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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; +2 more... Stinear, Timothy P; Howden, Benjamin P; (2015) Convergent adaptation in the dominant global hospital clone ST239 of methicillin-resistant Staphylococcus aureus. MBIO, 6 (2). e00080-. ISSN 2150-7511 DOI: https://doi.org/10.1128/mBio.00080-15

Baker, Stephen; Hanage, William P; Holt, Kathryn E; (2010) Navigating the future of bacterial molecular epidemiology. Current opinion in microbiology, 13 (5). pp. 640-645. ISSN 1369-5274 DOI: https://doi.org/10.1016/j.mib.2010.08.002

Baker, Stephen; Holt, Kathryn E; Clements, Archie CA; Karkey, Abhilasha; Arjyal, Amit; Boni, Maciej F; Dongol, Sabina; Hammond, Naomi; Koirala, Samir; Duy, Pham Thanh; +6 more... Nga, Tran Vu Thieu; Campbell, James I; Dolecek, Christiane; Basnyat, Buddha; Dougan, Gordon; Farrar, Jeremy J; (2011) Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission. Open biology, 1 (2). 110008-. ISSN 2046-2441 DOI: https://doi.org/10.1098/rsob.110008

Baker, Stephen; Holt, Kathryn; Whitehead, Sally; Goodhead, Ian; Perkins, Tim; Stocker, Bruce; Hardy, Jonathan; Dougan, Gordon; (2007) A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi. MOLECULAR MICROBIOLOGY, 66 (5). pp. 1207-1218. ISSN 0950-382X DOI: https://doi.org/10.1111/j.1365-2958.2007.05995.x

Baker, Stephen; Thomson, Nicholas; Weill, François-Xavier; Holt, Kathryn E; (2018) Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens. Science, 360 (6390). pp. 733-738. ISSN 0036-8075 DOI: https://doi.org/10.1126/science.aar3777

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; +2 more... Fonkoua, Marie-Christine; Weill, François-Xavier; (2015) Multidrug-resistant Salmonella enterica serotype Typhi, Gulf of Guinea Region, Africa. EMERGING INFECTIOUS DISEASES, 21 (4). pp. 655-659. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid2104.141355

Barber, Jake N; Nicholson, Luke C; Woods, Laura C; Judd, Louise M; Sezmis, Aysha L; Hawkey, Jane; Holt, Kathryn E; McDonald, Michael J; (2022) Species interactions constrain adaptation and preserve ecological stability in an experimental microbial community. The ISME Journal: Multidisciplinary Journal of Microbial Ecology, 16 (5). pp. 1442-1452. ISSN 1751-7362 DOI: https://doi.org/10.1038/s41396-022-01191-1

Berríos-Pastén, Camilo; Acevedo, Rodolfo; Arros, Patricio; Varas, Macarena A; Wyres, Kelly L; Lam, Margaret MC; Holt, Kathryn E; Lagos, Rosalba; Marcoleta, Andrés E; (2020) Properties of genes encoding transfer RNAs as integration sites for genomic islands and prophages in<i>Klebsiella pneumoniae</i>. bioRxiv preprint. DOI: https://doi.org/10.1101/2020.11.02.365908

Blackwell, Grace A; Holt, Kathryn E; Bentley, Stephen D; Hsu, Li Yang; Hall, Ruth M; (2017) Variants of AbGRI3 carrying the armA gene in extensively antibiotic-resistant Acinetobacter baumannii from Singapore. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 72 (4). pp. 1031-1039. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dkw542

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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; +4 more... Adhikari, Neelam; Dougan, Gordon; Holt, Kathryn E; Pollard, Andrew J; (2018) Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: Antimicrobial resistance and implications for vaccine policy. PLOS NEGLECTED TROPICAL DISEASES, 12 (4). e0006408-. ISSN 1935-2735 DOI: https://doi.org/10.1371/journal.pntd.0006408

Britto, Carl D; Dyson, Zoe A; Mathias, Sitarah; Bosco, Ashish; Dougan, Gordon; Jose, Sanju; Nagaraj, Savitha; Holt, Kathryn E; Pollard, Andrew J; (2020) Persistent circulation of a fluoroquinolone-resistant Salmonella enterica Typhi clone in the Indian subcontinent. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 75 (2). pp. 337-341. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dkz435

Brynildsrud, Ola B; Pepperell, Caitlin S; Suffys, Philip; Grandjean, Louis; Monteserin, Johana; Debech, Nadia; Bohlin, Jon; Alfsnes, Kristian; Pettersson, John O-H; Kirkeleite, Ingerid; +20 more... 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; (2018) Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation. SCIENCE ADVANCES, 4 (10). eaat5869-. ISSN 2375-2548 DOI: https://doi.org/10.1126/sciadv.aat5869

Cain, Amy K; Boinett, Christine J; Barquist, Lars; Dordel, Janina; Fookes, Maria; Mayho, Matthew; Ellington, Matthew J; Goulding, David; Pickard, Derek; Wick, Ryan R; +3 more... Holt, Kathryn E; Parkhill, Julian; Thomson, Nicholas R; (2018) Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin. Scientific reports, 8 (1). 9868-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-018-28199-y

Carey, Megan E; Dyson, Zoe A; Argimón, Silvia; Cerdeira, Louise; Yeats, Corin; Aanensen, David; Mboowa, Gerald; Baker, Stephen; Tessema, Sofonias K; Smith, Anthony M; +2 more... Okeke, Iruka N; Holt, Kathryn E; (2023) Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization. Open forum infectious diseases, 10 (Suppl ). S38-S46. ISSN 2328-8957 DOI: https://doi.org/10.1093/ofid/ofad044

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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; +3 more... Teasdale, Rohan D; Likić, Vladimir A; Lithgow, Trevor; (2012) A bioinformatic strategy for the detection, classification and analysis of bacterial autotransporters. PLOS ONE, 7 (8). e43245-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0043245

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; (2019) Small IncQ1 and Col-Like Plasmids Harboring blaKPC-2 and Non-Tn4401 Elements (NTEKPC-IId) in High-Risk Lineages of Klebsiella pneumoniae CG258. Antimicrobial agents and chemotherapy, 63 (3). ISSN 0066-4804 DOI: https://doi.org/10.1128/AAC.02140-18

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; +15 more... 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; (2019) Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei. Nature communications, 10 (1). 4828-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-019-12823-0

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; +12 more... 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; (2016) South Asia as a Reservoir for the Global Spread of Ciprofloxacin-Resistant Shigella sonnei: A Cross-Sectional Study. PLoS medicine, 13 (8). e1002055-. ISSN 1549-1277 DOI: https://doi.org/10.1371/journal.pmed.1002055

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; +9 more... Minh, Chau Nguyen Ngoc; Turner, Paul; Sar, Poda; Thwaites, Guy; Holt, Kathryn E; Thomson, Nicholas R; Bodhidatta, Ladaporn; Jeffries Mason, Carl; Baker, Stephen; (2015) Introduction and establishment of fluoroquinolone-resistant Shigella sonnei into Bhutan. Microbial genomics, 1 (6). e000042-. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000042

Comas, Iñaki; Coscolla, Mireia; Luo, Tao; Borrell, Sonia; Holt, Kathryn E; Kato-Maeda, Midori; Parkhill, Julian; Malla, Bijaya; Berg, Stefan; Thwaites, Guy; +12 more... 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; (2013) Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. NATURE GENETICS, 45 (10). pp. 1176-1182. ISSN 1061-4036 DOI: https://doi.org/10.1038/ng.2744

Cooper, Helena B; Vezina, Ben; Hawkey, Jane; Passet, Virginie; López-Fernández, Sebastián; Monk, Jonathan M; Brisse, Sylvain; Holt, Kathryn E; Wyres, Kelly L; (2024) A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex. Microbial genomics, 10 (2). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.001206

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; +2 more... Holt, Kathryn E; Flores, Heather A; (2021) wMel Wolbachia genome remains stable after 7 years in Australian Aedes aegypti field populations. Microbial genomics, 7 (9). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000641

Darton, Thomas C; Meiring, James E; Tonks, Susan; Khan, Md Arifuzzaman; Khanam, Farhana; Shakya, Mila; Thindwa, Deus; Baker, Stephen; Basnyat, Buddha; Clemens, John D; +11 more... 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; (2017) 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. BMJ OPEN, 7 (6). e016283-. ISSN 2044-6055 DOI: https://doi.org/10.1136/bmjopen-2017-016283

Davis, Jacky; Banks, Ian; Wrigley, David; Peedell, Clive; Pollock, Alyson; McPherson, Klim; McKee, Martin; Irving, William L; Crome, Peter; Greenhalgh, Trisha; +230 more... 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; (2013) 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. BMJ (Clinical research ed), 346 (mar20 ). f1819-. ISSN 0959-8138 DOI: https://doi.org/10.1136/bmj.f1819

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; (2012) On the origin of Mycobacterium ulcerans, the causative agent of Buruli ulcer. BMC GENOMICS, 13 (1). 258-. ISSN 1471-2164 DOI: https://doi.org/10.1186/1471-2164-13-258

Duchene, Sebastian; Duchene, David A; Geoghegan, Jemma L; Dyson, Zoe A; Hawkey, Jane; Holt, Kathryn E; (2018) Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods. BMC EVOLUTIONARY BIOLOGY, 18 (1). 95-. ISSN 1471-2148 DOI: https://doi.org/10.1186/s12862-018-1210-5

Duchêne, Sebastian; Holt, Kathryn E; Weill, François-Xavier; Le Hello, Simon; Hawkey, Jane; Edwards, David J; Fourment, Mathieu; Holmes, Edward C; (2016) Genome-scale rates of evolutionary change in bacteria. MICROBIAL GENOMICS, 2 (11). e000094-. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000094

Duchêne, Sebastián; Duchêne, David A; Di Giallonardo, Francesca; Eden, John-Sebastian; Geoghegan, Jemma L; Holt, Kathryn E; Ho, Simon YW; Holmes, Edward C; (2016) Cross-validation to select Bayesian hierarchical models in phylogenetics. BMC EVOLUTIONARY BIOLOGY, 16 (1). 115-. ISSN 1471-2148 DOI: https://doi.org/10.1186/s12862-016-0688-y

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; +11 more... 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; (2024) Pathogen diversity and antimicrobial resistance transmission of Salmonella enterica serovars Typhi and Paratyphi A in Bangladesh, Nepal, and Malawi: a genomic epidemiological study. The Lancet microbe, 5 (8). 100841-. ISSN 2666-5247 DOI: https://doi.org/10.1016/S2666-5247(24)00047-8

Dyson, Zoe A; Holt, Kathryn E; (2021) Five Years of GenoTyphi: Updates to the Global Salmonella Typhi Genotyping Framework. JOURNAL OF INFECTIOUS DISEASES, 224 (12 Sup). S775-S780. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jiab414

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; +1 more... Holt, Kathryn E; (2017) Whole Genome Sequence Analysis of Salmonella Typhi Isolated in Thailand before and after the Introduction of a National Immunization Program. PLoS neglected tropical diseases, 11 (1). e0005274-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0005274

Dyson, Zoe Anne; Malau, Elisheba; Horwood, Paul F; Ford, Rebecca; Siba, Valentine; Yoannes, Mition; Pomat, William; Passey, Megan; Judd, Louise M; Ingle, Danielle J; +4 more... Williamson, Deborah A; Dougan, Gordon; Greenhill, Andrew R; Holt, Kathryn E; (2022) Whole genome sequence analysis of Salmonella Typhi in Papua New Guinea reveals an established population of genotype 2.1.7 sensitive to antimicrobials. PLoS Neglected Tropical Diseases, 16 (3). e0010306-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0010306

Edwards, David J; Duchene, Sebastián; Pope, Bernard; Holt, Kathryn E; (2021) SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments. Microbial genomics, 7 (12). DOI: https://doi.org/10.1099/mgen.0.000694

Edwards, David J; Duchêne, Sebastián; Pope, Bernard; Holt, Kathryn E; (2020) SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments. bioRxiv preprint. DOI: https://doi.org/10.1101/2020.07.08.194480

Follador, Rainer; Heinz, Eva; Wyres, Kelly L; Ellington, Matthew J; Kowarik, Michael; Holt, Kathryn E; Thomson, Nicholas R; (2016) The diversity of Klebsiella pneumoniae surface polysaccharides. Microbial genomics, 2 (8). e000073-. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000073

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; +2 more... Brisse, Sylvain; Holt, Kathryn E; (2023) Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae. Microbial genomics, 9 (2). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000936

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; +2 more... Brisse, Sylvain; Holt, Kathryn E; (2023) Corrigendum: 'Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae'. Microbial genomics, 9 (8). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.001084

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; +1 more... Norwegian Study Group on Klebsiella pneumoniae; Norwegian Study Group on Klebsiella pneumoniae; (2021) A nationwide genomic study of clinical Klebsiella pneumoniae in Norway 2001-15: introduction and spread of ESBLs facilitated by clonal groups CG15 and CG307. The Journal of antimicrobial chemotherapy, 77 (3). pp. 665-674. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dkab463

Gomi, Ryota; Wyres, Kelly L; Holt, Kathryn E; (2021) Detection of plasmid contigs in draft genome assemblies using customized Kraken databases. Microbial genomics, 7 (4). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000550

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; +4 more... McGloughlin, Steve A; Spelman, Denis W; Jenney, Adam WJ; Holt, Kathryn E; (2017) Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients. CLINICAL INFECTIOUS DISEASES, 65 (2). pp. 208-215. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/cix270

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; +5 more... Hunter, Peter C; McGloughlin, Steve A; Spelman, Denis W; Jenney, Adam WJ; Holt, Kathryn E; (2018) Antimicrobial-Resistant Klebsiella pneumoniae Carriage and Infection in Specialized Geriatric Care Wards Linked to Acquisition in the Referring Hospital. CLINICAL INFECTIOUS DISEASES, 67 (2). pp. 161-170. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/ciy027

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; +9 more... 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; (2022) Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen. Nature communications, 13 (1). 3017-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-022-30717-6

Hamidian, Mohammad; Hawkey, Jane; Holt, Kathryn E; Hall, Ruth M; (2015) Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1. Genome announcements, 3 (6). ISSN 2169-8287 DOI: https://doi.org/10.1128/genomeA.01478-15

Hamidian, Mohammad; Hawkey, Jane; Wick, Ryan; Holt, Kathryn E; Hall, Ruth M; (2019) Evolution of a clade of Acinetobacter baumannii global clone 1, lineage 1 via acquisition of carbapenem- and aminoglycoside-resistance genes and dispersion of ISAba1. Microbial Genomics, 5 (1). DOI: https://doi.org/10.1099/mgen.0.000242

Hamidian, Mohammad; Holt, Kathryn E; Pickard, Derek; Dougan, Gordon; Hall, Ruth M; (2014) A GC1 Acinetobacter baumannii isolate carrying AbaR3 and the aminoglycoside resistance transposon TnaphA6 in a conjugative plasmid. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 69 (4). pp. 955-958. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dkt454

Hamidian, Mohammad; Holt, Kathryn E; Pickard, Derek; Hall, Ruth M; (2016) A small Acinetobacter plasmid carrying the tet39 tetracycline resistance determinant. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 71 (1). pp. 269-271. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dkv293

Hamidian, Mohammad; Wick, Ryan R; Hartstein, Rebecca M; Judd, Louise M; Holt, Kathryn E; Hall, Ruth M; (2019) Insights from the revised complete genome sequences of Acinetobacter baumannii strains AB307-0294 and ACICU belonging to global clones 1 and 2. Microbial genomics, 5 (10). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000298

Hamidian, Mohammad; Wick, Ryan R; Judd, Louise M; Holt, Kathryn E; Hall, Ruth M; (2019) Complete Genome Sequence of A388, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 1 Isolate from Greece. Microbiology resource announcements, 8 (41). ISSN 2576-098X DOI: https://doi.org/10.1128/MRA.00971-19

Hamidian, Mohammad; Wynn, Matthew; Holt, Kathryn E; Pickard, Derek; Dougan, Gordon; Hall, Ruth M; (2014) Identification of a marker for two lineages within the GC1 clone of Acinetobacter baumannii. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 69 (2). pp. 557-558. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dkt379

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; (2018) Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection. MICROBIAL GENOMICS, 4 (3). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000165

Hawkey, Jane; Cottingham, Hugh; Tokolyi, Alex; Wick, Ryan R; Judd, Louise M; Cerdeira, Louise; de Oliveira Garcia, Doroti; Wyres, Kelly L; Holt, Kathryn E; (2022) Linear plasmids in Klebsiella and other Enterobacteriaceae. Microbial genomics, 8 (4). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000807

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; +1 more... Weill, François-Xavier; (2019) Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198. Microbial genomics, 5 (7). DOI: https://doi.org/10.1099/mgen.0.000269

Hawkey, Jane; Monk, Jonathan M; Billman-Jacobe, Helen; Palsson, Bernhard; Holt, Kathryn E; (2020) Impact of insertion sequences on convergent evolution of Shigella species. PLOS GENETICS, 16 (7). e1008931-. ISSN 1553-7404 DOI: https://doi.org/10.1371/journal.pgen.1008931

Hawkey, Jane; Paranagama, Kalani; Baker, Kate S; Bengtsson, Rebecca J; Weill, François-Xavier; Thomson, Nicholas R; Baker, Stephen; Cerdeira, Louise; Iqbal, Zamin; Hunt, Martin; +5 more... Ingle, Danielle J; Dallman, Timothy J; Jenkins, Claire; Williamson, Deborah A; Holt, Kathryn E; (2021) Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei. Nature communications, 12 (1). 2684-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-021-22700-4

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; (2022) A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality. Genome research, 32 (5). pp. 1004-1014. ISSN 1088-9051 DOI: https://doi.org/10.1101/gr.276289.121

Hawkey, Jane; Wyres, Kelly L; Judd, Louise M; Harshegyi, Taylor; Blakeway, Luke; Wick, Ryan R; Jenney, Adam WJ; Holt, Kathryn E; (2022) ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting. Genome medicine, 14 (1). 97-. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-022-01103-0

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; +15 more... 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; (2010) Evolutionary dynamics of Clostridium difficile over short and long time scales. Proceedings of the National Academy of Sciences of the United States of America, 107 (16). pp. 7527-7532. ISSN 0027-8424 DOI: https://doi.org/10.1073/pnas.0914322107 Full text not available from this repository.

Heinz, Eva; Holt, Kathryn E; Meehan, Conor J; Sheppard, Samuel K; (2021) Addressing parachute research and removing barriers for LMIC researchers in Microbial Genomics. Microbial genomics, 7 (10). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000722

Hetland, Marit AK; Hawkey, Jane; Bernhoff, Eva; Bakksjø, Ragna-Johanne; Kaspersen, Håkon; Rettedal, Siren I; Sundsfjord, Arnfinn; Holt, Kathryn E; Löhr, Iren H; (2023) Within-patient and global evolutionary dynamics of Klebsiella pneumoniae ST17. Microbial genomics, 9 (5). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.001005

Hogg, Geoff; Dimovski, Karolina; Hiley, Lester; Holt, Kathryn E; (2013) Draft Genome Sequences for Ten Salmonella enterica Serovar Typhimurium Phage Type 135 Variants. Genome announcements, 1 (3). e00293-e00213. ISSN 2169-8287 DOI: https://doi.org/10.1128/genomeA.00293-13

Holt, Kathryn E; Aanensen, David M; Achtman, Mark; (2022) Genomic population structures of microbial pathogens. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 377 (1861). 20210230-. ISSN 0962-8436 DOI: https://doi.org/10.1098/rstb.2021.0230

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; +8 more... Choi, Seon Young; Kim, Su Hee; da Silveira, Wanderley D; Pickard, Derek J; Farrar, Jeremy J; Parkhill, Julian; Dougan, Gordon; Thomson, Nicholas R; (2012) Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nature genetics, 44 (9). pp. 1056-1059. ISSN 1061-4036 DOI: https://doi.org/10.1038/ng.2369

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; +4 more... Hien, Tran Tinh; Farrar, Jeremy; Dougan, Gordon; Baker, Stephen; (2011) Temporal fluctuation of multidrug resistant salmonella typhi haplotypes in the mekong river delta region of Vietnam. PLoS neglected tropical diseases, 5 (1). e929-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0000929

Holt, Kathryn E; Hamidian, Mohammad; Kenyon, Johanna J; Wynn, Matthew T; Hawkey, Jane; Pickard, Derek; Hall, Ruth M; (2015) Genome Sequence of Acinetobacter baumannii Strain A1, an Early Example of Antibiotic-Resistant Global Clone 1. Genome announcements, 3 (2). ISSN 2169-8287 DOI: https://doi.org/10.1128/genomeA.00032-15

Holt, Kathryn E; Lassalle, Florent; Wyres, Kelly L; Wick, Ryan; Mostowy, Rafal J; (2019) Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales. BioRxiv. DOI: https://doi.org/10.1101/709832

Holt, Kathryn E; Lassalle, Florent; Wyres, Kelly L; Wick, Ryan; Mostowy, Rafał J; (2022) Correction to: Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales. ISME JOURNAL, 16 (5). 1478-. ISSN 1751-7362 DOI: https://doi.org/10.1038/s41396-021-01181-9

Holt, Kathryn E; Lassalle, Florent; Wyres, Kelly L; Wick, Ryan; Mostowy, Rafał J; (2020) Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales. ISME JOURNAL, 14 (7). pp. 1713-1730. ISSN 1751-7362 DOI: https://doi.org/10.1038/s41396-020-0628-0

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; +11 more... 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; (2018) Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam. NATURE GENETICS, 50 (6). pp. 849-856. ISSN 1061-4036 DOI: https://doi.org/10.1038/s41588-018-0117-9

Holt, Kathryn E; Millar, A Harvey; Whelan, James; (2006) ModuleFinder and CoReg: alternative tools for linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants. PLANT METHODS, 2 (1). 8-. ISSN 1746-4811 DOI: https://doi.org/10.1186/1746-4811-2-8

Holt, Kathryn E; Parkhill, Julian; Mazzoni, Camila J; Roumagnac, Philippe; Weill, François-Xavier; Goodhead, Ian; Rance, Richard; Baker, Stephen; Maskell, Duncan J; Wain, John; +3 more... Dolecek, Christiane; Achtman, Mark; Dougan, Gordon; (2008) High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nature genetics, 40 (8). pp. 987-993. ISSN 1061-4036 DOI: https://doi.org/10.1038/ng.195 Full text not available from this repository.

Holt, Kathryn E; Teo, Yik Y; Li, Heng; Nair, Satheesh; Dougan, Gordon; Wain, John; Parkhill, Julian; (2009) Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA. BIOINFORMATICS, 25 (16). pp. 2074-2075. ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/btp344

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; +20 more... 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; (2013) Tracking the establishment of local endemic populations of an emergent enteric pathogen. Proceedings of the National Academy of Sciences of the United States of America, 110 (43). pp. 17522-17527. ISSN 0027-8424 DOI: https://doi.org/10.1073/pnas.1308632110 Full text not available from this repository.

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; +5 more... White, Brian; Bason, Nathalie; Mungall, Karen; Dougan, Gordon; Parkhill, Julian; (2009) Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi. BMC GENOMICS, 10 (1). 36-. ISSN 1471-2164 DOI: https://doi.org/10.1186/1471-2164-10-36

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; +18 more... 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; (2015) Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proceedings of the National Academy of Sciences of the United States of America, 112 (27). E3574-E3581. ISSN 0027-8424 DOI: https://doi.org/10.1073/pnas.1501049112 Full text not available from this repository.

Holt, Kathryn; Kenyon, Johanna J; Hamidian, Mohammad; Schultz, Mark B; Pickard, Derek J; Dougan, Gordon; Hall, Ruth; (2016) Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1. MICROBIAL GENOMICS, 2 (2). e000052-. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000052

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; (2013) Genomic insights to control the emergence of vancomycin-resistant enterococci. MBIO, 4 (4). ISSN 2150-7511 DOI: https://doi.org/10.1128/mBio.00412-13

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; +5 more... Khor, Chiea Chuen; Sly, Peter D; Holt, Patrick G; Holt, Kathryn E; Inouye, Michael; (2020) Neonatal genetics of gene expression reveal potential origins of autoimmune and allergic disease risk. NATURE COMMUNICATIONS, 11 (1). 3761-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-020-17477-x

Im, Justin; Islam, Md Taufiqul; Kim, Deok Ryun; Ahmmed, Faisal; Chon, Yun; Zaman, K; Khan, Ashraful Islam; Ali, Mohammad; Sur, Dipika; Kanungo, Suman; +8 more... Dutta, Shanta; Bhattacharya, Sujit K; Dougan, Gordon; Holt, Kathryn E; Marks, Florian; Kim, Jerome H; Qadri, Firdausi; Clemens, John D; (2020) Protection conferred by typhoid fever against recurrent typhoid fever in urban Kolkata. PLOS NEGLECTED TROPICAL DISEASES, 14 (8). e0008530-. ISSN 1935-2735 DOI: https://doi.org/10.1371/journal.pntd.0008530 Item availability may be restricted.

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; +7 more... Holt, Kathryn E; Chow, Eric PF; Fairley, Christopher K; Chen, Marcus Y; Kirk, Martyn D; Howden, Benjamin P; Williamson, Deborah A; (2019) Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in Australia. Clinical Infectious Diseases, 69 (9). pp. 1535-1544. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/ciz005

Ingle, Danielle J; Levine, Myron M; Kotloff, Karen L; Holt, Kathryn E; Robins-Browne, Roy M; (2018) Dynamics of antimicrobial resistance in intestinal Escherichia coli from children in community settings in South Asia and sub-Saharan Africa. Nature microbiology, 3 (9). pp. 1063-1073. ISSN 2058-5276 DOI: https://doi.org/10.1038/s41564-018-0217-4

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; (2019) Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers. PLoS neglected tropical diseases, 13 (9). e0007620-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0007620

Ingle, Danielle J; Valcanis, Mary; Kuzevski, Alex; Tauschek, Marija; Inouye, Michael; Stinear, Tim; Levine, Myron M; Robins-Browne, Roy M; Holt, Kathryn E; (2016) 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. MICROBIAL GENOMICS, 2 (7). e000064-. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000064

Inouye, Michael; Conway, Thomas C; Zobel, Justin; Holt, Kathryn E; (2012) Short read sequence typing (SRST): multi-locus sequence types from short reads. BMC GENOMICS, 13 (1). 338-. ISSN 1471-2164 DOI: https://doi.org/10.1186/1471-2164-13-338

Inouye, Michael; Dashnow, Harriet; Raven, Lesley-Ann; Schultz, Mark B; Pope, Bernard J; Tomita, Takehiro; Zobel, Justin; Holt, Kathryn E; (2014) SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. GENOME MEDICINE, 6 (11). 90-. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-014-0090-6

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; +22 more... 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; (2016) Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa. PLoS neglected tropical diseases, 10 (9). e0004781-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0004781

Jansen, Angela M; Hall, Lindsay J; Clare, Simon; Goulding, David; Holt, Kathryn E; Grant, Andrew J; Mastroeni, Piero; Dougan, Gordon; Kingsley, Robert A; (2011) A Salmonella Typhimurium-Typhi genomic chimera: a model to study Vi polysaccharide capsule function in vivo. PLOS PATHOGENS, 7 (7). e1002131-. ISSN 1553-7366 DOI: https://doi.org/10.1371/journal.ppat.1002131

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; +2 more... Peleg, Anton Y; START Trial Group; START Trial Group; (2021) Multicentre stepped-wedge cluster randomised controlled trial of an antimicrobial stewardship programme in residential aged care: protocol for the START trial. BMJ open, 11 (3). e046142-. ISSN 2044-6055 DOI: https://doi.org/10.1136/bmjopen-2020-046142

Kariuki, Samuel; Dyson, Zoe A; Mbae, Cecilia; Ngetich, Ronald; Kavai, Susan M; Wairimu, Celestine; Anyona, Stephen; Gitau, Naomi; Onsare, Robert Sanaya; Ongandi, Beatrice; +5 more... Duchene, Sebastian; Ali, Mohamed; Clemens, John David; Holt, Kathryn E; Dougan, Gordon; (2021) Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya. eLife, 10. ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.67852

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; +8 more... Duy, Pham Thanh; Day, Jeremy N; Campbell, James I; Dougan, Gordon; Dolecek, Christiane; Farrar, Jeremy; Basnyat, Buddha; Baker, Stephen; (2010) The burden and characteristics of enteric fever at a healthcare facility in a densely populated area of Kathmandu. PLOS ONE, 5 (11). e13988-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0013988

Karmakar, Malancha; Rodrigues, Carlos HM; Holt, Kathryn E; Dunstan, Sarah J; Denholm, Justin; Ascher, David B; (2019) Empirical ways to identify novel Bedaquiline resistance mutations in AtpE. PloS one, 14 (5). e0217169-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0217169

Khoury, Muin J; Holt, Kathryn E; (2021) The impact of genomics on precision public health: beyond the pandemic. Genome medicine, 13 (1). 67-. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-021-00886-y

Kingsley, Robert A; Kay, Sally; Connor, Thomas; Barquist, Lars; Sait, Leanne; Holt, Kathryn E; Sivaraman, Karthi; Wileman, Thomas; Goulding, David; Clare, Simon; +10 more... Hale, Christine; Seshasayee, Aswin; Harris, Simon; Thomson, Nicholas R; Gardner, Paul; Rabsch, Wolfgang; Wigley, Paul; Humphrey, Tom; Parkhill, Julian; Dougan, Gordon; (2013) Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar. MBIO, 4 (5). e00565-e00513. ISSN 2150-7511 DOI: https://doi.org/10.1128/mBio.00565-13

Lam, Margaret MC; Wick, Ryan R; Judd, Louise M; Holt, Kathryn E; Wyres, Kelly L; (2022) Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex. Microbial genomics, 8 (3). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000800

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Viehweger, Adrian; Blumenscheit, Christian; Lippmann, Norman; Wyres, Kelly L; Brandt, Christian; Hans, Jörg B; Hölzer, Martin; Irber, Luiz; Gatermann, Sören; Lübbert, Christoph; +3 more... Pletz, Mathias W; Holt, Kathryn E; König, Brigitte; (2021) Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae. Microbial genomics, 7 (12). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000741

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; (2021) Klebsiella pneumoniae with capsule type K64 is overrepresented among invasive disease in Vietnam. F1000Research, 10. p. 454. ISSN 2046-1402 DOI: https://doi.org/10.12688/f1000research.52799.1

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; +9 more... Holt, Kathryn E; Yu, Ly-Mee; Lockhart, Stephen; Farrar, Jeremy J; Sztein, Marcelo B; Dougan, Gordon; Angus, Brian; Levine, Myron M; Pollard, Andrew J; (2014) An outpatient, ambulant-design, controlled human infection model using escalating doses of Salmonella Typhi challenge delivered in sodium bicarbonate solution. CLINICAL INFECTIOUS DISEASES, 58 (9). pp. 1230-1240. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/ciu078

Walker, Michael L; Holt, Kathryn E; Anderson, Gary P; Teo, Shu Mei; Sly, Peter D; Holt, Patrick G; Inouye, Michael; (2014) Elucidation of pathways driving asthma pathogenesis: development of a systems-level analytic strategy. FRONTIERS IN IMMUNOLOGY, 5 (SEP). 447-. ISSN 1664-3224 DOI: https://doi.org/10.3389/fimmu.2014.00447

Wan, Yu; Wick, Ryan R; Zobel, Justin; Ingle, Danielle J; Inouye, Michael; Holt, Kathryn E; (2020) GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure. BMC GENOMICS, 21 (1). 658-. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-020-07019-6

Wan, Yu; Wick, Ryan R; Zobel, Justin; Ingle, Danielle J; Inouye, Michael; Holt, Kathryn E; (2020) GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene Associations Controlled for Population Structure. bioRxiv preprint. DOI: https://doi.org/10.1101/2020.02.29.970970

Watts, Stephen C; Holt, Kathryn E; (2019) hicap: In Silico Serotyping of the Haemophilus influenzae Capsule Locus. Journal of clinical microbiology, 57 (6). ISSN 0095-1137 DOI: https://doi.org/10.1128/JCM.00190-19

Watts, Stephen C; Judd, Louise M; Carzino, Rosemary; Ranganathan, Sarath; Holt, Kathryn E; (2021) Genomic Diversity and Antimicrobial Resistance of Haemophilus Colonizing the Airways of Young Children with Cystic Fibrosis. mSystems, 6 (4). e0017821-. ISSN 2379-5077 DOI: https://doi.org/10.1128/mSystems.00178-21

Watts, Stephen C; Ritchie, Scott C; Inouye, Michael; Holt, Kathryn E; (2018) FastSpar: rapid and scalable correlation estimation for compositional data. Bioinformatics, 35 (6). pp. 1064-1066. ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/bty734

Weill, François-Xavier; Domman, Daryl; Njamkepo, Elisabeth; Tarr, Cheryl; Rauzier, Jean; Fawal, Nizar; Keddy, Karen H; Salje, Henrik; Moore, Sandra; Mukhopadhyay, Asish K; +31 more... 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; (2017) Genomic history of the seventh pandemic of cholera in Africa. Science (New York, NY), 358 (6364). pp. 785-789. ISSN 0036-8075 DOI: https://doi.org/10.1126/science.aad5901 Full text not available from this repository.

Wick, Ryan R; Heinz, Eva; Holt, Kathryn E; Wyres, Kelly L; (2018) Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes. JOURNAL OF CLINICAL MICROBIOLOGY, 56 (6). ISSN 0095-1137 DOI: https://doi.org/10.1128/JCM.00197-18

Wick, Ryan R; Holt, Kathryn E; (2019) Benchmarking of long-read assemblers for prokaryote whole genome sequencing. F1000Research, 8. 2138-. ISSN 2046-1402 DOI: https://doi.org/10.12688/f1000research.21782.4

Wick, Ryan R; Holt, Kathryn E; (2022) Polypolish: Short-read polishing of long-read bacterial genome assemblies. PLoS computational biology, 18 (1). e1009802-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1009802

Wick, Ryan R; Judd, Louise M; Cerdeira, Louise T; Hawkey, Jane; Méric, Guillaume; Vezina, Ben; Wyres, Kelly L; Holt, Kathryn E; (2021) Trycycler: consensus long-read assemblies for bacterial genomes. Genome biology, 22 (1). 266-. ISSN 1474-7596 DOI: https://doi.org/10.1186/s13059-021-02483-z

Wick, Ryan R; Judd, Louise M; Gorrie, Claire L; Holt, Kathryn E; (2017) Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS COMPUTATIONAL BIOLOGY, 13 (6). e1005595-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1005595

Wick, Ryan R; Judd, Louise M; Gorrie, Claire L; Holt, Kathryn E; (2017) Completing bacterial genome assemblies with multiplex MinION sequencing. DOI: https://doi.org/10.1101/160614

Wick, Ryan R; Judd, Louise M; Gorrie, Claire L; Holt, Kathryn E; (2017) Completing bacterial genome assemblies with multiplex MinION sequencing. MICROBIAL GENOMICS, 3 (10). e000132-. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000132

Wick, Ryan R; Judd, Louise M; Holt, Kathryn E; (2018) Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks. PLoS computational biology, 14 (11). e1006583-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1006583

Wick, Ryan R; Judd, Louise M; Holt, Kathryn E; (2018) Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks. DOI: https://doi.org/10.1101/366526

Wick, Ryan R; Judd, Louise M; Holt, Kathryn E; (2019) Performance of neural network basecalling tools for Oxford Nanopore sequencing. GENOME BIOLOGY, 20 (1). 129-. ISSN 1474-760X DOI: https://doi.org/10.1186/s13059-019-1727-y

Wick, Ryan R; Judd, Louise M; Holt, Kathryn E; (2023) Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. PLOS Computational Biology, 19 (3). e1010905-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1010905

Wick, Ryan R; Judd, Louise M; Wyres, Kelly L; Holt, Kathryn E; (2021) Recovery of small plasmid sequences via Oxford Nanopore sequencing. Microbial genomics, 7 (8). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000631 Item availability may be restricted.

Wick, Ryan R; Schultz, Mark B; Zobel, Justin; Holt, Kathryn E; (2015) Bandage: interactive visualization of de novo genome assemblies. Bioinformatics, 31 (20). pp. 3350-3352. ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/btv383

Wong, Vanessa K; Baker, Stephen; Connor, Thomas R; Pickard, Derek; Page, Andrew J; Dave, Jayshree; Murphy, Niamh; Holliman, Richard; Sefton, Armine; Millar, Michael; +4 more... Dyson, Zoe A; Dougan, Gordon; Holt, Kathryn E; International Typhoid Consortium; (2016) An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid. Nature communications, 7 (1). 12827-. ISSN 2041-1723 DOI: https://doi.org/10.1038/ncomms12827

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; +64 more... 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; (2015) Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events. Nature genetics, 47 (6). pp. 632-639. ISSN 1061-4036 DOI: https://doi.org/10.1038/ng.3281 Full text not available from this repository.

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; +9 more... Ellison, Louise; Bautista, Ruben; McGee, Chris J; Kay, Sally J; Wileman, Thomas M; Kenney, Linda J; MacLennan, Calman A; Kingsley, Robert A; Dougan, Gordon; (2013) Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium. PLOS ONE, 8 (12). e84567-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0084567

Wyres, Kelly L; Cahill, Sarah M; Holt, Kathryn E; Hall, Ruth M; Kenyon, Johanna J; (2020) 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. MICROBIAL GENOMICS, 6 (3). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000339

Wyres, Kelly L; Gorrie, Claire; Edwards, David J; Wertheim, Heiman FL; Hsu, Li Yang; Van Kinh, Nguyen; Zadoks, Ruth; Baker, Stephen; Holt, Kathryn E; (2015) Extensive Capsule Locus Variation and Large-Scale Genomic Recombination within the Klebsiella pneumoniae Clonal Group 258. Genome biology and evolution, 7 (5). pp. 1267-1279. ISSN 1759-6653 DOI: https://doi.org/10.1093/gbe/evv062

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; (2018) Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307. DOI: https://doi.org/10.1101/352740

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; (2018) Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307. The Journal of antimicrobial chemotherapy, 74 (3). pp. 577-581. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dky492

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; +6 more... McGloughlin, Steve A; Abbott, Iain J; Macesic, Nenad; Spelman, Denis W; Jenney, Adam WJ; Holt, Kathryn E; (2021) Genomic surveillance of antimicrobial resistant bacterial colonisation and infection in intensive care patients. BMC infectious diseases, 21 (1). 683-. ISSN 1471-2334 DOI: https://doi.org/10.1186/s12879-021-06386-z

Wyres, Kelly L; Holt, Kathryn E; (2018) <i>Klebsiella pneumoniae</i> as a key trafficker of drug resistance genes from environmental to clinically important bacteria. PeerJ Preprints. DOI: https://doi.org/10.7287/peerj.preprints.26852

Wyres, Kelly L; Holt, Kathryn E; (2016) Klebsiella pneumoniae Population Genomics and Antimicrobial-Resistant Clones. TRENDS IN MICROBIOLOGY, 24 (12). pp. 944-956. ISSN 0966-842X DOI: https://doi.org/10.1016/j.tim.2016.09.007

Wyres, Kelly L; Holt, Kathryn E; (2018) Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria. Current opinion in microbiology, 45. pp. 131-139. ISSN 1369-5274 DOI: https://doi.org/10.1016/j.mib.2018.04.004

Wyres, Kelly L; Lam, Margaret MC; Holt, Kathryn E; (2018) Comment on: CG258 Klebsiella pneumoniae isolates without β-lactam resistance at the onset of the carbapenem-resistant Enterobacteriaceae epidemic in New York City. The Journal of Antimicrobial Chemotherapy, 74 (3). pp. 831-833. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dky472

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; +10 more... 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; (2020) Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia. Genome Medicine, 12 (1). 11-. DOI: https://doi.org/10.1186/s13073-019-0706-y

Wyres, Kelly L; Wick, Ryan R; Gorrie, Claire; Jenney, Adam; Follador, Rainer; Thomson, Nicholas R; Holt, Kathryn E; (2016) Identification of Klebsiella capsule synthesis loci from whole genome data. Microbial genomics, 2 (12). e000102-. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000102

Wyres, Kelly L; Wick, Ryan R; Gorrie, Claire; Jenney, Adam; Follador, Rainer; Thomson, Nicholas R; Holt, Kathryn E; (2016) Identification of<i>Klebsiella</i>capsule synthesis loci from whole genome data. BioRxiv. DOI: https://doi.org/10.1101/071415

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; (2018) Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of<i>Klebsiella pneumoniae</i>. DOI: https://doi.org/10.1101/414235

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; (2019) Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae. PLoS genetics, 15 (4). e1008114-. ISSN 1553-7390 DOI: https://doi.org/10.1371/journal.pgen.1008114

Wyrsch, Ethan R; Hawkey, Jane; Judd, Louise M; Haites, Ruth; Holt, Kathryn E; Djordjevic, Steven P; Billman-Jacobe, Helen; (2019) Z/I1 Hybrid Virulence Plasmids Carrying Antimicrobial Resistance genes in S. Typhimurium from Australian Food Animal Production. MICROORGANISMS, 7 (9). p. 299. ISSN 2076-2607 DOI: https://doi.org/10.3390/microorganisms7090299

Zhou, Kai; Xiao, Tingting; David, Sophia; Wang, Qin; Zhou, Yanzi; Guo, Lihua; Aanensen, David; Holt, Kathryn E; Thomson, Nicholas R; Grundmann, Hajo; +2 more... Shen, Ping; Xiao, Yonghong; (2020) Novel Subclone of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 with Enhanced Virulence and Transmissibility, China. EMERGING INFECTIOUS DISEASES, 26 (2). pp. 289-297. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid2602.190594

Zhou, Kai; Xue, Chun-Xu; Xu, Tingting; Shen, Ping; Wei, Sha; Wyres, Kelly L; Lam, Margaret MC; Liu, Jinquan; Lin, Haoyun; Chen, Yunbo; +3 more... Holt, Kathryn E; BRICS Working Group; Xiao, Yonghong; (2023) A point mutation in recC associated with subclonal replacement of carbapenem-resistant Klebsiella pneumoniae ST11 in China. Nature communications, 14 (1). 2464-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-023-38061-z