Dr Mathew A Beale

Senior Staff Scientist

I am a molecular and computational microbiologist, with broad wet and dry lab experience, expertise in genomic laboratory methods and bioinformatic 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.

Genomic population structure of T. pallidum in England (Beale et al, 2023)



Distribution of T. pallidum lineages and sublineages throughout England (Beale et al, 2023)


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.

Localised transmission network of Yaws in Papua New Guinea (Beale et al, 2020)

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.


Transmission of MDR K. pneumoniae within two Vietnamese ICUs (Pham et al, 2023)

My timeline


My publications

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