Holt Group

Holt group
2020 Holt group. L-R Back row: Mr Hugh Cottingham, Dr Zoe Dyson, Mr Stephen Watts, Mr Ryan Wick Middle row: Dr Kelly Wyres, Prof Kathryn Holt, Dr Louise Judd, Dr Margaret Lam Front row: Mr David Edwards*, Dr Jane Hawkey, Ms Taylor Harshegyi. Absent: Dr Louise Cerdeira, Dr Leonardos Mageiros, Mr Hassan Al-Mana, Ms Fatemah Mubarak

*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 Holt lab.

Group Head

Microbial Genomics

Key terms

  • genomics, bacteria, antimicrobial resistance, microbiome, hospital acquired infections, bioinformatics


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.

Visit Holt Lab website for more information on our research areas and funding; and our current & past group members.

Student research projects

Applying genomics to track the evolution and spread of hospital pathogens
Supervisor(s): Prof Kathryn Holt, Dr Jane Hawkey and Dr Kelly Wyres
Email: Kathryn.Holt@monash.edu
Applicable for: PhD, Masters, Honours, BMedSc(Hons)

Genomics and metabolic modelling of Klebsiella, a drug resistant priority pathogen
Supervisor(s): Dr Kelly Wyres, Prof Kathryn Holt and Dr Jane Hawkey
Email: Kelly.Wyres@monash.edu
Applicable for: PhD, Masters, Honours, BMedSc(Hons)

Investigating plasmid transmission in clinical pathogens
Supervisor(s): Dr Margaret Lam and Prof Kathryn Holt
Email: Margaret.Lam@monash.edu
Applicable for: Masters, Honours, BMedSc(Hons)

Pathogen detection and genotyping by sequencing direct from specimens
Supervisor(s): Prof Kathryn Holt, Dr Kelly Wyres and Dr Jane Hawkey
Email: Kathryn.Holt@monash.edu
Applicable for: PhD, Masters, Honours, BMedSc(Hons)


A full list of publications can be found at Google Scholar or PURE research output

Other Links