Group members


Lab Head – Prof Kat Holt (PhD)

ORCID • Google Scholar • PublonsPubMed • TwitterGitHub • MonashLSHTM

Postdoctoral researchers

Dr Kelly Wyres (DPhil)

Kelly is a NHMRC Emerging Leadership Fellow whose 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 is a Marie Curie research fellow based at LSHTM in London, focussing on genomic surveillance of the bacteria that cause typhoid fever (Salmonella Typhi). She uses genomic sequence analyses to understand how these bacteria spread within and between geographies and how they evolve drug resistance. Find Zoe on Google Scholar.

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.

Research assistant

Taylor Harshegyi

Taylor holds a MSc in Biomedical Science and joined the lab in 2019 to assist with wet lab experiments and sequencing projects.

Graduate students

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.

Hassan Al-Mana

Hassan is a PhD student who is using genomic approaches to understand the genetic basis for uropathogenicity of Klebsiella pneumoniae (i.e. how the bacterium causes urinary tract infections).

David Edwards

David joined the lab in 2010 as a Masters project student, wherein he developed RedDog for bacterial nucleotide variant and gene content analysis, and helped to write the Beginner’s Guide to Comparative Bacterial Genomics. David stayed on in the lab as a research assistant for several years before enrolling as a PhD student, investigating approaches for detecting different types of natural selection in pathogen populations, and developing SNPPar. David tragically passed away October 2020. He was a wonderful and generous colleague who will be sorely missed by the other members of the lab.


Honoraries, Visitors & Grad students based in other labs

2018 Lab Retreat at Rye


  • Dr Mark Schultz  (Postdoc) – A. baumannii phylogenomics and metagenomics
  • Sebastian Duchene (Postdoc) – Phylodynamics
  • Dr Paul McAdam (Postdoc) – TB phylogenomics
  • Dr Shu Mei Teo (Postdoc) – Human microbiome and asthma development (Inouye lab, Baker Institute)
  • Leonardos Mageiros (Postdoc) – Human microbiome signatures of typhoid fever susceptibility, disease and carriage
  • Louise Teixeira Cerdeira (Postdoc) – TyphiNET dashboard and ONT sequencing tools
  • Claire Gorrie (PhD) – K. pneumoniae genomic epidemiology
  • Danielle Ingle (PhD) – E. coli genomics
  • Stephen Watts (PhD) – Respiratory pathogens and microbiome in children
  • 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
  • Muhammad Fadli Bin Ismail (3rd-year Biochemistry research project) – K. oxytoca comparative genomics
  • Yu Wan (PhD) – detection of AMR gene transfer
  • Leo Featherstone (Honours) – cluster detection from phylogenies
  • Kalani Paranagama (3rd-year Biochemistry research project, Honours) – Shigella sonnei genotyping framework
  • Roni Froumine (MSc Bioinformatics) – CRISPR/Cas9 loci in K. pneumoniae
  • Hugh Cottingham (3rd-year Biochemistry research project, research assistant, Honours)
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.