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List of works by Stephen D Bentley

70th Anniversary Collection for the Microbiology Society: Microbial Genomics

scientific article published on 14 December 2015

A bad combination

scientific article published on 01 July 2003

A genomic approach to bacterial taxonomy: an examination and proposed reclassification of species within the genus Neisseria.

scientific article

A genomic infection control study for in two Ghanaian hospitals

scholarly article by Eric S Donkor et al published 2018 in Infection and Drug Resistance

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

scientific article

A high-resolution view of genome-wide pneumococcal transformation

scientific article

A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children

scientific article published on 2 October 2017

A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak

scientific article (publication date: 9 January 2013)

A simple method for directional transcriptome sequencing using Illumina technology

scientific article

A small predatory core genome in the divergent marine Bacteriovorax marinus SJ and the terrestrial Bdellovibrio bacteriovorus

scientific article

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

scientific article

Animal, vegetable or mineral?

scientific article published in October 2006

Antimicrobial exposure in sexual networks drives divergent evolution in modern gonococci

Antimicrobial resistance determinants and susceptibility profiles of pneumococcal isolates recovered in Trinidad and Tobago

scientific article published on 14 August 2017

Armed to the teeth

scientific article published on 01 April 2002

Association of Pneumococcal Protein Antigen Serology With Age and Antigenic Profile of Colonizing Isolates

scientific article published on 29 December 2016

Bacterial home from home

scientific article

Bacterial therapeutics

scientific article published in March 2007

Bayesian inference of ancestral dates on bacterial phylogenetic trees

Bioinformatic identification of novel regulatory DNA sequence motifs in Streptomyces coelicolor

scientific 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

Climate induces seasonality in pneumococcal transmission

scientific article published on 12 June 2015

Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core Genome

scientific article published on 10 August 2015

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

scientific article

Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome

scientific article

Comparative genomic analysis of ten Streptococcus pneumoniae temperate bacteriophages

scientific article published on 05 June 2009

Comparative genomic structure of prokaryotes

scientific article

Comparative genomics and proteomics of Helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen.

scientific article

Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens

scientific article

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

scientific article

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

scientific article

Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes

scientific article

Correction for van Tonder et al., Genomics Reveals the Worldwide Distribution of Multidrug-Resistant Serotype 6E Pneumococci

scientific article published on June 2016

Correction: Enemies within

scientific article published in 2005

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: Climate induces seasonality in pneumococcal transmission

scientific article published on 29 March 2016

Corrigendum: SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data

scholarly article published in Microbial genomics

Cryptic ecology among host generalist Campylobacter jejuni in domestic animals

scientific article

DORA Editorial

scientific article published on 01 January 2019

Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data

scientific article

Defining the estimated core genome of bacterial populations using a Bayesian decision model

scientific article

Dense genomic sampling identifies highways of pneumococcal recombination

scientific article published on 09 February 2014

Description and nomenclature of Neisseria meningitidis capsule locus

scientific article published on April 2013

Detection of recombination events in bacterial genomes from large population samples

scientific article

Determinants of invasiveness beneath the capsule of the pneumococcus

scientific article published on 5 September 2013

Developing insights into the mechanisms of evolution of bacterial pathogens from whole-genome sequences

scientific article

Diverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening

scientific article published on 04 January 2017

Diversification of bacterial genome content through distinct mechanisms over different timescales.

scientific article

Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection

scientific article (publication date: 2013)

Effect of Vaccination on Pneumococci Isolated from the Nasopharynx of Healthy Children and the Middle Ear of Children with Otitis Media in Iceland

scholarly article by Sigríður J Quirk et al published December 2018 in Journal of Clinical Microbiology

Effect on nasopharyngeal pneumococcal carriage of replacing PCV7 with PCV13 in the Expanded Programme of Immunization in The Gambia

scientific article

Emergence and genomic diversification of a virulent serogroup W:ST-2881(CC175) Neisseria meningitidis clone in the African meningitis belt

scientific article published on 21 June 2017

Emergence of a new epidemic Neisseria meningitidis serogroup A Clone in the African meningitis belt: high-resolution picture of genomic changes that mediate immune evasion.

scientific article

Erratum for Kulohoma et al., Comparative genomic analysis of meningitis- and bacteremia-causing pneumococci identifies a common core genome

scientific article published in December 2015

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

scientific article published on 12 May 2015

Eukaryotes: not beyond compare

scientific article published in 2004

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study.

scientific article

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

scientific article

Evidence for soft selective sweeps in the evolution of pneumococcal multidrug resistance and vaccine escape

scientific article

Evidence of antimicrobial resistance-conferring genetic elements among pneumococci isolated prior to 1974

scientific article

Evolution of the Rhodococcus equi vap pathogenicity island seen through comparison of host-associated vapA and vapB virulence plasmids

scientific article

Evolutionary dynamics of Clostridium difficile over short and long time scales

scientific article published on 20 April 2010

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

scientific article

Faecal matters

scholarly article by Alan Walker et al published August 2006 in Nature Reviews Microbiology

Fast and flexible bacterial genomic epidemiology with PopPUNK

scholarly article published 6 July 2018

Fitting the niche by genomic adaptation

scientific article published in November 2003

Five winters of pneumococcal serotype replacement in UK carriage following PCV introduction

scientific article

Food for thought

scientific article published on 01 December 2005

Frequency-dependent selection in vaccine-associated pneumococcal population dynamics

scientific article published on 16 October 2017

Frequent recombination of pneumococcal capsule highlights future risks of emergence of novel serotypes

article

Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes

scientific article

Genetic characterisation of Malawian pneumococci prior to the roll-out of the PCV13 vaccine using a high-throughput whole genome sequencing approach

scientific article published on 10 September 2012

Genetic relatedness of the Streptococcus pneumoniae capsular biosynthetic loci

scientific article published on 31 August 2007

Genome giants

scientific article published on 01 July 2002

Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp. sepedonicus suggests recent niche adaptation

scientific article (publication date: March 2008)

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

scientific article published on 4 July 2011

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-level analyses of Mycobacterium bovis lineages reveal the role of SNPs and antisense transcription in differential gene expression

scientific article

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

scientific article

Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork

scientific article

Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork

Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork

article published in 2016

Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter

scientific article

Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

scientific article

Genomic Analysis and Comparison of Two Gonorrhea Outbreaks

scientific article published on 28 June 2016

Genomic Epidemiology of Gonococcal Resistance to Extended-Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the United States, 2000-2013

scientific article (publication date: 15 November 2016)

Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis

scientific article published on 06 January 2013

Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

scientific article published on 11 May 2009

Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study

scientific article

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

scientific article

Genomic identification of a novel co-trimoxazole resistance genotype and its prevalence amongst Streptococcus pneumoniae in Malawi.

scientific article published on 29 September 2013

Genomic perspectives on the evolution and spread of bacterial pathogens

scientific article

Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei

scientific article

Genomic pot pourri

scientific article published in 2004

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

scientific article

Genomics Reveals the Worldwide Distribution of Multidrug-Resistant Serotype 6E Pneumococci

scientific article published on 13 May 2015

Genotypic and phenotypic modifications of Neisseria meningitidis after an accidental human passage

scientific article

Global Distribution of Invasive Serotype 35D Streptococcus pneumoniae Isolates following Introduction of 13-Valent Pneumococcal Conjugate Vaccine. ⬇️

scientific article

Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages

scientific article published on 04 December 2014

Heterogeneity Among Estimates Of The Core Genome And Pan-Genome In Different Pneumococcal Populations

article

Heterogeneity in the frequency and characteristics of homologous recombination in pneumococcal evolution

scientific article

High multiple carriage and emergence of Streptococcus pneumoniae vaccine serotype variants in Malawian children.

scientific article published on 20 June 2015

High rates of homologous recombination in the mite endosymbiont and opportunistic human pathogen Orientia tsutsugamushi

scientific article

Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict.

scientific article

Identification of pathogen-specific genes through microarray analysis of pathogenic and commensal Neisseria species

scientific article published in September 2005

Identification, variation and transcription of pneumococcal repeat sequences

scientific article

Identifying the effect of patient sharing on between-hospital genetic differentiation of methicillin-resistant Staphylococcus aureus

scientific article published on 13 February 2016

Improved detection of nasopharyngeal cocolonization by multiple pneumococcal serotypes by use of latex agglutination or molecular serotyping by microarray

scientific article

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

Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06.

scientific article

Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data

scientific article

Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

scientific article

Investigations into genome diversity of Haemophilus influenzae using whole genome sequencing of clinical isolates and laboratory transformants

scientific article

Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis

scholarly article

Key features of invasive pneumococcal isolates recovered in Lima, Peru determined through whole genome sequencing ⬇️

scientific article published on 22 July 2017

Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis

scientific article published on 31 January 2017

Large scale genomic analysis shows no evidence for repeated pathogen adaptation during the invasive phase of bacterial meningitis in humans

Lineage-specific virulence determinants of Haemophilus influenzae biogroup aegyptius

scientific article published in March 2012

Massive attack

scientific article published on August 2005

Meningococcal Two-Partner Secretion Systems and Their Association with Outcome in Patients with Meningitis

scientific article published on 20 June 2016

Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18.

scientific article

Methicillin resistantStaphylococcus aureusemerged long before the introduction of methicillin in to clinical practice

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 extensively drug-resistant tuberculosis in Russia

scientific article published on 31 January 2012

Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of Sodalis glossinidius, the secondary endosymbiont of tsetse flies

scientific article

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

scientific article published on 24 April 2013

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

scientific article

New knowledge from old: in silico discovery of novel protein domains in Streptomyces coelicolor

scientific article

Novel determinants of antibiotic resistance: identification of mutated loci in highly methicillin-resistant subpopulations of methicillin-resistant Staphylococcus aureus

scientific article published on 08 April 2014

Novel staphylococcal species that form part of a Staphylococcus aureus-related complex: the non-pigmented Staphylococcus argenteus sp. nov. and the non-human primate-associated Staphylococcus schweitzeri sp. nov.

scientific article

Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans

scientific article (publication date: October 2013)

PANINI: Pangenome Neighbour Identification for Bacterial Populations

scientific article published in 2019

Pathogenomics

scientific article published in December 2003

Phage-Derived Protein Induces Increased Platelet Activation and Is Associated with Mortality in Patients with Invasive Pneumococcal Disease

scientific article

Phylogenetic Analysis of Invasive Serotype 1 Pneumococcus in South Africa, 1989 to 2013.

scientific article published on 9 March 2016

Phylogenomic exploration of the relationships between strains of Mycobacterium avium subspecies paratuberculosis

scientific article published on 26 January 2016

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

scientific article published on 27 December 2012

Pneumococcal capsular switching: a historical perspective

scientific article published on 21 November 2012

Population genetic structure, antibiotic resistance, capsule switching and evolution of invasive pneumococci before conjugate vaccination in Malawi ⬇️

scientific article published on 12 July 2017

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

scientific article published on 4 July 2017

Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae

scientific article

Population genomics of post-vaccine changes in pneumococcal epidemiology.

scientific article published on 05 May 2013

Predicted functions and linkage specificities of the products of the Streptococcus pneumoniae capsular biosynthetic loci

scientific article published on 31 August 2007

Prediction of post-vaccine population structure of Streptococcus pneumoniae using accessory gene frequencies

article

Progressive genome-wide introgression in agricultural Campylobacter coli

scientific article published on 20 December 2012

Putatively novel serotypes and the potential for reduced vaccine effectiveness: capsular locus diversity revealed among 5405 pneumococcal genomes

scientific article published on October 2016

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 phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.

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

Rapid whole-genome sequencing for investigation of a suspected tuberculosis outbreak

scientific article published on 21 November 2012

Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence

scientific article

Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing

scientific article published on 22 May 2013

Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule

scientific article published on 27 September 2016

Region-specific diversification of the highly virulent serotype 1 Streptococcus pneumoniae

scientific article published on 11 August 2015

Role of conjugative elements in the evolution of the multidrug-resistant pandemic clone Streptococcus pneumoniaeSpain23F ST81

scientific article

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

scientific article (publication date: 2012)

Searching for clues

scientific article published in August 2002

Selective and genetic constraints on pneumococcal serotype switching

scientific article published on 31 March 2015

Sequence and functional analyses of Haemophilus spp. genomic islands

scientific article

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

scientific article published on 16 September 2016

Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei

scientific article (publication date: 22 February 2003)

SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data

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

scientific article

SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences

scientific article published on 26 September 2012

Streptomyces coelicolor A3(2) plasmid SCP2*: deductions from the complete sequence

scientific article published on February 2003

Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

scientific article

Tales of the unexpected

scientific article published on 01 June 2002

Temporal population structure of invasive Group B Streptococcus during a period of rising disease incidence shows expansion of a CC17 clone

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

scientific article

The Contribution of Genetic Variation of Streptococcus pneumoniae to the Clinical Manifestation of Invasive Pneumococcal Disease

scientific article published in 2018

The Contribution of Genetic Variation of Streptococcus pneumoniae to the Clinical Manifestation of Invasive Pneumococcal Disease

article published in 2019

The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants

scientific article

The contribution of genetic variation of Streptococcus pneumoniae to the clinical manifestation of invasive pneumococcal disease

The devil is in the detail

scientific article published on 01 June 2003

The effect of environmental and management associated factors on prevalence and diversity of Streptococcus suis in clinically healthy pig herds of China and UK.

scientific article published on 2 February 2018

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

scientific article published on 17 October 2008

The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex

scientific article published on 28 February 2012

The genome of a pathogenic rhodococcus: cooptive virulence underpinned by key gene acquisitions

scientific article (publication date: 30 September 2010)

The global distribution and diversity of protein vaccine candidate antigens in the highly virulent Streptococcus pnuemoniae serotype 1.

scientific article published on 09 January 2017

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 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 multidrug-resistant PMEN1 pneumococcus is a paradigm for genetic success

scientific article published on 16 November 2012

The post-vaccine microevolution of invasive Streptococcus pneumoniae ⬇️

scientific article

The value of comparison

scientific article published in 2003

Twenty-eight divergent polysaccharide loci specifying within- and amongst-strain capsule diversity in three strains of Bacteroides fragilis

scientific article

Two-phase importance sampling for inference about transmission trees

scientific article published in November 2014

Understanding pneumococcal serotype 1 biology through population genomic analysis

scientific article published on 8 November 2016

Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone

scientific article published on 23 June 2014

Variants of AbGRI3 carrying the armA gene in extensively antibiotic-resistant Acinetobacter baumannii from Singapore

scientific article

Where there's muck there's microbes

scientific article published on 01 September 2006

Whole genome sequencing to investigate a putative outbreak of the virulent community-associated methicillin-resistant Staphylococcus aureus ST93 clone in a remote Indigenous community

scientific article published on 12 December 2016

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

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 reveals clonal expansion of multiresistant Staphylococcus haemolyticus in European hospitals

scientific article

Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study

scientific article

Within-Host Sampling of a Natural Population Shows Signs of Selection on Pde1 during Bacterial Meningitis

scientific article published on 23 February 2017

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