Items where Author or Contributor is "Holt, Kathryn E"

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Number of items: 119.

2020

Repetti, Sonja I; Jackson, Christopher J; Judd, Louise M; Wick, Ryan R; Holt, Kathryn E; Verbruggen, Heroen; (2020) The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns. PEERJ, 8 (1). e8273-. ISSN 2167-8359 DOI: https://doi.org/10.7717/peerj.8273
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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
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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; +8 more... Langridge, Gemma C; Hadfield, James; Chau, Nguyen Van Vinh; Thwaites, Guy E; Parkhill, Julian; Thomson, Nicholas R; Holt, Kathryn E; Baker, Stephen; (2019) Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii. Microbial genomics, 5 (2). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000246
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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
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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). p. 4828. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-019-12823-0
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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
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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
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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
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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
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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
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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
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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
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Lam, Margaret MC; Wyres, Kelly L; Wick, Ryan R; Judd, Louise M; Fostervold, Aasmund; Holt, Kathryn E; Löhr, Iren Høyland; (2019) Convergence of virulence and MDR in a single plasmid vector in MDR Klebsiella pneumoniae ST15. The Journal of antimicrobial chemotherapy, 74 (5). pp. 1218-1222. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dkz028
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Méric, Guillaume; Wick, Ryan R; Watts, Stephen C; Holt, Kathryn E; Inouye, Michael; (2019) Correcting index databases improves metagenomic studies. bioRxiv. DOI: https://doi.org/10.1101/712166
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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
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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
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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
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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
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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; +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
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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
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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
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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
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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
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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
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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
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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
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Lam, Margaret MC; Wick, Ryan R; Wyres, Kelly L; Gorrie, Claire L; Judd, Louise M; Jenney, Adam WJ; Brisse, Sylvain; Holt, Kathryn E; (2018) Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations. MICROBIAL GENOMICS, 4 (9). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000196
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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; +4 more... Koh, Tse Hsien; Passet, Virginie; Brisse, Sylvain; Holt, Kathryn E; (2018) Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination. Nature communications, 9 (1). 2703-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-018-05114-7
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Lam, Margaret MC; Wyres, Kelly L; Judd, Louise M; Wick, Ryan R; Jenney, Adam; Brisse, Sylvain; Holt, Kathryn E; (2018) Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae. Genome medicine, 10 (1). 77-. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-018-0587-5
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Manna, S; Ortika, BD; Dunne, EM; Holt, KE; Kama, M; Russell, FM; Hinds, J; Satzke, C; (2018) A novel genetic variant of Streptococcus pneumoniae serotype 11A discovered in Fiji. CLINICAL MICROBIOLOGY AND INFECTION, 24 (4). 428.e1-428.e7. ISSN 1198-743X DOI: https://doi.org/10.1016/j.cmi.2017.06.031
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Mostowy, Rafał J; Holt, Kathryn E; (2018) Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating. Trends in microbiology, 26 (12). pp. 1008-1021. ISSN 0966-842X DOI: https://doi.org/10.1016/j.tim.2018.06.006
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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; +60 more... 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; (2018) The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa. Nature communications, 9 (1). 5094-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-018-07370-z
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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; +6 more... Simpson, Angela; Custovic, Adnan; Sly, Peter D; Holt, Patrick G; Holt, Kathryn E; Inouye, Michael; (2018) Abstract. ELIFE, 7. ISSN 2050-084X DOI: https://doi.org/10.7554/elife.35856.001
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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; +6 more... Simpson, Angela; Custovic, Adnan; Sly, Peter D; Holt, Patrick G; Holt, Kathryn E; Inouye, Michael; (2018) Trajectories of childhood immune development and respiratory health relevant to asthma and allergy. eLife, 7. ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.35856
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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; +9 more... 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; (2018) Airway Microbiota Dynamics Uncover a Critical Window for Interplay of Pathogenic Bacteria and Allergy in Childhood Respiratory Disease. Cell host & microbe, 24 (3). 341-352.e5. ISSN 1931-3128 DOI: https://doi.org/10.1016/j.chom.2018.08.005
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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
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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
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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
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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
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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
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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 Klebsiella pneumoniae. DOI: https://doi.org/10.1101/414235
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2017

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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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
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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
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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
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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; +19 more... 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; (2017) Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain. NATURE COMMUNICATIONS, 8 (1). 15483-. ISSN 2041-1723 DOI: https://doi.org/10.1038/ncomms15483
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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; 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
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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
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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; +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
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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
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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
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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
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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
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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
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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
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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
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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; +2 more... Holt, Kathryn E; Gan, Yunn-Hwen; (2016) Differential host susceptibility and bacterial virulence factors driving Klebsiella liver abscess in an ethnically diverse population. SCIENTIFIC REPORTS, 6 (1). 29316-. ISSN 2045-2322 DOI: https://doi.org/10.1038/srep29316
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Njamkepo, Elisabeth; Fawal, Nizar; Tran-Dien, Alicia; Hawkey, Jane; Strockbine, Nancy; Jenkins, Claire; Talukder, Kaisar A; Bercion, Raymond; Kuleshov, Konstantin; Kolínská, Renáta; +62 more... 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; (2016) Global phylogeography and evolutionary history of Shigella dysenteriae type 1. Nature microbiology, 1 (4). 16027-. ISSN 2058-5276 DOI: https://doi.org/10.1038/nmicrobiol.2016.27 Full text not available from this repository.

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; +13 more... 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; (2016) A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure. eLife, 5 (MARCH2). e14003-. ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.14003
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Pham Thanh, Duy; Thanh Tuyen, Ha; Nguyen Thi Nguyen, To; Chung The, Hao; Wick, Ryan R; Thwaites, Guy E; Baker, Stephen; Holt, Kathryn E; (2016) Inducible colistin resistance via a disrupted plasmid-borne mcr-1 gene in a 2008 Vietnamese Shigella sonnei isolate. The Journal of antimicrobial chemotherapy, 71 (8). pp. 2314-2317. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dkw173 Full text not available from this repository.

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; +8 more... Wong, Vanessa; Pickard, Derek; Thwaites, Guy E; Day, Nicholas; Dougan, Gordon; Turner, Paul; Parry, Christopher M; Baker, Stephen; (2016) The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia. PLoS neglected tropical diseases, 10 (6). e0004785-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0004785
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Ritchie, Scott C; Watts, Stephen; Fearnley, Liam G; Holt, Kathryn E; Abraham, Gad; Inouye, Michael; (2016) A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets. CELL SYSTEMS, 3 (1). pp. 71-82. ISSN 2405-4712 DOI: https://doi.org/10.1016/j.cels.2016.06.012
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Robins-Browne, Roy M; Holt, Kathryn E; Ingle, Danielle J; Hocking, Dianna M; Yang, Ji; Tauschek, Marija; (2016) Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing? FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, 6 (NOV). 141-. ISSN 2235-2988 DOI: https://doi.org/10.3389/fcimb.2016.00141
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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; +6 more... Thwaites, Guy; Thi Khanh Nhu, Nguyen; Hall, Ruth M; Fournier-Level, Alexandre; Baker, Stephen; Holt, Kathryn E; (2016) Repeated local emergence of carbapenem-resistant Acinetobacter baumannii in a single hospital ward. MICROBIAL GENOMICS, 2 (3). e000050-. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000050
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The, Hao Chung; Thanh, Duy Pham; Holt, Kathryn E; Thomson, Nicholas R; Baker, Stephen; (2016) The genomic signatures of Shigella evolution, adaptation and geographical spread. Nature reviews Microbiology, 14 (4). pp. 235-250. ISSN 1740-1526 DOI: https://doi.org/10.1038/nrmicro.2016.10 Full text not available from this repository.

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
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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
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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
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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; +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
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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
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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
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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
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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.

Nigro, Steven J; Holt, Kathryn E; Pickard, Derek; Hall, Ruth M; (2015) Carbapenem and amikacin resistance on a large conjugative Acinetobacter baumannii plasmid. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 70 (4). pp. 1259-1261. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dku486
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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
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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.

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
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2014

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
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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
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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
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Stinear, Timothy P; Holt, Kathryn E; Chua, Kyra; Stepnell, Justin; Tuck, Kellie L; Coombs, Geoffrey; Harrison, Paul Francis; Seemann, Torsten; Howden, Benjamin P; (2014) Adaptive change inferred from genomic population analysis of the ST93 epidemic clone of community-associated methicillin-resistant Staphylococcus aureus. GENOME BIOLOGY AND EVOLUTION, 6 (2). pp. 366-378. ISSN 1759-6653 DOI: https://doi.org/10.1093/gbe/evu022
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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
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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
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2013

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
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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
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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). S69-S82. ISSN 2169-8287 DOI: https://doi.org/10.1128/genomeA.00293-13
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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.

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
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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
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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; +2 more... Dougan, Gordon; Baker, Stephen; (2013) Identification of Salmonella enterica serovar Typhi genotypes by use of rapid multiplex ligation-dependent probe amplification. Journal of clinical microbiology, 51 (9). pp. 2950-2958. ISSN 0095-1137 DOI: https://doi.org/10.1128/JCM.01010-13
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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
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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; +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
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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
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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
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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
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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; +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
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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
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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
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2010

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
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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.

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
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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; +6 more... Arjyal, Amit; Koirala, Samir; Basnyat, Buddha; Dolecek, Christiane; Farrar, Jeremy; Baker, Stephen; (2010) The sensitivity of real-time PCR amplification targeting invasive Salmonella serovars in biological specimens. BMC INFECTIOUS DISEASES, 10 (1). 125-. ISSN 1471-2334 DOI: https://doi.org/10.1186/1471-2334-10-125
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Song, Yajun; Roumagnac, Philippe; Weill, François-Xavier; Wain, John; Dolecek, Christiane; Mazzoni, Camila J; Holt, Kathryn E; Achtman, Mark; (2010) A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 65 (8). pp. 1631-1641. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dkq175
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2009

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
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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
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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; +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.

2007

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
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2006

This list was generated on Mon Jun 1 06:30:33 2020 BST.