Welcome to the website of Kat Holt and her research group 

We use genome sequencing, phylogenetics, spatiotemporal analysis and epidemiology to study the evolution and transmission of bacterial pathogens, including tropical diseases such as typhoid, dysenteryE. coli diarrhea and tuberculosis; and hospital associated pathogens such as Klebsiella and Acinetobacter. We are particularly interested in the global health crisis of antimicrobial resistance, using genomic epidemiology tools to understand the evolutionary history and global dissemination of multidrug resistant pathogens, and developing new tools for prospective surveillance and tracking of emerging problems in the public health and clinical infectious disease space. We are also interested in human, animal and environmental microbiomes, and their role in chronic disease, infectious disease, and horizontal gene transfer. We develop bioinformatics software when needed, and have been having great fun working up lab and computational methods for nanopore sequencing (see links, top right). We publish open access wherever we can (usually with preprints available before peer review, links on the right), deposit all data in public databases, and release open source code.

Currently, a major focus of the group is genomic surveillance and epidemiology of Klebsiella pneumoniae, a pathogen recognised as critically important by the World Health Organisation due to its concerning levels of antimicrobial resistance (AMR). We use genomics to investigate Klebsiella populations, primarily those causing infections in humans; and translate our growing knowledge base into the informatics tools Kaptive (for capsule (K) and O antigen serotype prediction), and Kleborate (for speciation, AMR and virulence typing), to support global research and surveillance activities.

Another key focus is Salmonella Typhi, the agent of typhoid fever. In addition to applying genomics to investigate typhoid epidemiology, we developed and maintain the GenoTyphi genotyping scheme, helped establish and coordinate the Global Typhoid Genomics Consortium, and are developing the typhi.net dashboard for interactive visualisation of genomics-derived AMR and lineage data for Typhi.

To learn more about what we get up to in the lab, check out the recent preprints & papers listed on the right; the software we develop; our research areas; and our current & past group members.

Joining us

Kat is now based permanently at London School of Hygiene and Tropical Medicine, where she is Professor of Microbial Systems Genomics and Co-Director of the LSHTM AMR Centre.

Students interested in joining the group at the London School should read about the graduate research programmes at the London School of Hygiene and Tropical Medicine. We also host summer projects for LSHTM MSc students. We are based in the Department of Infection Biology, Faculty of Infectious and Tropical Diseases, located in Keppel Street, Bloomsbury.

Kat also maintains an Adjunct Professor (Research) position at Monash University’s Department of Infectious Diseases at the Alfred Hospital in Melbourne, with lots of ongoing projects in collaboration with Kelly Wyres, Margaret Lam, Nenad Macesic, Adam Jenney and Anton Peleg. Students interested in joining Melbourne-based projects should make contact directly with one of these Monash-based investigators.

Kat Holt – Bio

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 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).

In 2020 and 2021 Kat was named a Web of Science Highly Cited Researcher. A list of publications can be found via Google Scholar.