Items where Author or Contributor is "Holt, Kathryn E"
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Number of items: 188.
2024
Cooper, Helena B;
Vezina, Ben;
Hawkey, Jane;
Passet, Virginie;
López-Fernández, Sebastián;
Monk, Jonathan M;
Brisse, Sylvain;
Holt, Kathryn E;
Wyres, Kelly L;
(2024)
A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex.
Microbial genomics, 10 (2).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.001206
Dyson, Zoe A;
Ashton, Philip M;
Khanam, Farhana;
Chunga Chirambo, Angeziwa;
Shakya, Mila;
Meiring, James E;
Tonks, Susan;
Karkey, Abhilasha;
Msefula, Chisomo;
Clemens, John D;
+11 more...
Dunstan, Sarah J;
Baker, Stephen;
Dougan, Gordon;
Pitzer, Virginia E;
Basnyat, Buddha;
Qadri, Firdausi;
Heyderman, Robert S;
Gordon, Melita A;
Pollard, Andrew J;
Holt, Kathryn E;
STRATAA Study Group;
(2024)
Pathogen diversity and antimicrobial resistance transmission of Salmonella enterica serovars Typhi and Paratyphi A in Bangladesh, Nepal, and Malawi: a genomic epidemiological study.
The Lancet microbe, 5 (8).
100841-.
ISSN 2666-5247
DOI: https://doi.org/10.1016/S2666-5247(24)00047-8
Mills, Richael O;
Dadzie, Isaac;
Le-Viet, Thanh;
Baker, David J;
Addy, Humphrey PK;
Akwetey, Samuel A;
Donkoh, Irene E;
Quansah, Elvis;
Semanshia, Prince S;
Morgan, Jennifer;
+9 more...
Mensah, Abraham;
Adade, Nana E;
Ampah, Emmanuel O;
Owusu, Emmanuel;
Mwintige, Philimon;
Amoako, Eric O;
Spadar, Anton;
Holt, Kathryn E;
Foster-Nyarko, Ebenezer;
(2024)
Genomic diversity and antimicrobial resistance in clinical Klebsiella pneumoniae isolates from tertiary hospitals in Southern Ghana.
The Journal of antimicrobial chemotherapy, 79 (7).
pp. 1529-1539.
ISSN 0305-7453
DOI: https://doi.org/10.1093/jac/dkae123
Tsang, Kara K;
Lam, Margaret MC;
Wick, Ryan R;
Wyres, Kelly L;
Bachman, Michael;
Baker, Stephen;
Barry, Katherine;
Brisse, Sylvain;
Campino, Susana;
Chiaverini, Alexandra;
+65 more...
Cirillo, Daniela Maria;
Clark, Taane;
Corander, Jukka;
Corbella, Marta;
Cornacchia, Alessandra;
Cuénod, Aline;
D'Alterio, Nicola;
Di Marco, Federico;
Donado-Godoy, Pilar;
Egli, Adrian;
Farzana, Refath;
Feil, Edward J;
Fostervold, Aasmund;
Gorrie, Claire L;
Hassan, Brekhna;
Hetland, Marit Andrea Klokkhammer;
Hoa, Le Nguyen Minh;
Hoi, Le Thi;
Howden, Benjamin;
Ikhimiukor, Odion O;
Jenney, Adam WJ;
Kaspersen, Håkon;
Khokhar, Fahad;
Leangapichart, Thongpan;
Ligowska-Marzęta, Małgorzata;
Löhr, Iren Høyland;
Long, Scott W;
Mathers, Amy J;
McArthur, Andrew G;
Nagaraj, Geetha;
Oaikhena, Anderson O;
Okeke, Iruka N;
Perdigão, João;
Parikh, Hardik;
Pham, My H;
Pomilio, Francesco;
Raffelsberger, Niclas;
Rakotondrasoa, Andriniaina;
Kumar, KL Ravi;
Roberts, Leah W;
Rodrigues, Carla;
Samuelsen, Ørjan;
Sands, Kirsty;
Sassera, Davide;
Seth-Smith, Helena;
Shamanna, Varun;
Sherry, Norelle L;
Sia, Sonia;
Spadar, Anton;
Stoesser, Nicole;
Sunde, Marianne;
Sundsfjord, Arnfinn;
Thach, Pham Ngoc;
Thomson, Nicholas R;
Thorpe, Harry A;
Torok, M Estée;
Trang, Van Dinh;
Trung, Nguyen Vu;
Vornhagen, Jay;
Walsh, Timothy;
Warne, Ben;
Wilson, Hayley;
Wright, Gerard D;
Holt, Kathryn E;
KlebNET-Gsp Amr Genotype-Phenotype Group;
(2024)
Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae.
Microbial genomics, 10 (10).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.001294
2023
Carey, Megan E;
Dyson, Zoe A;
Argimón, Silvia;
Cerdeira, Louise;
Yeats, Corin;
Aanensen, David;
Mboowa, Gerald;
Baker, Stephen;
Tessema, Sofonias K;
Smith, Anthony M;
+2 more...
Okeke, Iruka N;
Holt, Kathryn E;
(2023)
Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization.
Open forum infectious diseases, 10 (Suppl ).
S38-S46.
ISSN 2328-8957
DOI: https://doi.org/10.1093/ofid/ofad044
Carey, Megan E;
Dyson, Zoe A;
Ingle, Danielle J;
Amir, Afreenish;
Aworh, Mabel K;
Chattaway, Marie Anne;
Chew, Ka Lip;
Crump, John A;
Feasey, Nicholas A;
Howden, Benjamin P;
+105 more...
Keddy, Karen H;
Maes, Mailis;
Parry, Christopher M;
Van Puyvelde, Sandra;
Webb, Hattie E;
Afolayan, Ayorinde Oluwatobiloba;
Alexander, Anna P;
Anandan, Shalini;
Andrews, Jason R;
Ashton, Philip M;
Basnyat, Buddha;
Bavdekar, Ashish;
Bogoch, Isaac I;
Clemens, John D;
da Silva, Kesia Esther;
De, Anuradha;
de Ligt, Joep;
Diaz Guevara, Paula Lucia;
Dolecek, Christiane;
Dutta, Shanta;
Ehlers, Marthie M;
Francois Watkins, Louise;
Garrett, Denise O;
Godbole, Gauri;
Gordon, Melita A;
Greenhill, Andrew R;
Griffin, Chelsey;
Gupta, Madhu;
Hendriksen, Rene S;
Heyderman, Robert S;
Hooda, Yogesh;
Hormazabal, Juan Carlos;
Ikhimiukor, Odion O;
Iqbal, Junaid;
Jacob, Jobin John;
Jenkins, Claire;
Jinka, Dasaratha Ramaiah;
John, Jacob;
Kang, Gagandeep;
Kanteh, Abdoulie;
Kapil, Arti;
Karkey, Abhilasha;
Kariuki, Samuel;
Kingsley, Robert A;
Koshy, Roshine Mary;
Lauer, AC;
Levine, Myron M;
Lingegowda, Ravikumar Kadahalli;
Luby, Stephen P;
Mackenzie, Grant Austin;
Mashe, Tapfumanei;
Msefula, Chisomo;
Mutreja, Ankur;
Nagaraj, Geetha;
Nagaraj, Savitha;
Nair, Satheesh;
Naseri, Take K;
Nimarota-Brown, Susana;
Njamkepo, Elisabeth;
Okeke, Iruka N;
Perumal, Sulochana Putli Bai;
Pollard, Andrew J;
Pragasam, Agila Kumari;
Qadri, Firdausi;
Qamar, Farah N;
Rahman, Sadia Isfat Ara;
Rambocus, Savitra Devi;
Rasko, David A;
Ray, Pallab;
Robins-Browne, Roy;
Rongsen-Chandola, Temsunaro;
Rutanga, Jean Pierre;
Saha, Samir K;
Saha, Senjuti;
Saigal, Karnika;
Sajib, Mohammad Saiful Islam;
Seidman, Jessica C;
Shakya, Jivan;
Shamanna, Varun;
Shastri, Jayanthi;
Shrestha, Rajeev;
Sia, Sonia;
Sikorski, Michael J;
Singh, Ashita;
Smith, Anthony M;
Tagg, Kaitlin A;
Tamrakar, Dipesh;
Tanmoy, Arif Mohammed;
Thomas, Maria;
Thomas, Mathew S;
Thomsen, Robert;
Thomson, Nicholas R;
Tupua, Siaosi;
Vaidya, Krista;
Valcanis, Mary;
Veeraraghavan, Balaji;
Weill, François-Xavier;
Wright, Jackie;
Dougan, Gordon;
Argimón, Silvia;
Keane, Jacqueline A;
Aanensen, David M;
Baker, Stephen;
Holt, Kathryn E;
Global Typhoid Genomics Consortium Group Authorship;
(2023)
Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes.
eLife, 12.
e85867-.
ISSN 2050-084X
DOI: https://doi.org/10.7554/eLife.85867
Foster-Nyarko, Ebenezer;
Cottingham, Hugh;
Wick, Ryan R;
Judd, Louise M;
Lam, Margaret MC;
Wyres, Kelly L;
Stanton, Thomas D;
Tsang, Kara K;
David, Sophia;
Aanensen, David M;
+2 more...
Brisse, Sylvain;
Holt, Kathryn E;
(2023)
Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae.
Microbial genomics, 9 (2).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000936
Foster-Nyarko, Ebenezer;
Cottingham, Hugh;
Wick, Ryan R;
Judd, Louise M;
Lam, Margaret MC;
Wyres, Kelly L;
Stanton, Thomas D;
Tsang, Kara K;
David, Sophia;
Aanensen, David M;
+2 more...
Brisse, Sylvain;
Holt, Kathryn E;
(2023)
Corrigendum: 'Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae'.
Microbial genomics, 9 (8).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.001084
Hetland, Marit AK;
Hawkey, Jane;
Bernhoff, Eva;
Bakksjø, Ragna-Johanne;
Kaspersen, Håkon;
Rettedal, Siren I;
Sundsfjord, Arnfinn;
Holt, Kathryn E;
Löhr, Iren H;
(2023)
Within-patient and global evolutionary dynamics of Klebsiella pneumoniae ST17.
Microbial genomics, 9 (5).
ISSN 2057-5858
DOI: https://doi.org/10.1099/mgen.0.001005
Miles, Sydney L;
Torraca, Vincenzo;
Dyson, Zoe A;
López-Jiménez, Ana Teresa;
Foster-Nyarko, Ebenezer;
Lobato-Márquez, Damián;
Jenkins, Claire;
Holt, Kathryn E;
Mostowy, Serge;
(2023)
Acquisition of a large virulence plasmid (pINV) promoted temperature-dependent virulence and global dispersal of O96:H19 enteroinvasive Escherichia coli.
mBio, 14 (4).
e0088223-.
ISSN 2150-7511
DOI: https://doi.org/10.1128/mbio.00882-23
Okomo, Uduak A;
Darboe, Saffiatou;
Bah, Saikou Y;
Ayorinde, Abigail;
Jarju, Sheikh;
Sesay, Abdul Karim;
Kebbeh, Ngange;
Gai, Abdou;
Dibbasey, Tida;
Grey-Johnson, Mary;
+4 more...
Le Doare, Kirsty;
Holt, Kathryn E;
Lawn, Joy E;
Kampmann, Beate;
(2023)
Maternal colonization and early-onset neonatal bacterial sepsis in the Gambia, West Africa: a genomic analysis of vertical transmission.
Clinical microbiology and infection, 29 (3).
386.e1-386.e9.
ISSN 1198-743X
DOI: https://doi.org/10.1016/j.cmi.2022.10.012
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
Zhou, Kai;
Xue, Chun-Xu;
Xu, Tingting;
Shen, Ping;
Wei, Sha;
Wyres, Kelly L;
Lam, Margaret MC;
Liu, Jinquan;
Lin, Haoyun;
Chen, Yunbo;
+3 more...
Holt, Kathryn E;
BRICS Working Group;
Xiao, Yonghong;
(2023)
A point mutation in recC associated with subclonal replacement of carbapenem-resistant Klebsiella pneumoniae ST11 in China.
Nature communications, 14 (1).
2464-.
ISSN 2041-1723
DOI: https://doi.org/10.1038/s41467-023-38061-z
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).
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;
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Addressing parachute research and removing barriers for LMIC researchers in Microbial Genomics.
Microbial genomics, 7 (10).
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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;
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Peleg, Anton Y;
START Trial Group;
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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).
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Kariuki, Samuel;
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Ngetich, Ronald;
Kavai, Susan M;
Wairimu, Celestine;
Anyona, Stephen;
Gitau, Naomi;
Onsare, Robert Sanaya;
Ongandi, Beatrice;
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Duchene, Sebastian;
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Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya.
eLife, 10.
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Genome medicine, 13 (1).
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Lam, Margaret MC;
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Hallam, Steven J;
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Mercury methylation by metabolically versatile and cosmopolitan marine bacteria.
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Cassimon, B;
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Phillips, Maile T;
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Thindwa, Deus;
Darton, Thomas C;
Dongol, Sabina;
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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;
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Warren, Joshua L;
Baker, Stephen;
Basnyat, Buddha;
Clemens, John D;
Dolecek, Christiane;
Dunstan, Sarah J;
Dougan, Gordon;
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Gordon, Melita A;
Thindwa, Deus;
Heyderman, Robert S;
Holt, Kathryn E;
Qadri, Firdausi;
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A Bayesian approach for estimating typhoid fever incidence from large-scale facility-based passive surveillance data.
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Löhr, Iren Høyland;
Andreassen, Lotte Leonore Eivindsdatter;
Brisse, Sylvain;
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Sundsfjord, Arnfinn;
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Gravningen, Kirsten;
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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).
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Viehweger, Adrian;
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Wyres, Kelly L;
Brandt, Christian;
Hans, Jörg B;
Hölzer, Martin;
Irber, Luiz;
Gatermann, Sören;
Lübbert, Christoph;
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Pletz, Mathias W;
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König, Brigitte;
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Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae.
Microbial genomics, 7 (12).
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Vu Thi Ngoc, Bich;
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Vu Tien Viet, Dung;
Holt, Kathryn E;
Nguyen Vu, Trung;
Tran Thi Kieu, Huong;
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Klebsiella pneumoniae with capsule type K64 is overrepresented among invasive disease in Vietnam.
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Genomic Diversity and Antimicrobial Resistance of Haemophilus Colonizing the Airways of Young Children with Cystic Fibrosis.
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Trycycler: consensus long-read assemblies for bacterial genomes.
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Recovery of small plasmid sequences via Oxford Nanopore sequencing.
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Wyres, Kelly L;
Hawkey, Jane;
Mirčeta, Mirianne;
Judd, Louise M;
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Watson, Kerrie M;
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McGloughlin, Steve A;
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Genomic surveillance of antimicrobial resistant bacterial colonisation and infection in intensive care patients.
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SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments.
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Ritchie, Scott C;
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Brozynska, Marta;
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Bakshi, Andrew;
Holt, Barbara J;
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Khor, Chiea Chuen;
Sly, Peter D;
Holt, Patrick G;
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Inouye, Michael;
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Neonatal genetics of gene expression reveal potential origins of autoimmune and allergic disease risk.
NATURE COMMUNICATIONS, 11 (1).
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Ahmmed, Faisal;
Chon, Yun;
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Ali, Mohammad;
Sur, Dipika;
Kanungo, Suman;
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Dutta, Shanta;
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Dougan, Gordon;
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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;
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Lawn, Joy E;
Bentley, Stephen D;
Kampmann, Beate;
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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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Khanam, Farhana;
Holt, Kathryn E;
Chowdhury, Emran Kabir;
Dougan, Gordon;
Qadri, Firdausi;
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Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016.
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Repetti, Sonja I;
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The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns.
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Ingle, Danielle J;
Inouye, Michael;
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GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure.
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Wan, Yu;
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GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene Associations Controlled for Population Structure.
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Wyres, Kelly L;
Cahill, Sarah M;
Holt, Kathryn E;
Hall, Ruth M;
Kenyon, Johanna J;
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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).
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Wyres, Kelly L;
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Lam, Margaret MC;
Judd, Louise M;
van Vinh Chau, Nguyen;
Dance, David AB;
Ip, Margaret;
Karkey, Abhilasha;
Ling, Clare L;
Miliya, Thyl;
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Newton, Paul N;
Lan, Nguyen Phu Huong;
Sengduangphachanh, Amphone;
Turner, Paul;
Veeraraghavan, Balaji;
Vinh, Phat Voong;
Vongsouvath, Manivanh;
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Baker, Stephen;
Holt, Kathryn E;
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Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia.
Genome Medicine, 12 (1).
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Zhou, Kai;
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Wang, Qin;
Zhou, Yanzi;
Guo, Lihua;
Aanensen, David;
Holt, Kathryn E;
Thomson, Nicholas R;
Grundmann, Hajo;
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Shen, Ping;
Xiao, Yonghong;
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Novel Subclone of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 with Enhanced Virulence and Transmissibility, China.
EMERGING INFECTIOUS DISEASES, 26 (2).
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Khanh, Nhu Nguyen Thi;
Thanh, Duy Pham;
Dordel, Janina;
Campbell, James I;
Lan, Nguyen Phu Huong;
Mayho, Matthew;
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Langridge, Gemma C;
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Thwaites, Guy E;
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Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii.
Microbial genomics, 5 (2).
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Cerdeira, Louise T;
Lam, Margaret MC;
Wyres, Kelly L;
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Judd, Louise M;
Lopes, Ralf;
Ribas, Rosineide M;
Morais, Marcia M;
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Lincopan, Nilton;
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Small IncQ1 and Col-Like Plasmids Harboring blaKPC-2 and Non-Tn4401 Elements (NTEKPC-IId) in High-Risk Lineages of Klebsiella pneumoniae CG258.
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Chung The, Hao;
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Howden, Benjamin P;
Valcanis, Mary;
De Lappe, Niall;
Cormican, Martin;
Wangchuk, Sonam;
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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;
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Rabaa, Maia A;
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Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei.
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Hamidian, Mohammad;
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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).
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Hamidian, Mohammad;
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Hall, Ruth M;
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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).
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Hamidian, Mohammad;
Wick, Ryan R;
Judd, Louise M;
Holt, Kathryn E;
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Complete Genome Sequence of A388, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 1 Isolate from Greece.
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Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198.
Microbial genomics, 5 (7).
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Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales.
BioRxiv.
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Seemann, Torsten;
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Carter, Glen P;
Gonçalves da Silva, Anders;
Adamopoulos, James;
Baines, Sarah L;
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Holt, Kathryn E;
Chow, Eric PF;
Fairley, Christopher K;
Chen, Marcus Y;
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Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in Australia.
Clinical Infectious Diseases, 69 (9).
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Dyson, Zoe A;
Day, Martin;
Freedman, Joanne;
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Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers.
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Karmakar, Malancha;
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Empirical ways to identify novel Bedaquiline resistance mutations in AtpE.
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hicap: In Silico Serotyping of the Haemophilus influenzae Capsule Locus.
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Benchmarking of long-read assemblers for prokaryote whole genome sequencing.
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Olanipekun, Grace;
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Alter, Roxanne;
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Le Hello, Simon;
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Carbapenem and amikacin resistance on a large conjugative Acinetobacter baumannii plasmid.
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Feasey, Nicholas A;
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Thomson, Nicholas R;
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Harris, Simon R;
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Singh, Shalini Pravin;
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Dimovski, Karolina;
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Edwards, David J;
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Extensive Capsule Locus Variation and Large-Scale Genomic Recombination within the Klebsiella pneumoniae Clonal Group 258.
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Hamidian, Mohammad;
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Hall, Ruth M;
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A GC1 Acinetobacter baumannii isolate carrying AbaR3 and the aminoglycoside resistance transposon TnaphA6 in a conjugative plasmid.
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Identification of a marker for two lineages within the GC1 clone of Acinetobacter baumannii.
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Inouye, Michael;
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SRST2: Rapid genomic surveillance for public health and hospital microbiology labs.
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Stinear, Timothy P;
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Holt, Kathryn E;
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An outpatient, ambulant-design, controlled human infection model using escalating doses of Salmonella Typhi challenge delivered in sodium bicarbonate solution.
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Elucidation of pathways driving asthma pathogenesis: development of a systems-level analytic strategy.
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Newell, Jo;
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Lee, Alan;
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Timmis, Alison;
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Caan, Woody;
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