Wyres lab

Kelly is currently Associate Professor & Research Group Leader, at Monash University Australia. She is also an Honorary Associate Professor at London School of Hygiene and Tropical Medicine, UK. Kelly co-leads the Monash University Department of Infectious Diseases, Infectious Diseases Genomics research stream and is a Centre Leader at the Monash University Centre to Impact AMR. Kelly is a Monash University Research Talent Accelerator Fellow 2024, former NHMRC (Australia) Emerging Leadership Fellow and recipient of multiple research funding awards, including from the Australian Research Council and the Gates Foundation. In 2024 and 2025 Kelly was named as a Clarivate Highly Cited Researcher, and in 2025 awarded the Australian Society of Microbiology’s prestigious Frank Fenner Award. You can learn about Kelly’s ongoing research here and see a list of highlighted papers here.

Kelly holds a BA (Hons) in Biological Sciences and DPhil in Zoology from the University of Oxford, where she was awarded a St Peter’s College Domus Scholarship and St Catherine’s College Graduate Scholarship (Sciences). Her doctoral thesis explored the genomic evolution of Streptococcus pneumoniae, a bacterial pathogen that causes pneumonia and meningitis in young children and the elderly. Kelly’s work focussed on understanding the evolution of penicillin resistance and vaccine escape in this globally important pathogen. As part of this work Kelly collected and characterised the largest sample (>400) of historical S. pneumoniae isolates of its time. She used a combination of microbiological and molecular biology laboratory techniques to characterise these isolates and select approximately 100 for whole-genome sequencing. The work was reported in three key publications, the most influential of which showed for the first time that recombination events resulting in capsule switching (relevant to vaccine design) have occurred commonly throughput the history of S. pneumoniae (Wyres et al JID 2013).

After completing her DPhil, Kelly moved to Australia and spent 2.5 years in an industry research role at IBM Research – Australia, first as a Staff Researcher and later as the Genomics Team Lead. Here her primary work focussed on the use of computing to facilitate the adoption of high-throughput DNA sequencing in clinical and public health microbiology labs. Kelly led a scoping review of computational tools available to support genomic analyses in these settings, highlighting the need for user friendly, reproducible analysis softwares. She led the microbial genomics strategy and contributed to an IBM executive report, The evolving promise of genomic medicine. During this time Kelly also continued to expand her foundational genomics research expertise through investigation of collateral drug susceptibility in Mycobacterium tuberculosis– the causal agent of tuberculosis.

In September 2015 Kelly transitioned back to an academic research role as a Post-Doctoral Research Fellow in the Microbial Genomics lab led by Kathryn Holt. It was here that Kelly developed her enthusiasm for Klebsiella genomic epidemiology and evolution, initially though the exploration of K. pneumoniae capsule synthesis loci, drawing on her biological knowledge about bacterial capsule genetics (gained through her doctorate) and then on her experiences at IBM in designing user-friendly genomic analysis tools. Kelly established the first standardised database and nomenclature for K. pneumoniae capsule locus typing and lead the development of Kaptive and Kaptive Web, tools for rapid identification of capsule loci from whole genome sequences. She also led several key stone K. pneumoniae genomics analyses, including a comparative analysis of the evolutionary dynamics of 28 distinct K. pneumoniae clones (closely related groups of K. pneumoniae) and contributed to the development of Kleborate, now the gold standard K. pneumoniae genomic typing tool.

Following award of an NHMRC Investigator Grant and ARC Discovery Project in 2019, Kelly started building her own team from within the Holt lab. In 2021 the team span out into an independent research group.