Items where Author or Contributor is "Holt, Kathryn E"
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Number of items: 167.
2022
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
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
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.
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).
p. 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).
p. 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;
+1 more...
Peleg, Anton Y;
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).
p. 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;
+13 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;
(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).
p. 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).
p. 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).
p. 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.
The Lancet Microbe, 1 (3).
e119-e129.
ISSN 2666-5247
DOI: https://doi.org/10.1016/S2666-5247(20)30061-6
Rahman, Sadia Isfat Ara;
Dyson, Zoe A;
Klemm, Elizabeth J;
Khanam, Farhana;
Holt, Kathryn E;
Chowdhury, Emran Kabir;
Dougan, Gordon;
Qadri, Firdausi;
(2020)
Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016.
PLOS NEGLECTED TROPICAL DISEASES, 14 (2).
e0008036.
ISSN 1935-2735
DOI: https://doi.org/10.1371/journal.pntd.0008036
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
Wan, Yu;
Wick, Ryan R;
Zobel, Justin;
Ingle, Danielle J;
Inouye, Michael;
Holt, Kathryn E;
(2020)
GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure.
BMC GENOMICS, 21 (1).
p. 658.
ISSN 1471-2164
DOI: https://doi.org/10.1186/s12864-020-07019-6
Wan, Yu;
Wick, Ryan R;
Zobel, Justin;
Ingle, Danielle J;
Inouye, Michael;
Holt, Kathryn E;
(2020)
GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene Associations Controlled for Population Structure.
bioRxiv preprint.
DOI: https://doi.org/10.1101/2020.02.29.970970
Wyres, Kelly L;
Cahill, Sarah M;
Holt, Kathryn E;
Hall, Ruth M;
Kenyon, Johanna J;
(2020)
Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive.
MICROBIAL GENOMICS, 6 (3).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000339
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 bla KPC-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.21782.4
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.
e35856-.
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;
Judd, Louise M;
Froumine, Roni;
Tokolyi, Alex;
Gorrie, Claire L;
Lam, Margaret MC;
Duchêne, Sebastián;
Jenney, Adam;
Holt, Kathryn E;
(2018)
Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of<i>Klebsiella pneumoniae</i>.
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;
+11 more...
Dougan, Gordon;
Dolecek, Christiane;
Dunstan, Sarah J;
Gordon, Melita A;
Heyderman, Robert S;
Holt, Kathryn E;
Pitzer, Virginia E;
Qadri, Firdausi;
Zaman, K;
Pollard, Andrew J;
STRATAA Study Consortium;
(2017)
The STRATAA study protocol: a programme to assess the burden of enteric fever in Bangladesh, Malawi and Nepal using prospective population census, passive surveillance, serological studies and healthcare utilisation surveys.
BMJ OPEN, 7 (6).
e016283-.
ISSN 2044-6055
DOI: https://doi.org/10.1136/bmjopen-2017-016283
Dyson, Zoe A;
Thanh, Duy Pham;
Bodhidatta, Ladaporn;
Mason, Carl Jeffries;
Srijan, Apichai;
Rabaa, Maia A;
Vinh, Phat Voong;
Thanh, Tuyen Ha;
Thwaites, Guy E;
Baker, Stephen;
+1 more...
Holt, Kathryn E;
(2017)
Whole Genome Sequence Analysis of Salmonella Typhi Isolated in Thailand before and after the Introduction of a National Immunization Program.
PLoS neglected tropical diseases, 11 (1).
e0005274-.
ISSN 1935-2727
DOI: https://doi.org/10.1371/journal.pntd.0005274
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 (1).
15483-.
ISSN 2041-1723
DOI: https://doi.org/10.1038/ncomms15483
Weill, François-Xavier;
Domman, Daryl;
Njamkepo, Elisabeth;
Tarr, Cheryl;
Rauzier, Jean;
Fawal, Nizar;
Keddy, Karen H;
Salje, Henrik;
Moore, Sandra;
Mukhopadhyay, Asish K;
+31 more...
Bercion, Raymond;
Luquero, Francisco J;
Ngandjio, Antoinette;
Dosso, Mireille;
Monakhova, Elena;
Garin, Benoit;
Bouchier, Christiane;
Pazzani, Carlo;
Mutreja, Ankur;
Grunow, Roland;
Sidikou, Fati;
Bonte, Laurence;
Breurec, Sébastien;
Damian, Maria;
Njanpop-Lafourcade, Berthe-Marie;
Sapriel, Guillaume;
Page, Anne-Laure;
Hamze, Monzer;
Henkens, Myriam;
Chowdhury, Goutam;
Mengel, Martin;
Koeck, Jean-Louis;
Fournier, Jean-Michel;
Dougan, Gordon;
Grimont, Patrick AD;
Parkhill, Julian;
Holt, Kathryn E;
Piarroux, Renaud;
Ramamurthy, Thandavarayan;
Quilici, Marie-Laure;
Thomson, Nicholas R;
(2017)
Genomic history of the seventh pandemic of cholera in Africa.
Science (New York, NY), 358 (6364).
pp. 785-789.
ISSN 0036-8075
DOI: https://doi.org/10.1126/science.aad5901
Full text not available from this repository.
Wick, Ryan R;
Judd, Louise M;
Gorrie, Claire L;
Holt, Kathryn E;
(2017)
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.
PLOS COMPUTATIONAL BIOLOGY, 13 (6).
e1005595-.
ISSN 1553-734X
DOI: https://doi.org/10.1371/journal.pcbi.1005595
Wick, Ryan R;
Judd, Louise M;
Gorrie, Claire L;
Holt, Kathryn E;
(2017)
Completing bacterial genome assemblies with multiplex MinION sequencing.
DOI: https://doi.org/10.1101/160614
Wick, Ryan R;
Judd, Louise M;
Gorrie, Claire L;
Holt, Kathryn E;
(2017)
Completing bacterial genome assemblies with multiplex MinION sequencing.
MICROBIAL GENOMICS, 3 (10).
e000132-.
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000132
2016
Chung The, Hao;
Rabaa, Maia A;
Pham Thanh, Duy;
De Lappe, Niall;
Cormican, Martin;
Valcanis, Mary;
Howden, Benjamin P;
Wangchuk, Sonam;
Bodhidatta, Ladaporn;
Mason, Carl J;
+12 more...
Nguyen Thi Nguyen, To;
Vu Thuy, Duong;
Thompson, Corinne N;
Phu Huong Lan, Nguyen;
Voong Vinh, Phat;
Ha Thanh, Tuyen;
Turner, Paul;
Sar, Poda;
Thwaites, Guy;
Thomson, Nicholas R;
Holt, Kathryn E;
Baker, Stephen;
(2016)
South Asia as a Reservoir for the Global Spread of Ciprofloxacin-Resistant Shigella sonnei: A Cross-Sectional Study.
PLoS medicine, 13 (8).
e1002055-.
ISSN 1549-1277
DOI: https://doi.org/10.1371/journal.pmed.1002055
Duchêne, Sebastian;
Holt, Kathryn E;
Weill, François-Xavier;
Le Hello, Simon;
Hawkey, Jane;
Edwards, David J;
Fourment, Mathieu;
Holmes, Edward C;
(2016)
Genome-scale rates of evolutionary change in bacteria.
MICROBIAL GENOMICS, 2 (11).
e000094-.
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000094
Duchêne, Sebastián;
Duchêne, David A;
Di Giallonardo, Francesca;
Eden, John-Sebastian;
Geoghegan, Jemma L;
Holt, Kathryn E;
Ho, Simon YW;
Holmes, Edward C;
(2016)
Cross-validation to select Bayesian hierarchical models in phylogenetics.
BMC EVOLUTIONARY BIOLOGY, 16 (1).
115-.
ISSN 1471-2148
DOI: https://doi.org/10.1186/s12862-016-0688-y
Follador, Rainer;
Heinz, Eva;
Wyres, Kelly L;
Ellington, Matthew J;
Kowarik, Michael;
Holt, Kathryn E;
Thomson, Nicholas R;
(2016)
The diversity of Klebsiella pneumoniae surface polysaccharides.
Microbial genomics, 2 (8).
e000073-.
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000073
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).
e000052-.
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).
e000064-.
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000064
International Typhoid Consortium;
Wong, Vanessa K;
Holt, Kathryn E;
Okoro, Chinyere;
Baker, Stephen;
Pickard, Derek J;
Marks, Florian;
Page, Andrew J;
Olanipekun, Grace;
Munir, Huda;
+22 more...
Alter, Roxanne;
Fey, Paul D;
Feasey, Nicholas A;
Weill, Francois-Xavier;
Le Hello, Simon;
Hart, Peter J;
Kariuki, Samuel;
Breiman, Robert F;
Gordon, Melita A;
Heyderman, Robert S;
Jacobs, Jan;
Lunguya, Octavie;
Msefula, Chisomo;
MacLennan, Calman A;
Keddy, Karen H;
Smith, Anthony M;
Onsare, Robert S;
De Pinna, Elizabeth;
Nair, Satheesh;
Amos, Ben;
Dougan, Gordon;
Obaro, Stephen;
(2016)
Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa.
PLoS neglected tropical diseases, 10 (9).
e0004781-.
ISSN 1935-2727
DOI: https://doi.org/10.1371/journal.pntd.0004781
Lee, I Russel;
Molton, James S;
Wyres, Kelly L;
Gorrie, Claire;
Wong, Jocelyn;
Hoh, Chu Han;
Teo, Jeanette;
Kalimuddin, Shirin;
Lye, David C;
Archuleta, Sophia;
+2 more...
Holt, Kathryn E;
Gan, Yunn-Hwen;
(2016)
Differential host susceptibility and bacterial virulence factors driving Klebsiella liver abscess in an ethnically diverse population.
SCIENTIFIC REPORTS, 6 (1).
29316-.
ISSN 2045-2322
DOI: https://doi.org/10.1038/srep29316
Njamkepo, Elisabeth;
Fawal, Nizar;
Tran-Dien, Alicia;
Hawkey, Jane;
Strockbine, Nancy;
Jenkins, Claire;
Talukder, Kaisar A;
Bercion, Raymond;
Kuleshov, Konstantin;
Kolínská, Renáta;
+62 more...
Russell, Julie E;
Kaftyreva, Lidia;
Accou-Demartin, Marie;
Karas, Andreas;
Vandenberg, Olivier;
Mather, Alison E;
Mason, Carl J;
Page, Andrew J;
Ramamurthy, Thandavarayan;
Bizet, Chantal;
Gamian, Andrzej;
Carle, Isabelle;
Sow, Amy Gassama;
Bouchier, Christiane;
Wester, Astrid Louise;
Lejay-Collin, Monique;
Fonkoua, Marie-Christine;
Le Hello, Simon;
Blaser, Martin J;
Jernberg, Cecilia;
Ruckly, Corinne;
Mérens, Audrey;
Page, Anne-Laure;
Aslett, Martin;
Roggentin, Peter;
Fruth, Angelika;
Denamur, Erick;
Venkatesan, Malabi;
Bercovier, Hervé;
Bodhidatta, Ladaporn;
Chiou, Chien-Shun;
Clermont, Dominique;
Colonna, Bianca;
Egorova, Svetlana;
Pazhani, Gururaja P;
Ezernitchi, Analia V;
Guigon, Ghislaine;
Harris, Simon R;
Izumiya, Hidemasa;
Korzeniowska-Kowal, Agnieszka;
Lutyńska, Anna;
Gouali, Malika;
Grimont, Francine;
Langendorf, Céline;
Marejková, Monika;
Peterson, Lorea AM;
Perez-Perez, Guillermo;
Ngandjio, Antoinette;
Podkolzin, Alexander;
Souche, Erika;
Makarova, Mariia;
Shipulin, German A;
Ye, Changyun;
Žemličková, Helena;
Herpay, Mária;
Grimont, Patrick AD;
Parkhill, Julian;
Sansonetti, Philippe;
Holt, Kathryn E;
Brisse, Sylvain;
Thomson, Nicholas R;
Weill, François-Xavier;
(2016)
Global phylogeography and evolutionary history of Shigella dysenteriae type 1.
Nature microbiology, 1 (4).
16027-.
ISSN 2058-5276
DOI: https://doi.org/10.1038/nmicrobiol.2016.27
Full text not available from this repository.
Pham Thanh, Duy;
Karkey, Abhilasha;
Dongol, Sabina;
Ho Thi, Nhan;
Thompson, Corinne N;
Rabaa, Maia A;
Arjyal, Amit;
Holt, Kathryn E;
Wong, Vanessa;
Tran Vu Thieu, Nga;
+13 more...
Voong Vinh, Phat;
Ha Thanh, Tuyen;
Pradhan, Ashish;
Shrestha, Saroj Kumar;
Gajurel, Damoder;
Pickard, Derek;
Parry, Christopher M;
Dougan, Gordon;
Wolbers, Marcel;
Dolecek, Christiane;
Thwaites, Guy E;
Basnyat, Buddha;
Baker, Stephen;
(2016)
A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure.
eLife, 5 (MARCH2).
e14003-.
ISSN 2050-084X
DOI: https://doi.org/10.7554/eLife.14003
Pham Thanh, Duy;
Thanh Tuyen, Ha;
Nguyen Thi Nguyen, To;
Chung The, Hao;
Wick, Ryan R;
Thwaites, Guy E;
Baker, Stephen;
Holt, Kathryn E;
(2016)
Inducible colistin resistance via a disrupted plasmid-borne mcr-1 gene in a 2008 Vietnamese Shigella sonnei isolate.
The Journal of antimicrobial chemotherapy, 71 (8).
pp. 2314-2317.
ISSN 0305-7453
DOI: https://doi.org/10.1093/jac/dkw173
Full text not available from this repository.
Pham Thanh, Duy;
Thompson, Corinne N;
Rabaa, Maia A;
Sona, Soeng;
Sopheary, Sun;
Kumar, Varun;
Moore, Catrin;
Tran Vu Thieu, Nga;
Wijedoru, Lalith;
Holt, Kathryn E;
+8 more...
Wong, Vanessa;
Pickard, Derek;
Thwaites, Guy E;
Day, Nicholas;
Dougan, Gordon;
Turner, Paul;
Parry, Christopher M;
Baker, Stephen;
(2016)
The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia.
PLoS neglected tropical diseases, 10 (6).
e0004785-.
ISSN 1935-2727
DOI: https://doi.org/10.1371/journal.pntd.0004785
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).
141-.
ISSN 2235-2988
DOI: https://doi.org/10.3389/fcimb.2016.00141
Schultz, Mark B;
Pham Thanh, Duy;
Tran Do Hoan, Nhu;
Wick, Ryan R;
Ingle, Danielle J;
Hawkey, Jane;
Edwards, David J;
Kenyon, Johanna J;
Phu Huong Lan, Nguyen;
Campbell, James I;
+6 more...
Thwaites, Guy;
Thi Khanh Nhu, Nguyen;
Hall, Ruth M;
Fournier-Level, Alexandre;
Baker, Stephen;
Holt, Kathryn E;
(2016)
Repeated local emergence of carbapenem-resistant Acinetobacter baumannii in a single hospital ward.
MICROBIAL GENOMICS, 2 (3).
e000050-.
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000050
The, Hao Chung;
Thanh, Duy Pham;
Holt, Kathryn E;
Thomson, Nicholas R;
Baker, Stephen;
(2016)
The genomic signatures of Shigella evolution, adaptation and geographical spread.
Nature reviews Microbiology, 14 (4).
pp. 235-250.
ISSN 1740-1526
DOI: https://doi.org/10.1038/nrmicro.2016.10
Full text not available from this repository.
Wong, Vanessa K;
Baker, Stephen;
Connor, Thomas R;
Pickard, Derek;
Page, Andrew J;
Dave, Jayshree;
Murphy, Niamh;
Holliman, Richard;
Sefton, Armine;
Millar, Michael;
+4 more...
Dyson, Zoe A;
Dougan, Gordon;
Holt, Kathryn E;
International Typhoid Consortium;
(2016)
An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid.
Nature communications, 7 (1).
12827-.
ISSN 2041-1723
DOI: https://doi.org/10.1038/ncomms12827
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
Wyres, Kelly L;
Wick, Ryan R;
Gorrie, Claire;
Jenney, Adam;
Follador, Rainer;
Thomson, Nicholas R;
Holt, Kathryn E;
(2016)
Identification of Klebsiella capsule synthesis loci from whole genome data.
Microbial genomics, 2 (12).
e000102-.
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000102
2015
Baines, Sarah L;
Holt, Kathryn E;
Schultz, Mark B;
Seemann, Torsten;
Howden, Brian O;
Jensen, Slade O;
van Hal, Sebastiaan J;
Coombs, Geoffrey W;
Firth, Neville;
Powell, David R;
+2 more...
Stinear, Timothy P;
Howden, Benjamin P;
(2015)
Convergent adaptation in the dominant global hospital clone ST239 of methicillin-resistant Staphylococcus aureus.
MBIO, 6 (2).
e00080-.
ISSN 2150-7511
DOI: https://doi.org/10.1128/mBio.00080-15
Baltazar, Murielle;
Ngandjio, Antoinette;
Holt, Kathryn Elizabeth;
Lepillet, Elodie;
Pardos de la Gandara, Maria;
Collard, Jean-Marc;
Bercion, Raymond;
Nzouankeu, Ariane;
Le Hello, Simon;
Dougan, Gordon;
+2 more...
Fonkoua, Marie-Christine;
Weill, François-Xavier;
(2015)
Multidrug-resistant Salmonella enterica serotype Typhi, Gulf of Guinea Region, Africa.
EMERGING INFECTIOUS DISEASES, 21 (4).
pp. 655-659.
ISSN 1080-6040
DOI: https://doi.org/10.3201/eid2104.141355
Chung The, Hao;
Rabaa, Maia A;
Thanh, Duy Pham;
Ruekit, Sirigade;
Wangchuk, Sonam;
Dorji, Tshering;
Tshering, Kinzang Pem;
Nguyen, To Nguyen Thi;
Vinh, Phat Voong;
Thanh, Tuyen Ha;
+9 more...
Minh, Chau Nguyen Ngoc;
Turner, Paul;
Sar, Poda;
Thwaites, Guy;
Holt, Kathryn E;
Thomson, Nicholas R;
Bodhidatta, Ladaporn;
Jeffries Mason, Carl;
Baker, Stephen;
(2015)
Introduction and establishment of fluoroquinolone-resistant Shigella sonnei into Bhutan.
Microbial genomics, 1 (6).
e000042-.
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000042
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
Holt, Kathryn E;
Wertheim, Heiman;
Zadoks, Ruth N;
Baker, Stephen;
Whitehouse, Chris A;
Dance, David;
Jenney, Adam;
Connor, Thomas R;
Hsu, Li Yang;
Severin, Juliëtte;
+18 more...
Brisse, Sylvain;
Cao, Hanwei;
Wilksch, Jonathan;
Gorrie, Claire;
Schultz, Mark B;
Edwards, David J;
Nguyen, Kinh Van;
Nguyen, Trung Vu;
Dao, Trinh Tuyet;
Mensink, Martijn;
Minh, Vien Le;
Nhu, Nguyen Thi Khanh;
Schultsz, Constance;
Kuntaman, Kuntaman;
Newton, Paul N;
Moore, Catrin E;
Strugnell, Richard A;
Thomson, Nicholas R;
(2015)
Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health.
Proceedings of the National Academy of Sciences of the United States of America, 112 (27).
E3574-E3581.
ISSN 0027-8424
DOI: https://doi.org/10.1073/pnas.1501049112
Full text not available from this repository.
Nigro, Steven J;
Holt, Kathryn E;
Pickard, Derek;
Hall, Ruth M;
(2015)
Carbapenem and amikacin resistance on a large conjugative Acinetobacter baumannii plasmid.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 70 (4).
pp. 1259-1261.
ISSN 0305-7453
DOI: https://doi.org/10.1093/jac/dku486
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
Wong, Vanessa K;
Baker, Stephen;
Pickard, Derek J;
Parkhill, Julian;
Page, Andrew J;
Feasey, Nicholas A;
Kingsley, Robert A;
Thomson, Nicholas R;
Keane, Jacqueline A;
Weill, François-Xavier;
+64 more...
Edwards, David J;
Hawkey, Jane;
Harris, Simon R;
Mather, Alison E;
Cain, Amy K;
Hadfield, James;
Hart, Peter J;
Thieu, Nga Tran Vu;
Klemm, Elizabeth J;
Glinos, Dafni A;
Breiman, Robert F;
Watson, Conall H;
Kariuki, Samuel;
Gordon, Melita A;
Heyderman, Robert S;
Okoro, Chinyere;
Jacobs, Jan;
Lunguya, Octavie;
Edmunds, W John;
Msefula, Chisomo;
Chabalgoity, Jose A;
Kama, Mike;
Jenkins, Kylie;
Dutta, Shanta;
Marks, Florian;
Campos, Josefina;
Thompson, Corinne;
Obaro, Stephen;
MacLennan, Calman A;
Dolecek, Christiane;
Keddy, Karen H;
Smith, Anthony M;
Parry, Christopher M;
Karkey, Abhilasha;
Mulholland, E Kim;
Campbell, James I;
Dongol, Sabina;
Basnyat, Buddha;
Dufour, Muriel;
Bandaranayake, Don;
Naseri, Take Toleafoa;
Singh, Shalini Pravin;
Hatta, Mochammad;
Newton, Paul;
Onsare, Robert S;
Isaia, Lupeoletalalei;
Dance, David;
Davong, Viengmon;
Thwaites, Guy;
Wijedoru, Lalith;
Crump, John A;
De Pinna, Elizabeth;
Nair, Satheesh;
Nilles, Eric J;
Thanh, Duy Pham;
Turner, Paul;
Soeng, Sona;
Valcanis, Mary;
Powling, Joan;
Dimovski, Karolina;
Hogg, Geoff;
Farrar, Jeremy;
Holt, Kathryn E;
Dougan, Gordon;
(2015)
Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events.
Nature genetics, 47 (6).
pp. 632-639.
ISSN 1061-4036
DOI: https://doi.org/10.1038/ng.3281
Full text not available from this repository.
Wyres, Kelly L;
Gorrie, Claire;
Edwards, David J;
Wertheim, Heiman FL;
Hsu, Li Yang;
Van Kinh, Nguyen;
Zadoks, Ruth;
Baker, Stephen;
Holt, Kathryn E;
(2015)
Extensive Capsule Locus Variation and Large-Scale Genomic Recombination within the Klebsiella pneumoniae Clonal Group 258.
Genome biology and evolution, 7 (5).
pp. 1267-1279.
ISSN 1759-6653
DOI: https://doi.org/10.1093/gbe/evv062
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).
90-.
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).
447-.
ISSN 1664-3224
DOI: https://doi.org/10.3389/fimmu.2014.00447
2013
Comas, Iñaki;
Coscolla, Mireia;
Luo, Tao;
Borrell, Sonia;
Holt, Kathryn E;
Kato-Maeda, Midori;
Parkhill, Julian;
Malla, Bijaya;
Berg, Stefan;
Thwaites, Guy;
+12 more...
Yeboah-Manu, Dorothy;
Bothamley, Graham;
Mei, Jian;
Wei, Lanhai;
Bentley, Stephen;
Harris, Simon R;
Niemann, Stefan;
Diel, Roland;
Aseffa, Abraham;
Gao, Qian;
Young, Douglas;
Gagneux, Sebastien;
(2013)
Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans.
NATURE GENETICS, 45 (10).
pp. 1176-1182.
ISSN 1061-4036
DOI: https://doi.org/10.1038/ng.2744
Davis, Jacky;
Banks, Ian;
Wrigley, David;
Peedell, Clive;
Pollock, Alyson;
McPherson, Klim;
McKee, Martin;
Irving, William L;
Crome, Peter;
Greenhalgh, Trisha;
+230 more...
Holland, Walter;
Evans, David;
Maryon-Davis, Alan;
Smyth, Alan;
Fleming, Peter;
Coleman, Michel;
Sharp, Deborah J;
Whincup, Peter;
Logan, Stuart;
Cook, Derek;
Moore, Robert;
Rawaf, Salman;
McEewen, J;
West, Robert;
Yudkin, John S;
Clarke, Aileen;
Finer, Nick;
Domizio, Paola;
Bambra, Clare;
Jones, Anna;
Feder, Gene;
Scott-Samuel, Alex;
Irvine, Louise;
Sharma, Ajay;
Fitchett, Mike;
Boomla, Kambiz;
Folb, Jonathan;
Paul, Ashish;
McCoy, David;
Tallis, Ray;
Burgess-Allen, Jilla;
Edwards, Mark;
Tomlinson, Jonathon;
Colvin, Deborah;
Gore, Jonathan;
Brown, Kirsten;
Mitchel, Sarah;
Lau, Alice;
Sayer, Mel;
Clark, Leon;
Silverman, Ruth;
Marmot, Saul;
Rainbow, Daniel;
Carter, Lucy;
Mann, Nick;
Fielding, Richard;
Logan, Jane;
Tebboth, Louise;
Arnold, Natasha;
Stobbart, Kate;
Cabot, Kate;
Finer, Sarah;
Edwards, Martin;
Davies, David;
Buttivant, Helen;
Kraemer, Sebastian;
Newell, Jo;
Griffiths, Alun;
Fitzgerald, Richard;
Macgibbon, Robert;
Lee, Alan;
Macklon, AF;
Hobson, Esther;
Jenner, David;
Jacobson, Bobbie;
Timmis, Alison;
Salim, Asad;
Evans-Jones, John;
Caan, Woody;
Awsare, Ninaad;
Pride, Neil;
Suckling, Ruth;
Bratty, Catherine;
Rossiter, Brian;
Hawkins, David;
Currie, Jonny;
Camilleri-Ferrante, Corinne;
Fluxman, Jonathan;
Bhatti, Osman;
Anson, James;
Etherington, Robert;
Lawrence, David;
Fell, Henry;
Clarke, Edward;
Ormerod, Julian;
Ormerod, Oliver;
Ireland, Maggie;
Duncan, John AT;
Chandy, Rajiv;
Mindell, Jennifer;
Mullen, Paul;
Bennett-Richards, Phillip;
Hirst, Julie;
Murphy, E;
Martin, P;
Lowes, Simon;
Fleming, Peter;
Grunewald, Richard;
Reeve, Joanne;
Schweiger, Martin;
Coates, Jonathan;
Farrelly, George;
Chamberlain, MA;
Lewis, Geoffrey;
Young, Jane;
Scott, Brian;
Gibbs, John;
Landers, Aileen;
Deveson, Pete;
Ingrams, Grant;
Leigh, Martha;
Gawler, Jeff;
Ford, Amy;
Nixon, Jonathan;
McCartney, Margaret;
Bareford, David;
Singh, Surinder;
Lockwood, Kate;
Cripwell, Michael;
Ehrhardt, Peter;
Bell, David;
Wortley, Pam;
Tomlinson, Laurie;
Hotchkiss, Julie;
Ford, Steven;
Turner, Gill;
Reissman, Gerard;
Lewis, David;
Johnstone, Chris;
Tomson, Mike;
Torabi, Payam;
Bell, David;
Tomson, D;
Tulloch, Alex;
Johnston, Sally;
Dickinson, Jane;
McElderry, Elisabeth;
Ross, Wendy;
Holt, Kim;
Logan, Mary;
Klonin, Hilary;
Jenner, David;
Danby, Jude;
Goodger, V;
Puntis, John;
Dickson, Harriet;
Gould, Derek A;
Livingstone, Anna;
Lefevre, Dianne;
Kendall, Bryony;
Singh, G;
Hall, Peter;
Darling, Jonathan;
Hamlyn, Adrian N;
Patel, Anita;
Erskine, Jonathan;
Fisher, Brian;
Hughes, Richard;
Highton, Clare;
Venning, Helen;
Singer, Ron;
Brearey, Steve;
Sikorski, Jim;
Paintin, David;
Feehally, John;
Savage, Wendy;
Freud, Kathy McAdam;
Holt, Victoria J;
Gill, Alison;
Waterston, Tony;
Souza, Richard de;
Hopkinson, Nicholas;
Beadsworth, Mike;
Franks, Andrea;
Daley, Helen;
Cullinan, Paul;
Basarab, Adriana;
Folb, Jonathan;
Gurling, Hugh;
Zinkin, Pam;
Kirwin, Simon;
Buhrs, Ernst;
Brown, Raymond;
West, Andrew;
Marlowe, Gary;
Fellows, Griffith;
Main, John;
Applebee, Jackie;
Koperski, M;
Jones, Phil;
Macfarlane, Alison;
Beer, Naomi;
Mason, Rebecca;
West, Robert;
Eisner, Maggie;
Smailes, Alison;
Timms, Philip;
Knight, David;
Jones, Coral;
Wesby, Barbara;
Lyttelton, Laura;
Morrison, Richard;
Bossano, David;
Walker, Jonathan;
Davies, Gerry;
Godfrey, Peter;
Wolfe, Ingrid;
Nsutebu, Emmanuel;
Stevenson, Nicola;
Cheeroth, Sheila;
Miller, Jo;
Johnson, Guy;
Noor, R;
Hall, Alyson;
Bostock, David;
Michael, Benedict;
Sharvill, John;
Macpherson, Jamie;
Lewis, David;
Ma, Richard;
Middleton, John;
Jeffreys, Anne;
Cole, Jim;
Boswell, John P;
Bury, Bob;
Mitchison, Sally;
Kinmonth, Ann-Louise;
Young, Gail;
Maclennan, Iain;
Munday, Pat;
(2013)
Act now against new NHS competition regulations: an open letter to the BMA and the Academy of Medical Royal Colleges calls on them to make a joint public statement of opposition to the amended section 75 regulations.
BMJ (Clinical research ed), 346 (mar20 ).
f1819-.
ISSN 0959-8138
DOI: https://doi.org/10.1136/bmj.f1819
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).
e00293-e00213.
ISSN 2169-8287
DOI: https://doi.org/10.1128/genomeA.00293-13
Holt, Kathryn E;
Thieu Nga, Tran Vu;
Thanh, Duy Pham;
Vinh, Ha;
Kim, Dong Wook;
Vu Tra, My Phan;
Campbell, James I;
Hoang, Nguyen Van Minh;
Vinh, Nguyen Thanh;
Minh, Pham Van;
+20 more...
Thuy, Cao Thu;
Nga, Tran Thi Thu;
Thompson, Corinne;
Dung, Tran Thi Ngoc;
Nhu, Nguyen Thi Khanh;
Vinh, Phat Voong;
Tuyet, Pham Thi Ngoc;
Phuc, Hoang Le;
Lien, Nguyen Thi Nam;
Phu, Bui Duc;
Ai, Nguyen Thi Thuy;
Tien, Nguyen Manh;
Dong, Nguyen;
Parry, Christopher M;
Hien, Tran Tinh;
Farrar, Jeremy J;
Parkhill, Julian;
Dougan, Gordon;
Thomson, Nicholas R;
Baker, Stephen;
(2013)
Tracking the establishment of local endemic populations of an emergent enteric pathogen.
Proceedings of the National Academy of Sciences of the United States of America, 110 (43).
pp. 17522-17527.
ISSN 0027-8424
DOI: https://doi.org/10.1073/pnas.1308632110
Full text not available from this repository.
Howden, Benjamin P;
Holt, Kathryn E;
Lam, Margaret MC;
Seemann, Torsten;
Ballard, Susan;
Coombs, Geoffrey W;
Tong, Steven YC;
Grayson, M Lindsay;
Johnson, Paul DR;
Stinear, Timothy P;
(2013)
Genomic insights to control the emergence of vancomycin-resistant enterococci.
MBIO, 4 (4).
ISSN 2150-7511
DOI: https://doi.org/10.1128/mBio.00412-13
Kingsley, Robert A;
Kay, Sally;
Connor, Thomas;
Barquist, Lars;
Sait, Leanne;
Holt, Kathryn E;
Sivaraman, Karthi;
Wileman, Thomas;
Goulding, David;
Clare, Simon;
+10 more...
Hale, Christine;
Seshasayee, Aswin;
Harris, Simon;
Thomson, Nicholas R;
Gardner, Paul;
Rabsch, Wolfgang;
Wigley, Paul;
Humphrey, Tom;
Parkhill, Julian;
Dougan, Gordon;
(2013)
Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar.
MBIO, 4 (5).
e00565-e00513.
ISSN 2150-7511
DOI: https://doi.org/10.1128/mBio.00565-13
Pham Thanh, Duy;
Tran Vu Thieu, Nga;
Tran Thuy, Chau;
Lodén, Martin;
Tuin, Kiki;
Campbell, James I;
Van Minh Hoang, Nguyen;
Voong Vinh, Phat;
Farrar, Jeremy J;
Holt, Kathryn E;
+2 more...
Dougan, Gordon;
Baker, Stephen;
(2013)
Identification of Salmonella enterica serovar Typhi genotypes by use of rapid multiplex ligation-dependent probe amplification.
Journal of clinical microbiology, 51 (9).
pp. 2950-2958.
ISSN 0095-1137
DOI: https://doi.org/10.1128/JCM.01010-13
Wong, Vanessa K;
Pickard, Derek J;
Barquist, Lars;
Sivaraman, Karthikeyan;
Page, Andrew J;
Hart, Peter J;
Arends, Mark J;
Holt, Kathryn E;
Kane, Leanne;
Mottram, Lynda F;
+9 more...
Ellison, Louise;
Bautista, Ruben;
McGee, Chris J;
Kay, Sally J;
Wileman, Thomas M;
Kenney, Linda J;
MacLennan, Calman A;
Kingsley, Robert A;
Dougan, Gordon;
(2013)
Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium.
PLOS ONE, 8 (12).
e84567-.
ISSN 1932-6203
DOI: https://doi.org/10.1371/journal.pone.0084567
2012
Celik, Nermin;
Webb, Chaille T;
Leyton, Denisse L;
Holt, Kathryn E;
Heinz, Eva;
Gorrell, Rebecca;
Kwok, Terry;
Naderer, Thomas;
Strugnell, Richard A;
Speed, Terence P;
+3 more...
Teasdale, Rohan D;
Likić, Vladimir A;
Lithgow, Trevor;
(2012)
A bioinformatic strategy for the detection, classification and analysis of bacterial autotransporters.
PLOS ONE, 7 (8).
e43245-.
ISSN 1932-6203
DOI: https://doi.org/10.1371/journal.pone.0043245
Doig, Kenneth D;
Holt, Kathryn E;
Fyfe, Janet AM;
Lavender, Caroline J;
Eddyani, Miriam;
Portaels, Françoise;
Yeboah-Manu, Dorothy;
Pluschke, Gerd;
Seemann, Torsten;
Stinear, Timothy P;
(2012)
On the origin of Mycobacterium ulcerans, the causative agent of Buruli ulcer.
BMC GENOMICS, 13 (1).
258-.
ISSN 1471-2164
DOI: https://doi.org/10.1186/1471-2164-13-258
Holt, Kathryn E;
Baker, Stephen;
Weill, François-Xavier;
Holmes, Edward C;
Kitchen, Andrew;
Yu, Jun;
Sangal, Vartul;
Brown, Derek J;
Coia, John E;
Kim, Dong Wook;
+8 more...
Choi, Seon Young;
Kim, Su Hee;
da Silveira, Wanderley D;
Pickard, Derek J;
Farrar, Jeremy J;
Parkhill, Julian;
Dougan, Gordon;
Thomson, Nicholas R;
(2012)
Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe.
Nature genetics, 44 (9).
pp. 1056-1059.
ISSN 1061-4036
DOI: https://doi.org/10.1038/ng.2369
Inouye, Michael;
Conway, Thomas C;
Zobel, Justin;
Holt, Kathryn E;
(2012)
Short read sequence typing (SRST): multi-locus sequence types from short reads.
BMC GENOMICS, 13 (1).
338-.
ISSN 1471-2164
DOI: https://doi.org/10.1186/1471-2164-13-338
2011
Baker, Stephen;
Holt, Kathryn E;
Clements, Archie CA;
Karkey, Abhilasha;
Arjyal, Amit;
Boni, Maciej F;
Dongol, Sabina;
Hammond, Naomi;
Koirala, Samir;
Duy, Pham Thanh;
+6 more...
Nga, Tran Vu Thieu;
Campbell, James I;
Dolecek, Christiane;
Basnyat, Buddha;
Dougan, Gordon;
Farrar, Jeremy J;
(2011)
Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission.
Open biology, 1 (2).
110008-.
ISSN 2046-2441
DOI: https://doi.org/10.1098/rsob.110008
Holt, Kathryn E;
Dolecek, Christiane;
Chau, Tran Thuy;
Duy, Pham Thanh;
La, Tran Thi Phi;
Hoang, Nguyen Van Minh;
Nga, Tran Vu Thieu;
Campbell, James I;
Manh, Bui Huu;
Vinh Chau, Nguyen Van;
+4 more...
Hien, Tran Tinh;
Farrar, Jeremy;
Dougan, Gordon;
Baker, Stephen;
(2011)
Temporal fluctuation of multidrug resistant salmonella typhi haplotypes in the mekong river delta region of Vietnam.
PLoS neglected tropical diseases, 5 (1).
e929-.
ISSN 1935-2727
DOI: https://doi.org/10.1371/journal.pntd.0000929
Jansen, Angela M;
Hall, Lindsay J;
Clare, Simon;
Goulding, David;
Holt, Kathryn E;
Grant, Andrew J;
Mastroeni, Piero;
Dougan, Gordon;
Kingsley, Robert A;
(2011)
A Salmonella Typhimurium-Typhi genomic chimera: a model to study Vi polysaccharide capsule function in vivo.
PLOS PATHOGENS, 7 (7).
e1002131-.
ISSN 1553-7366
DOI: https://doi.org/10.1371/journal.ppat.1002131
2010
Baker, Stephen;
Hanage, William P;
Holt, Kathryn E;
(2010)
Navigating the future of bacterial molecular epidemiology.
Current opinion in microbiology, 13 (5).
pp. 640-645.
ISSN 1369-5274
DOI: https://doi.org/10.1016/j.mib.2010.08.002
He, Miao;
Sebaihia, Mohammed;
Lawley, Trevor D;
Stabler, Richard A;
Dawson, Lisa F;
Martin, Melissa J;
Holt, Kathryn E;
Seth-Smith, Helena MB;
Quail, Michael A;
Rance, Richard;
+15 more...
Brooks, Karen;
Churcher, Carol;
Harris, David;
Bentley, Stephen D;
Burrows, Christine;
Clark, Louise;
Corton, Craig;
Murray, Vicky;
Rose, Graham;
Thurston, Scott;
van Tonder, Andries;
Walker, Danielle;
Wren, Brendan W;
Dougan, Gordon;
Parkhill, Julian;
(2010)
Evolutionary dynamics of Clostridium difficile over short and long time scales.
Proceedings of the National Academy of Sciences of the United States of America, 107 (16).
pp. 7527-7532.
ISSN 0027-8424
DOI: https://doi.org/10.1073/pnas.0914322107
Full text not available from this repository.
Karkey, Abhilasha;
Arjyal, Amit;
Anders, Katherine L;
Boni, Maciej F;
Dongol, Sabina;
Koirala, Samir;
My, Phan Vu Tra;
Nga, Tran Vu Thieu;
Clements, Archie CA;
Holt, Kathryn E;
+8 more...
Duy, Pham Thanh;
Day, Jeremy N;
Campbell, James I;
Dougan, Gordon;
Dolecek, Christiane;
Farrar, Jeremy;
Basnyat, Buddha;
Baker, Stephen;
(2010)
The burden and characteristics of enteric fever at a healthcare facility in a densely populated area of Kathmandu.
PLOS ONE, 5 (11).
e13988-.
ISSN 1932-6203
DOI: https://doi.org/10.1371/journal.pone.0013988
Nga, Tran Vu Thieu;
Karkey, Abhilasha;
Dongol, Sabina;
Thuy, Hang Nguyen;
Dunstan, Sarah;
Holt, Kathryn;
Tu, Le Thi Phuong;
Campbell, James I;
Chau, Tran Thuy;
Chau, Nguyen Van Vinh;
+6 more...
Arjyal, Amit;
Koirala, Samir;
Basnyat, Buddha;
Dolecek, Christiane;
Farrar, Jeremy;
Baker, Stephen;
(2010)
The sensitivity of real-time PCR amplification targeting invasive Salmonella serovars in biological specimens.
BMC INFECTIOUS DISEASES, 10 (1).
125-.
ISSN 1471-2334
DOI: https://doi.org/10.1186/1471-2334-10-125
Song, Yajun;
Roumagnac, Philippe;
Weill, François-Xavier;
Wain, John;
Dolecek, Christiane;
Mazzoni, Camila J;
Holt, Kathryn E;
Achtman, Mark;
(2010)
A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 65 (8).
pp. 1631-1641.
ISSN 0305-7453
DOI: https://doi.org/10.1093/jac/dkq175
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