Kathryn Holt

Professor

  • Level 2, The Burnet Institute 85 Commercial Road Melbourne 3004

    Australia

Accepting PhD Students

20052023

Research output per year

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Research Output

2020

Persistent circulation of a fluoroquinolone-resistant Salmonella enterica Typhi clone in the Indian subcontinent

Britto, C. D., Dyson, Z. A., Mathias, S., Bosco, A., Dougan, G., Jose, S., Nagaraj, S., Holt, K. E. & Pollard, A. J., 1 Feb 2020, In : Journal of Antimicrobial Chemotherapy. 75, 2, p. 337-341 5 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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2019

Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii

Boinett, C. J., Cain, A. K., Hawkey, J., Do Hoang, N. T., Khanh, N. N. T., Thanh, D. P., Dordel, J., Campbell, J. I., Lan, N. P. H., Mayho, M., Langridge, G. C., Hadfield, J., Chau, N. V. V., Thwaites, G. E., Parkhill, J., Thomson, N. R., Holt, K. E. & Baker, S., 1 Feb 2019, In : Microbial genomics. 5, 2, 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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2 Citations (Scopus)

Co-circulation of Multidrug-resistant Shigella among Men Who Have Sex with Men in Australia

Ingle, D. J., Easton, M., Valcanis, M., Seemann, T., Kwong, J. C., Stephens, N., Carter, G. P., Goncalves da Silva, A., Adamopoulos, J., Baines, S. L., Holt, K. E., Chow, E. P. F., Fairley, C., Chen, M. Y., Kirk, M. D., Howden, B. P. & Williamson, D. A., 15 Oct 2019, In : Clinical Infectious Diseases. 69, 9, p. 1535-1544 10 p.

Research output: Contribution to journalArticleResearchpeer-review

7 Citations (Scopus)

Convergence of virulence and MDR in a single plasmid vector in MDR Klebsiella pneumoniae ST15

Lam, M. M. C., Wyres, K. L., Wick, R. R., Judd, L. M., Fostervold, A., Holt, K. E. & Löhr, I. H., May 2019, In : Journal of Antimicrobial Chemotherapy. 74, 5, p. 1218-1222 5 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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7 Citations (Scopus)

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae

Wyres, K. L., Wick, R. R., Judd, L. M., Froumine, R., Tokolyi, A., Gorrie, C. L., Lam, M. M. C., Duchêne, S., Jenney, A. & Holt, K. E., 1 Apr 2019, In : PLoS Genetics. 15, 4, 25 p., e1008114.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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9 Citations (Scopus)

Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307

Wyres, K. L., Hawkey, J., Hetland, M. A. K., Fostervold, A., Wick, R. R., Judd, L. M., Hamidian, M., Howden, B. P., Löhr, I. H. & Holt, K. E., 1 Mar 2019, In : Journal of Antimicrobial Chemotherapy. 74, 3, p. 577-581 5 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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14 Citations (Scopus)

Empirical ways to identify novel Bedaquiline resistance mutations in AtpE

Karmakar, M., Rodrigues, C. H. M., Holt, K. E., Dunstan, S. J., Denholm, J. & Ascher, D. B., 1 May 2019, In : PLoS ONE. 14, 5, 14 p., e0217169.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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3 Citations (Scopus)

Evolution of a clade of Acinetobacter baumannii global clone 1, lineage 1 via acquisition of carbapenem- and aminoglycoside-resistance genes and dispersion of ISAba1

Hamidian, M., Hawkey, J., Wick, R., Holt, K. E. & Hall, R. M., 1 Jan 2019, In : Microbial genomics. 5, 1, 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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7 Citations (Scopus)

FastSpar: Rapid and scalable correlation estimation for compositional data

Watts, S. C., Ritchie, S. C., Inouye, M. & Holt, K. E., 15 Mar 2019, In : Bioinformatics. 35, 6, p. 1064-1066 3 p.

Research output: Contribution to journalArticleOtherpeer-review

Open Access
3 Citations (Scopus)

Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198

Hawkey, J., Le Hello, S., Doublet, B., Granier, S. A., Hendriksen, R. S., Florian Fricke, W., Ceyssens, P. J., Gomart, C., Billman-Jacobe, H., Holt, K. E. & Weill, F. X., 1 Jul 2019, In : Microbial genomics. 5, 7, 12 p., 000269.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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6 Citations (Scopus)

Performance of neural network basecalling tools for Oxford Nanopore sequencing

Wick, R. R., Judd, L. M. & Holt, K. E., 24 Jun 2019, In : Genome Biology. 20, 1, 10 p., 129.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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16 Citations (Scopus)

Small IncQ1 and col-like plasmids harboring bla KPC-2 and non-Tn4401 elements (NTE KPC -IId) in high-risk lineages of Klebsiella pneumoniae CG258

Cerdeira, L. T., Lam, M. M. C., Wyres, K. L., Wick, R. R., Judd, L. M., Lopes, R., Ribas, R. M., Morais, M. M., Holt, K. E. & Lincopan, N., 1 Mar 2019, In : Antimicrobial Agents and Chemotherapy. 63, 3, 4 p., e02140-18.

Research output: Contribution to journalLetterResearchpeer-review

1 Citation (Scopus)
2018

Airway Microbiota Dynamics Uncover a Critical Window for Interplay of Pathogenic Bacteria and Allergy in Childhood Respiratory Disease

Teo, S. M., Tang, H. H. F., Mok, D., Judd, L. M., Watts, S. C., Pham, K., Holt, B. J., Kusel, M., Serralha, M., Troy, N., Bochkov, Y. A., Grindle, K., Lemanske, R. F., Johnston, S. L., Gern, J. E., Sly, P. D., Holt, P. G., Holt, K. E. & Inouye, M., 12 Sep 2018, In : Cell Host and Microbe. 24, 3, p. 341-352.e5 17 p.

Research output: Contribution to journalArticleResearchpeer-review

18 Citations (Scopus)

A novel genetic variant of Streptococcus pneumoniae serotype 11A discovered in Fiji

Manna, S., Ortika, B. D., Dunne, E. M., Holt, K. E., Kama, M., Russell, F. M., Hinds, J. & Satzke, C., 1 Apr 2018, In : Clinical Microbiology and Infection. 24, 4, p. 428.e1-428.e7 7 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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8 Citations (Scopus)

Antimicrobial-resistant klebsiella pneumoniae carriage and infection in specialized geriatric care wards linked to acquisition in the referring hospital

Gorrie, C. L., Mirceta, M., Wick, R. R., Judd, L. M., Wyres, K. L., Thomson, N. R., Strugnell, R. A., Pratt, N. F., Garlick, J. S., Watson, K. M., Hunter, P. C., McGloughlin, S. A., Spelman, D. W., Jenney, A. W. J. & Holt, K. E., 2 Jul 2018, In : Clinical Infectious Diseases. 67, 2, p. 161-170 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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24 Citations (Scopus)

Complete genome sequence of wm99c, an antibiotic-resistant acinetobacter baumannii global clone 2 (gc2) strain representing an australian gc2 lineage

Nigro, S. J., Wick, R., Holt, K. E. & Hall, R. M., 6 Dec 2018, In : Microbiology Resource Announcements. 7, 22, 2 p., e01199-18.

Research output: Contribution to journalArticleOtherpeer-review

Open Access
1 Citation (Scopus)

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks

Wick, R. R., Judd, L. M. & Holt, K. E., 1 Nov 2018, In : PLoS Computational Biology. 14, 11, 11 p., e1006583.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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10 Citations (Scopus)

Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating

Mostowy, R. J. & Holt, K. E., 1 Dec 2018, In : Trends in Microbiology. 26, 12, p. 1008-1021 14 p.

Research output: Contribution to journalReview ArticleResearchpeer-review

Open Access
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14 Citations (Scopus)

Dynamics of antimicrobial resistance in intestinal Escherichia coli from children in community settings in South Asia and sub-Saharan Africa

Ingle, D. J., Levine, M. M., Kotloff, K. L., Holt, K. E. & Robins-Browne, R. M., 1 Sep 2018, In : Nature Microbiology. 3, 9, p. 1063-1073 11 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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10 Citations (Scopus)

Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection

Hawkey, J., Ascher, D. B., Judd, L. M., Wick, R. R., Kostoulias, X., Cleland, H., Spelman, D. W., Padiglione, A., Peleg, A. Y. & Holt, K. E., Mar 2018, In : Microbial genomics. 4, 3, 11 p., 000165.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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14 Citations (Scopus)

Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam

Holt, K. E., McAdam, P., Thai, P. V. K., Thuong, N. T. T., Ha, D. T. M., Lan, N. N., Lan, N. H., Nhu, N. T. Q., Hai, H. T., Ha, V. T. N., Thwaites, G., Edwards, D. J., Nath, A. P., Pham, K., Ascher, D. B., Farrar, J., Khor, C. C., Teo, Y. Y., Inouye, M., Caws, M. & 1 others, Dunstan, S. J., 1 Jun 2018, In : Nature Genetics. 50, 6, p. 849-856 8 p.

Research output: Contribution to journalArticleResearchpeer-review

35 Citations (Scopus)

Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations

Lam, M. MC., Wick, R. R., Wyres, K. L., Gorrie, C. L., Judd, L. M., Jenney, A. WJ., Brisse, S. & Holt, K. E., 1 Sep 2018, In : Microbial genomics. 4, 9, 14 p., 000196.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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37 Citations (Scopus)

Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens

Baker, S., Thomson, N., Weill, F. X. & Holt, K. E., 18 May 2018, In : Science. 360, 6390, p. 733-738 6 p.

Research output: Contribution to journalReview ArticleResearchpeer-review

Open Access
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41 Citations (Scopus)

Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation

Brynildsrud, O. B., Pepperell, C. S., Suffys, P., Grandjean, L., Monteserin, J., Debech, N., Bohlin, J., Alfsnes, K., Pettersson, J. O. H., Kirkeleite, I., Fandinho, F., Da Silva, M. A., Perdigao, J., Portugal, I., Viveiros, M., Clark, T., Caws, M., Dunstan, S., Thai, P. V. K., Lopez, B. & 10 others, Ritacco, V., Kitchen, A., Brown, T. S., Van Soolingen, D., O'Neill, M. B., Holt, K. E., Feil, E. J., Mathema, B., Balloux, F. & Eldholm, V., 17 Oct 2018, In : Science Advances. 4, 10, 11 p., eaat5869.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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18 Citations (Scopus)

Kaptive web: User-Friendly capsule and lipopolysaccharide serotype prediction for Klebsiella genomes

Wick, R. R., Heinz, E., Holt, K. E. & Wyres, K. L., 1 Jun 2018, In : Journal of Clinical Microbiology. 56, 6, 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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23 Citations (Scopus)

Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria

Wyres, K. L. & Holt, K. E., 1 Oct 2018, In : Current Opinion in Microbiology. 45, p. 131-139 9 p.

Research output: Contribution to journalReview ArticleResearchpeer-review

Open Access
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29 Citations (Scopus)

Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: Antimicrobial resistance and implications for vaccine policy

Britto, C. D., Dyson, Z. A., Duchene, S., Carter, M. J., Gurung, M., Kelly, D. F., Murdoch, D. R., Ansari, I., Thorson, S., Shrestha, S., Adhikari, N., Dougan, G., Holt, K. E. & Pollard, A. J., 23 Apr 2018, In : PLoS Neglected Tropical Diseases. 12, 4, 19 p., e0006408.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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12 Citations (Scopus)

Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin

Cain, A. K., Boinett, C. J., Barquist, L., Dordel, J., Fookes, M., Mayho, M., Ellington, M. J., Goulding, D., Pickard, D., Wick, R. R., Holt, K. E., Parkhill, J. & Thomson, N. R., 1 Dec 2018, In : Scientific Reports. 8, 1, 11 p., 9868.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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2 Citations (Scopus)

Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination

Lam, M. M. C., Wyres, K. L., Duchêne, S., Wick, R. R., Judd, L. M., Gan, Y. H., Hoh, C. H., Archuleta, S., Molton, J. S., Kalimuddin, S., Koh, T. H., Passet, V., Brisse, S. & Holt, K. E., 1 Dec 2018, In : Nature Communications. 9, 1, 10 p., 2703.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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27 Citations (Scopus)

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa

Park, S. E., Pham, D. T., Boinett, C., Wong, V. K., Pak, G. D., Panzner, U., Espinoza, L. M. C., von Kalckreuth, V., Im, J., Schütt-Gerowitt, H., Crump, J. A., Breiman, R. F., Adu-Sarkodie, Y., Owusu-Dabo, E., Rakotozandrindrainy, R., Soura, A. B., Aseffa, A., Gasmelseed, N., Keddy, K. H., May, J. & 50 others, Sow, A. G., Aaby, P., Biggs, H. M., Hertz, J. T., Montgomery, J. M., Cosmas, L., Olack, B., Fields, B., Sarpong, N., Razafindrabe, T. J. L., Raminosoa, T. M., Kabore, L. P., Sampo, E., Teferi, M., Yeshitela, B., El Tayeb, M. A., Sooka, A., Meyer, C. G., Krumkamp, R., Dekker, D. M., Jaeger, A., Poppert, S., Tall, A., Niang, A., Bjerregaard-Andersen, M., Løfberg, S. V., Seo, H. J., Jeon, H. J., Deerin, J. F., Park, J., Konings, F., Ali, M., Clemens, J. D., Hughes, P., Sendagala, J. N., Vudriko, T., Downing, R., Ikumapayi, U. N., Mackenzie, G. A., Obaro, S., Argimon, S., Aanensen, D. M., Page, A., Keane, J. A., Duchene, S., Dyson, Z., Holt, K. E., Dougan, G., Marks, F. & Baker, S., 1 Dec 2018, In : Nature Communications. 9, 1, 10 p., 5094.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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8 Citations (Scopus)

Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae

Lam, M. M. C., Wyres, K. L., Judd, L. M., Wick, R. R., Jenney, A., Brisse, S. & Holt, K. E., 29 Oct 2018, In : Genome Medicine. 10, 1, 15 p., 77.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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9 Citations (Scopus)

Trajectories of childhood immune development and respiratory health relevant to asthma and allergy

Tang, H. H. F., Teo, S. M., Belgrave, D. C. M., Evans, M. D., Jackson, D. J., Brozynska, M., Kusel, M. M. H., Johnston, S. L., Gern, J. E., Lemanske, R. F., Simpson, A., Custovic, A., Sly, P. D., Holt, P. G., Holt, K. E. & Inouye, M., 1 Oct 2018, In : eLife. 7, 31 p., e35856.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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2 Citations (Scopus)
2017

Comparative genomics of Crohn's disease-Associated adherent-invasive Escherichia coli

O'Brien, C. L., Bringer, M. A., Holt, K. E., Gordon, D. M., Dubois, A. L., Barnich, N., Darfeuille-Michaud, A. & Pavli, P., 1 Aug 2017, In : Gut. 66, 8, p. 1382-1389 8 p.

Research output: Contribution to journalArticleResearchpeer-review

24 Citations (Scopus)

Completing bacterial genome assemblies with multiplex MinION sequencing

Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E., 1 Oct 2017, In : Microbial genomics. 3, 10, 7 p., 000132.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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71 Citations (Scopus)

Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain

Perrin, A., Larsonneur, E., Nicholson, A. C., Edwards, D. J., Gundlach, K. M., Whitney, A. M., Gulvik, C. A., Bell, M. E., Rendueles, O., Cury, J., Hugon, P., Clermont, D., Enouf, V., Loparev, V., Juieng, P., Monson, T., Warshauer, D., Elbadawi, L. I., Walters, M. S., Crist, M. B. & 9 others, Noble-Wang, J., Borlaug, G., Rocha, E. P. C., Criscuolo, A., Touchon, M., Davis, J. P., Holt, K. E., McQuiston, J. R. & Brisse, S., 24 May 2017, In : Nature Communications. 8, 12 p., 15483.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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32 Citations (Scopus)

Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients

Gorrie, C. L., Mirc Eta, M., Wick, R. R., Edwards, D. J., Thomson, N. R., Strugnell, R. A., Pratt, N. F., Garlick, J. S., Watson, K. M., Pilcher, D. V., McGloughlin, S. A., Spelman, D. W., Jenney, A. W. J. & Holt, K. E., 15 Jul 2017, In : Clinical Infectious Diseases. 65, 2, p. 208-215 8 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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64 Citations (Scopus)

Genomic history of the seventh pandemic of cholera in Africa

Weill, F. X., Domman, D., Njamkepo, E., Tarr, C., Rauzier, J., Fawal, N., Keddy, K. H., Salje, H., Moore, S., Mukhopadhyay, A. K., Bercion, R., Luquero, F. J., Ngandjio, A., Dosso, M., Monakhova, E., Garin, B., Bouchier, C., Pazzani, C., Mutreja, A., Grunow, R. & 21 others, Sidikou, F., Bonte, L., Breurec, S., Damian, M., Njanpop-Lafourcade, B. M., Sapriel, G., Page, A. L., Hamze, M., Henkens, M., Chowdhury, G., Mengel, M., Koeck, J. L., Fournier, J. M., Dougan, G., Grimont, P. A. D., Parkhill, J., Holt, K. E., Piarroux, R., Ramamurthy, T., Quilici, M. L. & Thomson, N. R., 10 Nov 2017, In : Science. 358, 6364, p. 785-789 5 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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55 Citations (Scopus)

Prediction of antibiotic resistance from antibiotic resistance genes detected in antibiotic-resistant commensal Escherichia coli using PCR or WGS

Moran, R. A., Anantham, S., Holt, K. E. & Hall, R. M., 1 Mar 2017, In : Journal of Antimicrobial Chemotherapy. 72, 3, p. 700-704 5 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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13 Citations (Scopus)

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

Darton, T. C., Meiring, J. E., Tonks, S., Khan, M. A., Khanam, F., Shakya, M., Thindwa, D., Baker, S., Basnyat, B., Clemens, J. D., Dougan, G., Dolecek, C., Dunstan, S. J., Gordon, M. A., Heyderman, R. S., Holt, K. E., Pitzer, V. E., Qadri, F., Kamarul Zaman, T., Pollard, A. J. & 1 others, STRATAA Study Consortium, 1 Jun 2017, In : BMJ Open. 7, 6, 9 p., e016283.

Research output: Contribution to journalReview ArticleOtherpeer-review

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17 Citations (Scopus)

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E., 1 Jun 2017, In : PLoS Computational Biology. 13, 6, 22 p., e1005595.

Research output: Contribution to journalArticleResearchpeer-review

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454 Citations (Scopus)

Variants of AbGRI3 carrying the armA gene in extensively antibiotic-resistant Acinetobacter baumannii from Singapore

Blackwell, G. A., Holt, K. E., Bentley, S. D., Hsu, L. Y. & Hall, R. M., 1 Jan 2017, In : Journal of Antimicrobial Chemotherapy. 72, 4, p. 1031-1039 9 p.

Research output: Contribution to journalArticleResearchpeer-review

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15 Citations (Scopus)

Vitamin D over the first decade and susceptibility to childhood allergy and asthma

Hollams, E. M., Teo, S. M., Kusel, M., Holt, B. J., Holt, K. E., Inouye, M., De Klerk, N. H., Zhang, G., Sly, P. D., Hart, P. H. & Holt, P. G., 1 Feb 2017, In : Journal of Allergy and Clinical Immunology. 139, 2, p. 472-481.e9 19 p.

Research output: Contribution to journalArticleResearchpeer-review

38 Citations (Scopus)

Whole Genome Sequence Analysis of Salmonella Typhi Isolated in Thailand before and after the Introduction of a National Immunization Program

Dyson, Z. A., Thanh, D. P., Bodhidatta, L., Mason, C. J., Srijan, A., Rabaa, M. A., Vinh, P. V., Thanh, T. H., Thwaites, G. E., Baker, S. & Holt, K. E., 6 Jan 2017, In : PLoS Neglected Tropical Diseases. 11, 1, 15 p., e0005274.

Research output: Contribution to journalArticleResearchpeer-review

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9 Citations (Scopus)
2016

An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid

Wong, V. K., Baker, S., Connor, T. R., Pickard, D., Page, A. J., Dave, J., Murphy, N. C., Holliman, R., Sefton, A., Millar, M., Dyson, Z. A., Dougan, G., Holt, K. E. & International Typhoid Consortium, 5 Oct 2016, In : Nature Communications. 7, 11 p., 12827.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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36 Citations (Scopus)

A novel ciprofloxacin-resistant subclade of h58. Salmonella typhi is associated with fluoroquinolone treatment failure

Thanh, D. P., Karkey, A., Dongol, S., Thi, N. H., Thompson, C. N., Rabaa, M. A., Arjyal, A., Holt, K. E., Wong, V., Thieu, N. T. V., Vinh, P. V., Thanh, T. H., Pradhan, A., Shrestha, S. K., Gajurel, D., Pickard, D., Parry, C. M., Dougan, G., Wolbers, M., Dolecek, C. & 3 others, Thwaites, G. E., Basnyat, B. & Baker, S., 14 Mar 2016, In : eLife. 5, 13 p., e14003.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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38 Citations (Scopus)

Are Escherichia coli pathotypes still relevant in the era of whole-genome sequencing?

Robins-Browne, R. M., Holt, K. E., Ingle, D. J., Hocking, D. M., Yang, J. & Tauschek, M., 18 Nov 2016, In : Frontiers in Cellular and Infection Microbiology. 6, NOV, 9 p., 141.

Research output: Contribution to journalReview ArticleResearchpeer-review

Open Access
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26 Citations (Scopus)

A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets

Ritchie, S. C., Watts, S., Fearnley, L. G., Holt, K. E., Abraham, G. & Inouye, M., 27 Jul 2016, In : Cell Systems. 3, 1, p. 71-82 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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9 Citations (Scopus)

A small Acinetobacter plasmid carrying the tet39 tetracycline resistance determinant

Hamidian, M., Holt, K. E., Pickard, D. & Hall, R. M., 1 Jan 2016, In : Journal of Antimicrobial Chemotherapy. 71, 1, p. 269-271 3 p.

Research output: Contribution to journalLetterOtherpeer-review

Open Access
9 Citations (Scopus)

Cross-validation to select Bayesian hierarchical models in phylogenetics

Duchêne, S., Duchêne, D. A., Di Giallonardo, F., Eden, J. S., Geoghegan, J. L., Holt, K. E., Ho, S. Y. W. & Holmes, E. C., 26 May 2016, In : BMC Evolutionary Biology. 16, 1, 8 p., 115.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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9 Citations (Scopus)