Projects per year
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 typhoid, dysentery, E. 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.
Expertise related to UN Sustainable Development Goals
In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):
Education/Academic qualification
Epidemiology, MEpi, University of Melbourne
Award Date: 2 Dec 2011
Molecular Biology, PhD, University of Cambridge
Award Date: 12 Nov 2009
Biochemistry, Applied Statistics, Philosophy, BSc/BA (Hons), University of Western Australia
Award Date: 2 Dec 2005
External positions
Honorary Research Fellow, University of Melbourne
2019
Professor of Microbial Systems Genomics, London School of Hygiene & Tropical Medicine
Apr 2018 → …
Research area keywords
- Infectious disease genomics
- Computational genomics
- Genome sequencing
- Phylogenetics
- Spatiotemporal analysis
- Epidemiology
- Bacterial pathogens
- Tropical diseases
- Antimicrobial resistance
Collaborations and top research areas from the last five years
Recent external collaboration on country/territory level. Dive into details by clicking on the dots or
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KlebNET 2: An integrated platform for K. pneumoniae genomic surveillance
Holt, K. (Primary Chief Investigator (PCI)), Wyres, K. (Chief Investigator (CI)), Lam, M. (Chief Investigator (CI)), Stanton, T. (Chief Investigator (CI)), Brisse, S. (Chief Investigator (CI)), Aaenensen, D. (Chief Investigator (CI)), Ott, S. (Chief Investigator (CI)), McArthur, A. (Chief Investigator (CI)), Dramowksi, A. (Chief Investigator (CI)), Jolley, K. A. (Chief Investigator (CI)), Brancotte , B. (Chief Investigator (CI)), Raffestin , B. (Chief Investigator (CI)), Dyer, N. (Chief Investigator (CI)) & Tsang, K. (Chief Investigator (CI))
1/01/25 → 31/12/27
Project: Research
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META-GP: Delivering a Clinical Metagenomics Platform for Australia
Stinear, T. P. (Primary Chief Investigator (PCI)), Williamson, D. A. (Chief Investigator (CI)), Howden, B. P. (Chief Investigator (CI)), Coin, L. J. M. (Chief Investigator (CI)), Tong, S. Y. C. (Chief Investigator (CI)), Denholm, J. T. (Chief Investigator (CI)), Seemann, T. (Chief Investigator (CI)), Andersson, P. (Chief Investigator (CI)), Slavin, M. A. (Chief Investigator (CI)), Thursky, K. A. (Chief Investigator (CI)), Bryant, P. A. (Chief Investigator (CI)), Peleg, A. (Chief Investigator (CI)), Holt, K. (Chief Investigator (CI)), Kwong, J. C. (Chief Investigator (CI)), Holmes, E. C. (Chief Investigator (CI)), Sintchenko, V. (Chief Investigator (CI)), Britton, P. N. (Chief Investigator (CI)), Eden, J.-S. (Chief Investigator (CI)), Whiley, D. (Chief Investigator (CI)), Trembizki, E. (Chief Investigator (CI)), Jennison, A. (Chief Investigator (CI)), Schlebusch, S. (Chief Investigator (CI)), Dwyer, D. E. (Chief Investigator (CI)), Kok, J. (Chief Investigator (CI)), Sintchenko, V. (Chief Investigator (CI)) & Badrick, T. (Chief Investigator (CI))
Department of Health and Aged Care (Australia)
6/01/21 → 30/06/25
Project: Research
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Unlocking the secrets of metabolic variation in a highly diverse bacterium
Wyres, K. (Primary Chief Investigator (PCI)), Holt, K. (Partner Investigator (PI)), Monk, J. (Partner Investigator (PI)) & Brisse, S. (Partner Investigator (PI))
19/10/20 → 31/12/25
Project: Research
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Genomics, Digital Health and Machine Learning: the SuperbugAi Flagship
Peleg, A. (Primary Chief Investigator (PCI)), Holt, K. (Chief Investigator (CI)), Song, J. (Chief Investigator (CI)), Macesic, N. (Chief Investigator (CI)), Ananda-Rajah, M. (Chief Investigator (CI)), Webb, G. (Chief Investigator (CI)), Korman, T. (Chief Investigator (CI)), Stuart, R. (Chief Investigator (CI)), Cheng, A. (Chief Investigator (CI)), Peel, T. (Chief Investigator (CI)), Stewardson, A. (Chief Investigator (CI)), Ayton, D. (Chief Investigator (CI)) & Bain, C. (Chief Investigator (CI))
2/01/21 → 7/12/24
Project: Research
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Enabling Klebsiella pneumoniae genomic surveillance and sero-epidemiology
Holt, K. (Primary Chief Investigator (PCI)) & Wyres, K. (Chief Investigator (CI))
7/09/20 → 30/09/21
Project: Research
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A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex
Cooper, H. B., Vezina, B., Hawkey, J., Passet, V., López-Fernández, S., Monk, J. M., Brisse, S., Holt, K. E. & Wyres, K. L., 20 Feb 2024, In: Microbial Genomics. 10, 2, 16 p., 001206.Research output: Contribution to journal › Article › Research › peer-review
Open Access2 Citations (Scopus) -
High-level nitrofurantoin resistance in a clinical isolate of Klebsiella pneumoniae: a comparative genomics and metabolomics analysis
Hussein, M., Sun, Z., Hawkey, J., Allobawi, R., Judd, L. M., Carbone, V., Sharma, R., Thombare, V., Baker, M., Rao, G. G., Li, J., Holt, K. E. & Velkov, T., 23 Jan 2024, In: mSystems. 9, 1, 16 p., e00972-23.Research output: Contribution to journal › Article › Research › peer-review
Open Access3 Citations (Scopus) -
A point mutation in recC associated with subclonal replacement of carbapenem-resistant Klebsiella pneumoniae ST11 in China
Zhou, K., Xue, C. X., Xu, T., Shen, P., Wei, S., Wyres, K. L., Lam, M. M. C., Liu, J., Lin, H., Chen, Y., Holt, K. E., the BRICS Working Group & Xiao, Y., 28 Apr 2023, In: Nature Communications. 14, 1, 14 p., 2464.Research output: Contribution to journal › Article › Research › peer-review
Open Access32 Citations (Scopus) -
Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models
Vezina, B., Watts, S. C., Hawkey, J., Cooper, H. B., Judd, L. M., Jenney, A. W. J., Monk, J. M., Holt, K. E. & Wyres, K. L., Oct 2023, In: eLife. 12, 22 p., e87406.Research output: Contribution to journal › Article › Research › peer-review
Open Access5 Citations (Scopus) -
Comment on: MDR carbapenemase-producing Klebsiella pneumoniae of the hypervirulence-associated ST23 clone in Poland, 2009–19
Lam, M. M. C., Holt, K. & Wyres, K. L., 3 Apr 2023, In: Journal of Antimicrobial Chemotherapy. 78, 4, p. 1132-1134 3 p.Research output: Contribution to journal › Comment / Debate › Other › peer-review
Open Access4 Citations (Scopus)