Dr Simon Harris | Senior Staff Scientist

Simon is a Senior Staff Scientist in the Pathogen Genomics Group. His research involves analysis of whole genome DNA sequence data to study the evolution and population dynamics of bacterial pathogens.

My current work is focussed on the genomics of pathogenic Neisseria and Mycobacteria, combining population genomics, epidemiology and phenotypic approaches to understand their evolution and transmission.

I am particularly interested in the ways bacteria adapt and thrive in the face of changing selective pressures such as moving between host species, transitioning between carriage and disease or in response to antimicrobial therapy. Improving our understanding of these processes of adaptation requires the application and development of innovative bioinformatic techniques to reconstruct the evolutionary history of the entire genomes of large bacterial populations.

During my time at the Institute I have worked on many innovative projects using genomic data to both reconstruct the historical spread of some of the most important causes of transmissible disease, and to illustrate the potential of whole genome sequencing in informing clinical practice in real-time.

Publications

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

    Harris SR, Robinson C, Steward KF, Webb KS, Paillot R et al.

    Genome research 2015;25;9;1360-71

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

    Hsu LY, Harris SR, Chlebowicz MA, Lindsay JA, Koh TH et al.

    Genome biology 2015;16;81

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

    Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA et al.

    Nucleic acids research 2015;43;3;e15

  • Dense genomic sampling identifies highways of pneumococcal recombination.

    Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P et al.

    Nature genetics 2014;46;3;305-9

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

    Harris SR, Cartwright EJ, Török ME, Holden MT, Brown NM et al.

    The Lancet. Infectious diseases 2013;13;2;130-6

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

    Quail MA, Smith M, Coupland P, Otto TD, Harris SR et al.

    BMC genomics 2012;13;341

  • A high-resolution view of genome-wide pneumococcal transformation.

    Croucher NJ, Harris SR, Barquist L, Parkhill J and Bentley SD

    PLoS pathogens 2012;8;6;e1002745

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

    Harris SR, Clarke IN, Seth-Smith HM, Solomon AW, Cutcliffe LT et al.

    Nature genetics 2012;44;4;413-9, S1

  • Rapid pneumococcal evolution in response to clinical interventions.

    Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J et al.

    Science (New York, N.Y.) 2011;331;6016;430-4

  • Evolution of MRSA during hospital transmission and intercontinental spread.

    Harris SR, Feil EJ, Holden MT, Quail MA, Nickerson EK et al.

    Science (New York, N.Y.) 2010;327;5964;469-74

  • Circlator: automated circularization of genome assemblies using long sequencing reads.

    Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA and Harris SR

    Genome biology 2015;16;294

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

    Judge K, Harris SR, Reuter S, Parkhill J and Peacock SJ

    The Journal of antimicrobial chemotherapy 2015;70;10;2775-8

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

    Kulohoma BW, Cornick JE, Chaguza C, Yalcin F, Harris SR et al.

    Infection and immunity 2015;83;10;4165-73

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

    Harris SR, Robinson C, Steward KF, Webb KS, Paillot R et al.

    Genome research 2015;25;9;1360-71

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

    Baker KS, Dallman TJ, Ashton PM, Day M, Hughes G et al.

    The Lancet. Infectious diseases 2015;15;8;913-21

  • Genomic analysis of isolates from the United Kingdom 2012 pertussis outbreak reveals that vaccine antigen genes are unusually fast evolving.

    Sealey KL, Harris SR, Fry NK, Hurst LD, Gorringe AR et al.

    The Journal of infectious diseases 2015;212;2;294-301

  • Complete Genome Sequence of Bordetella pertussis D420.

    Boinett CJ, Harris SR, Langridge GC, Trainor EA, Merkel TJ and Parkhill J

    Genome announcements 2015;3;3

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

    Wong VK, Baker S, Pickard DJ, Parkhill J, Page AJ et al.

    Nature genetics 2015;47;6;632-9

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

    Bolz M, Bratschi MW, Kerber S, Minyem JC, Um Boock A et al.

    PLoS neglected tropical diseases 2015;9;6;e0003802

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

    Steward KF, Harrison T, Robinson C, Slater J, Maskell DJ et al.

    Microbiology (Reading, England) 2015;161;Pt 5;1105-12

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

    Ellington MJ, Reuter S, Harris SR, Holden MT, Cartwright EJ et al.

    International journal of antimicrobial agents 2015;45;5;477-84

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

    Hsu LY, Harris SR, Chlebowicz MA, Lindsay JA, Koh TH et al.

    Genome biology 2015;16;81

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

    Paterson GK, Harrison EM, Murray GG, Welch JJ, Warland JH et al.

    Nature communications 2015;6;6560

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

    Chung The H, Karkey A, Pham Thanh D, Boinett CJ, Cain AK et al.

    EMBO molecular medicine 2015;7;3;227-39

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

    Okoro CK, Barquist L, Connor TR, Harris SR, Clare S et al.

    PLoS neglected tropical diseases 2015;9;3;e0003611

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

    Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA et al.

    Nucleic acids research 2015;43;3;e15

  • Genomic Investigations unmask Mycoplasma amphoriforme, a new respiratory pathogen.

    Gillespie SH, Ling CL, Oravcova K, Pinheiro M, Wells L et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2015;60;3;381-8

  • Whole Genome Sequencing of a Methicillin-Resistant Staphylococcus aureus Pseudo-Outbreak in a Professional Football Team.

    Anderson DJ, Harris SR, Godofsky E, Toriscelli T, Rude TH et al.

    Open forum infectious diseases 2014;1;3;ofu096

  • Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis.

    Bos KI, Harkins KM, Herbig A, Coscolla M, Weber N et al.

    Nature 2014;514;7523;494-7

  • 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.

    Lamelas A, Harris SR, Röltgen K, Dangy JP, Hauser J et al.

    mBio 2014;5;5;e01974-14

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

    Chewapreecha C, Marttinen P, Croucher NJ, Salter SJ, Harris SR et al.

    PLoS genetics 2014;10;8;e1004547

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

    Török ME, Harris SR, Cartwright EJ, Raven KE, Brown NM et al.

    The Journal of antimicrobial chemotherapy 2014;69;8;2238-45

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

    Croucher NJ, Chewapreecha C, Hanage WP, Harris SR, McGee L et al.

    Genome biology and evolution 2014;6;7;1589-602

  • Parallel independent evolution of pathogenicity within the genus Yersinia.

    Reuter S, Connor TR, Barquist L, Walker D, Feltwell T et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;18;6768-73

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

    Mostowy R, Croucher NJ, Hanage WP, Harris SR, Bentley S and Fraser C

    PLoS genetics 2014;10;5;e1004300

  • Global population structure and evolution of Bordetella pertussis and their relationship with vaccination.

    Bart MJ, Harris SR, Advani A, Arakawa Y, Bottero D et al.

    mBio 2014;5;2;e01074

  • Dense genomic sampling identifies highways of pneumococcal recombination.

    Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P et al.

    Nature genetics 2014;46;3;305-9

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

    Casali N, Nikolayevskyy V, Balabanova Y, Harris SR, Ignatyeva O et al.

    Nature genetics 2014;46;3;279-86

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

    Grad YH, Kirkcaldy RD, Trees D, Dordel J, Harris SR et al.

    The Lancet. Infectious diseases 2014;14;3;220-6

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

    Cornick JE, Harris SR, Parry CM, Moore MJ, Jassi C et al.

    The Journal of antimicrobial chemotherapy 2014;69;2;368-74

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

    Seth-Smith HM, Harris SR, Scott P, Parmar S, Marsh P et al.

    Nature protocols 2013;8;12;2404-12

  • Playing fast and loose with mutation.

    Mather AE and Harris SR

    Nature reviews. Microbiology 2013;11;12;822

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

    Bryant JM, Harris SR, Parkhill J, Dawson R, Diacon AH et al.

    The Lancet. Respiratory medicine 2013;1;10;786-92

  • Genomic characterisation of invasive non-typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans isolates from Malawi.

    Bronowski C, Fookes MC, Gilderthorp R, Ashelford KE, Harris SR et al.

    PLoS neglected tropical diseases 2013;7;11;e2557

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

    Comas I, Coscolla M, Luo T, Borrell S, Holt KE et al.

    Nature genetics 2013;45;10;1176-82

  • Transcriptional regulation of Culex pipiens mosquitoes by Wolbachia influences cytoplasmic incompatibility.

    Pinto SB, Stainton K, Harris S, Kambris Z, Sutton ER et al.

    PLoS pathogens 2013;9;10;e1003647

  • Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts.

    Mather AE, Reid SW, Maskell DJ, Parkhill J, Fookes MC et al.

    Science (New York, N.Y.) 2013;341;6153;1514-7

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

    Reuter S, Ellington MJ, Cartwright EJ, Köser CU, Török ME et al.

    JAMA internal medicine 2013;173;15;1397-404

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

    Harris SR, Török ME, Cartwright EJ, Quail MA, Peacock SJ and Parkhill J

    Nature biotechnology 2013;31;7;592-4

  • Horizontally acquired glycosyltransferase operons drive salmonellae lipopolysaccharide diversity.

    Davies MR, Broadbent SE, Harris SR, Thomson NR and van der Woude MW

    PLoS genetics 2013;9;6;e1003568

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

    Bryant JM, Grogono DM, Greaves D, Foweraker J, Roddick I et al.

    Lancet (London, England) 2013;381;9877;1551-60

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

    Seth-Smith HM, Harris SR, Skilton RJ, Radebe FM, Golparian D et al.

    Genome research 2013;23;5;855-66

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

    Holden MT, Hsu LY, Kurt K, Weinert LA, Mather AE et al.

    Genome research 2013;23;4;653-64

  • 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.

    O'Neill CE, Seth-Smith HM, Van Der Pol B, Harris SR, Thomson NR et al.

    Microbiology (Reading, England) 2013;159;Pt 4;748-56

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

    Harrison EM, Paterson GK, Holden MT, Larsen J, Stegger M et al.

    EMBO molecular medicine 2013;5;4;509-15

  • Bacterial genomes in epidemiology--present and future.

    Croucher NJ, Harris SR, Grad YH and Hanage WP

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2013;368;1614;20120202

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

    Carver T, Harris SR, Otto TD, Berriman M, Parkhill J and McQuillan JA

    Briefings in bioinformatics 2013;14;2;203-12

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

    Hon PY, Chan KS, Holden MT, Harris SR, Tan TY et al.

    Antimicrobial agents and chemotherapy 2013;57;3;1563-4

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

    Bryant JM, Schürch AC, van Deutekom H, Harris SR, de Beer JL et al.

    BMC infectious diseases 2013;13;110

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

    Harris SR, Cartwright EJ, Török ME, Holden MT, Brown NM et al.

    The Lancet. Infectious diseases 2013;13;2;130-6

  • Emergence and global spread of epidemic healthcare-associated Clostridium difficile.

    He M, Miyajima F, Roberts P, Ellison L, Pickard DJ et al.

    Nature genetics 2013;45;1;109-13

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

    Okoro CK, Kingsley RA, Connor TR, Harris SR, Parry CM et al.

    Nature genetics 2012;44;11;1215-21

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

    Quail MA, Smith M, Coupland P, Otto TD, Harris SR et al.

    BMC genomics 2012;13;341

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

    Köser CU, Holden MT, Ellington MJ, Cartwright EJ, Brown NM et al.

    The New England journal of medicine 2012;366;24;2267-75

  • Microevolution of extensively drug-resistant tuberculosis in Russia.

    Casali N, Nikolayevskyy V, Balabanova Y, Ignatyeva O, Kontsevaya I et al.

    Genome research 2012;22;4;735-45

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

    Harris SR, Clarke IN, Seth-Smith HM, Solomon AW, Cutcliffe LT et al.

    Nature genetics 2012;44;4;413-9, S1

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

    Seth-Smith HM, Fookes MC, Okoro CK, Baker S, Harris SR et al.

    Journal of bacteriology 2012;194;6;1494-504

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

    Murchison EP, Schulz-Trieglaff OB, Ning Z, Alexandrov LB, Bauer MJ et al.

    Cell 2012;148;4;780-91

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

    Carver T, Harris SR, Berriman M, Parkhill J and McQuillan JA

    Bioinformatics (Oxford, England) 2012;28;4;464-9

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

    Bentley SD, Comas I, Bryant JM, Walker D, Smith NH et al.

    PLoS neglected tropical diseases 2012;6;2;e1552

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

    Heinz E, Williams TA, Nakjang S, Noël CJ, Swan DC et al.

    PLoS pathogens 2012;8;10;e1002979

  • A high-resolution view of genome-wide pneumococcal transformation.

    Croucher NJ, Harris SR, Barquist L, Parkhill J and Bentley SD

    PLoS pathogens 2012;8;6;e1002745

  • Optimal enzymes for amplifying sequencing libraries.

    Quail MA, Otto TD, Gu Y, Harris SR, Skelly TF et al.

    Nature methods 2011;9;1;10-1

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

    Mutreja A, Kim DW, Thomson NR, Connor TR, Lee JH et al.

    Nature 2011;477;7365;462-5

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

    Castillo-Ramírez S, Harris SR, Holden MT, He M, Parkhill J et al.

    PLoS pathogens 2011;7;7;e1002129

  • Genome sequence of the zoonotic pathogen Chlamydophila psittaci.

    Seth-Smith HM, Harris SR, Rance R, West AP, Severin JA et al.

    Journal of bacteriology 2011;193;5;1282-3

  • Rapid pneumococcal evolution in response to clinical interventions.

    Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J et al.

    Science (New York, N.Y.) 2011;331;6016;430-4

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

    Unemo M, Seth-Smith HM, Cutcliffe LT, Skilton RJ, Barlow D et al.

    Microbiology (Reading, England) 2010;156;Pt 5;1394-404

  • Evolution of MRSA during hospital transmission and intercontinental spread.

    Harris SR, Feil EJ, Holden MT, Quail MA, Nickerson EK et al.

    Science (New York, N.Y.) 2010;327;5964;469-74

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

    Seth-Smith HM, Harris SR, Persson K, Marsh P, Barron A et al.

    BMC genomics 2009;10;239

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

    Silby MW, Cerdeño-Tárraga AM, Vernikos GS, Giddens SR, Jackson RW et al.

    Genome biology 2009;10;5;R51

  • The archaebacterial origin of eukaryotes.

    Cox CJ, Foster PG, Hirt RP, Harris SR and Embley TM

    Proceedings of the National Academy of Sciences of the United States of America 2008;105;51;20356-61

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

    Smíd O, Matusková A, Harris SR, Kucera T, Novotný M et al.

    PLoS pathogens 2008;4;12;e1000243

  • Investigating stagnation in morphological phylogenetics using consensus data.

    Harris SR, Pisani D, Gower DJ and Wilkinson M

    Systematic biology 2007;56;1;125-9

  • Molecular evidence for dim-light vision in the last common ancestor of the vertebrates.

    Pisani D, Mohun SM, Harris SR, McInerney JO and Wilkinson M

    Current biology : CB 2006;16;9;R318-9; author reply R320

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

    Wilkinson M, Cotton JA, Creevey C, Eulenstein O, Harris SR et al.

    Systematic biology 2005;54;3;419-31

  • Phylogenetic methods and aetosaur interrelationships: a rejoinder.

    Harris SR, Gower DJ and Wilkinson M

    Systematic biology 2003;52;6;851-2

  • Intraorganismal homology, character construction, and the phylogeny of aetosaurian archosaurs (reptilia, diapsida).

    Harris SR, Gower DJ and Wilkinson M

    Systematic biology 2003;52;2;239-52

Harris, Simon
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Simon's Timeline
2014

Senior Staff Scientist, Wellcome Trust Sanger Institute

2010

Staff Scientist, Wellcome Trust Sanger Institute

2008

Post-Doctoral Research Assistant, Wellcome Trust Sanger Institute

2005

BBSRC Post-Doctoral Research Assistant, Newcastle University

2000

PhD, University of Bristol

1997

BSc Joint Honours in Biology and Geology, University of Bristol