Mathew Beale

Publications

• The global epidemiology of emerging Histoplasma species in recent years
• On the effective depth of viral sequence data
• Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African HIV/AIDS cohort.
• Genomic epidemiology of syphilis reveals independent emergence of macrolide resistance across multiple circulating lineages
• A Population Genomics Approach to Assessing the Genetic Basis of Within-Host Microevolution Underlying Recurrent Cryptococcal Meningitis Infection
• Tracing Genetic Exchange and Biogeography of Cryptococcus neoformans var. grubii at the Global Population Level
• Identification of novel adenovirus genotype 90 in children from Bangladesh
• Whole genome sequencing of Herpes Simplex Virus 1 directly from human cerebrospinal fluid reveals selective constraints in neurotropic viruses
• Trial of Three Rounds of Mass Azithromycin Administration for Yaws Eradication.
• Clinical and biological insights from viral genome sequencing.
• An integrated national scale SARS-CoV-2 genomic surveillance network
• SARS-CoV-2 genomics as a springboard for future disease mitigation in LMICs
• Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis
• AIDS-related mycoses: the way forward.
• Is there evidence of recent hepatitis E virus infection in English and North Welsh blood donors?
• The genetic backbone modulates the phenotype of Hepatitis B surface antigen mutants
• Illuminating choices for library prep: A comparison of library preparation methods for whole genome sequencing of cryptococcus neoformans using Illumina HiSeq
• Efficient phagocytosis and laccase activity affect the outcome of HIV-associated cryptococcosis
• Genotypic Diversity Is Associated with Clinical Outcome and Phenotype in Cryptococcal Meningitis across Southern Africa.
• Genomic Context of Azole Resistance Mutations in Aspergillus fumigatus Determined Using Whole-Genome Sequencing
• A genomic epidemiology investigation of yaws re-emergence and bacterial drug resistance selection
• Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen
• A genomic appraisal of invasive Salmonella Typhimurium and associated antibiotic resistance in sub-Saharan Africa
• Genus-wide research provides insights into pathogen evolution
• Investigating the role of whole genome sequencing in syphilis epidemiology: an English case study
• Household geckos as a potential vector forSalmonellatransmission in Malawi
• Genomic epidemiology of the cholera outbreak in Yemen reveals the spread of a multi-drug resistance plasmid between diverse lineages of Vibrio cholerae
• Conference report: the first bacterial genome sequencing pan-European network conference
• One Health in Eastern Africa: No barriers for ESBL producingE. colitransmission or independent antimicrobial resistance gene flow across ecological compartments
• Evidence of widespread endemic populations of highly multidrug resistant Klebsiella pneumoniae in hospital settings in Hanoi, Vietnam: a prospective cohort study
• Genomic analysis of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli colonising adults in Blantyre, Malawi reveals previously undescribed diversity
• Genomic epidemiology of syphilis in England: a population-based study
• Genomic epidemiology on the move
• The Effect of Repeated Mass Drug Administration on the Transmission of Yaws: A Genomic Epidemiology Study
• Characterisation of Treponema pallidum lineages within the contemporary syphilis outbreak in Australia: a genomic epidemiological analysis
• Genomic and antigenic diversity of colonizing Klebsiella pneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi
• Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission
• Colonization dynamics of extended-spectrum beta-lactamase-producing Enterobacterales in the gut of Malawian adults
• Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity
• Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission
• Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study
• SARS-CoV-2 Testing in the Community: Testing Positive Samples with the TaqMan SARS-CoV-2 Mutation Panel To Find Variants in Real Time
• Trial of Three Rounds of Mass Azithromycin Administration for Yaws Eradication
• Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England
• Changes in symptomatology, re-infection and transmissibility associated with SARS-CoV-2 variant B.1.1.7: An ecological study
• Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study
• Early analysis of a potential link between viral load and the N501Y mutation in the SARS-COV-2 spike protein
• Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity
• Dynamics of gut mucosal colonisation with extended spectrum beta-lactamase producing Enterobacterales in Malawi
• Epidemiologic and genomic reidentifi cation of yaws, liberia
• SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies
• Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7
• Genomic epidemiology of covid-19 in care homes in the east of England
• Exploring genetic diversity, population structure, and phylogeography in Paracoccidioides species using AFLP markers
• Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic
• Genomic reconstruction of the SARS-CoV-2 epidemic in England
• Trends in the molecular epidemiology and population genetics of emerging Sporothrix species
• Salmonella carriage by geckos detected within households in Malawi
• Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data
• Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies
• Archaeogenetics: What Can Ancient Genomes Tell Us about the Origin of Syphilis?
• Genotypic diversity is associated with clinical outcome and phenotype in cryptococcal meningitis across Southern Africa
• Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African HIV/AIDS cohort
• Clinical and biological insights from viral genome sequencing
• Yaws re-emergence and bacterial drug resistance selection after mass administration of azithromycin: a genomic epidemiology investigation
• Phylo-Plex: A phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology