Items where Author or Contributor is "Holt, Kathryn E"
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Number of items: 151.
2021
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
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).
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, Colin;
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.
p. 6638780.
ISSN 2090-6625
DOI: https://doi.org/10.1155/2021/6638780
![[img]](/style/images/fileicons/text.png)
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
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 Klebsiella pneumoniae.
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)
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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.
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International Typhoid Consortium;
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Alter, Roxanne;
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Le Hello, Simon;
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Onsare, Robert S;
De Pinna, Elizabeth;
Nair, Satheesh;
Amos, Ben;
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Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa.
PLoS neglected tropical diseases, 10 (9).
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Lee, I Russel;
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Differential host susceptibility and bacterial virulence factors driving Klebsiella liver abscess in an ethnically diverse population.
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The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia.
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Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1.
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Genome Sequence of Acinetobacter baumannii Strain A1, an Early Example of Antibiotic-Resistant Global Clone 1.
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Carbapenem and amikacin resistance on a large conjugative Acinetobacter baumannii plasmid.
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Kingsley, Robert A;
Thomson, Nicholas R;
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Hawkey, Jane;
Harris, Simon R;
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Hart, Peter J;
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Nair, Satheesh;
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Dimovski, Karolina;
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Wyres, Kelly L;
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Edwards, David J;
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Van Kinh, Nguyen;
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Hamidian, Mohammad;
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Inouye, Michael;
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Schultz, Mark B;
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Holt, Kathryn E;
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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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Stepnell, Justin;
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Holt, Kathryn E;
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Elucidation of pathways driving asthma pathogenesis: development of a systems-level analytic strategy.
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Sharma, Ajay;
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Clark, Leon;
Silverman, Ruth;
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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;
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Hirst, Julie;
Murphy, E;
Martin, P;
Lowes, Simon;
Fleming, Peter;
Grunewald, Richard;
Reeve, Joanne;
Schweiger, Martin;
Coates, Jonathan;
Farrelly, George;
Chamberlain, MA;
Lewis, Geoffrey;
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Scott, Brian;
Gibbs, John;
Landers, Aileen;
Deveson, Pete;
Ingrams, Grant;
Leigh, Martha;
Gawler, Jeff;
Ford, Amy;
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McCartney, Margaret;
Bareford, David;
Singh, Surinder;
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Cripwell, Michael;
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Hotchkiss, Julie;
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