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
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
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
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).
p. 4828.
ISSN 2041-1723
DOI: https://doi.org/10.1038/s41467-019-12823-0
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;
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
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
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
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;
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
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
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
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
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
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.21782.2
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
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
2018
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
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
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
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
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
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
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
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
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
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
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
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
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
Nigro, Steven J;
Wick, Ryan;
Holt, Kathryn E;
Hall, Ruth M;
(2018)
Complete Genome Sequence of WM99c, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 2 (GC2) Strain Representing an Australian GC2 Lineage.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS, 7 (22).
ISSN 2576-098X
DOI: https://doi.org/10.1128/MRA.01199-18
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
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
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
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
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
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;
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
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;
Holt, Kathryn E;
(2018)
Klebsiella pneumoniae 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;
(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;
Wick, Ryan R;
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Variants of AbGRI3 carrying the armA gene in extensively antibiotic-resistant Acinetobacter baumannii from Singapore.
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Dougan, Gordon;
Dolecek, Christiane;
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Whole Genome Sequence Analysis of Salmonella Typhi Isolated in Thailand before and after the Introduction of a National Immunization Program.
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Watson, Kerri M;
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Holt, Kathryn E;
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Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients.
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Enouf, Vincent;
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Juieng, Phalasy;
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Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain.
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Tarr, Cheryl;
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Fawal, Nizar;
Keddy, Karen H;
Salje, Henrik;
Moore, Sandra;
Mukhopadhyay, Asish K;
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Bercion, Raymond;
Luquero, Francisco J;
Ngandjio, Antoinette;
Dosso, Mireille;
Monakhova, Elena;
Garin, Benoit;
Bouchier, Christiane;
Pazzani, Carlo;
Mutreja, Ankur;
Grunow, Roland;
Sidikou, Fati;
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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;
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Genomic history of the seventh pandemic of cholera in Africa.
Science (New York, NY), 358 (6364).
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Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.
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Completing bacterial genome assemblies with multiplex MinION sequencing.
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South Asia as a Reservoir for the Global Spread of Ciprofloxacin-Resistant Shigella sonnei: A Cross-Sectional Study.
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Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1.
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Okoro, Chinyere;
Baker, Stephen;
Pickard, Derek J;
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Page, Andrew J;
Olanipekun, Grace;
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Fey, Paul D;
Feasey, Nicholas A;
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Le Hello, Simon;
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Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa.
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Kalimuddin, Shirin;
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Differential host susceptibility and bacterial virulence factors driving Klebsiella liver abscess in an ethnically diverse population.
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Russell, Julie E;
Kaftyreva, Lidia;
Accou-Demartin, Marie;
Karas, Andreas;
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Fonkoua, Marie-Christine;
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Herpay, Mária;
Grimont, Patrick AD;
Parkhill, Julian;
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Dongol, Sabina;
Ho Thi, Nhan;
Thompson, Corinne N;
Rabaa, Maia A;
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Holt, Kathryn E;
Wong, Vanessa;
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Voong Vinh, Phat;
Ha Thanh, Tuyen;
Pradhan, Ashish;
Shrestha, Saroj Kumar;
Gajurel, Damoder;
Pickard, Derek;
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A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure.
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Pham Thanh, Duy;
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Chung The, Hao;
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Baker, Stephen;
Holt, Kathryn E;
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Inducible colistin resistance via a disrupted plasmid-borne mcr-1 gene in a 2008 Vietnamese Shigella sonnei isolate.
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Rabaa, Maia A;
Sona, Soeng;
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Kumar, Varun;
Moore, Catrin;
Tran Vu Thieu, Nga;
Wijedoru, Lalith;
Holt, Kathryn E;
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Wong, Vanessa;
Pickard, Derek;
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Day, Nicholas;
Dougan, Gordon;
Turner, Paul;
Parry, Christopher M;
Baker, Stephen;
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The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia.
PLoS neglected tropical diseases, 10 (6).
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Ritchie, Scott C;
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A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets.
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Yang, Ji;
Tauschek, Marija;
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Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, 6 (NOV).
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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;
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Thwaites, Guy;
Thi Khanh Nhu, Nguyen;
Hall, Ruth M;
Fournier-Level, Alexandre;
Baker, Stephen;
Holt, Kathryn E;
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Repeated local emergence of carbapenem-resistant Acinetobacter baumannii in a single hospital ward.
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The, Hao Chung;
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The genomic signatures of Shigella evolution, adaptation and geographical spread.
Nature reviews Microbiology, 14 (4).
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Wong, Vanessa K;
Baker, Stephen;
Connor, Thomas R;
Pickard, Derek;
Page, Andrew J;
Dave, Jayshree;
Murphy, Niamh;
Holliman, Richard;
Sefton, Armine;
Millar, Michael;
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Dyson, Zoe A;
Dougan, Gordon;
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International Typhoid Consortium;
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An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid.
Nature communications, 7 (1).
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Wyres, Kelly L;
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Klebsiella pneumoniae Population Genomics and Antimicrobial-Resistant Clones.
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Wyres, Kelly L;
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Identification of Klebsiella capsule synthesis loci from whole genome data.
Microbial genomics, 2 (12).
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Baines, Sarah L;
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Howden, Brian O;
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Stinear, Timothy P;
Howden, Benjamin P;
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Convergent adaptation in the dominant global hospital clone ST239 of methicillin-resistant Staphylococcus aureus.
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Baltazar, Murielle;
Ngandjio, Antoinette;
Holt, Kathryn Elizabeth;
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Pardos de la Gandara, Maria;
Collard, Jean-Marc;
Bercion, Raymond;
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Fonkoua, Marie-Christine;
Weill, François-Xavier;
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Multidrug-resistant Salmonella enterica serotype Typhi, Gulf of Guinea Region, Africa.
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Chung The, Hao;
Rabaa, Maia A;
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Wangchuk, Sonam;
Dorji, Tshering;
Tshering, Kinzang Pem;
Nguyen, To Nguyen Thi;
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Minh, Chau Nguyen Ngoc;
Turner, Paul;
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Thwaites, Guy;
Holt, Kathryn E;
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Bodhidatta, Ladaporn;
Jeffries Mason, Carl;
Baker, Stephen;
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Introduction and establishment of fluoroquinolone-resistant Shigella sonnei into Bhutan.
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Hamidian, Mohammad;
Hawkey, Jane;
Holt, Kathryn E;
Hall, Ruth M;
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Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1.
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ISSN 2169-8287
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Holt, Kathryn E;
Hamidian, Mohammad;
Kenyon, Johanna J;
Wynn, Matthew T;
Hawkey, Jane;
Pickard, Derek;
Hall, Ruth M;
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Genome Sequence of Acinetobacter baumannii Strain A1, an Early Example of Antibiotic-Resistant Global Clone 1.
Genome announcements, 3 (2).
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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;
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Brisse, Sylvain;
Cao, Hanwei;
Wilksch, Jonathan;
Gorrie, Claire;
Schultz, Mark B;
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Nguyen, Kinh Van;
Nguyen, Trung Vu;
Dao, Trinh Tuyet;
Mensink, Martijn;
Minh, Vien Le;
Nhu, Nguyen Thi Khanh;
Schultsz, Constance;
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Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health.
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Nigro, Steven J;
Holt, Kathryn E;
Pickard, Derek;
Hall, Ruth M;
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Carbapenem and amikacin resistance on a large conjugative Acinetobacter baumannii plasmid.
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Wong, Vanessa K;
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Parkhill, Julian;
Page, Andrew J;
Feasey, Nicholas A;
Kingsley, Robert A;
Thomson, Nicholas R;
Keane, Jacqueline A;
Weill, François-Xavier;
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Edwards, David J;
Hawkey, Jane;
Harris, Simon R;
Mather, Alison E;
Cain, Amy K;
Hadfield, James;
Hart, Peter J;
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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;
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Campbell, James I;
Dongol, Sabina;
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BMJ (Clinical research ed), 346 (mar20).
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Draft Genome Sequences for Ten Salmonella enterica Serovar Typhimurium Phage Type 135 Variants.
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Vu Tra, My Phan;
Campbell, James I;
Hoang, Nguyen Van Minh;
Vinh, Nguyen Thanh;
Minh, Pham Van;
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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;
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Parkhill, Julian;
Dougan, Gordon;
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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).
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Howden, Benjamin P;
Holt, Kathryn E;
Lam, Margaret MC;
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Ballard, Susan;
Coombs, Geoffrey W;
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Genomic insights to control the emergence of vancomycin-resistant enterococci.
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Kay, Sally;
Connor, Thomas;
Barquist, Lars;
Sait, Leanne;
Holt, Kathryn E;
Sivaraman, Karthi;
Wileman, Thomas;
Goulding, David;
Clare, Simon;
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Hale, Christine;
Seshasayee, Aswin;
Harris, Simon;
Thomson, Nicholas R;
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Rabsch, Wolfgang;
Wigley, Paul;
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Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar.
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Pham Thanh, Duy;
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Lodén, Martin;
Tuin, Kiki;
Campbell, James I;
Van Minh Hoang, Nguyen;
Voong Vinh, Phat;
Farrar, Jeremy J;
Holt, Kathryn E;
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Dougan, Gordon;
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Identification of Salmonella enterica serovar Typhi genotypes by use of rapid multiplex ligation-dependent probe amplification.
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Sivaraman, Karthikeyan;
Page, Andrew J;
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Arends, Mark J;
Holt, Kathryn E;
Kane, Leanne;
Mottram, Lynda F;
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Ellison, Louise;
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MacLennan, Calman A;
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Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium.
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Celik, Nermin;
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Heinz, Eva;
Gorrell, Rebecca;
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Naderer, Thomas;
Strugnell, Richard A;
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Teasdale, Rohan D;
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A bioinformatic strategy for the detection, classification and analysis of bacterial autotransporters.
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Doig, Kenneth D;
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Portaels, Françoise;
Yeboah-Manu, Dorothy;
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On the origin of Mycobacterium ulcerans, the causative agent of Buruli ulcer.
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Holt, Kathryn E;
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Holmes, Edward C;
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Yu, Jun;
Sangal, Vartul;
Brown, Derek J;
Coia, John E;
Kim, Dong Wook;
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Choi, Seon Young;
Kim, Su Hee;
da Silveira, Wanderley D;
Pickard, Derek J;
Farrar, Jeremy J;
Parkhill, Julian;
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Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe.
Nature genetics, 44 (9).
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Inouye, Michael;
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Zobel, Justin;
Holt, Kathryn E;
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Short read sequence typing (SRST): multi-locus sequence types from short reads.
BMC GENOMICS, 13 (1).
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Baker, Stephen;
Holt, Kathryn E;
Clements, Archie CA;
Karkey, Abhilasha;
Arjyal, Amit;
Boni, Maciej F;
Dongol, Sabina;
Hammond, Naomi;
Koirala, Samir;
Duy, Pham Thanh;
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Nga, Tran Vu Thieu;
Campbell, James I;
Dolecek, Christiane;
Basnyat, Buddha;
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Farrar, Jeremy J;
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Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission.
Open biology, 1 (2).
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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;
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Hien, Tran Tinh;
Farrar, Jeremy;
Dougan, Gordon;
Baker, Stephen;
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Temporal fluctuation of multidrug resistant salmonella typhi haplotypes in the mekong river delta region of Vietnam.
PLoS neglected tropical diseases, 5 (1).
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Jansen, Angela M;
Hall, Lindsay J;
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Holt, Kathryn E;
Grant, Andrew J;
Mastroeni, Piero;
Dougan, Gordon;
Kingsley, Robert A;
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A Salmonella Typhimurium-Typhi genomic chimera: a model to study Vi polysaccharide capsule function in vivo.
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Baker, Stephen;
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Holt, Kathryn E;
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Navigating the future of bacterial molecular epidemiology.
Current opinion in microbiology, 13 (5).
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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;
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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;
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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).
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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;
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Duy, Pham Thanh;
Day, Jeremy N;
Campbell, James I;
Dougan, Gordon;
Dolecek, Christiane;
Farrar, Jeremy;
Basnyat, Buddha;
Baker, Stephen;
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The burden and characteristics of enteric fever at a healthcare facility in a densely populated area of Kathmandu.
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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;
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Arjyal, Amit;
Koirala, Samir;
Basnyat, Buddha;
Dolecek, Christiane;
Farrar, Jeremy;
Baker, Stephen;
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The sensitivity of real-time PCR amplification targeting invasive Salmonella serovars in biological specimens.
BMC INFECTIOUS DISEASES, 10 (1).
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Song, Yajun;
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Weill, François-Xavier;
Wain, John;
Dolecek, Christiane;
Mazzoni, Camila J;
Holt, Kathryn E;
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A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A.
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Holt, Kathryn E;
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Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.
BIOINFORMATICS, 25 (16).
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Holt, Kathryn E;
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Langridge, Gemma C;
Hasan, Rumina;
Bhutta, Zulfiqar A;
Quail, Michael A;
Norbertczak, Halina;
Walker, Danielle;
Simmonds, Mark;
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White, Brian;
Bason, Nathalie;
Mungall, Karen;
Dougan, Gordon;
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Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi.
BMC GENOMICS, 10 (1).
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Holt, Kathryn E;
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Mazzoni, Camila J;
Roumagnac, Philippe;
Weill, François-Xavier;
Goodhead, Ian;
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Baker, Stephen;
Maskell, Duncan J;
Wain, John;
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High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.
Nature genetics, 40 (8).
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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;
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A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi.
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Holt, Kathryn E;
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ModuleFinder and CoReg: alternative tools for linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants.
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