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, dysentery, E. coli diarrhoea and tuberculosis; and hospital associated pathogens such as Klebsiella and Acinetobacter.

We are particularly interested in the global health crisis of antimicrobial resistance (AMR), 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 developed 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 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 developed 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.

Meet the team

Kat Holt 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; and former Editor-in-Chief of the UK Microbiology Society journal Microbial Genomics. Full bio here.

Current and past group members are listed here.

Joining us

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. LSHTM has highly flexible work arrangements, and our team do a mix of working from home and coming in to recently-renovated, bright and sunny, open-plan office and lab space at Keppel Street.

Kat was previously based in Monash University’s Department of Infectious Diseases at the Alfred Hospital in Melbourne. The LSHTM team retains strong links there, including lots of ongoing projects in collaboration with Kelly Wyres, Margaret Lam, Jane Hawkey, 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.