Projects per year
Personal profile
Biography
I am an NHMRC Emerging Leadership Fellow based in the Department of Infectious Diseases, where I co-lead the Fundamental Microbial Genomics research program. I use comparative genomics techniques and metabolic modelling to investigate the diversity of Klebsiella pneumoniae, a bacterium that causes large numbers of hospital-associated infections with high rates of drug resistance. I am particularly interested in diversity of surface antigens (targets for novel anti-Klebsiella vaccines and phage therapies), as well as the features and evolution of closely related groups of K. pneumoniae, called ‘clones,’ that seem to be associated with distinct behaviours and clinical risks (e.g. some are particularly good at becoming drug-resistant while others are particularly virulent).
I am a co-developer of Kaptive and Kaptive Web (tools for identification of Klebsiella surface polysaccharide loci in whole genome sequence data) and Kleborate a comprehensive K. pneumoniae genotyping tool, which are used by research and public health labs globally. My team has also recently developed Bactabolize, a tool for rapid generation of strain-specific metabolic models and growth phenotype predictions from genome assemblies, which we are applying to understand how K. pneumoniae metabolic diversity is associated with ecology and clinical risk.
I am a direct contributor to the KlebNET-GSP project (Klebsiella genomic surveillance platform), which aims to implement accessible and harmonised tools that support global genomic surveillance for K. pneumoniae and closely related species. As part of this work, I chair the Epidemiology Working Group, comprising colleagues from around the globe working to build a genomically-informed K. pneumoniae clone risk framework.
My prior experience includes 2 ½ years as a Staff Researcher at IBM Research – Australia where I was a founding member of the IBM Research – Australia Genomics Team and later became the Team Lead. My team was interested in exploring the use of computing for clinical and public health genomics. We collaborated with colleagues around the world and contributed to a number of applied and pure research projects, including an evolutionary exploration of drug-resistant Mycobacterium tuberculosis, the bacterium that causes TB.
Before moving to Australia and joining IBM I completed my Bachelor’s and Doctoral degrees at the University of Oxford, UK. During my doctoral degree, I studied the genomic evolution of another important disease-causing bacterium, Streptococcus pneumoniae. I focused on the evolution of penicillin resistance and capsule switching, which is important for vaccine design.
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
Zoology, DPhil, Genome evolution of Streptococcus pneumoniae, University of Oxford
Jan 2009 → Sept 2012
Award Date: 8 Mar 2014
BA (Hons) Oxon Biological Sciences, University of Oxford
Oct 2004 → Jun 2007
Award Date: 15 Sept 2007
External positions
Post-Doctoral Research Fellow, University of Melbourne
Sept 2015 → Dec 2018
Staff Researcher & Genomics Team Lead, IBM Research (Australia)
Jan 2015 → Sept 2015
Staff Researcher, IBM Research (Australia)
Feb 2013 → Dec 2014
DPhil Candidate, University of Oxford
Jan 2009 → Sept 2012
Laboratory Technician, University of Oxford
Oct 2007 → Dec 2008
Research area keywords
- Comparative genomics
- Metabolic modelling
- Microbial genomics
- Kelbsiella pneumoniae
- Clinical genomics
- Public health genomics
- Mycobacterium tuberculosis
Collaborations and top research areas from the last five years
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Unlocking the secrets of metabolic variation in a highly diverse bacterium
Wyres, K., Holt, K., Monk, J. & Brisse, S.
19/10/20 → 19/10/24
Project: Research
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A clone-specific risk framework for Klebsiella pneumoniae transmission and AMR
1/01/20 → 30/06/25
Project: Research
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Klebsiella pneumoniae – a key driver in the global spread of antimicrobial resistance and a target for new approaches in diagnostics, surveillance and alternative therapeutics (KLEB-GAP).
Sundsfjord, A., Hoyland Lohr, I., Samuelsen, O., Sunde, M., Lunestad, B. T., Brisse, S., Giske, C. G., Bengoechea, J., Holt, K., Frantzen, C. & Wyres, K.
30/06/19 → 31/12/23
Project: Research
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Enabling Klebsiella pneumoniae genomic surveillance and sero-epidemiology
7/09/20 → 30/09/21
Project: Research
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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 Access -
Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models
Vezina, B., Watts, S., Cooper, H., Judd, L., Jenney, A. W. J., Monk, J. M., Holt, K. E. & Wyres, K. L., 30 May 2023, (Accepted/In press) 27 p. eLife Sciences Organisation, Ltd.Research output: Other contribution › Research › peer-review
Open Access -
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 Access -
Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae
Foster-Nyarko, E., Cottingham, H., Wick, R. R., Judd, L. M., Lam, M. M. C., Wyres, K. L., Stanton, T. D., Tsang, K. K., David, S., Aanensen, D. M., Brisse, S. & Holt, K. E., 2023, In: Microbial Genomics. 9, 2, 16 p., 000936.Research output: Contribution to journal › Article › Research › peer-review
Open Access3 Citations (Scopus) -
A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality
Hawkey, J., Vezina, B., Monk, J. M., Judd, L. M., Harshegyi, T., López-Fernández, S., Rodrigues, C., Brisse, S., Holt, K. E. & Wyres, K. L., May 2022, In: Genome Research. 32, 5, p. 1004-1014 11 p.Research output: Contribution to journal › Article › Research › peer-review
Open Access2 Citations (Scopus)
Activities
- 1 Patents
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IBM - International Business Machines Corporation (United States) (External organisation)
Thomas C. Conway (Member) & Kelly Wyres (Member)
10 Oct 2014Activity: Industry, Government and Philanthropy Engagement and Partnerships › Patents › Patent