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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

Award Date: 8 Mar 2014

University of Oxford

Oct 2004Jun 2007

Award Date: 15 Sep 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

Research Output

Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales

Holt, K. E., Lassalle, F., Wyres, K. L., Wick, R. & Mostowy, R. J., 6 Apr 2020, (Accepted/In press) In : ISME Journal. 18 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File

Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia

Wyres, K. L., Nguyen, T. N. T., Lam, M. M. C., Judd, L. M., van Vinh Chau, N., Dance, D. A. B., Ip, M., Karkey, A., Ling, C. L., Miliya, T., Newton, P. N., Lan, N. P. H., Sengduangphachanh, A., Turner, P., Veeraraghavan, B., Vinh, P. V., Vongsouvath, M., Thomson, N. R., Baker, S. & Holt, K. E., 16 Jan 2020, In : Genome Medicine. 12, 1, 16 p., 11.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
4 Citations (Scopus)
Open Access
File
4 Citations (Scopus)

Population genomics of Klebsiella pneumoniae

Wyres, K. L., Lam, M. M. C. & Holt, K. E., 1 Jun 2020, In : Nature Reviews Microbiology. 18, 6, p. 344-359 16 p.

Research output: Contribution to journalReview ArticleResearchpeer-review

1 Citation (Scopus)