Items where Author or Contributor is "Holt, Kathryn E"
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Number of items: 174.
2023
Wick, Ryan R;
Judd, Louise M;
Holt, Kathryn E;
(2023)
Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing.
PLOS Computational Biology, 19 (3).
e1010905-.
ISSN 1553-734X
DOI: https://doi.org/10.1371/journal.pcbi.1010905
2022
Azarian, Taj;
Sherry, Norelle L;
Baker, Kate;
Holt, Kathryn E;
Okeke, Iruka N;
(2022)
Making microbial genomics work for clinical and public health microbiology.
Microbial genomics, 8 (9).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000900
Barber, Jake N;
Nicholson, Luke C;
Woods, Laura C;
Judd, Louise M;
Sezmis, Aysha L;
Hawkey, Jane;
Holt, Kathryn E;
McDonald, Michael J;
(2022)
Species interactions constrain adaptation and preserve ecological stability in an experimental microbial community.
The ISME Journal: Multidisciplinary Journal of Microbial Ecology, 16 (5).
pp. 1442-1452.
ISSN 1751-7362
DOI: https://doi.org/10.1038/s41396-022-01191-1
Dyson, Zoe Anne;
Malau, Elisheba;
Horwood, Paul F;
Ford, Rebecca;
Siba, Valentine;
Yoannes, Mition;
Pomat, William;
Passey, Megan;
Judd, Louise M;
Ingle, Danielle J;
+4 more...
Williamson, Deborah A;
Dougan, Gordon;
Greenhill, Andrew R;
Holt, Kathryn E;
(2022)
Whole genome sequence analysis of Salmonella Typhi in Papua New Guinea reveals an established population of genotype 2.1.7 sensitive to antimicrobials.
PLoS Neglected Tropical Diseases, 16 (3).
e0010306-.
ISSN 1935-2727
DOI: https://doi.org/10.1371/journal.pntd.0010306
Gorrie, Claire L;
Mirčeta, Mirjana;
Wick, Ryan R;
Judd, Louise M;
Lam, Margaret MC;
Gomi, Ryota;
Abbott, Iain J;
Thomson, Nicholas R;
Strugnell, Richard A;
Pratt, Nigel F;
+9 more...
Garlick, Jill S;
Watson, Kerrie M;
Hunter, Peter C;
Pilcher, David V;
McGloughlin, Steve A;
Spelman, Denis W;
Wyres, Kelly L;
Jenney, Adam WJ;
Holt, Kathryn E;
(2022)
Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen.
Nature communications, 13 (1).
3017-.
ISSN 2041-1723
DOI: https://doi.org/10.1038/s41467-022-30717-6
Hawkey, Jane;
Cottingham, Hugh;
Tokolyi, Alex;
Wick, Ryan R;
Judd, Louise M;
Cerdeira, Louise;
de Oliveira Garcia, Doroti;
Wyres, Kelly L;
Holt, Kathryn E;
(2022)
Linear plasmids in Klebsiella and other Enterobacteriaceae.
Microbial genomics, 8 (4).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000807
Hawkey, Jane;
Vezina, Ben;
Monk, Jonathan M;
Judd, Louise M;
Harshegyi, Taylor;
López-Fernández, Sebastián;
Rodrigues, Carla;
Brisse, Sylvain;
Holt, Kathryn E;
Wyres, Kelly L;
(2022)
A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality.
Genome research, 32 (5).
pp. 1004-1014.
ISSN 1088-9051
DOI: https://doi.org/10.1101/gr.276289.121
Hawkey, Jane;
Wyres, Kelly L;
Judd, Louise M;
Harshegyi, Taylor;
Blakeway, Luke;
Wick, Ryan R;
Jenney, Adam WJ;
Holt, Kathryn E;
(2022)
ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting.
Genome medicine, 14 (1).
97-.
ISSN 1756-994X
DOI: https://doi.org/10.1186/s13073-022-01103-0
Holt, Kathryn E;
Aanensen, David M;
Achtman, Mark;
(2022)
Genomic population structures of microbial pathogens.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 377 (1861).
20210230-.
ISSN 0962-8436
DOI: https://doi.org/10.1098/rstb.2021.0230
Holt, Kathryn E;
Lassalle, Florent;
Wyres, Kelly L;
Wick, Ryan;
Mostowy, Rafał J;
(2022)
Correction to: Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales.
ISME JOURNAL, 16 (5).
1478-.
ISSN 1751-7362
DOI: https://doi.org/10.1038/s41396-021-01181-9
Lam, Margaret MC;
Wick, Ryan R;
Judd, Louise M;
Holt, Kathryn E;
Wyres, Kelly L;
(2022)
Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex.
Microbial genomics, 8 (3).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000800
Le, Mi Nguyen-Tra;
Kayama, Shizuo;
Wyres, Kelly L;
Yu, Liansheng;
Hisatsune, Junzo;
Suzuki, Masato;
Yahara, Koji;
Terachi, Tsuneko;
Sawa, Kana;
Takahashi, Shin;
+6 more...
Okuhara, Toshihiko;
Kohama, Kunihiko;
Holt, Kathryn E;
Mizutani, Tetsu;
Ohge, Hiroki;
Sugai, Motoyuki;
(2022)
Genomic epidemiology and temperature dependency of hypermucoviscous Klebsiella pneumoniae in Japan.
Microbial genomics, 8 (5).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000827
Lindstedt, Kenneth;
Buczek, Dorota;
Pedersen, Torunn;
Hjerde, Erik;
Raffelsberger, Niclas;
Suzuki, Yutaka;
Brisse, Sylvain;
Holt, Kathryn;
Samuelsen, Ørjan;
Sundsfjord, Arnfinn;
(2022)
Detection of Klebsiella pneumoniae human gut carriage: a comparison of culture, qPCR, and whole metagenomic sequencing methods.
Gut Microbes, 14 (1).
2118500-.
ISSN 1949-0976
DOI: https://doi.org/10.1080/19490976.2022.2118500
Qiu, Shaofu;
Liu, Kangkang;
Yang, Chaojie;
Xiang, Ying;
Min, Kaiyuan;
Zhu, Kunpeng;
Liu, Hongbo;
Du, Xinying;
Yang, Mingjuan;
Wang, Ligui;
+12 more...
Sun, Yong;
Zhou, Haijian;
Mahe, Muti;
Zhao, Jiayong;
Li, Shijun;
Yu, Deshan;
Hawkey, Jane;
Holt, Kathryn E;
Baker, Stephen;
Yang, Juntao;
Xu, Xuebin;
Song, Hongbin;
(2022)
A Shigella sonnei clone with extensive drug resistance associated with waterborne outbreaks in China.
Nature communications, 13 (1).
p. 7365.
ISSN 2041-1723
DOI: https://doi.org/10.1038/s41467-022-35136-1
Stewart, James;
Judd, Louise M;
Jenney, Adam;
Holt, Kathryn E;
Wyres, Kelly L;
Hawkey, Jane;
(2022)
Epidemiology and genomic analysis of Klebsiella oxytoca from a single hospital network in Australia.
BMC Infectious Diseases, 22 (1).
704-.
ISSN 1471-2334
DOI: https://doi.org/10.1186/s12879-022-07687-7
Vezina, Ben;
Judd, Louise M;
McDougall, Fiona K;
Boardman, Wayne SJ;
Power, Michelle L;
Hawkey, Jane;
Brisse, Sylvain;
Monk, Jonathan M;
Holt, Kathryn E;
Wyres, Kelly L;
(2022)
Transmission of Klebsiella strains and plasmids within and between grey-headed flying fox colonies.
Environmental microbiology, 24 (9).
pp. 4425-4436.
ISSN 1462-2912
DOI: https://doi.org/10.1111/1462-2920.16047
Wick, Ryan R;
Holt, Kathryn E;
(2022)
Polypolish: Short-read polishing of long-read bacterial genome assemblies.
PLoS computational biology, 18 (1).
e1009802-.
ISSN 1553-734X
DOI: https://doi.org/10.1371/journal.pcbi.1009802
2021
Argimón, Silvia;
David, Sophia;
Underwood, Anthony;
Abrudan, Monica;
Wheeler, Nicole E;
Kekre, Mihir;
Abudahab, Khalil;
Yeats, Corin A;
Goater, Richard;
Taylor, Ben;
+11 more...
Harste, Harry;
Muddyman, Dawn;
Feil, Edward J;
Brisse, Sylvain;
Holt, Kathryn;
Donado-Godoy, Pilar;
Ravikumar, KL;
Okeke, Iruka N;
Carlos, Celia;
Aanensen, David M;
NIHR Global Health Research Unit on Genomic Surveillance of Anti;
NIHR Global Health Research Unit on Genomic Surveillance;
(2021)
Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 73 (Suppl_).
S325-S335.
ISSN 1058-4838
DOI: https://doi.org/10.1093/cid/ciab784
Argimón, Silvia;
Yeats, Corin A;
Goater, Richard J;
Abudahab, Khalil;
Taylor, Benjamin;
Underwood, Anthony;
Sánchez-Busó, Leonor;
Wong, Vanessa K;
Dyson, Zoe A;
Nair, Satheesh;
+8 more...
Park, Se Eun;
Marks, Florian;
Page, Andrew J;
Keane, Jacqueline A;
Baker, Stephen;
Holt, Kathryn E;
Dougan, Gordon;
Aanensen, David M;
(2021)
A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch.
Nature communications, 12 (1).
2879-.
ISSN 2041-1723
DOI: https://doi.org/10.1038/s41467-021-23091-2
Dainty, Kimberley R;
Hawkey, Jane;
Judd, Louise M;
Pacidônio, Etiene C;
Duyvestyn, Johanna M;
Gonçalves, Daniela S;
Lin, Silk Yu;
O'Donnell, Tanya B;
O'Neill, Scott L;
Simmons, Cameron P;
+2 more...
Holt, Kathryn E;
Flores, Heather A;
(2021)
wMel Wolbachia genome remains stable after 7 years in Australian Aedes aegypti field populations.
Microbial genomics, 7 (9).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000641
Dyson, Zoe A;
Holt, Kathryn E;
(2021)
Five Years of GenoTyphi: Updates to the Global Salmonella Typhi Genotyping Framework.
JOURNAL OF INFECTIOUS DISEASES, 224 (12 Sup).
S775-S780.
ISSN 0022-1899
DOI: https://doi.org/10.1093/infdis/jiab414
Edwards, David J;
Duchene, Sebastián;
Pope, Bernard;
Holt, Kathryn E;
(2021)
SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments.
Microbial genomics, 7 (12).
DOI: https://doi.org/10.1099/mgen.0.000694
Fostervold, Aasmund;
Hetland, Marit AK;
Bakksjø, Ragna;
Bernhoff, Eva;
Holt, Kathryn E;
Samuelsen, Ørjan;
Simonsen, Gunnar Skov;
Sundsfjord, Arnfinn;
Wyres, Kelly L;
Löhr, Iren Høyland;
+1 more...
Norwegian Study Group on Klebsiella pneumoniae;
Norwegian Study Group on Klebsiella pneumoniae;
(2021)
A nationwide genomic study of clinical Klebsiella pneumoniae in Norway 2001-15: introduction and spread of ESBLs facilitated by clonal groups CG15 and CG307.
The Journal of antimicrobial chemotherapy, 77 (3).
pp. 665-674.
ISSN 0305-7453
DOI: https://doi.org/10.1093/jac/dkab463
Gomi, Ryota;
Wyres, Kelly L;
Holt, Kathryn E;
(2021)
Detection of plasmid contigs in draft genome assemblies using customized Kraken databases.
Microbial genomics, 7 (4).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000550
Hawkey, Jane;
Paranagama, Kalani;
Baker, Kate S;
Bengtsson, Rebecca J;
Weill, François-Xavier;
Thomson, Nicholas R;
Baker, Stephen;
Cerdeira, Louise;
Iqbal, Zamin;
Hunt, Martin;
+5 more...
Ingle, Danielle J;
Dallman, Timothy J;
Jenkins, Claire;
Williamson, Deborah A;
Holt, Kathryn E;
(2021)
Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei.
Nature communications, 12 (1).
2684-.
ISSN 2041-1723
DOI: https://doi.org/10.1038/s41467-021-22700-4
Heinz, Eva;
Holt, Kathryn E;
Meehan, Conor J;
Sheppard, Samuel K;
(2021)
Addressing parachute research and removing barriers for LMIC researchers in Microbial Genomics.
Microbial genomics, 7 (10).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000722
Jokanovic, Natali;
Haines, Terry;
Cheng, Allen C;
Holt, Kathryn E;
Hilmer, Sarah N;
Jeon, Yun-Hee;
Stewardson, Andrew J;
Stuart, Rhonda L;
Spelman, Tim;
Peel, Trisha N;
+2 more...
Peleg, Anton Y;
START Trial Group;
START Trial Group;
(2021)
Multicentre stepped-wedge cluster randomised controlled trial of an antimicrobial stewardship programme in residential aged care: protocol for the START trial.
BMJ open, 11 (3).
e046142-.
ISSN 2044-6055
DOI: https://doi.org/10.1136/bmjopen-2020-046142
Kariuki, Samuel;
Dyson, Zoe A;
Mbae, Cecilia;
Ngetich, Ronald;
Kavai, Susan M;
Wairimu, Celestine;
Anyona, Stephen;
Gitau, Naomi;
Onsare, Robert Sanaya;
Ongandi, Beatrice;
+5 more...
Duchene, Sebastian;
Ali, Mohamed;
Clemens, John David;
Holt, Kathryn E;
Dougan, Gordon;
(2021)
Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya.
eLife, 10.
ISSN 2050-084X
DOI: https://doi.org/10.7554/eLife.67852
Khoury, Muin J;
Holt, Kathryn E;
(2021)
The impact of genomics on precision public health: beyond the pandemic.
Genome medicine, 13 (1).
67-.
ISSN 1756-994X
DOI: https://doi.org/10.1186/s13073-021-00886-y
Lam, Margaret MC;
Wick, Ryan R;
Watts, Stephen C;
Cerdeira, Louise T;
Wyres, Kelly L;
Holt, Kathryn E;
(2021)
A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex.
Nature communications, 12 (1).
4188-.
ISSN 2041-1723
DOI: https://doi.org/10.1038/s41467-021-24448-3
Lee, V Vern;
Judd, Louise M;
Jex, Aaron R;
Holt, Kathryn E;
Tonkin, Christopher J;
Ralph, Stuart A;
(2021)
Direct Nanopore Sequencing of mRNA Reveals Landscape of Transcript Isoforms in Apicomplexan Parasites.
mSystems, 6 (2).
e01081-e01020.
ISSN 2379-5077
DOI: https://doi.org/10.1128/mSystems.01081-20
Lin, Heyu;
Ascher, David B;
Myung, Yoochan;
Lamborg, Carl H;
Hallam, Steven J;
Gionfriddo, Caitlin M;
Holt, Kathryn E;
Moreau, John W;
(2021)
Mercury methylation by metabolically versatile and cosmopolitan marine bacteria.
The ISME journal, 15 (6).
pp. 1810-1825.
ISSN 1751-7362
DOI: https://doi.org/10.1038/s41396-020-00889-4
Macleod, CK;
Khokhar, FA;
Warne, B;
Wick, R;
Butcher, R;
Cassimon, B;
Hayden, P;
Holt, K;
Török, ME;
(2021)
Rapid Whole Genome Sequencing of Serotype K1 Hypervirulent Klebsiella pneumoniae from an Undocumented Chinese Migrant.
Case reports in infectious diseases, 2021.
6638780-.
ISSN 2090-6625
DOI: https://doi.org/10.1155/2021/6638780
![[img]](/style/images/fileicons/text.png)
Meiring, James E;
Shakya, Mila;
Khanam, Farhana;
Voysey, Merryn;
Phillips, Maile T;
Tonks, Susan;
Thindwa, Deus;
Darton, Thomas C;
Dongol, Sabina;
Karkey, Abilasha;
+14 more...
Zaman, K;
Baker, Stephen;
Dolecek, Christiane;
Dunstan, Sarah J;
Dougan, Gordon;
Holt, Kathryn E;
Heyderman, Robert S;
Qadri, Firdausi;
Pitzer, Virginia E;
Basnyat, Buddha;
Gordon, Melita A;
Clemens, John;
Pollard, Andrew J;
STRATAA Study Group;
STRATAA Study Group;
(2021)
Burden of enteric fever at three urban sites in Africa and Asia: a multicentre population-based study.
The Lancet. Global health, 9 (12).
e1688-e1696.
ISSN 2214-109X
DOI: https://doi.org/10.1016/S2214-109X(21)00370-3
Phillips, Maile T;
Meiring, James E;
Voysey, Merryn;
Warren, Joshua L;
Baker, Stephen;
Basnyat, Buddha;
Clemens, John D;
Dolecek, Christiane;
Dunstan, Sarah J;
Dougan, Gordon;
+8 more...
Gordon, Melita A;
Thindwa, Deus;
Heyderman, Robert S;
Holt, Kathryn E;
Qadri, Firdausi;
Pollard, Andrew J;
Pitzer, Virginia E;
STRATAA Study Group;
(2021)
A Bayesian approach for estimating typhoid fever incidence from large-scale facility-based passive surveillance data.
Statistics in medicine, 40 (26).
pp. 5853-5870.
ISSN 0277-6715
DOI: https://doi.org/10.1002/sim.9159
Raffelsberger, Niclas;
Hetland, Marit Andrea Klokkhammer;
Svendsen, Kristian;
Småbrekke, Lars;
Löhr, Iren Høyland;
Andreassen, Lotte Leonore Eivindsdatter;
Brisse, Sylvain;
Holt, Kathryn E;
Sundsfjord, Arnfinn;
Samuelsen, Ørjan;
+1 more...
Gravningen, Kirsten;
(2021)
Gastrointestinal carriage of Klebsiella pneumoniae in a general adult population: a cross-sectional study of risk factors and bacterial genomic diversity.
Gut microbes, 13 (1).
1939599-.
ISSN 1949-0976
DOI: https://doi.org/10.1080/19490976.2021.1939599
Viehweger, Adrian;
Blumenscheit, Christian;
Lippmann, Norman;
Wyres, Kelly L;
Brandt, Christian;
Hans, Jörg B;
Hölzer, Martin;
Irber, Luiz;
Gatermann, Sören;
Lübbert, Christoph;
+3 more...
Pletz, Mathias W;
Holt, Kathryn E;
König, Brigitte;
(2021)
Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae.
Microbial genomics, 7 (12).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000741
Watts, Stephen C;
Judd, Louise M;
Carzino, Rosemary;
Ranganathan, Sarath;
Holt, Kathryn E;
(2021)
Genomic Diversity and Antimicrobial Resistance of Haemophilus Colonizing the Airways of Young Children with Cystic Fibrosis.
mSystems, 6 (4).
e0017821-.
ISSN 2379-5077
DOI: https://doi.org/10.1128/mSystems.00178-21
Wick, Ryan R;
Judd, Louise M;
Cerdeira, Louise T;
Hawkey, Jane;
Méric, Guillaume;
Vezina, Ben;
Wyres, Kelly L;
Holt, Kathryn E;
(2021)
Trycycler: consensus long-read assemblies for bacterial genomes.
Genome biology, 22 (1).
266-.
ISSN 1474-7596
DOI: https://doi.org/10.1186/s13059-021-02483-z
Wick, Ryan R;
Judd, Louise M;
Wyres, Kelly L;
Holt, Kathryn E;
(2021)
Recovery of small plasmid sequences via Oxford Nanopore sequencing.
Microbial genomics, 7 (8).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000631
Item availability may be restricted.
Wyres, Kelly L;
Hawkey, Jane;
Mirčeta, Mirianne;
Judd, Louise M;
Wick, Ryan R;
Gorrie, Claire L;
Pratt, Nigel F;
Garlick, Jill S;
Watson, Kerrie M;
Pilcher, David V;
+6 more...
McGloughlin, Steve A;
Abbott, Iain J;
Macesic, Nenad;
Spelman, Denis W;
Jenney, Adam WJ;
Holt, Kathryn E;
(2021)
Genomic surveillance of antimicrobial resistant bacterial colonisation and infection in intensive care patients.
BMC infectious diseases, 21 (1).
683-.
ISSN 1471-2334
DOI: https://doi.org/10.1186/s12879-021-06386-z
2020
Berríos-Pastén, Camilo;
Acevedo, Rodolfo;
Arros, Patricio;
Varas, Macarena A;
Wyres, Kelly L;
Lam, Margaret MC;
Holt, Kathryn E;
Lagos, Rosalba;
Marcoleta, Andrés E;
(2020)
Properties of genes encoding transfer RNAs as integration sites for genomic islands and prophages in <i>Klebsiella pneumoniae</i>.
bioRxiv preprint.
DOI: https://doi.org/10.1101/2020.11.02.365908
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
Edwards, David J;
Duchêne, Sebastián;
Pope, Bernard;
Holt, Kathryn E;
(2020)
SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments.
bioRxiv preprint.
DOI: https://doi.org/10.1101/2020.07.08.194480
Hawkey, Jane;
Monk, Jonathan M;
Billman-Jacobe, Helen;
Palsson, Bernhard;
Holt, Kathryn E;
(2020)
Impact of insertion sequences on convergent evolution of Shigella species.
PLOS GENETICS, 16 (7).
e1008931-.
ISSN 1553-7404
DOI: https://doi.org/10.1371/journal.pgen.1008931
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
Huang, Qin Qin;
Tang, Howard HF;
Teo, Shu Mei;
Mok, Danny;
Ritchie, Scott C;
Nath, Artika P;
Brozynska, Marta;
Salim, Agus;
Bakshi, Andrew;
Holt, Barbara J;
+5 more...
Khor, Chiea Chuen;
Sly, Peter D;
Holt, Patrick G;
Holt, Kathryn E;
Inouye, Michael;
(2020)
Neonatal genetics of gene expression reveal potential origins of autoimmune and allergic disease risk.
NATURE COMMUNICATIONS, 11 (1).
3761-.
ISSN 2041-1723
DOI: https://doi.org/10.1038/s41467-020-17477-x
Im, Justin;
Islam, Md Taufiqul;
Kim, Deok Ryun;
Ahmmed, Faisal;
Chon, Yun;
Zaman, K;
Khan, Ashraful Islam;
Ali, Mohammad;
Sur, Dipika;
Kanungo, Suman;
+8 more...
Dutta, Shanta;
Bhattacharya, Sujit K;
Dougan, Gordon;
Holt, Kathryn E;
Marks, Florian;
Kim, Jerome H;
Qadri, Firdausi;
Clemens, John D;
(2020)
Protection conferred by typhoid fever against recurrent typhoid fever in urban Kolkata.
PLOS NEGLECTED TROPICAL DISEASES, 14 (8).
e0008530-.
ISSN 1935-2735
DOI: https://doi.org/10.1371/journal.pntd.0008530
Item availability may be restricted.
Okomo, Uduak;
Senghore, Madikay;
Darboe, Saffiatou;
Bojang, Ebrima;
Zaman, Syed MA;
Hossain, Mohammad Jahangir;
Nwakanma, Davis;
Le Doare, Kirsty;
Holt, Kathryn E;
Hos, Nina Judith;
+3 more...
Lawn, Joy E;
Bentley, Stephen D;
Kampmann, Beate;
(2020)
Investigation of sequential outbreaks of Burkholderia cepacia and multidrug-resistant extended spectrum β-lactamase producing Klebsiella species in a West African tertiary hospital neonatal unit: a retrospective genomic analysis.
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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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Wong, Vanessa K;
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Page, Andrew J;
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Dyson, Zoe A;
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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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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;
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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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Act now against new NHS competition regulations: an open letter to the BMA and the Academy of Medical Royal Colleges calls on them to make a joint public statement of opposition to the amended section 75 regulations.
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Vu Tra, My Phan;
Campbell, James I;
Hoang, Nguyen Van Minh;
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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;
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Ai, Nguyen Thi Thuy;
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Dong, Nguyen;
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Howden, Benjamin P;
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Lam, Margaret MC;
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Genomic insights to control the emergence of vancomycin-resistant enterococci.
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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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Lodén, Martin;
Tuin, Kiki;
Campbell, James I;
Van Minh Hoang, Nguyen;
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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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Kane, Leanne;
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Ellison, Louise;
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Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium.
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On the origin of Mycobacterium ulcerans, the causative agent of Buruli ulcer.
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Choi, Seon Young;
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Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe.
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Short read sequence typing (SRST): multi-locus sequence types from short reads.
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Nga, Tran Vu Thieu;
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Hoang, Nguyen Van Minh;
Nga, Tran Vu Thieu;
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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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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
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).
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