Wyres lab

Kelly is a computational microbiologist with a background in bacterial population genetics and genomics. She is Associate Professor, Research Group Leader and Co-Lead for the Infectious Diseases Genomics program at the Department of Infectious Diseases, Monash University. She is also a Centre Leader for the Monash University Centre to Impact AMR and Co-Lead for the KlebNET Genomic Surveillance Platform, a multi-national consortium working to develop and harmonise resources that support global genomic surveillance for Klebsiella and Escherichia coli. Kelly has received numerous research funding awards, including a National Health and Medical Research Council of Australia Investigator Grant, Australian Research Council Discovery Project award and Gates Foundation Investment Grants. In 2024 Kelly was named a Clarivate Highly Cited Researcher and in 2025 received the Australian Society for Microbiology’s Frank Fenner Award.

Kelly completed her undergraduate and doctoral degrees at 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. Following a move to Australia in 2012, Kelly 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 work focussed on the use of computing to facilitate the adoption of high-throughput DNA sequencing in clinical and public health microbiology labs.

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. In 2020 Kelly started building her own team from within the Holt lab and in 2021 the team span out into an independent research group.

Outside of the lab Kelly is busy parenting an energetic pre-schooler and tries to find time to practice pilates.

Tom is a postdoctoral researcher working on K. pneumoniae sero-epidemiology and the ongoing development of our tools for typing capsule and lipopolysaccharide loci from bacterial genome data- Kaptive and Kaptive Web. This includes improving Kaptive’s accuracy for prediction of K. pneumoniae capsule phenotypes. Tom holds a PhD from the University of Edinburgh, UK.

Hina is a data management specialist leading a community effort to collate and curate a standardised meta-data collection for publicly available Klebsiella genome sequences. Hina holds a Master’s in Public Health and International Health from The University of New South Wales.

Naosie is a postdoctoral researcher developing and applying novel Kaptive databases for Klebsiella oxytoca O antigen loci and E. coli capsule loci, to explore the sero-epidemiology of these important pathogens. Naoise holds a PhD in Clinical Microbiology from Trinity College Dublin, Ireland.

Kalani is a third year PhD student using metabolic modelling to investigate the association between K. pneumoniae species complex metabolic traits and ecological niche. Kalani previously completed a Masters of Data Science and a Bachelor of Science (Hons) at Monash University, focussing on Shigella sonnei genomics.

Hassan is a PhD student working to identify K. pneumoniae genomic and metabolic factors associated with isolates that cause urinary tract infections in hospitalised patients. Hassan is co-supervised and based with Prof Kathryn Holt, London School of Hygiene and Tropical Medicine, UK.

Jiahui is a PhD student investigating the composition of K. pneumoniae surface membranes and the impact of porin mutations. Jiahui is co-supervised and based with Prof Trevor Lithgow, Monash University, Australia.

Abhinaba is a PhD student investigating the prevalence and diversity of bacteriocins within the K. pneumoniae population. Bacteriocins are antimicrobial peptides produced by the bacteria to kill competing cells. Abhinaba is co-supervised by Dr Ben Vezina and Prof Sheena McGowan (Monash University).

Ella is working towards an Honours degree. She is using transposon mutagenesis to identify K. pneumoniae genes required for growth on different carbon sources. Ella is co-supervised with Dr Fran Short (Monash University).

Claire is an Honours student working on K. pneumoniae plasmid diversity and dynamics. Claire is co-supervised and based with Dr Margaret Lam and Dr Ben Vezina (Monash University).