holt, Kathryn E

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks. (2018) Wick, Ryan R; Judd, Louise M; Holt, Kathryn E

Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks. (2018) Wick, Ryan R; Judd, Louise M; Holt, Kathryn E

Performance of neural network basecalling tools for Oxford Nanopore sequencing. (2019) Wick, Ryan R; Judd, Louise M; Holt, Kathryn E

Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. (2023) Wick, Ryan R; Judd, Louise M; Holt, Kathryn E

Bandage: interactive visualization of de novo genome assemblies. (2015) Wick, Ryan R; Schultz, Mark B; Zobel, Justin; Holt, Kathryn E

An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid. (2016) Wong, Vanessa K; Baker, Stephen; Connor, Thomas R; Pickard, Derek; Page, Andrew J; Dave, Jayshree; Murphy, Niamh; Holliman, Richard; Sefton, Armine; Millar, Michael; Dyson, Zoe A; Dougan, Gordon; Holt, Kathryn E; International Typhoid Consortium

Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium. (2013) Wong, Vanessa K; Pickard, Derek J; Barquist, Lars; Sivaraman, Karthikeyan; Page, Andrew J; Hart, Peter J; Arends, Mark J; Holt, Kathryn E; Kane, Leanne; Mottram, Lynda F; Ellison, Louise; Bautista, Ruben; McGee, Chris J; Kay, Sally J; Wileman, Thomas M; Kenney, Linda J; MacLennan, Calman A; Kingsley, Robert A; Dougan, Gordon

Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive. (2020) Wyres, Kelly L; Cahill, Sarah M; Holt, Kathryn E; Hall, Ruth M; Kenyon, Johanna J

Extensive Capsule Locus Variation and Large-Scale Genomic Recombination within the Klebsiella pneumoniae Clonal Group 258. (2015) Wyres, Kelly L; Gorrie, Claire; Edwards, David J; Wertheim, Heiman FL; Hsu, Li Yang; Van Kinh, Nguyen; Zadoks, Ruth; Baker, Stephen; Holt, Kathryn E

Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307. (2018) Wyres, Kelly L; Hawkey, Jane; Hetland, Marit AK; Fostervold, Aasmund; Wick, Ryan R; Judd, Louise M; Hamidian, Mohammad; Howden, Benjamin P; Löhr, Iren H; Holt, Kathryn E

Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307. (2018) Wyres, Kelly L; Hawkey, Jane; Hetland, Marit AK; Fostervold, Aasmund; Wick, Ryan R; Judd, Louise M; Hamidian, Mohammad; Howden, Benjamin P; Löhr, Iren H; Holt, Kathryn E

Genomic surveillance of antimicrobial resistant bacterial colonisation and infection in intensive care patients. (2021) Wyres, Kelly L; Hawkey, Jane; Mirčeta, Mirianne; Judd, Louise M; Wick, Ryan R; Gorrie, Claire L; Pratt, Nigel F; Garlick, Jill S; Watson, Kerrie M; Pilcher, David V; McGloughlin, Steve A; Abbott, Iain J; Macesic, Nenad; Spelman, Denis W; Jenney, Adam WJ; Holt, Kathryn E

<i>Klebsiella pneumoniae</i> as a key trafficker of drug resistance genes from environmental to clinically important bacteria. (2018) Wyres, Kelly L; Holt, Kathryn E

Klebsiella pneumoniae Population Genomics and Antimicrobial-Resistant Clones. (2016) Wyres, Kelly L; Holt, Kathryn E

Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria. (2018) Wyres, Kelly L; Holt, Kathryn E

Comment on: CG258 Klebsiella pneumoniae isolates without β-lactam resistance at the onset of the carbapenem-resistant Enterobacteriaceae epidemic in New York City. (2018) Wyres, Kelly L; Lam, Margaret MC; Holt, Kathryn E

Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia. (2020) Wyres, Kelly L; Nguyen, To NT; Lam, Margaret MC; Judd, Louise M; van Vinh Chau, Nguyen; Dance, David AB; Ip, Margaret; Karkey, Abhilasha; Ling, Clare L; Miliya, Thyl; Newton, Paul N; Lan, Nguyen Phu Huong; Sengduangphachanh, Amphone; Turner, Paul; Veeraraghavan, Balaji; Vinh, Phat Voong; Vongsouvath, Manivanh; Thomson, Nicholas R; Baker, Stephen; Holt, Kathryn E

Identification of Klebsiella capsule synthesis loci from whole genome data. (2016) Wyres, Kelly L; Wick, Ryan R; Gorrie, Claire; Jenney, Adam; Follador, Rainer; Thomson, Nicholas R; Holt, Kathryn E

Identification of<i>Klebsiella</i>capsule synthesis loci from whole genome data. (2016) Wyres, Kelly L; Wick, Ryan R; Gorrie, Claire; Jenney, Adam; Follador, Rainer; Thomson, Nicholas R; Holt, Kathryn E

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of<i>Klebsiella pneumoniae</i>. (2018) Wyres, Kelly L; Wick, Ryan R; Judd, Louise M; Froumine, Roni; Tokolyi, Alex; Gorrie, Claire L; Lam, Margaret MC; Duchêne, Sebastián; Jenney, Adam; Holt, Kathryn E

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae. (2019) Wyres, Kelly L; Wick, Ryan R; Judd, Louise M; Froumine, Roni; Tokolyi, Alex; Gorrie, Claire L; Lam, Margaret MC; Duchêne, Sebastián; Jenney, Adam; Holt, Kathryn E

Z/I1 Hybrid Virulence Plasmids Carrying Antimicrobial Resistance genes in S. Typhimurium from Australian Food Animal Production. (2019) Wyrsch, Ethan R; Hawkey, Jane; Judd, Louise M; Haites, Ruth; Holt, Kathryn E; Djordjevic, Steven P; Billman-Jacobe, Helen

Novel Subclone of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 with Enhanced Virulence and Transmissibility, China. (2020) Zhou, Kai; Xiao, Tingting; David, Sophia; Wang, Qin; Zhou, Yanzi; Guo, Lihua; Aanensen, David; Holt, Kathryn E; Thomson, Nicholas R; Grundmann, Hajo; Shen, Ping; Xiao, Yonghong

A point mutation in recC associated with subclonal replacement of carbapenem-resistant Klebsiella pneumoniae ST11 in China. (2023) Zhou, Kai; Xue, Chun-Xu; Xu, Tingting; Shen, Ping; Wei, Sha; Wyres, Kelly L; Lam, Margaret MC; Liu, Jinquan; Lin, Haoyun; Chen, Yunbo; Holt, Kathryn E; BRICS Working Group; Xiao, Yonghong

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Protection conferred by typhoid fever against recurrent typhoid fever in urban Kolkata. (2020) Im, Justin; Islam, Md Taufiqul; Kim, Deok Ryun; Ahmmed, Faisal; Chon, Yun; Zaman, K; Khan, Ashraful Islam; Ali, Mohammad; Sur, Dipika; Kanungo, Suman; Dutta, Shanta; Bhattacharya, Sujit K; Dougan, Gordon; Holt, Kathryn E; Marks, Florian; Kim, Jerome H; Qadri, Firdausi; Clemens, John D picture_as_pdf

Recovery of small plasmid sequences via Oxford Nanopore sequencing. (2021) Wick, Ryan R; Judd, Louise M; Wyres, Kelly L; Holt, Kathryn E picture_as_pdf