Items where Author or Contributor is "Holt, KE"
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Number of items: 79.
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.
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 bla KPC-2 and non-Tn4401 Elements (NTEKPC-IId) in High-Risk Lineages of Klebsiella pneumoniae CG258.
Antimicrobial agents and chemotherapy.
ISSN 0066-4804
DOI: https://doi.org/10.1128/aac.02140-18
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
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.
DOI: https://doi.org/10.1099/mgen.0.000269
Holt, Kathryn;
Lassalle, Florent;
Wyres, Kelly;
Wick, Ryan;
Mostowy, Rafał;
(2019)
Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales.
BioRxiv.
https://researchonline.lshtm.ac.uk/id/eprint/4653801
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;
Howden, Benjamin P;
Williamson, Deborah A;
(2019)
Co-circulation of multidrug-resistant Shigella among men who have sex with men, Australia.
Clinical Infectious Diseases.
ISSN 1058-4838
DOI: https://doi.org/10.1093/cid/ciz005
Item availability may be restricted.
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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
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.
ISSN 0305-7453
DOI: https://doi.org/10.1093/jac/dkz028
Méric, Guillaume;
Wick, Ryan;
Watts, Stephen;
Holt, Kathryn;
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;
Judd, Louise M;
Holt, Kathryn E;
(2019)
Performance of neural network basecalling tools for Oxford Nanopore sequencing.
GENOME BIOLOGY, 20 (1).
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).
ISSN 1553-7390
DOI: https://doi.org/10.1371/journal.pgen.1008114
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).
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;
Phan, Vuong Khac Thai;
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).
ISSN 2375-2548
DOI: https://doi.org/10.1126/sciadv.aat5869
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).
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;
Phan, Vuong Khac Thai;
Nguyen, Thuy Thuong Thuong;
Dang, Thi Minh Ha;
Nguyen, Ngoc Lan;
Nguyen, Huu Lan;
Nguyen, Thi Quynh Nhu;
Hoang, Thanh Hai;
Vu, Thi Ngoc Ha;
+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).
849-+.
ISSN 1061-4036
DOI: https://doi.org/10.1038/s41588-018-0117-9
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
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).
ISSN 1198-743X
DOI: https://doi.org/10.1016/j.cmi.2017.06.031
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)
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.35856.001
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
Watts, Stephen C;
Ritchie, Scott C;
Inouye, Michael;
Holt, Kathryn E;
(2018)
FastSpar: Rapid and scalable correlation estimation for compositional data.
Bioinformatics.
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;
Judd, Louise;
Holt, Kathryn;
(2018)
Deepbinner: 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.
The Journal of antimicrobial chemotherapy.
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.
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.
ISSN 0305-7453
DOI: https://doi.org/10.1093/jac/dky472
Wyres, Kelly;
Hawkey, Jane;
Hetland, Marit;
Fostervold, Aasmund;
Wick, Ryan;
Judd, Louise;
Hamidian, Mohammad;
Howden, Benjamin;
Lohr, Iren;
Holt, Kathryn;
(2018)
Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307.
DOI: https://doi.org/10.1101/352740
Wyres, Kelly;
Holt, Kathryn;
(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;
Wick, Ryan;
Judd, Louise;
Froumine, Roni;
Tokolyi, Alex;
Gorrie, Claire;
Lam, Margaret;
Duchene, Sebastian;
Jenney, Adam;
Holt, Kathryn;
(2018)
Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae.
DOI: https://doi.org/10.1101/414235
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
Darton, Thomas C;
Meiring, James E;
Tonks, Susan;
Khan, Md Arifuzzaman;
Khanam, Farhana;
Shakya, Mila;
Thindwa, Deus;
Baker, Stephen;
Basnyat, Buddha;
Clemens, John D;
+10 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;
(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).
ISSN 2044-6055
DOI: https://doi.org/10.1136/bmjopen-2017-016283
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
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.
ISSN 2041-1723
DOI: https://doi.org/10.1038/ncomms15483
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).
ISSN 1553-734X
DOI: https://doi.org/10.1371/journal.pcbi.1005595
Wick, Ryan R;
Judd, Louise M;
Gorrie, Claire L;
Holt, Kathryn E;
(2017)
Completing bacterial genome assemblies with multiplex MinION sequencing.
MICROBIAL GENOMICS, 3 (10).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000132
Wick, Ryan;
Judd, Louise;
Gorrie, Claire;
Holt, Kathryn;
(2017)
Completing bacterial genome assemblies with multiplex MinION sequencing.
DOI: https://doi.org/10.1101/160614
2016
Duchene, Sebastian;
Duchene, 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).
ISSN 1471-2148
DOI: https://doi.org/10.1186/s12862-016-0688-y
Duchene, Sebastian;
Holt, Kathryn E;
Weill, Francois-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).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000094
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
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).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000052
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).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000064
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.
ISSN 2045-2322
DOI: https://doi.org/10.1038/srep29316
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
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).
ISSN 2235-2988
DOI: https://doi.org/10.3389/tcimb.2016.00141
Schultz, Mark B;
Duy, Pham Thanh;
Nhu, Tran Do Hoan;
Wick, Ryan R;
Ingle, Danielle J;
Hawkey, Jane;
Edwards, David J;
Kenyon, Johanna J;
Nguyen, Phu Huong Lan;
Campbell, James I;
+6 more...
Thwaites, Guy;
Nguyen, Thi Khanh Nhu;
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).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000050
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
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).
ISSN 2150-7511
DOI: https://doi.org/10.1128/mBio.00080-15
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, Francois-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
Hamidian, Mohammad;
Hawkey, Jane;
Holt, Kathryn E;
Hall, Ruth M;
(2015)
Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1.
Genome announcements, 3 (6).
ISSN 2169-8287
DOI: https://doi.org/10.1128/genomeA.01478-15
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
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
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
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
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
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).
ISSN 1756-994X
DOI: https://doi.org/10.1186/s13073-014-0090-6
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
Waddington, Claire S;
Darton, Thomas C;
Jones, Claire;
Haworth, Kathryn;
Peters, Anna;
John, Tessa;
Thompson, Ben AV;
Kerridge, Simon A;
Kingsley, Robert A;
Zhou, Liqing;
+9 more...
Holt, Kathryn E;
Yu, Ly-Mee;
Lockhart, Stephen;
Farrar, Jeremy J;
Sztein, Marcelo B;
Dougan, Gordon;
Angus, Brian;
Levine, Myron M;
Pollard, Andrew J;
(2014)
An Outpatient, Ambulant-Design, Controlled Human Infection Model Using Escalating Doses of Salmonella Typhi Challenge Delivered in Sodium Bicarbonate Solution.
CLINICAL INFECTIOUS DISEASES, 58 (9).
pp. 1230-1240.
ISSN 1058-4838
DOI: https://doi.org/10.1093/cid/ciu078
Walker, Michael L;
Holt, Kathryn E;
Anderson, Gary P;
Teo, Shu Mei;
Sly, Peter D;
Holt, Patrick G;
Inouye, Michael;
(2014)
Elucidation of pathways driving asthma pathogenesis: development of a systems-level analytic strategy.
FRONTIERS IN IMMUNOLOGY, 5 (SEP).
pp. 1-16.
ISSN 1664-3224
DOI: https://doi.org/10.3389/fimmu.2014.00447
2013
Comas, Inaki;
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).
1176-U311.
ISSN 1061-4036
DOI: https://doi.org/10.1038/ng.2744
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
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
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).
ISSN 2150-7511
DOI: https://doi.org/10.1128/mBio.00565-13
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).
ISSN 1932-6203
DOI: https://doi.org/10.1371/journal.pone.0084567
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;
Likic, Vladimir A;
Lithgow, Trevor;
(2012)
A Bioinformatic Strategy for the Detection, Classification and Analysis of Bacterial Autotransporters.
PLOS ONE, 7 (8).
ISSN 1932-6203
DOI: https://doi.org/10.1371/journal.pone.0043245
Doig, Kenneth D;
Holt, Kathryn E;
Fyfe, Janet AM;
Lavender, Caroline J;
Eddyani, Miriam;
Portaels, Francoise;
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).
ISSN 1471-2164
DOI: https://doi.org/10.1186/1471-2164-13-258
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).
ISSN 1471-2164
DOI: https://doi.org/10.1186/1471-2164-13-338
2011
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).
ISSN 1553-7366
DOI: https://doi.org/10.1371/journal.ppat.1002131
2010
Karkey, Abhilasha;
Arjyal, Amit;
Anders, Katherine L;
Boni, Maciej F;
Dongol, Sabina;
Koirala, Samir;
Phan, Vu Tra My;
Tran, Vu Thieu Nga;
Clements, Archie CA;
Holt, Kathryn E;
+8 more...
Pham, Thanh Duy;
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).
ISSN 1932-6203
DOI: https://doi.org/10.1371/journal.pone.0013988
Song, Yajun;
Roumagnac, Philippe;
Weill, Francois-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
Tran, Vu Thieu Nga;
Karkey, Abhilasha;
Dongol, Sabina;
Hang, Nguyen Thuy;
Dunstan, Sarah;
Holt, Kathryn;
Le, Thi Phuong Tu;
Campbell, James I;
Tran, Thuy Chau;
Nguyen, Van Vinh Chau;
+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).
ISSN 1471-2334
DOI: https://doi.org/10.1186/1471-2334-10-125
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
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).
ISSN 1471-2164
DOI: https://doi.org/10.1186/1471-2164-10-36
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
2006
Holt, Kathryn E;
Millar, A Harvey;
Whelan, James;
(2006)
ModuleFinder and CoReg: alternative tools for linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants.
PLANT METHODS, 2 (1).
ISSN 1746-4811
DOI: https://doi.org/10.1186/1746-4811-2-8