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List of works by Matthew Holden

"Gene accordions" cause genotypic and phenotypic heterogeneity in clonal populations of Staphylococcus aureus

scientific article published on 14 July 2020

2015 Epidemic of Severe Streptococcus agalactiae Sequence Type 283 Infections in Singapore Associated With the Consumption of Raw Freshwater Fish: A Detailed Analysis of Clinical, Epidemiological, and Bacterial Sequencing Data

scientific article

A Staphylococcus xylosus isolate with a new mecC allotype

scientific article published on 28 December 2012

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

scientific article

A highly conserved complete accessory Escherichia coli type III secretion system 2 is widespread in bloodstream isolates of the ST69 lineage

scientific article published on 05 March 2020

A novel hybrid SCCmec-mecC region in Staphylococcus sciuri

scientific article published on 02 December 2013

A novel streptococcal integrative conjugative element involved in iron acquisition.

scientific article published on December 2008

A shared population of epidemic methicillin-resistant Staphylococcus aureus 15 circulates in humans and companion animals.

scientific article

A single multilocus sequence typing (MLST) scheme for seven pathogenic Leptospira species

scientific article

A very early-branching Staphylococcus aureus lineage lacking the carotenoid pigment staphyloxanthin

scientific article

An Outbreak of Streptococcus pyogenes in a Mental Health Facility: Advantage of Well-Timed Whole-Genome Sequencing Over emm Typing

scientific article published on 09 May 2018

Antimicrobial resistance in atopic dermatitis: Need for an urgent rethink

scientific article published on 29 November 2018

Antimicrobial resistance to ceftazidime involving loss of penicillin-binding protein 3 in Burkholderia pseudomallei

scientific article

Arginine catabolic mobile element in methicillin-resistant Staphylococcus aureus (MRSA) clonal group ST239-MRSA-III isolates in Singapore: implications for PCR-based screening tests

scientific article published on 14 January 2013

Armed to the teeth

scientific article published on 01 April 2002

Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics

scientific article published on 27 May 2019

Author Correction: Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics

scientific article published on 1 August 2019

Author Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland ⬇️

correction of a scholarly article

Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland

scientific article published on 15 December 2015

Burkholderia Hep_Hag autotransporter (BuHA) proteins elicit a strong antibody response during experimental glanders but not human melioidosis

scientific article published on 15 March 2007

Burkholderia pseudomallei genome plasticity associated with genomic island variation

scientific article

Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles

article published in 2015

Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles.

scientific article

Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission

scientific article

Characterisation of a mobilisable plasmid conferring florfenicol and chloramphenicol resistance in Actinobacillus pleuropneumoniae

scientific article

Characterization of pneumonia due to Streptococcus equi subsp. zooepidemicus in dogs

scientific article

Chlamydia trachomatis: genome sequence analysis of lymphogranuloma venereum isolates

scientific article

Chlorhexidine and octenidine use, carriage of qac genes, and reduced antiseptic susceptibility in methicillin-resistant Staphylococcus aureus isolates from a healthcare network

scientific article published on 06 January 2019

Clinical Perspectives in Integrating Whole Genome Sequencing into the Investigation of Healthcare and Public Health Outbreaks - Hype or Help?

scientific article published on 09 November 2020

Colony morphology variation of Burkholderia pseudomallei is associated with antigenic variation and O-polysaccharide modification

scientific article published on 16 March 2015

Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica

scientific article

Comparative epidemiology and factors associated with major healthcare-associated methicillin-resistant Staphylococcus aureus clones among interconnected acute, intermediate- and long-term healthcare facilities in Singapore

scientific article published on 29 July 2020

Comparative genomics of vancomycin-resistant Staphylococcus aureus strains and their positions within the clade most commonly associated with Methicillin-resistant S. aureus hospital-acquired infection in the United States

scientific article

Comparative sequence analysis of the capsular polysaccharide loci of Actinobacillus pleuropneumoniae serovars 1-18, and development of two multiplex PCRs for comprehensive capsule typing.

scientific article

Comparative whole genome sequence analysis of the carcinogenic bacterial model pathogen Helicobacter felis

scientific article

Comparisons of dN/dS are time dependent for closely related bacterial genomes

scientific article

Complete Genome Sequence of MIDG2331, a Genetically Tractable Serovar 8 Clinical Isolate of Actinobacillus pleuropneumoniae

scientific article

Complete genome of acute rheumatic fever-associated serotype M5 Streptococcus pyogenes strain manfredo.

scientific article published on 29 September 2006

Complete genome sequence and lytic phase transcription profile of a Coccolithovirus

scientific article

Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18

scientific article

Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance

scientific article

Cooking with GAS

scientific article published on 01 April 2010

Corrigendum: Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland

scientific article published on September 2017

Corrigendum: Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline

scientific article published on 28 January 2015

Design, validation, and application of a seven-strain Staphylococcus aureus PCR product microarray for comparative genomics

scientific article published on November 2005

Development of a Multilocus Sequence Typing Scheme for Molecular Typing of Mycoplasma pneumoniae

scientific article

Distinct evolutionary patterns of Neisseria meningitidis serogroup B disease outbreaks at two universities in the USA.

scientific article published on 4 April 2018

Diversity of Streptococcus equi subsp. zooepidemicus strains isolated from the Spanish sheep and goat population and the identification, function and prevalence of a novel arbutin utilisation system

scientific article

Draft Genome Sequences of the Type Strains of Actinobacillus indolicus (46K2C) and Actinobacillus porcinus (NM319), Two NAD-Dependent Bacterial Species Found in the Respiratory Tract of Pigs

scientific article published on 02 January 2020

Emergence of a New Highly Successful Acapsular Group A Streptococcus Clade of Genotype emm89 in the United Kingdom

scientific article

Emergence of methicillin resistance predates the clinical use of antibiotics

scientific article published on 05 January 2022

Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance

scientific article published on 17 November 2014

Emergent and evolving antimicrobial resistance cassettes in community-associated fusidic acid and meticillin-resistant Staphylococcus aureus.

scientific article published on 19 February 2015

Enhanced nasopharyngeal infection and shedding associated with an epidemic lineage of emm3 group A Streptococcus

scientific article published on May 2017

Erratum: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

scientific article published on 12 May 2015

Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis

scientific article

Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent

scientific article published on 26 November 2019

Evolutionary History of the Coccolithoviridae

article

Evolutionary Trade-Offs Underlie the Multi-faceted Virulence of Staphylococcus aureus

scientific article published on 2 September 2015

Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system.

scientific article

Extensive DNA Inversions in the B. fragilis Genome Control Variable Gene Expression

scientific article

Fitting the niche by genomic adaptation

scientific article published in November 2003

Food for thought

scientific article published on 01 December 2005

Functional analysis of the EsaB component of the Staphylococcus aureus Type VII secretion system.

scientific article published on 22 November 2017

Gene exchange drives the ecological success of a multi-host bacterial pathogen

article

Gene expression changes linked to antimicrobial resistance, oxidative stress, iron depletion and retained motility are observed when Burkholderia cenocepacia grows in cystic fibrosis sputum

scientific article

GeneDB--an annotation database for pathogens

scientific article

Genetic analysis of invasive Escherichia coli in Scotland reveals determinants of healthcare-associated versus community-acquired infections

scientific article published on 22 June 2018

Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei

scientific article published on 22 November 2019

Genome giants

scientific article published on 01 July 2002

Genome sequence of Staphylococcus lugdunensis N920143 allows identification of putative colonization and virulence factors

scientific article published on 4 July 2011

Genome sequence of Yersinia pestis, the causative agent of plague

scientific article

Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes

scientific article published on 22 May 2007

Genome sequence of a recently emerged, highly transmissible, multi-antibiotic- and antiseptic-resistant variant of methicillin-resistant Staphylococcus aureus, sequence type 239 (TW).

scientific article published on 30 November 2009

Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors.

scholarly article

Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting

scientific article published on 9 December 2014

Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection

scientific article

Genome watch: Brothers in arms

article published in 2005

Genome-wide analysis reveals loci encoding anti-macrophage factors in the human pathogen Burkholderia pseudomallei K96243

scientific article

Genomes beyond compare

scientific article published on 01 August 2004

Genomic Analysis of Global <i>Staphylococcus argenteus</i> Strains Reveals Distinct Lineages With Differing Virulence and Antibiotic Resistance Gene Content

scientific article published on 02 December 2021

Genomic Dissection of an Icelandic Epidemic of Respiratory Disease in Horses and Associated Zoonotic Cases

scientific article

Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland

scholarly article

Genomic evidence for the evolution of Streptococcus equi: host restriction, increased virulence, and genetic exchange with human pathogens

scientific article

Genomic identification of cryptic susceptibility to penicillins and β-lactamase inhibitors in methicillin-resistant Staphylococcus aureus

scientific article published on 24 June 2019

Genomic insights into the emergence and spread of international clones of healthcare-, community- and livestock-associated meticillin-resistant Staphylococcus aureus: Blurring of the traditional definitions

scientific article

Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei

scientific article

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

scientific article

Genomics of Natural Populations of Staphylococcus aureus.

scientific article published on 29 July 2016

Global Scale Dissemination of ST93: A Divergent Epidemic Lineage That Has Recently Emerged From Remote Northern Australia

article

Global and regional dissemination and evolution of Burkholderia pseudomallei

scientific article published on 23 January 2017

Guidelines for reporting novel mecA gene homologues

scientific article

Haem-iron plays a key role in the regulation of the Ess/type VII secretion system of Staphylococcus aureus RN6390.

scientific article

ICEApl1, an Integrative Conjugative Element Related to ICEHin1056, Identified in the Pig Pathogen Actinobacillus pleuropneumoniae

scientific article

Identification of three novel superantigen-encoding genes in Streptococcus equi subsp. zooepidemicus, szeF, szeN, and szeP.

scientific article

Improved characterisation of MRSA transmission using within-host bacterial sequence diversity

scientific article published on 08 October 2019

In vivo evolution of antimicrobial resistance in a series of Staphylococcus aureus patient isolates: the entire picture or a cautionary tale?

scientific article published on 18 September 2013

Innate immunity. A Spaetzle-like role for nerve growth factor β in vertebrate immunity to Staphylococcus aureus

scientific article

Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines

scientific article published on 01 June 2020

Lost and found

scientific article published on 01 November 2001

LuxS: its role in central metabolism and the in vitro synthesis of 4-hydroxy-5-methyl-3(2H)-furanone.

scientific article

MRSA Transmission Dynamics Among Interconnected Acute, Intermediate-Term, and Long-Term Healthcare Facilities in Singapore

scientific article published on May 2017

Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice

scientific article

Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study

scientific article published on August 2011

Microbial mariners

scientific article published in 2005

Microevolution of Burkholderia pseudomallei during an acute infection

scientific article

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

scientific article (publication date: 30 November 2016)

Mobile-Genetic-Element-Encoded Hypertolerance to Copper Protects Staphylococcus aureus from Killing by Host Phagocytes ⬇️

scientific article published on 16 October 2018

Molecular analysis of an outbreak of lethal postpartum sepsis caused by Streptococcus pyogenes.

scientific article published on 24 April 2013

Molecular epidemiology and expression of capsular polysaccharides in Staphylococcus aureus clinical isolates in the United States

scientific article published in PLoS ONE

Molecular genetics of carbapenem antibiotic biosynthesis.

scientific article

Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus ⬇️

scientific article

Molecular tracing of the emergence, diversification, and transmission of S. aureus sequence type 8 in a New York community

scientific article (publication date: 6 May 2014)

Multiplex PCR assay for unequivocal differentiation of Actinobacillus pleuropneumoniae serovars 1 to 3, 5 to 8, 10, and 12.

scientific article

Naturally occurring polymorphisms in the virulence regulator Rsp modulate Staphylococcus aureus survival in blood and antibiotic susceptibility.

scientific article

New signal molecules on the quorum-sensing block

scientific article published on 01 March 2000

Nonrandom distribution of Burkholderia pseudomallei clones in relation to geographical location and virulence

scientific article published on July 2006

Novel mutations in penicillin-binding protein genes in clinical Staphylococcus aureus isolates that are methicillin resistant on susceptibility testing, but lack the mec gene

scientific article published on 11 November 2013

Old Drugs To Treat Resistant Bugs: Methicillin-Resistant Staphylococcus aureus Isolates with mecC Are Susceptible to a Combination of Penicillin and Clavulanic Acid.

scientific article published on 21 September 2015

Origin, maintenance and spread of antibiotic resistance genes within plasmids and chromosomes of bloodstream isolates of Escherichia coli

scientific article published on 11 March 2020

Pan-genomic perspective on the evolution of the Staphylococcus aureus USA300 epidemic

scientific article published on 31 May 2016

Pathogenomics of non-pathogens

scientific article published in 2004

Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus

scientific article published on 27 December 2012

PinR mediates the generation of reversible population diversity in Streptococcus zooepidemicus.

scientific article published on 20 February 2015

Population genetic structuring of methicillin-resistant Staphylococcus aureus clone EMRSA-15 within UK reflects patient referral patterns

scientific article published on 4 July 2017

Predicting the virulence of MRSA from its genome sequence

scientific article

Properties of a novel PBP2A protein homolog from Staphylococcus aureus strain LGA251 and its contribution to the β-lactam-resistant phenotype.

scientific article published on 12 September 2012

Proposal of serovars 17 and 18 of Actinobacillus pleuropneumoniae based on serological and genotypic analysis

scientific article published on 16 February 2018

Pseudomonas aeruginosa intensive care unit outbreak: winnowing of transmissions with molecular and genomic typing

scientific article published on 8 December 2017

Publisher Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland ⬇️

correction of a scholarly article

Publisher Correction: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

scientific article published on 22 November 2019

Quorum-sensing cross talk: isolation and chemical characterization of cyclic dipeptides from Pseudomonas aeruginosa and other Gram-negative bacteria

article

Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology

scientific article

Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis

scientific article

Rapid single-colony whole-genome sequencing of bacterial pathogens

scientific article

Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak

scientific article published on June 2012

Roary: rapid large-scale prokaryote pan genome analysis

scientific article

Routine use of microbial whole genome sequencing in diagnostic and public health microbiology

scientific article (publication date: 2012)

ST3268: a geographically widespread primate MRSA clone.

scientific article published on 21 April 2017

Searching for clues

scientific article published in August 2002

Shrinking genomics

scientific article published in January 2004

Single-molecule sequencing reveals the molecular basis of multidrug-resistance in ST772 methicillin-resistant Staphylococcus aureus

scientific article

Size matters?

scientific article published in August 2001

Some like it hot

scientific article published on 01 September 2004

SpeS: A Novel Superantigen and Its Potential as a Vaccine Adjuvant against Strangles

scientific article published on 23 June 2020

Split personalities

scientific article published on 01 March 2002

Staphylococcus aureus: superbug, super genome?

scientific article published in August 2004

Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline

scientific article

Structure, activity and evolution of the group I thiolactone peptide quorum-sensing system of Staphylococcus aureus.

scientific article published in July 2001

Superantigenic activity of emm3 Streptococcus pyogenes is abrogated by a conserved, naturally occurring smeZ mutation

scientific article

T Cell Immunity to the Alkyl Hydroperoxide Reductase of Burkholderia pseudomallei: A Correlate of Disease Outcome in Acute Melioidosis

scientific article published on 10 April 2015

Tales of the unexpected

scientific article published on 01 June 2002

The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation

scientific article

The Emergence of Successful Streptococcus pyogenes Lineages through Convergent Pathways of Capsule Loss and Recombination Directing High Toxin Expression

scientific article published on 10 December 2019

The Ess/Type VII secretion system of Staphylococcus aureus shows unexpected genetic diversity

scientific article

The Full Monty

scientific article published on 01 September 2001

The G5 domain: a potential N-acetylglucosamine recognition domain involved in biofilm formation

scientific article published on 14 December 2004

The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients

scientific article published in April 2009

The Global Posttranscriptional Regulator RsmA Modulates Production of Virulence Determinants and N-Acylhomoserine Lactones in Pseudomonas aeruginosa.

scientific article published in January 2002

The Microevolution and Epidemiology of Staphylococcus aureus Colonization during Atopic Eczema Disease Flare.

scientific article

The Streptococcus equi prophage-encoded protein SEQ2045 is a hyaluronan-specific hyaluronate lyase that is produced during equine infection

scientific article published in February 2009

The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129

scientific article

The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081.

scientific article published in December 2006

The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients

scientific article published on 17 October 2008

The genus Serratia revisited by genomics

scientific article published in 2022

The good, the bad and the ugly?

scientific article published on 01 May 2003

The grapes of wrath

scientific article published on 01 November 2006

The hyper-transmissible SARS-CoV-2 Omicron variant exhibits significant antigenic change, vaccine escape and a switch in cell entry mechanism

The impact of recombination on dN/dS within recently emerged bacterial clones

scientific article (publication date: July 2011)

The magnificent seven

scientific article published on 01 January 2003

The molecular basis of thioalcohol production in human body odour

scientific article published on 27 July 2020

The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome

scientific article

The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis

scientific article published on 24 December 2014

The widespread use of topical antimicrobials enriches for resistance in Staphylococcus aureus isolated from Atopic Dermatitis patients.

scientific article published on 5 May 2018

Turner et al. Reply to "Emergence of the Same Successful Clade among Distinct Populations of emm89 Streptococcus pyogenes in Multiple Geographic Regions".

scientific article published in December 2015

Understanding the rise of the superbug: investigation of the evolution and genomic variation of Staphylococcus aureus

scientific article

Whole Genome Sequencing for Surveillance of Antimicrobial Resistance in Actinobacillus pleuropneumoniae

scientific article published on 06 March 2017

Whole genome investigation of a divergent clade of the pathogen Streptococcus suis

scientific article

Whole genome sequencing identifies zoonotic transmission of MRSA isolates with the novel mecA homologue mecC

scientific article

Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe

scientific article

Whole-genome sequencing confirms that Burkholderia pseudomallei multilocus sequence types common to both Cambodia and Australia are due to homoplasy

scientific article

Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study.

scientific article published on 14 November 2012

Whole-genome sequencing of a quarter-century melioidosis outbreak in temperate Australia uncovers a region of low-prevalence endemicity

scientific article published on 11 July 2016

Whole-genome sequencing reveals clonal expansion of multiresistant Staphylococcus haemolyticus in European hospitals

scientific article

Whole-genome sequencing to investigate a non-clonal melioidosis cluster on a remote Australian island

scientific article published on 13 June 2017

Zero tolerance for healthcare-associated MRSA bacteraemia: is it realistic?

scientific article

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