Group members


Lab Head – Prof Kat Holt (PhD)

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Postdoctoral researchers

Dr Kelly Wyres (DPhil)

Kelly joined the lab as a post-doctoral researcher in 2015. Her work focusses on understanding the evolution and epidemiology of Klebsiella pneumoniae, in particular how and why this species is subdivided into hundreds of distinct clones that cause different clinical problems. Click here to read more or find Kelly on Google Scholar.

Dr Margaret Lam (PhD)

Margaret (Maggie) joined the group in July 2015 as an RA before starting as a postdoctoral fellow the following year. Here, her research has largely focussed on using comparative genomics and computation biology to unravel the incredible genetic diversity and mobilisation mechanisms of key virulence loci in Klebsiella pneumoniae. Prior to this, Maggie completed a Bachelor in Biomedical Science, Honours in Science and a Doctoral degree at The University of Melbourne. Find Maggie on Google Scholar.

Dr Jane Hawkey (PhD)

Jane joined the lab in 2013 as a PhD student, with a focus on the mobile elements that are responsible for disseminating antimicrobial resistance. During her PhD she developed the software ISMapper for enabling the detection of insertion sequences from short-read sequencing data. After the completion of her PhD in 2017, Jane became a Post-doctoral Research Fellow in the group. She is interested in the genomic evolution of hospital pathogens, particularly regarding mobile genetic elements that are shared between species. Find Jane on Google Scholar.

Dr Zoe Dyson (PhD)

Zoe’s research focusses on the bacterial cause of Typhoid fever. She uses genomic sequence analyses to understand how these bacteria spread within and between geographies and how they evolve drug-resistance. Zoe is currently seconded to the University of Cambridge (UK) working on the Strategic Alliance for Typhoid in Asia and Africa (STRATAA) project. Find Zoe on Google Scholar.

Dr Ryota Gomi (PhD)

Ryota was born and raised in Tokyo, Japan. He completed his PhD. in Engineering at Kyoto University. During his PhD, he studied microbial source tracking methods for identifying sources of microbial contamination in environmental water. He is visiting the lab a year, beginning August 2018. In the Holt lab, he is doing research on environmental Klebsiella species.

Lab Manager

Dr Louise Judd (PhD)

Louise manages the group’s wet lab space and equipment, and performs the majority of our wet lab experiments. These include DNA or RNA extractions and sequencing, and bacterial phenotyping e.g. antibiotic susceptibility testing. Louise developed the lab’s protocol for multiplexed long read sequencing on the Oxford Nanopore platform, which has become an integral component of many of our projects. Find Louise on Google Scholar.

Graduate students

Stephen Watts

Stephen is a PhD student investigating respiratory pathogens. He uses a combination of 16S RNA sequence and whole genome sequence data to explore the ecology and evolution of bacteria that colonise or cause disease in the respiratory tract. As part of this work Stephen developed FastSpar and HiCap.

Ryan Wick

Ryan Wick is a PhD student and research assistant. He developed Bandage & Unicycler. His work mainly focuses on bacterial genome assembly with an emphasis on the use of data from Oxford Nanopore’s sequencing platforms. His broader academic interests include machine learning, metagenomics and phylogenomics. Find Ryan on Google Scholar.

David Edwards

David originally joined the lab as a Masters project student, wherein he developed RedDog for bacterial nucleotide variant and gene content analysis. David is now a PhD student investigating approaches for detecting different types of natural selection in pathogen populations. Find David on Google Scholar.

Yu Wan

Wan recently submitted his PhD thesis, within which he combined bacterial genome-wide association, network analysis and genome assembly graph analyses to explore the co-occurrence of antibiotic resistance genes in Klebsiella pneumoniae and Escherichia coli.

Masters & Honours students

Roni Froumine

Roni is working towards an MSc in Bioinformatics. She is using bioinformatics approaches to investigate CRISPR/Cas locus diversity and activity in Klebsiella pneumoniae.

Leo Featherstone

Leo is an Honours student, working on phylodynamics in collaboration with alumni Sebastian Duchene at the University of Melbourne. He is working on detecting outbreaks of infectious bacteria using their DNA and statistics. He previously studied evolutionary biology and mathematics.

Kalani Paranagama

Kalani is an Honours student, working on developing a rapid genotyping scheme for Shigella sonnei. She is interested in learning how computational biology can be applied in a diagnostic setting.


Honoraries, Visitors & Grad students based in other labs

2018 Lab Retreat at Rye


  • Claire Gorrie (PhD) – K. pneumoniae genomic epidemiology
  • Danielle Ingle (PhD) – E. coli genomics
  • Dr Mark Schultz  (Postdoc) – A. baumannii phylogenomics and metagenomics
  • Sebastian Duchene (Postdoc) – Phylodynamics
  • Dr Paul McAdam (Postdoc) – TB phylogenomics
  • Macgregor Todd (MSc Bioinformatics)
  • Marialena Michanetzi (MSc Bioinformatics)
  • Cassandra Litchfield (MSc Bioinformatics)
  • Damien Zammit (MSc Bioinformatics) – Recombination analysis
  • Alex Tokolyi (Honours) – Plasmid genomics
  • Harriet Dashnow (VLSCI intern) – SRST2 early development
  • Partha Sarathi Gope (MPhil) – Plasmid bioinformatics
  • Louise Cerdeira (Visiting PhD student from University of São Paulo) – KPC plasmids
  • Carl Britto (Visiting PhD student from Oxford University) – Enteric fever
  • Gittan Blezer (MSc internship project from University of Utrecht) – K. pneumoniae core genome
  • Morgan Cerqueira Alves (3rd-year Biochemistry research project) – ESBL in K. pneumoniae
  • Wassif Kabir (3rd-year Biochemistry research project) – Salmonella Kentucky phylogenomics
  • Roni Froumine (3rd-year Microbiology research project) – CRISPR in K. pneumoniae
  • Muhammad Fadli Bin Ismail (3rd-year Biochemistry research project) – K. oxytoca comparative genomics
  • Hugh Cottingham (3rd-year Biochemistry research project) – Microbial enrichment from nasopharyngeal samples
  • Kalani Paranagama (3rd-year Microbiology research project) – IS elements in K. pneumoniae
Some of the lab attending AMIGOS in Sydney (Ryan, Paul, Claire, Jane, Harriet, Shu Mei, Stephen, Wan)
Some of the lab attending AMIGOS in Sydney (Ryan, Paul, Claire, Jane, Harriet, Shu Mei, Stephen, Wan)
Lab members working on a team project to analyse the genomes of vancomycin resistant Enterococcus isolated from a local hospital.
Lab members working on a team project to analyse the genomes of vancomycin resistant Enterococcus isolated from a local hospital.