Items where Author is "Holt, Kathryn E"
Number of items: 193.
2025
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
A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs. (2025)
Hetland, Marit AK; Winkler, Mia A; Kaspersen, Håkon P; Håkonsholm, Fredrik; Bakksjø, Ragna-Johanne; Bernhoff, Eva; Delgado-Blas, Jose F; Brisse, Sylvain; Correia, Annapaula; Fostervold, Aasmund; Lam, Margaret MC; Lunestad, Bjørn-Tore; Marathe, Nachiket P; Raffelsberger, Niclas; Samuelsen, Ørjan; Sunde, Marianne; Sundsfjord, Arnfinn; Urdahl, Anne Margrete; Wick, Ryan R; Löhr, Iren H; Holt, Kathryn E
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Complete genomes of 568 diverse Klebsiella pneumoniae species
complex isolates from humans, animals, and marine sources in
Norway from 2001 to 2020. (2025)
Hetland, Marit AK; Winkler, Mia A; Kaspersen, Håkon; Håkonsholm, Fredrik; Bakksjø, Ragna-Johanne; Bernhoff, Eva; Delgado-Blas, Jose F; Brisse, Sylvain; Correia, Annapaula; Fostervold, Aasmund; Lam, Margaret MC; Lunestad, Bjørn-Tore; Marathe, Nachiket P; Raffelsberger, Niclas; Samuelsen, Ørjan; Sunde, Marianne; Sundsfjord, Arnfinn; Urdahl, Anne Margrete; Wick, Ryan R; Holt, Kathryn E; Löhr, Iren H
Using zebrafish to study the evolution and pathogenesis of Shigella. (2025)
Miles, SL
The characterization of Klebsiella pneumoniae associated with neonatal sepsis in low- and middle-income countries to inform vaccine design. (2025)
Nonne, Francesca; Molfetta, Mariagrazia; Belciug, Gianina Florentina; Carducci, Martina; Cianchi, Virginia; Zakroff, Casey; Durante, Salvatore; Zellmer, Caroline; Baker, Stephen; Stanton, Thomas D; Holt, Kathryn E; Wyres, Kelly; Ravenscroft, Neil; Gasperini, Gianmarco; Rossi, Omar; Giannelli, Carlo; Berlanda Scorza, Francesco; Micoli, Francesca
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Fast and accurate in silico antigen typing with Kaptive 3. (2025)
Stanton, Thomas David; Hetland, Marit AK; Löhr, Iren H; Holt, Kathryn E; Wyres, Kelly L
2024
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
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
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, 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
2023
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
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
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
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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
Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. (2023)
Wick, Ryan R; Judd, Louise M; Holt, Kathryn E
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
2022
Making microbial genomics work for clinical and public health microbiology. (2022)
Azarian, Taj; Sherry, Norelle L; Baker, Kate; Holt, Kathryn E; Okeke, Iruka N
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
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
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
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
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
Genomic population structures of microbial pathogens. (2022)
Holt, Kathryn E; Aanensen, David M; Achtman, Mark
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
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
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
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
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
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
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
Polypolish: Short-read polishing of long-read bacterial genome assemblies. (2022)
Wick, Ryan R; Holt, Kathryn E
2021
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
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
Five Years of GenoTyphi: Updates to the Global Salmonella Typhi Genotyping Framework. (2021)
Dyson, Zoe A; 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
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
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
Addressing parachute research and removing barriers for LMIC researchers in Microbial Genomics. (2021)
Heinz, Eva; Holt, Kathryn E; Meehan, Conor J; Sheppard, Samuel K
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 impact of genomics on precision public health: beyond the pandemic. (2021)
Khoury, Muin J; Holt, Kathryn E
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
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
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
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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
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
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
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
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
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
Recovery of small plasmid sequences via Oxford Nanopore sequencing. (2021)
Wick, Ryan R; Judd, Louise M; Wyres, Kelly L; Holt, Kathryn E
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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
2020
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
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
SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments. (2020)
Edwards, David J; Duchêne, Sebastián; Pope, Bernard; Holt, Kathryn E
Impact of insertion sequences on convergent evolution of Shigella species. (2020)
Hawkey, Jane; Monk, Jonathan M; Billman-Jacobe, Helen; Palsson, Bernhard; Holt, Kathryn E
Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales. (2020)
Holt, Kathryn E; Lassalle, Florent; Wyres, Kelly L; Wick, Ryan; Mostowy, Rafał J
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
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
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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
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
Shigella sonnei. (2020)
Torraca, Vincenzo; Holt, Kathryn; Mostowy, Serge
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
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
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
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
2019
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
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
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
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
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
Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales. (2019)
Holt, Kathryn E; Lassalle, Florent; Wyres, Kelly L; Wick, Ryan; Mostowy, Rafal J
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
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
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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
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
Correcting index databases improves metagenomic studies. (2019)
Méric, Guillaume; Wick, Ryan R; Watts, Stephen C; Holt, Kathryn E; Inouye, Michael
hicap: In Silico Serotyping of the Haemophilus influenzae Capsule Locus. (2019)
Watts, Stephen C; Holt, Kathryn E
Benchmarking of long-read assemblers for prokaryote whole genome sequencing. (2019)
Wick, Ryan R; Holt, Kathryn E
Performance of neural network basecalling tools for Oxford Nanopore sequencing. (2019)
Wick, Ryan R; Judd, Louise M; 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
2018
Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens. (2018)
Baker, Stephen; Thomson, Nicholas; Weill, François-Xavier; Holt, Kathryn E
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
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
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
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
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
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
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
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
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
Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating. (2018)
Mostowy, Rafał J; Holt, Kathryn E
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
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
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
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
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
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
<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 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
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
2017
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
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
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
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
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
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
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
2016
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
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
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
A small Acinetobacter plasmid carrying the tet39 tetracycline resistance determinant. (2016)
Hamidian, Mohammad; Holt, Kathryn E; Pickard, Derek; Hall, Ruth M
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
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
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
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
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
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
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 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
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
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
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
Klebsiella pneumoniae Population Genomics and Antimicrobial-Resistant Clones. (2016)
Wyres, Kelly L; 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
2015
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
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
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
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
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
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
Carbapenem and amikacin resistance on a large conjugative Acinetobacter baumannii plasmid. (2015)
Nigro, Steven J; Holt, Kathryn E; Pickard, Derek; Hall, Ruth M
Bandage: interactive visualization of de novo genome assemblies. (2015)
Wick, Ryan R; Schultz, Mark B; Zobel, Justin; Holt, Kathryn E
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
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
2014
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
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
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
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
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
2013
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
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
Draft Genome Sequences for Ten Salmonella enterica Serovar Typhimurium Phage Type 135 Variants. (2013)
Hogg, Geoff; Dimovski, Karolina; Hiley, Lester; Holt, Kathryn E
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 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
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
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
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
2012
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
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
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
Short read sequence typing (SRST): multi-locus sequence types from short reads. (2012)
Inouye, Michael; Conway, Thomas C; Zobel, Justin; Holt, Kathryn E
2011
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
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
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
2010
Navigating the future of bacterial molecular epidemiology. (2010)
Baker, Stephen; Hanage, William P; Holt, Kathryn E
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
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
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
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
2009
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
2008
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