Matthew T. G. Holden
A5047037920- Antimicrobial Resistance in Staphylococcus
- Bacterial Identification and Susceptibility Testing
- Streptococcal Infections and Treatments
- Bacterial biofilms and quorum sensing
- Microbial infections and disease research
- Genomics and Phylogenetic Studies
- Antibiotic Resistance in Bacteria
- Bacteriophages and microbial interactions
- SARS-CoV-2 and COVID-19 Research
- Bacterial Genetics and Biotechnology
- Antibiotic Use and Resistance
- COVID-19 Clinical Research Studies
- Neonatal and Maternal Infections
- Urinary Tract Infections Management
- Plant Pathogenic Bacteria Studies
- Burkholderia infections and melioidosis
- Infective Endocarditis Diagnosis and Management
- Vibrio bacteria research studies
- Global Maternal and Child Health
- Laser Design and Applications
- SARS-CoV-2 detection and testing
- Animal Virus Infections Studies
- Atomic and Molecular Physics
- Mycobacterium research and diagnosis
- Biochemical and Structural Characterization
University of St Andrews
2016-2025
Public Health Scotland
2020-2024
Catholic University of Health and Allied Sciences
2023
Imperial College London
2022
Quadram Institute
2022
Wellcome Sanger Institute
2012-2021
Exosome Diagnostics (United States)
2021
Public Health England
2021
R&D Systems (United States)
2021
Faculty of Public Health
2021
Abstract Summary: A typical prokaryote population sequencing study can now consist of hundreds or thousands isolates. Interrogating these datasets provide detailed insights into the genetic structure prokaryotic genomes. We introduce Roary, a tool that rapidly builds large-scale pan genomes, identifying core and accessory genes. Roary makes construction genome samples possible on standard desktop without compromising accuracy results. Using single CPU produce consisting 1000 isolates in 4.5...
The Gram-negative bacterium Yersinia pestis is the causative agent of systemic invasive infectious disease classically referred to as plague, and has been responsible for three human pandemics: Justinian plague (sixth eighth centuries), Black Death (fourteenth nineteenth centuries) modern (nineteenth century present day). recent identification strains resistant multiple drugs potential use Y. an biological warfare mean that still poses a threat health. Here we report complete genome sequence...
Current methods for differentiating isolates of predominant lineages pathogenic bacteria often do not provide sufficient resolution to define precise relationships. Here, we describe a high-throughput genomics approach that provides high-resolution view the epidemiology and microevolution dominant strain methicillin-resistant Staphylococcus aureus (MRSA). This reveals global geographic structure within lineage, its intercontinental transmission through four decades, potential trace...
Staphylococcus aureus is an important nosocomial and community-acquired pathogen. Its genetic plasticity has facilitated the evolution of many virulent drug-resistant strains, presenting a major constantly changing clinical challenge. We sequenced approximately 2.8-Mbp genomes two disease-causing S. strains isolated from distinct settings: recent hospital-acquired representative epidemic methicillin-resistant EMRSA-16 clone (MRSA252), clinically globally prevalent lineage; invasive...
Burkholderia pseudomallei is a recognized biothreat agent and the causative of melioidosis. This Gram-negative bacterium exists as soil saprophyte in melioidosis-endemic areas world accounts for 20% community-acquired septicaemias northeastern Thailand where half those affected die. Here we report complete genome B. pseudomallei, which composed two chromosomes 4.07 megabase pairs 3.17 pairs, showing significant functional partitioning genes between them. The large chromosome encodes many...
Visualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple genomes as a tree provides framework onto which associated data (geographical, temporal, phenotypic and epidemiological) are added generate hypotheses explore dynamics system under investigation. Selected static images then within publications highlight key findings wider audience. However, these very inadequate way exploring interpreting...
Isolates of methicillin-resistant Staphylococcus aureus (MRSA) belonging to a single lineage are often indistinguishable by means current typing techniques. Whole-genome sequencing may provide improved resolution define transmission pathways and characterize outbreaks.
The emergence of meticillin-resistant Staphylococcus aureus (MRSA) that can persist in the community and replace existing hospital-adapted lineages MRSA means it is necessary to understand transmission dynamics terms hospitals as one entity. We assessed use whole-genome sequencing enhance detection between these settings.We studied a putative outbreak on special care baby unit (SCBU) at National Health Service Foundation Trust Cambridge, UK. used validate expand findings from an...
In cell‐free Pseudomonas aeruginosa culture supernatants, we identified two compounds capable of activating an N ‐acylhomoserine lactone (AHL) biosensor. Mass spectrometry and NMR spectroscopy revealed that these were not AHLs but the diketopiperazines (DKPs), cyclo(ΔAla‐ l ‐Val) cyclo( ‐Pro‐ ‐Tyr) respectively. These also found in supernatants from Proteus mirabilis , Citrobacter freundii Enterobacter agglomerans [cyclo(ΔAla‐ only]. Although both DKPs absent fluorescens alcaligenes...
Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone public health response to COVID-19. The emergence hypermutated, increasingly transmissible variants concern (VOCs) threaten this strategy. Omicron (B.1.1.529), fifth VOC be described, harbours multiple amino acid mutations in spike, half which lie within receptor-binding domain. Here we demonstrate substantial evasion neutralization by BA.1 and BA.2 vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2...
The widespread use of antibiotics in association with high-density clinical care has driven the emergence drug-resistant bacteria that are adapted to thrive hospitalized patients. Of particular concern globally disseminated methicillin-resistant Staphylococcus aureus (MRSA) clones cause outbreaks and epidemics associated health care. most rapidly spreading tenacious health-care-associated clone Europe currently is EMRSA-15, which was first detected UK early 1990s subsequently spread...
We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike ΔH69/V70 in multiple independent lineages, often occurring after acquisition of receptor binding motif replacements such as N439K and Y453F, known to increase affinity the ACE2 confer antibody escape. In vitro, we show that, although itself is not an evasion mechanism, it increases infectivity associated with enhanced incorporation cleaved into virions. able partially rescue proteins that have acquired Y453F escape...
The bacterial family Enterobacteriaceae is notable for its well studied human pathogens, including Salmonella , Yersinia Shigella and Escherichia spp. However, it also contains several plant pathogens. We report the genome sequence of a pathogenic enterobacterium, Erwinia carotovora subsp. atroseptica ( Eca ) strain SCRI1043, causative agent soft rot blackleg potato diseases. Approximately 33% genes are not shared with sequenced enterobacterial some predicted to facilitate unexpected...
ABSTRACT Bacterial infections of the lungs cystic fibrosis (CF) patients cause major complications in treatment this common genetic disease. Burkholderia cenocepacia infection is particularly problematic since organism has high levels antibiotic resistance, making it difficult to eradicate; resulting chronic are associated with severe declines lung function and increased mortality rates. B. strain J2315 was isolated from a CF patient member epidemic ET12 lineage that originated Canada or...
The spread of drug-resistant bacterial pathogens poses a major threat to global health. It is widely recognised that the widespread use antibiotics has generated selective pressures have driven emergence resistant strains. Methicillin-resistant Staphylococcus aureus (MRSA) was first observed in 1960, less than one year after introduction this second generation beta-lactam antibiotic into clinical practice. Epidemiological evidence always suggested resistance arose around period, when mecA...
GeneDB (http://www.genedb.org) is a genome database for prokaryotic and eukaryotic pathogens closely related organisms. The resource provides portal to sequence annotation data, which primarily generated by the Pathogen Genomics group at Wellcome Trust Sanger Institute. It combines data from completed ongoing projects with curated annotation, readily accessible web based resource. development of in recent years has focused on providing database-driven tools pipelines, as well catering...