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List of works by Simon R Harris

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

scientific article

A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae

scientific article published on 20 February 2015

A high-resolution view of genome-wide pneumococcal transformation

scientific article

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

scientific article

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers

scientific article

Adaptation to the cervical environment is associated with increased antibiotic susceptibility in Neisseria gonorrhoeae

scientific article published on 17 August 2020

An unusual Burkholderia gladioli double chain-initiating nonribosomal peptide synthetase assembles ‘fungal’ icosalide antibiotics

scientific article published on 25 April 2019

Antimicrobial exposure in sexual networks drives divergent evolution in modern gonococci

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

scientific article

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

Bacterial genomes in epidemiology--present and future.

scientific article published on 04 February 2013

BamView: visualizing and interpretation of next-generation sequencing read alignments

scientific article (publication date: March 2013)

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

scientific article

Chlamydia trachomatis clinical isolates identified as tetracycline resistant do not exhibit resistance in vitro: whole-genome sequencing reveals a mutation in porB but no evidence for tetracycline resistance genes.

scientific article published on February 2013

Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain

scientific article

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

scientific article published on 10 August 2015

Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches

scientific article published in Scientific Reports

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

scientific article

Convergent evolution and topologically disruptive polymorphisms among multidrug-resistant tuberculosis in Peru.

scientific article

Correction: Signatures of Adaptation in Human Invasive Salmonella Typhimurium ST313 Populations from Sub-Saharan Africa

scientific article published on 15 June 2015

Dense genomic sampling identifies highways of pneumococcal recombination

scientific article published on 09 February 2014

Detection of recombination events in bacterial genomes from large population samples

scientific article

Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings

scientific article published on 22 August 2016

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

scientific article (publication date: 2013)

Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila

scientific article

Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes

scientific article published on 28 July 2015

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 and global spread of epidemic healthcare-associated Clostridium difficile

scientific article published on 9 December 2012

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

Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host

scientific article published on 25 January 2016

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

scientific article published on 19 February 2015

Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread

scientific article published on 29 July 2019

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: Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings

scientific article published in March 2017

Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data

scientific article published on 03 September 2019

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

scientific article

Evidence for several waves of global transmission in the seventh cholera pandemic

scientific article

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

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

Evolution and transmission of drug-resistant tuberculosis in a Russian population

scientific article published on 26 January 2014

Evolution of mobile genetic element composition in an epidemic methicillin-resistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events

scientific article published on 4 September 2017

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

scientific article

Fast and flexible bacterial genomic epidemiology with PopPUNK

scientific article published on 24 January 2019

Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA.

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

scientific article published on 22 November 2019

Genetic variation regulates the activation and specificity of Restriction-Modification systems in Neisseria gonorrhoeae

scientific article published on 11 October 2019

Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar

scientific article published on 27 August 2013

Genome sequence of the zoonotic pathogen Chlamydophila psittaci

scientific article published on 23 December 2010

Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer

scientific article published in February 2012

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

scientific article

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

scientific article

Genomic Analysis and Comparison of Two Gonorrhea Outbreaks

scientific article published on 28 June 2016

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

scientific article

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

scientific article published on 11 May 2009

Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex

scientific article published on 12 June 2019

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

scientific article

Global and regional dissemination and evolution of Burkholderia pseudomallei

scientific article published on 23 January 2017

Global phylogeography and evolutionary history of Shigella dysenteriae type 1.

scientific article

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

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

Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study

scientific article published on 27 April 2015

Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa

scientific article

Investigating stagnation in morphological phylogenetics using consensus data

scientific article

Locally Confined Clonal Complexes of Mycobacterium ulcerans in Two Buruli Ulcer Endemic Regions of Cameroon

scientific article

Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 2005-2010.

scientific article published on April 2016

Microevolution of extensively drug-resistant tuberculosis in Russia

scientific article published on 31 January 2012

Optimal enzymes for amplifying sequencing libraries

scientific article published on 28 December 2011

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

scientific article (publication date: October 2013)

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

scientific article published on 31 May 2016

Parallel independent evolution of pathogenicity within the genus Yersinia

scientific article

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

scientific article published on 26 January 2016

Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

scientific article published on 11 May 2015

Rapid Pneumococcal Evolution in Response to Clinical Interventions ⬇️

scientific article (publication date: 28 January 2011)

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

scientific article

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

scientific article

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

scientific article published on June 2012

Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks

scientific article published in July 2013

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

scientific article published on 27 September 2016

Reductive evolution of the mitochondrial processing peptidases of the unicellular parasites trichomonas vaginalis and giardia intestinalis

scientific article

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

scientific article published on 11 August 2015

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

scientific article published on 16 September 2016

Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from sub-Saharan Africa.

scientific article

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

scientific article

Spatiotemporal Co-existence of Two Mycobacterium ulcerans Clonal Complexes in the Offin River Valley of Ghana

scientific article

Structure, diversity, and mobility of the Salmonella pathogenicity island 7 family of integrative and conjugative elements within Enterobacteriaceae

scientific article published on 13 January 2012

Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131.

scientific article published on 18 July 2017

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

scientific article

The Swedish new variant of Chlamydia trachomatis: genome sequence, morphology, cell tropism and phenotypic characterization

scientific article published on 21 January 2010

The archaebacterial origin of eukaryotes

scientific article

The evolutionary path to extraintestinal pathogenic, drug-resistant Escherichia coli is marked by drastic reduction in detectable recombination within the core genome

scientific article published on January 2013

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 the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution

scientific article published on 25 October 2012

The impact of antimicrobials on gonococcal evolution

scientific article published on 29 July 2019

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

scientific article (publication date: July 2011)

The shape of supertrees to come: tree shape related properties of fourteen supertree methods

scientific article published in June 2005

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

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

scientific article

Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing

scientific article

Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture

scientific article published on 22 March 2013

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

scientific article

Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study

scientific article published on 29 March 2013

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

scientific article

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