We are a computational genomics and sequencing group using 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 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.
To learn more about what we get up to in the lab, check out the blog posts on recent papers; recent preprints & papers listed on the right; the software we develop; our research areas and funding; and our current & past group members.
Interested in joining or visiting?
Students interested in joining the lab in Melbourne should first read about graduate research programmes at Monash University and contact Kat to discuss potential projects. From January 2019 we are based in the Department Infectious Diseases (Central Clinical School, Faculty of Medicine, Nursing & Health Sciences), located at the Alfred Hospital Precinct.
Students interested in projects based at the London School should read about the graduate research programmes at the London School of Hygiene and Tropical Medicine. We are based in the Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, located in Keppel Street, Bloomsbury.
Kat Holt – Bio
Kat is a computational biologist specialising in infectious disease genomics, and a Professor at Monash University and the London School of Hygiene and Tropical Medicine. She is currently a HHMI-Gates International Research Scholar and Viertel Foundation Senior Medical Research Fellow, and Senior Editor 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 also held Early Career (2010-2013) and Career Development (2014-2017) Fellowships from the NHMRC of Australia.
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).