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Personal profile

Biography

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 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 an NHMRC Emerging Leadership Fellow based in the Microbial Genomics Lab in the Department of Infectious Diseases. I am a co-developer of Kaptive and Kaptive Web (tools for identification of Klebsiella surface polysaccharide loci in whole genome sequence data) and recently completed a large-scale genomic comparison of 28 distinct K. pneumoniae clones, which revealed key differences in their evolutionary dynamics.

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.

Education/Academic qualification

Zoology, DPhil, University of Oxford

Jan 2009Sep 2012

University of Oxford

Oct 2004Jun 2007

External positions

Post-Doctoral Research Fellow, University of Melbourne

Sep 2015Dec 2018

Staff Researcher & Genomics Team Lead, IBM Research - Australia

Jan 2015Sep 2015

Staff Researcher, IBM Research - Australia

Feb 2013Dec 2014

DPhil Candidate, University of Oxford

Jan 2009Sep 2012

Laboratory Technician, University of Oxford

Oct 2007Dec 2008

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Projects 2019 2024

Research Output 2010 2019

5 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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8 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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8 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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1 Citation (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