Lab Head – Prof Kat Holt (PhD)
ORCID • Google Scholar • Publons • PubMed • Twitter • GitHub • Monash • LSHTM
London School of Hygiene & Tropical Medicine
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 and twitter @msmicrobiocode.
Dr Ebenezer Foster-Nyarko (PhD)
Ebenn is a clinical microbiologist and recently completed a PhD on E. coli genomics. He joined the lab in 2021 to work on the KlebNET Genomic Surveillance Platform, aiming to improve antimicrobial resistance and virulence prediction for Klebsiella pneumoniae to support global genomic surveillance. Find Ebenn on LinkedIn, Google Scholar and twitter @EFosterNyarko.
Dr Kara Tsang (PhD)
Kara is a computational biologist who joined the lab in 2021. She is leading the antimicrobial resistance prediction component of the KlebNET Genomic Surveillance Platform project. Find Kara on Google Scholar and twitter @KaraKTsang.
Tom Stanton
Tom combines microbiology and bioinformatics to study the genetic basis for clinically important phenotypes in Klebsiella and related pathogens. He is currently working with Kelly and Kat on understanding the relationship between genetic variation in the K (capsule synthesis) locus and serotype, and investigating sero-epidemiology of K. pneumoniae. Find Tom on twitter @tomstantonmicro.
Sydney Miles
Sydney is undertaking a PhD with Kat and Serge Mostowy at LSHTM, under the London Interdisciplinary Doctoral (LIDo) Training Programme. She is combining comparative genomics and in vivo infection modelling to investigate the evolution of pathogenicity and epidemiological success of Shigella sonnei lineages.
Monash University
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 and twitter @KelWyres.
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 and twitter @yekwah.
Dr Louise Judd (PhD) – Lab Manager
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.
Taylor Harshegyi – Research Assistant
Taylor is a research assistant in the lab. She holds a MSc in Biomedical Science and joined the lab in 2019 to assist with wet lab experiments and sequencing projects.
PhD students
Ryan Wick
Ryan Wick is a PhD student and research assistant. He developed the software packages Bandage, Unicycler and Trycycler, and also maintains our Kleborate and Kaptive software. 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, github and twitter @rrwick.
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).
Hugh Cottingham
Hugh did Honours in the lab in 2020, exploring the potential for using CRISPR-Cas9 coupled with nanopore sequencing for detection and typing of drug resistant Klebsiella. He commenced a PhD project in 2021, working with Kat, Jane, Nenad Macesic and Anton Peleg on nanopore sequencing-based approaches for clinical microbiology in the hospital setting.
Helena Cooper
Helena commenced a PhD program in 2021 with Kelly and Kat, working on metabolic modelling of Klebsiella pneumoniae.
Honoraries, Visitors & Grad students based in other labs
- Dr Guillaume Meric (Postdoc) – Pathogen and microbiome genomics (Inouye lab, Baker Institute)
- Jake Barber (PhD student) – Experimental evolution (McDonald lab, Monash University)
- Heyu Lin (PhD student) – Mercury methylation (Moreau lab, University of Melbourne Earth Sciences)
- Marit Hetland (PhD student) – Klebsiella population genomics (Stavanger University Hospital)
Alumni
- David Edwards tragically passed away October 2020. He was a wonderful and generous colleague who will be sorely missed by the other members of the lab. 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.
- 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
Holt Lab 