Kathryn Holt

Professor

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

    Australia

Accepting PhD Students

20072022
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Personal profile

Biography

Kat is a computational biologist specialising in infectious disease genomics, and a Professor at Monash University and the London School of Hygiene and Tropical Medicine. She is currently a HHMI-Gates International Research Scholar and Viertel Foundation Senior Medical Research Fellow, and Editor in Chief of the UK Microbiology Society journal Microbial Genomics.

Kat has a BA/BSc from the University of Western Australia majoring in Biochemistry, Applied Statistics and Philosophy, with Honours in Genetics (2004); a PhD in Molecular Biology from the University of Cambridge and the Wellcome Trust Sanger Institute on the genomics of typhoid fever, supervised by Gordon Dougan, Julian Parkhill and Duncan Maskell (2009); and a Masters in Epidemiology from the University of Melbourne (2011). She has also held Early Career (2010-2013) and Career Development (2014-2017) Fellowships from the NHMRC of Australia.

Kat has been awarded the Australian Academy of Science’s Gottschalk Medal for Medical Research (2017), a Georgina Sweet Award for Women in Quantitative Biomedical Science (2016), L’Oréal-UNESCO Rising Talents Fellowship (2015), the NHMRC Research Excellence Award for the Top-Ranked Career Development Fellow (2014) and L’Oréal For Women In Science Australia & NZ Fellowship (2013).

Research interests

Kat runs a computational genomics research group utilising genome sequencing, phylogenetics, spatiotemporal analysis and epidemiology to study the evolution and transmission of bacterial pathogens, including tropical diseases such as typhoiddysenteryE. coli diarrheaand tuberculosis; and hospital associated pathogens such as Klebsiella and Acinetobacter. Her lab is particularly interested in the global health crisis of antimicrobial resistance, using genomic epidemiology tools to understand the evolutionary history and global dissemination of multidrug resistant pathogens, and developing new tools for prospective surveillance and tracking of emerging problems in the public health and clinical infectious disease space. The lab are also interested in human, animal and environmental microbiomes, and their role in chronic disease, infectious disease, and horizontal gene transfer. They develop bioinformatics software when needed, including laboratory and computational methods for nanopore sequencing. The lab publishes open access papers (usually with preprints available before peer review, links on the right), deposits all data in public databases, and releases open source code.

Education/Academic qualification

Epidemiology, MEpi, The University of Melbourne

Molecular Biology, PhD, University of Cambridge

Biochemistry, Applied Statistics, Philosophy, BSc/BA (Hons), The University of Western Australia

External positions

Honorary Research Fellow, The University of Melbourne

2019

Professor of Microbial Systems Genomics, London School of Hygiene & Tropical Medicine

Apr 2018 → …

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Projects 2019 2022

Research Output 2007 2017

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
File

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 othersSTRATAA Study Consortium, 1 Jun 2017, In : BMJ Open. 7, 6, 9 p., e016283.

Research output: Contribution to journalReview ArticleOtherpeer-review

Open Access
File

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
File

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 othersThwaites, G. E., Basnyat, B. & Baker, S., 14 Mar 2016, In : eLife. 5, 13 p., e14003.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File

Evolution of atypical enteropathogenic E. Coli by repeated acquisition of LEE pathogenicity island variants

Ingle, D. J., Tauschek, M., Edwards, D. J., Hocking, D. M., Pickard, D. J., Azzopardi, K. I., Amarasena, T. H., Bennett-Wood, V. R., Pearson, J. S., Tamboura, B., Antonio, M., Ochieng, J. B., Oundo, J., Mandomando, I., Qureshi, S. M., Ramamurthy, T., Hossain, A., Kotloff, K. L., Nataro, J. P., Dougan, G. & 3 othersLevine, M. M., Robins-Browne, R. M. & Holt, K. E., 18 Jan 2016, In : Nature Microbiology. 1, 2, 9 p., 15010.

Research output: Contribution to journalArticleResearchpeer-review