Group members

Lab Head – Prof Kat Holt (PhD)

ORCID • Google Scholar • PubMed • BlueSky • GitHub

Kat is a computational biologist specialising in infectious disease genomics. She is Professor of Microbial Systems Genomics at the London School of Hygiene and Tropical Medicine (LSHTM) Department of Infection Biology, and Co-Director of the LSHTM AMR Centre. She is also an Adjunct Professor (Research) at Monash University’s Department of Infectious Diseases in Melbourne, Australia; a HHMI-Gates International Research Scholar; and former Editor-in-Chief of the UK Microbiology Society journal Microbial Genomics.

Kat has a BA/BSc from the University of Western Australia majoring in Biochemistry, Applied Statistics and Philosophy, with Honours in Genetics (2004); a PhD in Molecular Biology from the University of Cambridge and the Wellcome Trust Sanger Institute on the genomics of typhoid fever, supervised by Gordon Dougan, Julian Parkhill and Duncan Maskell (2009); and a Masters in Epidemiology from the University of Melbourne (2011). She has held Early Career (2010-2013) and Career Development (2014-2017) Fellowships from the NHMRC of Australia, and a Senior Medical Research Fellowship from the Viertel Foundation of Australia (2018-2021).

Kat has been awarded the Australian Academy of Science’s Gottschalk Medal for Medical Research (2017), a Georgina Sweet Award for Women in Quantitative Biomedical Science (2016), L’Oréal-UNESCO Rising Talents Fellowship (2015), the NHMRC Research Excellence Award for the Top-Ranked Career Development Fellow (2014) and L’Oréal For Women In Science Australia & NZ Fellowship (2013). Since 2020 Kat has been named a Web of Science Highly Cited Researcher. A list of publications can be found via Google Scholar.

London School based team

Assistant Professor Zoe Dyson (PhD)

Zoe is a former 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, and is a coordinator of the Global Typhoid Genomics Consortium. Find Zoe on Google Scholar and BlueSky @msmicrobiocode.bsky.social.

Dr Kara Tsang (PhD) – Honorary Assistant Professor

Kara is a computational biologist who joined the lab in 2021, before moving to McMaster University in 2025. She is leading the antimicrobial resistance prediction component of the KlebNET Genomic Surveillance Platform project. Find Kara on Google Scholar and twitter @KaraKTsang.

Dr Ebenezer Foster-Nyarko (PhD)

Ebenn is a clinical microbiologist with a PhD in 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 BlueSky @efosternyarko.bsky.social.

Dr Shaun Keegan (PhD)

Shaun is applying his expertise in modelling and statistics to study K and O antigen distribution in Klebsiella pneumoniae, to inform development of polysaccharide-based vaccines against neonatal sepsis. Find Shaun on BlueSky @shaunkeegan.bsky.social.

Erkison Odih (PhD)

Erkison is a microbial genomics and bioinformatics expert, investigating the dynamics of K and O locus turnover in Klebsiella pneumoniae to inform vaccine development efforts. He is also working on cluster identification and estimating the burden of neonatal sepsis that is associated with nosocomial transmission. Find Erkison on twitter @bioinfo_erkison.

Assistant Professor Charlene Rodrigues (DPhil)

Charlene is a paediatric infectious diseases clinician with a PhD in meningococcal genomics. She is currently working on the KlebNET Genomic Surveillance Platform project, where she will contribute to the devlopment of global genomic surveillance for Klebsiella pneumoniae, including applying her expertise in reporting of genomic results for a clinical and public health audience. Find Charlene on twitter @cmc_rodrigues and Google Scholar.

Megan Carey (PhD)

Megan is an expert in public health interventions for typhoid fever and recently graduated from the University of Cambridge. She works with us as Policy Fellow on the AMRnet project, and is a coordinator of the Global Typhoid Genomics Consortium. Find Megan on BlueSky @meganecarey.bsky.social, Google Scholar and ORCID.

Dr Louise Cerdeira (PhD)

Louise is a computational biologist and software engineer. She focuses on developing tools and genomic data analysis using the One Health approach to support global genomic surveillance. She has a PhD in Sciences focusing on microbial genomics, an MSc in Genetics and Molecular Biology, and a BSc in Computer Science. She first joined the lab in 2020 to work on the TyphiNET dashboard, and returned in 2023 to develop the the AMRnet Platform System Architecture. Find Louise on Google Scholar, LinkedIn, GitHub and BlueSky.

Anton Spadar (PhD)

Anton is a computational biologist. He joined the lab in 2023, and his current work focuses on design of amplicons for environmental surveillance of Salmonella Typhi. His PhD investigated epidemiology, AMR and virulence genes of K. pneumoniae. In addition, he has worked on host-pathogen genomics of flaviviruses transmitted by Aedes mosquitoes. Find Anton on Linkedin and Google Scholar.

Mary Maranga (PhD)

Mary is a bioinformatician specialising in microbial genomics. She is working on the AMRnet project, where she will be contributing to the development of open-access software to support the use of pathogen genomic data for AMR surveillance. Find Mary on twitter @gathoni_maranga.

Laura Phillips (PhD)

Laura is a computational biologist who joined the lab in 2024. She is currently working on a project to investigate the transmission of Klebsiella pneumoniae in a neonatal unit in Zambia, as well as being part of a Community of Practice on investigating pathogen transmission in neonatal units in low-resource settings.

Shaojie Bao

Shaojie is a Project Manager with over 8 years of combined experience in higher education and business environment within the UK, including a pivotal role as a Project Coordinator in Department of Infection Biology (DIB). He is currently managing the portfolio of research projects for Prof. Kat Holt and her team, primarily focuses on projects related to Klebsiella pneumoniae genomics for neonatal sepsis, supported by the Bill & Melinda Gates Foundation. Find Shaojie on Linkedin.

Vandana Sharma

Vandana is a software developer with a BTech and Masters in Computer Games. She is working in the lab as a research software engineer on the AMRnet dashboard.

Hassan Al-Mana

Hassan is a PhD student whose project focuses on using genomic approaches to understand the genetic basis for uropathogenicity of Klebsiella pneumoniae (i.e. how the bacterium causes urinary tract infections). He is co-supervised by Nick Furnham at LSHTM and Kelly Wyres at Monash University. Find Hassan on Google Scholar.

Dana Itani

Dana is a PhD student with a background in antimicrobial resistance (AMR), who is working on evaluating the benefits of including whole genome sequencing in national AMR surveillance programs. She is working closely with the National Reference Lab of AMR in Tunisia, in collaboration with the Quadram Institute.

Max Wallat

Max is a PhD student in the MRC-LID program, combining experimental work (with Jodi Lindsay at St George’s), genomics (with us) and modelling (with Gwen Knight at LSHTM) to investigate phage-mediated evolution of AMR in Staph aureus. Find Max on twitter @MaxWallat and ORCID.

Team members based elsewhere

Kat retains an Adjunct Professorship at Monash University in Melbourne and continues to work closely with former group members Dr Kelly Wyres, Dr Margaret Lam (who are members of the KlebNet project team) and Dr Jane Hawkey. Kat is also external supervisor to staff and students based outside LSHTM, who join the LSHTM team for regular group meetings and share code, data and resources – they are listed below.

Kalani Paranagama – Monash University

Marit Hetland – Stavanger University Hospital & University of Bergen

Marit has been collaborating with the Monash team on Klebsiella genomics since 2018, and is now undertaking a PhD at the University of Bergen in Norway, utilising isolates and data from the KLEB-GAP project to investigate genomic determinants of Klebsiella pneumoniae infection and transmission. Her primary supervisors are Iren Löhr and Bjørn Tore Lunestad; Ørjan Samuelsen (UiT) and Kat are co-supervisors.

Former lab group members

  • Dr Kelly Wyres (Postdoc, Unimelb & Monash) – K. pneumoniae genomics and capsule variation
  • Dr Jane Hawkey (PhD & Postdoc, Unimelb & Monash) – Microbial genomics
  • Dr Margaret Lam (Postdoc, Unimelb & Monash) – K. pneumoniae virulence genetics
  • Dr Ryan Wick (MSc Bioinformatics, RA, PhD & Postdoc, Unimelb & Monash) – Genome assembly
  • Dr Mark Schultz  (Postdoc, Unimelb) – A. baumannii phylogenomics and metagenomics
  • Dr Sebastian Duchene (Postdoc, Unimelb) – Phylodynamics
  • Dr Paul McAdam (Postdoc, Unimelb) – TB phylogenomics
  • Dr Shu Mei Teo (Postdoc, Unimelb) – Human microbiome and asthma development
  • Dr Leonardos Mageiros (Postdoc, Monash) – Human microbiome signatures of typhoid fever susceptibility, disease and carriage
  • Dr Tom Stanton (Postdoc, LSHTM) – Klebsiella K/O antigen sero-epi and Kaptive development
  • Louise Judd (Research Lab Manager, Unimelb & Monash)
  • Taylor Harshegyi (Research Assistant, Monash) – Wet lab molecular and microbiology
  • Claire Gorrie (PhD, Unimelb) – K. pneumoniae genomic epidemiology
  • Danielle Ingle (PhD, Unimelb) – E. coli genomics
  • Stephen Watts (PhD, Unimelb) – Respiratory pathogens and microbiome in children
  • Yu Wan (PhD, Unimelb) – Detection of AMR gene transfer
  • Jake Barber (PhD, Monash) – Experimental evolution
  • Heyu Lin (PhD, Unimelb) – Mercury methylation
  • Macgregor Todd (MSc Bioinformatics, Unimelb)
  • Marialena Michanetzi (MSc Bioinformatics, Unimelb)
  • Cassandra Litchfield (MSc Bioinformatics, Unimelb)
  • Damien Zammit (MSc Bioinformatics, Unimelb) – Recombination analysis
  • Roni Froumine (MSc Bioinformatics, Unimelb) – CRISPR/Cas9 loci in K. pneumoniae
  • Alex Tokolyi (Honours, Unimelb) – Plasmid genomics
  • Harriet Dashnow (VLSCI intern, Unimelb) – SRST2 early development
  • Partha Sarathi Gope (MPhil, Unimelb) – Plasmid bioinformatics
  • Carl Britto (Visiting PhD student from Oxford University, Unimelb) – Enteric fever
  • Gittan Blezer (MSc internship project from University of Utrecht, Unimelb) – K. pneumoniae core genome
  • Leo Featherstone (Honours, Monash) – Cluster detection from phylogenies
  • Kalani Paranagama (Honours & 3rd-year Biochemistry research project, Monash 2019) – Shigella sonnei genotyping framework
  • Morgan Cerqueira Alves (3rd-year Biochemistry research project, Unimelb) – ESBL in K. pneumoniae
  • Wassif Kabir (3rd-year Biochemistry research project, Unimelb) – Salmonella Kentucky phylogenomics
  • Muhammad Fadli Bin Ismail (3rd-year Biochemistry research project, Unimelb) – K. oxytoca comparative genomics
  • Ojonugwa Abubakar (MSc project & RA, LSHTM)
  • Iana Amke (MSc project & RA, LSHTM)
  • Dr Guillaume Meric (honorary Postdoc, Unimelb & Monash) – Pathogen and microbiome genomics
  • David Edwards (MSc Bioinformatics & RA & PhD, Unimelb & Monash). 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. He 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. His PhD thesis was awarded posthumously in 2022.