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. 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. ISSN 0066-4804 DOI: https://doi.org/10.1128/aac.02140-18

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

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. DOI: https://doi.org/10.1099/mgen.0.000269

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; Howden, Benjamin P; Williamson, Deborah A; (2019) Co-circulation of multidrug-resistant Shigella among men who have sex with men, Australia. Clinical Infectious Diseases. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/ciz005 Item availability may be restricted.

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. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dkz028

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

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). ISSN 1553-7390 DOI: https://doi.org/10.1371/journal.pgen.1008114

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). 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; Phan, Vuong Khac Thai; 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). ISSN 2375-2548 DOI: https://doi.org/10.1126/sciadv.aat5869

Cain, AK; Boinett, CJ; Barquist, L; Dordel, J; Fookes, M; Mayho, M; Ellington, MJ; Goulding, D; Pickard, D; Wick, RR; +3 more... Holt, KE; Parkhill, J; Thomson, NR; (2018) Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin. Scientific reports, 8 (1). p. 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). 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; Phan, Vuong Khac Thai; Nguyen, Thuy Thuong Thuong; Dang, Thi Minh Ha; Nguyen, Ngoc Lan; Nguyen, Huu Lan; Nguyen, Thi Quynh Nhu; Hoang, Thanh Hai; Vu, Thi Ngoc Ha; +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). 849-+. ISSN 1061-4036 DOI: https://doi.org/10.1038/s41588-018-0117-9

Ingle, DJ; Levine, MM; Kotloff, KL; Holt, KE; Robins-Browne, RM; (2018) Dynamics of antimicrobial resistance in intestinal Escherichia coli from children in community settings in South Asia and sub-Saharan Africa. Nature microbiology. ISSN 2058-5276 DOI: https://doi.org/10.1038/s41564-018-0217-4

Lam, MMC; Wyres, KL; Judd, LM; Wick, RR; Jenney, A; Brisse, S; Holt, KE; (2018) Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae. Genome medicine, 10 (1). p. 77. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-018-0587-5

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

M C Lam, M; Wyres, KL; Duchêne, S; Wick, RR; Judd, LM; Gan, YH; Hoh, CH; Archuleta, S; Molton, JS; Kalimuddin, S; +4 more... Koh, TH; Passet, V; Brisse, S; Holt, KE; (2018) Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination. Nature communications, 9 (1). p. 2703. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-018-05114-7

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). ISSN 1198-743X DOI: https://doi.org/10.1016/j.cmi.2017.06.031

Mostowy, RJ; Holt, KE; (2018) Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating. Trends in microbiology. 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) Trajectories of childhood immune development and respiratory health relevant to asthma and allergy. ELIFE, 7. ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.35856.001

Tang, Howard Hf; Teo, Shu Mei; Belgrave, Danielle Cm; Evans, Michael D; Jackson, Daniel J; Brozynska, Marta; Kusel, Merci Mh; Johnston, Sebastian L; Gern, James E; Lemanske, Robert F; +6 more... Simpson, Angela; Custovic, Adnan; Sly, Peter D; Holt, Patrick G; Holt, Kathryn E; Inouye, Michael; (2018) Trajectories of childhood immune development and respiratory health relevant to asthma and allergy. eLife, 7. ISSN 2050-084X DOI: https://doi.org/10.7554/elife.35856

Teo, SM; Tang, HHF; Mok, D; Judd, LM; Watts, SC; Pham, K; Holt, BJ; Kusel, M; Serralha, M; Troy, N; +9 more... Bochkov, YA; Grindle, K; Lemanske, RFJr; Johnston, SL; Gern, JE; Sly, PD; Holt, PG; Holt, KE; Inouye, M; (2018) Airway Microbiota Dynamics Uncover a Critical Window for Interplay of Pathogenic Bacteria and Allergy in Childhood Respiratory Disease. Technical Report. Elsevier (Cell Press). DOI: https://doi.org/10.1016/j.chom.2018.08.005 Full text not available from this repository.

Watts, Stephen C; Ritchie, Scott C; Inouye, Michael; Holt, Kathryn E; (2018) FastSpar: Rapid and scalable correlation estimation for compositional data. Bioinformatics. 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; Judd, Louise; Holt, Kathryn; (2018) Deepbinner: 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. The Journal of antimicrobial chemotherapy. 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. 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. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dky472

Wyres, Kelly; Hawkey, Jane; Hetland, Marit; Fostervold, Aasmund; Wick, Ryan; Judd, Louise; Hamidian, Mohammad; Howden, Benjamin; Lohr, Iren; Holt, Kathryn; (2018) Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307. DOI: https://doi.org/10.1101/352740

Wyres, Kelly; Holt, Kathryn; (2018) Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria. DOI: https://doi.org/10.7287/peerj.preprints.26852 Item availability may be restricted.

Wyres, Kelly; Wick, Ryan; Judd, Louise; Froumine, Roni; Tokolyi, Alex; Gorrie, Claire; Lam, Margaret; Duchene, Sebastian; Jenney, Adam; Holt, Kathryn; (2018) Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae. DOI: https://doi.org/10.1101/414235 Item availability may be restricted.

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; +10 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; (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). ISSN 2044-6055 DOI: https://doi.org/10.1136/bmjopen-2017-016283

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. ISSN 2041-1723 DOI: https://doi.org/10.1038/ncomms15483

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). 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. MICROBIAL GENOMICS, 3 (10). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000132

Wick, Ryan; Judd, Louise; Gorrie, Claire; Holt, Kathryn; (2017) Completing bacterial genome assemblies with multiplex MinION sequencing. DOI: https://doi.org/10.1101/160614

Duchene, Sebastian; Duchene, 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). ISSN 1471-2148 DOI: https://doi.org/10.1186/s12862-016-0688-y

Duchene, Sebastian; Holt, Kathryn E; Weill, Francois-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). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000094

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). 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). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000064

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. ISSN 2045-2322 DOI: https://doi.org/10.1038/srep29316

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). ISSN 2235-2988 DOI: https://doi.org/10.3389/tcimb.2016.00141

Schultz, Mark B; Duy, Pham Thanh; Nhu, Tran Do Hoan; Wick, Ryan R; Ingle, Danielle J; Hawkey, Jane; Edwards, David J; Kenyon, Johanna J; Nguyen, Phu Huong Lan; Campbell, James I; +6 more... Thwaites, Guy; Nguyen, Thi Khanh Nhu; 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). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000050

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

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). 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, Francois-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

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

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

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). 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). pp. 1-16. ISSN 1664-3224 DOI: https://doi.org/10.3389/fimmu.2014.00447

Comas, Inaki; 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). 1176-U311. ISSN 1061-4036 DOI: https://doi.org/10.1038/ng.2744

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). S69-S82. ISSN 2169-8287 DOI: https://doi.org/10.1128/genomeA.00293-13

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). ISSN 2150-7511 DOI: https://doi.org/10.1128/mBio.00565-13

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). ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0084567

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; Likic, Vladimir A; Lithgow, Trevor; (2012) A Bioinformatic Strategy for the Detection, Classification and Analysis of Bacterial Autotransporters. PLOS ONE, 7 (8). 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, Francoise; 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). ISSN 1471-2164 DOI: https://doi.org/10.1186/1471-2164-13-258 Item availability may be restricted.

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). ISSN 1471-2164 DOI: https://doi.org/10.1186/1471-2164-13-338

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). ISSN 1553-7366 DOI: https://doi.org/10.1371/journal.ppat.1002131

Karkey, Abhilasha; Arjyal, Amit; Anders, Katherine L; Boni, Maciej F; Dongol, Sabina; Koirala, Samir; Phan, Vu Tra My; Tran, Vu Thieu Nga; Clements, Archie CA; Holt, Kathryn E; +8 more... Pham, Thanh Duy; 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). ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0013988

Song, Yajun; Roumagnac, Philippe; Weill, Francois-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

Tran, Vu Thieu Nga; Karkey, Abhilasha; Dongol, Sabina; Hang, Nguyen Thuy; Dunstan, Sarah; Holt, Kathryn; Le, Thi Phuong Tu; Campbell, James I; Tran, Thuy Chau; Nguyen, Van Vinh Chau; +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). ISSN 1471-2334 DOI: https://doi.org/10.1186/1471-2334-10-125

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). ISSN 1471-2164 DOI: https://doi.org/10.1186/1471-2164-10-36

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

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). ISSN 1746-4811 DOI: https://doi.org/10.1186/1746-4811-2-8