Items where Author or Contributor is "Holt, Kathryn E"
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Number of items: 123.
2020
Britto, Carl D;
Dyson, Zoe A;
Mathias, Sitarah;
Bosco, Ashish;
Dougan, Gordon;
Jose, Sanju;
Nagaraj, Savitha;
Holt, Kathryn E;
Pollard, Andrew J;
(2020)
Persistent circulation of a fluoroquinolone-resistant Salmonella enterica Typhi clone in the Indian subcontinent.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 75 (2).
pp. 337-341.
ISSN 0305-7453
DOI: https://doi.org/10.1093/jac/dkz435
Holt, Kathryn E;
Lassalle, Florent;
Wyres, Kelly L;
Wick, Ryan;
Mostowy, Rafał J;
(2020)
Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales.
ISME JOURNAL, 14 (7).
pp. 1713-1730.
ISSN 1751-7362
DOI: https://doi.org/10.1038/s41396-020-0628-0
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
Torraca, Vincenzo;
Holt, Kathryn;
Mostowy, Serge;
(2020)
Shigella sonnei.
Trends in Microbiology, 28 (8).
pp. 696-697.
ISSN 0966-842X
DOI: https://doi.org/10.1016/j.tim.2020.02.011
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
Zhou, Kai;
Xiao, Tingting;
David, Sophia;
Wang, Qin;
Zhou, Yanzi;
Guo, Lihua;
Aanensen, David;
Holt, Kathryn E;
Thomson, Nicholas R;
Grundmann, Hajo;
+2 more...
Shen, Ping;
Xiao, Yonghong;
(2020)
Novel Subclone of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 with Enhanced Virulence and Transmissibility, China.
EMERGING INFECTIOUS DISEASES, 26 (2).
pp. 289-297.
ISSN 1080-6040
DOI: https://doi.org/10.3201/eid2602.190594
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).
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.21782.3
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;
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Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.
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Pradhan, Ashish;
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The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia.
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A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets.
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Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?
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Schultz, Mark B;
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Hawkey, Jane;
Edwards, David J;
Kenyon, Johanna J;
Phu Huong Lan, Nguyen;
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Thwaites, Guy;
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Baker, Stephen;
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Wong, Vanessa K;
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Connor, Thomas R;
Pickard, Derek;
Page, Andrew J;
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Holliman, Richard;
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Dyson, Zoe A;
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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.
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Klebsiella pneumoniae Population Genomics and Antimicrobial-Resistant Clones.
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Identification of Klebsiella capsule synthesis loci from whole genome data.
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Convergent adaptation in the dominant global hospital clone ST239 of methicillin-resistant Staphylococcus aureus.
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Fonkoua, Marie-Christine;
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Minh, Chau Nguyen Ngoc;
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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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Holt, Kathryn E;
Hamidian, Mohammad;
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Hawkey, Jane;
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Genome Sequence of Acinetobacter baumannii Strain A1, an Early Example of Antibiotic-Resistant Global Clone 1.
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Holt, Kathryn E;
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Brisse, Sylvain;
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Nigro, Steven J;
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Howden, Benjamin P;
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Wileman, Thomas;
Goulding, David;
Clare, Simon;
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Hale, Christine;
Seshasayee, Aswin;
Harris, Simon;
Thomson, Nicholas R;
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Lodén, Martin;
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Campbell, James I;
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Farrar, Jeremy J;
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Dougan, Gordon;
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Sivaraman, Karthikeyan;
Page, Andrew J;
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Holt, Kathryn E;
Kane, Leanne;
Mottram, Lynda F;
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Short read sequence typing (SRST): multi-locus sequence types from short reads.
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Hoang, Nguyen Van Minh;
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Temporal fluctuation of multidrug resistant salmonella typhi haplotypes in the mekong river delta region of Vietnam.
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Karkey, Abhilasha;
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Dongol, Sabina;
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My, Phan Vu Tra;
Nga, Tran Vu Thieu;
Clements, Archie CA;
Holt, Kathryn E;
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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
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
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).
8-.
ISSN 1746-4811
DOI: https://doi.org/10.1186/1746-4811-2-8