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Mycobacterium ulcerans Population Genomics To Inform on the Spread of Buruli Ulcer across Central Africa.

Vandelannoote K, Phanzu DM, Kibadi K, Eddyani M, Meehan CJ, Jordaens K, Leirs H, Portaels F, Stinear TP, Harris SR, de Jong BC.

mSphere. 2019 Feb 6;4(1). pii: e00472-18. doi: 10.1128/mSphere.00472-18.


Ovarian cancer metastases to internal mammary nodes.

Harris SR.

Breast J. 2019 Feb 6. doi: 10.1111/tbj.13226. [Epub ahead of print] No abstract available.


Using genomics to understand antimicrobial resistance and transmission in Neisseria gonorrhoeae.

Sánchez-Busó L, Harris SR.

Microb Genom. 2019 Jan 30. doi: 10.1099/mgen.0.000239. [Epub ahead of print]


Fast and flexible bacterial genomic epidemiology with PopPUNK.

Lees JA, Harris SR, Tonkin-Hill G, Gladstone RA, Lo SW, Weiser JN, Corander J, Bentley SD, Croucher NJ.

Genome Res. 2019 Feb;29(2):304-316. doi: 10.1101/gr.241455.118. Epub 2019 Jan 24.


Psychogenic movement disorders in children and adolescents: an update.

Harris SR.

Eur J Pediatr. 2019 Jan 11. doi: 10.1007/s00431-019-03317-8. [Epub ahead of print]


Bayesian inference of ancestral dates on bacterial phylogenetic trees.

Didelot X, Croucher NJ, Bentley SD, Harris SR, Wilson DJ.

Nucleic Acids Res. 2018 Dec 14;46(22):e134. doi: 10.1093/nar/gky783.


Bilateral Versus Single Internal Mammary Artery Use in Coronary Artery Bypass Grafting: A Propensity Matched Analysis.

Zhu YY, Seco M, Harris SR, Koullouros M, Ramponi F, Wilson M, Bannon PG, Vallely MP.

Heart Lung Circ. 2018 Apr 4. pii: S1443-9506(18)30138-0. doi: 10.1016/j.hlc.2018.03.022. [Epub ahead of print]


Loss of Genomic Diversity in a Neisseria meningitidis Clone Through a Colonization Bottleneck.

Lamelas A, Hamid AM, Dangy JP, Hauser J, Jud M, Röltgen K, Hodgson A, Junghanss T, Harris SR, Parkhill J, Bentley SD, Pluschke G.

Genome Biol Evol. 2018 Aug 1;10(8):2102-2109. doi: 10.1093/gbe/evy152.


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

Otchere ID, Coscollá M, Sánchez-Busó L, Asante-Poku A, Brites D, Loiseau C, Meehan C, Osei-Wusu S, Forson A, Laryea C, Yahayah AI, Baddoo A, Ansa GA, Aboagye SY, Asare P, Borrell S, Gehre F, Beckert P, Kohl TA, N'dira S, Beisel C, Antonio M, Niemann S, de Jong BC, Parkhill J, Harris SR, Gagneux S, Yeboah-Manu D.

Sci Rep. 2018 Jul 26;8(1):11269. doi: 10.1038/s41598-018-29620-2.


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

van Hal SJ, Steinig EJ, Andersson P, Holden MTG, Harris SR, Nimmo GR, Williamson DA, Heffernan H, Ritchie SR, Kearns AM, Ellington MJ, Dickson E, de Lencastre H, Coombs GW, Bentley SD, Parkhill J, Holt DC, Giffard PM, Tong SYC.

Front Microbiol. 2018 Jul 9;9:1453. doi: 10.3389/fmicb.2018.01453. eCollection 2018.


Practice Roles and Characteristics of Integrative and Functional Nutrition Registered Dietitian Nutritionists.

Goodman EM, Redmond J, Elia D, Harris SR, Augustine MB, Hand RK.

J Acad Nutr Diet. 2018 Dec;118(12):2356-2368.e1. doi: 10.1016/j.jand.2018.03.027. Epub 2018 Jun 23. No abstract available.


Assessing Clinical Judgment and Critical Thinking Skills in a Group of Experienced Integrative and Functional Nutrition Registered Dietitian Nutritionists.

Goodman EM, Redmond J, Elia D, Harris SR, Augustine MB, Hand RK.

J Acad Nutr Diet. 2018 Dec;118(12):2346-2355.e4. doi: 10.1016/j.jand.2018.03.026. Epub 2018 Jun 23. No abstract available.


Axillary Web Syndrome in Breast Cancer: A Prevalent But Under-Recognized Postoperative Complication.

Harris SR.

Breast Care (Basel). 2018 Apr;13(2):132-135. doi: 10.1159/000485023. Epub 2018 Feb 1. Review.


Public health surveillance of multidrug-resistant clones of Neisseria gonorrhoeae in Europe: a genomic survey.

Harris SR, Cole MJ, Spiteri G, Sánchez-Busó L, Golparian D, Jacobsson S, Goater R, Abudahab K, Yeats CA, Bercot B, Borrego MJ, Crowley B, Stefanelli P, Tripodo F, Abad R, Aanensen DM, Unemo M; Euro-GASP study group.

Lancet Infect Dis. 2018 Jul;18(7):758-768. doi: 10.1016/S1473-3099(18)30225-1. Epub 2018 May 15.


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

Lees JA, Kendall M, Parkhill J, Colijn C, Bentley SD, Harris SR.

Wellcome Open Res. 2018 Mar 23;3:33. doi: 10.12688/wellcomeopenres.14265.2. eCollection 2018.


Genomic evidence that the live Chlamydia abortus vaccine strain 1B is not attenuated and has the potential to cause disease.

Longbottom D, Sait M, Livingstone M, Laroucau K, Sachse K, Harris SR, Thomson NR, Seth-Smith HMB.

Vaccine. 2018 Jun 14;36(25):3593-3598. doi: 10.1016/j.vaccine.2018.05.042.


Zoonotic Transfer of Clostridium difficile Harboring Antimicrobial Resistance between Farm Animals and Humans.

Knetsch CW, Kumar N, Forster SC, Connor TR, Browne HP, Harmanus C, Sanders IM, Harris SR, Turner L, Morris T, Perry M, Miyajima F, Roberts P, Pirmohamed M, Songer JG, Weese JS, Indra A, Corver J, Rupnik M, Wren BW, Riley TV, Kuijper EJ, Lawley TD.

J Clin Microbiol. 2018 Feb 22;56(3). pii: e01384-17. doi: 10.1128/JCM.01384-17. Print 2018 Mar.


Correction: Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila.

David S, Sánchez-Busó L, Harris SR, Marttinen P, Rusniok C, Buchrieser C, Harrison TG, Parkhill J.

PLoS Genet. 2017 Dec 1;13(12):e1007116. doi: 10.1371/journal.pgen.1007116. eCollection 2017 Dec.


ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads.

Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J, Keane JA, Harris SR.

Microb Genom. 2017 Sep 4;3(10):e000131. doi: 10.1099/mgen.0.000131. eCollection 2017 Oct.


Phandango: an interactive viewer for bacterial population genomics.

Hadfield J, Croucher NJ, Goater RJ, Abudahab K, Aanensen DM, Harris SR.

Bioinformatics. 2017 Sep 25. doi: 10.1093/bioinformatics/btx610. [Epub ahead of print]


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

Lamelas A, Hauser J, Dangy JP, Hamid AM, Röltgen K, Abdul Sater MR, Hodgson A, Sie A, Junghanss T, Harris SR, Parkhill J, Bentley SD, Pluschke G.

Microb Genom. 2017 Jun 21;3(8):e000120. doi: 10.1099/mgen.0.000120. eCollection 2017 Aug.


Genomic epidemiology of a national outbreak of post-surgical Mycobacterium abscessus wound infections in Brazil.

Everall I, Nogueira CL, Bryant JM, Sánchez-Busó L, Chimara E, Duarte RDS, Ramos JP, Lima KVB, Lopes ML, Palaci M, Kipnis A, Monego F, Floto RA, Parkhill J, Leão SC, Harris SR.

Microb Genom. 2017 May 3;3(5):e000111. doi: 10.1099/mgen.0.000111. eCollection 2017 May.


Unloading knee brace is a cost-effective method to bridge and delay surgery in unicompartmental knee arthritis.

Lee PY, Winfield TG, Harris SR, Storey E, Chandratreya A.

BMJ Open Sport Exerc Med. 2017 Feb 21;2(1):e000195. doi: 10.1136/bmjsem-2016-000195. eCollection 2016.


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

Jamrozy D, Coll F, Mather AE, Harris SR, Harrison EM, MacGowan A, Karas A, Elston T, Estée Török M, Parkhill J, Peacock SJ.

BMC Genomics. 2017 Sep 4;18(1):684. doi: 10.1186/s12864-017-4065-z.


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

Björnsdóttir S, Harris SR, Svansson V, Gunnarsson E, Sigurðardóttir ÓG, Gammeljord K, Steward KF, Newton JR, Robinson C, Charbonneau ARL, Parkhill J, Holden MTG, Waller AS.

MBio. 2017 Aug 1;8(4). pii: e00826-17. doi: 10.1128/mBio.00826-17.


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.

Steward KF, Robinson C, Holden MTG, Harris SR, Ros AF, Pérez GC, Baselga R, Waller AS.

Vet Microbiol. 2017 Aug;207:231-238. doi: 10.1016/j.vetmic.2017.06.020. Epub 2017 Jul 1.


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

Kallonen T, Brodrick HJ, Harris SR, Corander J, Brown NM, Martin V, Peacock SJ, Parkhill J.

Genome Res. 2017 Jul 18. doi: 10.1101/gr.216606.116. [Epub ahead of print]


Early motor delays as diagnostic clues in autism spectrum disorder.

Harris SR.

Eur J Pediatr. 2017 Sep;176(9):1259-1262. doi: 10.1007/s00431-017-2951-7. Epub 2017 Jun 28. Review.


The Past, Present, and Future of Neurorehabilitation: From NUSTEP Through IV STEP and Beyond.

Harris SR, Winstein CJ.

Pediatr Phys Ther. 2017 Jul;29 Suppl 3:S2-S9. doi: 10.1097/PEP.0000000000000376.


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

David S, Sánchez-Busó L, Harris SR, Marttinen P, Rusniok C, Buchrieser C, Harrison TG, Parkhill J.

PLoS Genet. 2017 Jun 26;13(6):e1006855. doi: 10.1371/journal.pgen.1006855. eCollection 2017 Jun. Erratum in: PLoS Genet. 2017 Dec 1;13(12 ):e1007116.


The Past, Present, and Future of Neurorehabilitation: From NUSTEP Through IV STEP and Beyond.

Harris SR, Winstein CJ.

J Neurol Phys Ther. 2017 Jul;41 Suppl 3:S3-S9. doi: 10.1097/NPT.0000000000000193.


Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion.

Hadfield J, Harris SR, Seth-Smith HMB, Parmar S, Andersson P, Giffard PM, Schachter J, Moncada J, Ellison L, Vaulet MLG, Fermepin MR, Radebe F, Mendoza S, Ouburg S, Morré SA, Sachse K, Puolakkainen M, Korhonen SJ, Sonnex C, Wiggins R, Jalal H, Brunelli T, Casprini P, Pitt R, Ison C, Savicheva A, Shipitsyna E, Hadad R, Kari L, Burton MJ, Mabey D, Solomon AW, Lewis D, Marsh P, Unemo M, Clarke IN, Parkhill J, Thomson NR.

Genome Res. 2017 Jul;27(7):1220-1229. doi: 10.1101/gr.212647.116. Epub 2017 Jun 6.


Discovery and Biosynthesis of Gladiolin: A Burkholderia gladioli Antibiotic with Promising Activity against Mycobacterium tuberculosis.

Song L, Jenner M, Masschelein J, Jones C, Bull MJ, Harris SR, Hartkoorn RC, Vocat A, Romero-Canelon I, Coupland P, Webster G, Dunn M, Weiser R, Paisey C, Cole ST, Parkhill J, Mahenthiralingam E, Challis GL.

J Am Chem Soc. 2017 Jun 14;139(23):7974-7981. doi: 10.1021/jacs.7b03382. Epub 2017 Jun 5.


European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures.

Seth-Smith HMB, Busó LS, Livingstone M, Sait M, Harris SR, Aitchison KD, Vretou E, Siarkou VI, Laroucau K, Sachse K, Longbottom D, Thomson NR.

BMC Genomics. 2017 May 4;18(1):344. doi: 10.1186/s12864-017-3657-y.


Collaborative Occupational Therapy: Teachers' Impressions of the Partnering for Change (P4C) Model.

Wilson AL, Harris SR.

Phys Occup Ther Pediatr. 2018 May;38(2):130-142. doi: 10.1080/01942638.2017.1297988. Epub 2017 Apr 14.


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

Feasey NA, Hadfield J, Keddy KH, Dallman TJ, Jacobs J, Deng X, Wigley P, Barquist L, Langridge GC, Feltwell T, Harris SR, Mather AE, Fookes M, Aslett M, Msefula C, Kariuki S, Maclennan CA, Onsare RS, Weill FX, Le Hello S, Smith AM, McClelland M, Desai P, Parry CM, Cheesbrough J, French N, Campos J, Chabalgoity JA, Betancor L, Hopkins KL, Nair S, Humphrey TJ, Lunguya O, Cogan TA, Tapia MD, Sow SO, Tennant SM, Bornstein K, Levine MM, Lacharme-Lora L, Everett DB, Kingsley RA, Parkhill J, Heyderman RS, Dougan G, Gordon MA, Thomson NR.

Nat Genet. 2017 Mar 30;49(4):651. doi: 10.1038/ng0417-651c. No abstract available.


Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data.

Page AJ, De Silva N, Hunt M, Quail MA, Parkhill J, Harris SR, Otto TD, Keane JA.

Microb Genom. 2016 Aug 25;2(8):e000083. doi: 10.1099/mgen.0.000083. eCollection 2016 Aug.


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

Jamrozy DM, Harris SR, Mohamed N, Peacock SJ, Tan CY, Parkhill J, Anderson AS, Holden MT.

Microb Genom. 2016 May 31;2(5):e000058. doi: 10.1099/mgen.0.000058. eCollection 2016 May.


SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments.

Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T, Keane JA, Harris SR.

Microb Genom. 2016 Apr 29;2(4):e000056. doi: 10.1099/mgen.0.000056. eCollection 2016 Apr.


Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand.

Crispell J, Zadoks RN, Harris SR, Paterson B, Collins DM, de-Lisle GW, Livingstone P, Neill MA, Biek R, Lycett SJ, Kao RR, Price-Carter M.

BMC Genomics. 2017 Feb 16;18(1):180. doi: 10.1186/s12864-017-3569-x.


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

Skwark MJ, Croucher NJ, Puranen S, Chewapreecha C, Pesonen M, Xu YY, Turner P, Harris SR, Beres SB, Musser JM, Parkhill J, Bentley SD, Aurell E, Corander J.

PLoS Genet. 2017 Feb 16;13(2):e1006508. doi: 10.1371/journal.pgen.1006508. eCollection 2017 Feb.


Seeding and Establishment of Legionella pneumophila in Hospitals: Implications for Genomic Investigations of Nosocomial Legionnaires' Disease.

David S, Afshar B, Mentasti M, Ginevra C, Podglajen I, Harris SR, Chalker VJ, Jarraud S, Harrison TG, Parkhill J.

Clin Infect Dis. 2017 May 1;64(9):1251-1259. doi: 10.1093/cid/cix153.


Global and regional dissemination and evolution of Burkholderia pseudomallei.

Chewapreecha C, Holden MT, Vehkala M, Välimäki N, Yang Z, Harris SR, Mather AE, Tuanyok A, De Smet B, Le Hello S, Bizet C, Mayo M, Wuthiekanun V, Limmathurotsakul D, Phetsouvanh R, Spratt BG, Corander J, Keim P, Dougan G, Dance DA, Currie BJ, Parkhill J, Peacock SJ.

Nat Microbiol. 2017 Jan 23;2:16263. doi: 10.1038/nmicrobiol.2016.263.


The First population structure and comparative genomics analysis of Mycobacterium africanum strains from Ghana reveals higher diversity of Lineage 5.

Otchere ID, Harris SR, Busso SL, Asante-Poku A, Osei-Wusu S, Koram K, Parkhill J, Gagneux S, Yeboah-Manu D.

Int J Mycobacteriol. 2016 Dec;5 Suppl 1:S80-S81. doi: 10.1016/j.ijmyco.2016.09.051. Epub 2016 Nov 11.


Genomic variations leading to alterations in cell morphology of Campylobacter spp.

Esson D, Mather AE, Scanlan E, Gupta S, de Vries SP, Bailey D, Harris SR, McKinley TJ, Méric G, Berry SK, Mastroeni P, Sheppard SK, Christie G, Thomson NR, Parkhill J, Maskell DJ, Grant AJ.

Sci Rep. 2016 Dec 2;6:38303. doi: 10.1038/srep38303.


Emergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacterium.

Bryant JM, Grogono DM, Rodriguez-Rincon D, Everall I, Brown KP, Moreno P, Verma D, Hill E, Drijkoningen J, Gilligan P, Esther CR, Noone PG, Giddings O, Bell SC, Thomson R, Wainwright CE, Coulter C, Pandey S, Wood ME, Stockwell RE, Ramsay KA, Sherrard LJ, Kidd TJ, Jabbour N, Johnson GR, Knibbs LD, Morawska L, Sly PD, Jones A, Bilton D, Laurenson I, Ruddy M, Bourke S, Bowler IC, Chapman SJ, Clayton A, Cullen M, Daniels T, Dempsey O, Denton M, Desai M, Drew RJ, Edenborough F, Evans J, Folb J, Humphrey H, Isalska B, Jensen-Fangel S, Jönsson B, Jones AM, Katzenstein TL, Lillebaek T, MacGregor G, Mayell S, Millar M, Modha D, Nash EF, O'Brien C, O'Brien D, Ohri C, Pao CS, Peckham D, Perrin F, Perry A, Pressler T, Prtak L, Qvist T, Robb A, Rodgers H, Schaffer K, Shafi N, van Ingen J, Walshaw M, Watson D, West N, Whitehouse J, Haworth CS, Harris SR, Ordway D, Parkhill J, Floto RA.

Science. 2016 Nov 11;354(6313):751-757. doi: 10.1126/science.aaf8156.


Understanding pneumococcal serotype 1 biology through population genomic analysis.

Chaguza C, Cornick JE, Harris SR, Andam CP, Bricio-Moreno L, Yang M, Yalcin F, Ousmane S, Govindpersad S, Senghore M, Ebruke C, Du Plessis M, Kiran AM, Pluschke G, Sigauque B, McGee L, Klugman KP, Turner P, Corander J, Parkhill J, Collard JM, Antonio M, von Gottberg A, Heyderman RS, French N, Kadioglu A, Hanage WP, Everett DB, Bentley SD; PAGe Consortium.

BMC Infect Dis. 2016 Nov 8;16(1):649.


Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently.

David S, Rusniok C, Mentasti M, Gomez-Valero L, Harris SR, Lechat P, Lees J, Ginevra C, Glaser P, Ma L, Bouchier C, Underwood A, Jarraud S, Harrison TG, Parkhill J, Buchrieser C.

Genome Res. 2016 Nov;26(11):1555-1564. Epub 2016 Sep 23.


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

Grad YH, Harris SR, Kirkcaldy RD, Green AG, Marks DS, Bentley SD, Trees D, Lipsitch M.

J Infect Dis. 2016 Nov 15;214(10):1579-1587. Epub 2016 Sep 16.


Erratum: Global phylogeography and evolutionary history of Shigella dysenteriae type 1.

Njamkepo E, Fawal N, Tran-Dien A, Hawkey J, Strockbine N, Jenkins C, Talukder KA, Bercion R, Kuleshov K, Kolínská R, Russell JE, Kaftyreva L, Accou-Demartin M, Karas A, Vandenberg O, Mather AE, Mason CJ, Page AJ, Ramamurthy T, Bizet C, Gamian A, Carle I, Sow AG, Bouchier C, Wester AL, Lejay-Collin M, Fonkoua MC, Le Hello S, Blaser MJ, Jernberg C, Ruckly C, Mérens A, Page AL, Aslett M, Roggentin P, Fruth A, Denamur E, Venkatesan M, Bercovier H, Bodhidatta L, Chiou CS, Clermont D, Colonna B, Egorova S, Pazhani GP, Ezernitchi AV, Guigon G, Harris SR, Izumiya H, Korzeniowska-Kowal A, Lutyńska A, Gouali M, Grimont F, Langendorf C, Marejková M, Peterson LA, Perez-Perez G, Ngandjio A, Podkolzin A, Souche E, Makarova M, Shipulin GA, Ye C, Žemličková H, Herpay M, Grimont PA, Parkhill J, Sansonetti P, Holt KE, Brisse S, Thomson NR, Weill FX.

Nat Microbiol. 2016 Oct 3;1(11):16209. doi: 10.1038/nmicrobiol.2016.209. No abstract available.


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