Kathryn Holt


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


Accepting PhD Students

If you made any changes in Pure these will be visible here soon.

Personal profile


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


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

Apr 2018 → …

Network Recent external collaboration on country level. Dive into details by clicking on the dots.

Projects 2019 2022

Research Output 2005 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

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., Kirk, M., Howden, B. & Williamson, D. A., 2019, (Accepted/In press) In : Clinical Infectious Diseases. p. 1-10 10 p.

Research output: Contribution to journalArticleResearchpeer-review

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

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