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An Interdisciplinary Research Centre at the University of Cambridge

I am a molecular and computational microbiologist, with a broad wet and dry lab experience, expertise in genomic laboratory methods and bioinformatics analysis of pathogen genomes, working with viral, fungal and bacterial human pathogens.

My research focuses on the use of genome sequencing and population genomics to address questions of inter- and intra-host evolutionary and transmission dynamics, population structure, host adaptation and acquisition of virulence. In my current research in the Thomson group at WSI, I have continued previous work on direct sequencing approaches for pathogen genomics, developing laboratory and computational approaches for difficult to sequence (primarily bacterial) pathogens, and this has included substantial metagenomics. My primary research focuses on bacterial sexually transmitted infections (STIs) and neglected tropical diseases (NTDs), with a current emphasis on Treponema species (e.g. Syphilis, Yaws), where I am addressing questions around global genomic diversity, evolutionary drivers and history, and disease transmission epidemiology.

Sexually Transmitted Infections (STIs)
Incidence of sexually transmitted infections has been rising in many high income countries over the last two decades. My work uses whole genome sequencing to study the genetic diversity and epidemiological correlates of STI transmission. This includes projects on Neisseria gonorrhoea, Chlamydia trachomatis and Treponema pallidum. In particular, my work on T. pallidum (causative agent of syphilis) has helped to characterise the global genetic diversity and spread of this organism. I am currently a Co-Investigator on a BMGF-funded project to conduct aetiological and genomic surveillance of genital ulcer disease (GUD) in LMICs.

Neglected Tropical Diseases
I also work on neglected tropical diseases, and infectious diseases that disproportionately affect low and middle income countries (LMICS). This includes past work on viruses (such as Hepatitis B) and fungal pathogens (such as Cryptococcus). My current work is focussed on Yaws, a form of tropical ulcer associated with Treponema pallidum subspecies pertenue. I am using genomics to explore the genetic diversity and evolution of this bacterial pathogen, with a particular emphasis on the evolution of antimicrobial resistance, the effect of erradication efforts such as mass drug administration on the bacterial population structure, and how molecular and genomic epidemiology approaches can be developed and used to inform elimination efforts.

Antimicrobial Resistance
Within the Thomson group, I also support and oversee a number of projects focussing on the evolution and epidemiology of antimicrobial resistance – particularly in enterobacteriaciae such as Klebsiella pneumoniae and Escherichia coli. This includes extensive phylogenetics and analysis of mobile genetic elements. We have been investigating the acquisition of extended-spectrum Beta-lactamase resistant species in both a hospital and community environment, with a particular focus on longitudinal sampling.

Key Projects, Countries, and Partners:

  • Molecular and Genomic Surveillance of Genital Ulcer Disease in LMICs (Ghana, Uganda, Botswana, Zimbabwe, Argentina)
  • Genomic Surveillance of Syphilis (Global: USA, Canada, Europe(most), Zimbabwe, Argentina, Australia)
  • Genomic surveillance of Yaws: Papua New Guinea, Ghana, Liberia (+potentially Togo, Cote d'Ivoire)
  • Genomic Surveillance of AMR: Malawi
  • Genomic Surveillance of STIs: Singapore (past)
Postdoctoral Fellow, Parasites and Microbes Programme, Wellcome Sanger Institute
Molecular Microbiology, Bioinformatics, Phylogenetics, Phylodynamics, Molecular/Genomic Epidemiology, Genomic Surveillance. Sexually Transmitted Infections, Neglected Tropical Diseases, Global Health.
Not available for consultancy