Mathew A. Beale

Phylo-Plex: A phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology

Phylo-Plex is a low-cost amplicon sequencing method for high-resolution genomic epidemiology, achieving fine-scale lineage discrimination comparable to whole-genome sequencing in resource-limited settings.

Aeromonas: Genomic Insights into an Environmental Pathogen and Reservoir of Antimicrobial Resistance

This study analyzes 1,853 Aeromonas genomes, revealing high genetic diversity, widespread AMR genes, and frequent misidentification as Vibrio cholerae.

One Health in Eastern Africa: No barriers for ESBL producing E. coli transmission or independent antimicrobial resistance gene flow across ecological compartments

The paper uses whole genome sequencing to show high diversity and transmission of ESBL-Ec across human, animal, and environmental compartments in low-income settings, supporting the One Health approach for AMR control.

Genomic epidemiology of syphilis reveals independent emergence of macrolide resistance across multiple circulating lineages

The paper shows that macrolide resistance in syphilis emerged independently in multiple lineages, not just the SS14 lineage, challenging the idea that resistance drove its spread.

Population Genomics Of Cryptococcus neoformans var. grubii Reveals New Biogeographic Relationships And Finely Maps Hybridization

This study analyzes the population genomics of Cryptococcus neoformans var. grubii, revealing hybridization, biogeographic relationships, and genetic structure across global isolates.

A population genomics approach to assessing the genetic basis of within-host microevolution underlying recurrent cryptococcal meningitis infection

The paper uses whole-genome sequencing to determine whether recurrent cryptococcal meningitis in HIV patients results from relapse or reinfection, finding clonal relationships in most cases and novel hypermutator mechanisms in others.