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Items: 1 to 50 of 205

1.

Genome-wide epistasis and co-selection study using mutual information.

Pensar J, Puranen S, Arnold B, MacAlasdair N, Kuronen J, Tonkin-Hill G, Pesonen M, Xu Y, Sipola A, Sánchez-Busó L, Lees JA, Chewapreecha C, Bentley SD, Harris SR, Parkhill J, Croucher NJ, Corander J.

Nucleic Acids Res. 2019 Jul 30. pii: gkz656. doi: 10.1093/nar/gkz656. [Epub ahead of print]

PMID:
31361894
2.

The impact of antimicrobials on gonococcal evolution.

Sánchez-Busó L, Golparian D, Corander J, Grad YH, Ohnishi M, Flemming R, Parkhill J, Bentley SD, Unemo M, Harris SR.

Nat Microbiol. 2019 Jul 29. doi: 10.1038/s41564-019-0501-y. [Epub ahead of print]

PMID:
31358980
3.

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

Davies MR, McIntyre L, Mutreja A, Lacey JA, Lees JA, Towers RJ, Duchêne S, Smeesters PR, Frost HR, Price DJ, Holden MTG, David S, Giffard PM, Worthing KA, Seale AC, Berkley JA, Harris SR, Rivera-Hernandez T, Berking O, Cork AJ, Torres RSLA, Lithgow T, Strugnell RA, Bergmann R, Nitsche-Schmitz P, Chhatwal GS, Bentley SD, Fraser JD, Moreland NJ, Carapetis JR, Steer AC, Parkhill J, Saul A, Williamson DA, Currie BJ, Tong SYC, Dougan G, Walker MJ.

Nat Genet. 2019 Aug;51(8):1295. doi: 10.1038/s41588-019-0482-z.

PMID:
31324894
4.

Methylation Warfare: Interaction of Pneumococcal Bacteriophages with Their Host.

Furi L, Crawford LA, Rangel-Pineros G, Manso AS, De Ste Croix M, Haigh RD, Kwun MJ, Engelsen Fjelland K, Gilfillan GD, Bentley SD, Croucher NJ, Clokie MR, Oggioni MR.

J Bacteriol. 2019 Sep 6;201(19). pii: e00370-19. doi: 10.1128/JB.00370-19. Print 2019 Oct 1.

5.

Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study.

Lo SW, Gladstone RA, van Tonder AJ, Lees JA, du Plessis M, Benisty R, Givon-Lavi N, Hawkins PA, Cornick JE, Kwambana-Adams B, Law PY, Ho PL, Antonio M, Everett DB, Dagan R, von Gottberg A, Klugman KP, McGee L, Breiman RF, Bentley SD; Global Pneumococcal Sequencing Consortium.

Lancet Infect Dis. 2019 Jul;19(7):759-769. doi: 10.1016/S1473-3099(19)30297-X. Epub 2019 Jun 10.

6.

Putative novel cps loci in a large global collection of pneumococci.

van Tonder AJ, Gladstone RA, Lo SW, Nahm MH, du Plessis M, Cornick J, Kwambana-Adams B, Madhi SA, Hawkins PA, Benisty R, Dagan R, Everett D, Antonio M, Klugman KP, von Gottberg A, Breiman RF, McGee L, Bentley SD, The Global Pneumococcal Sequencing Consortium.

Microb Genom. 2019 Jul;5(7). doi: 10.1099/mgen.0.000274. Epub 2019 Jun 11.

7.

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

Davies MR, McIntyre L, Mutreja A, Lacey JA, Lees JA, Towers RJ, Duchêne S, Smeesters PR, Frost HR, Price DJ, Holden MTG, David S, Giffard PM, Worthing KA, Seale AC, Berkley JA, Harris SR, Rivera-Hernandez T, Berking O, Cork AJ, Torres RSLA, Lithgow T, Strugnell RA, Bergmann R, Nitsche-Schmitz P, Chhatwal GS, Bentley SD, Fraser JD, Moreland NJ, Carapetis JR, Steer AC, Parkhill J, Saul A, Williamson DA, Currie BJ, Tong SYC, Dougan G, Walker MJ.

Nat Genet. 2019 Jun;51(6):1035-1043. doi: 10.1038/s41588-019-0417-8. Epub 2019 May 27. Erratum in: Nat Genet. 2019 Jul 19;:.

PMID:
31133745
8.

Early signals of vaccine driven perturbation seen in pneumococcal carriage population genomic data.

Chaguza C, Heinsbroek E, Gladstone RA, Tafatatha T, Alaerts M, Peno C, Cornick JE, Musicha P, Bar-Zeev N, Kamng'ona A, Kadioglu A, McGee L, Hanage WP, Breiman RF, Heyderman RS, French N, Everett DB, Bentley SD.

Clin Infect Dis. 2019 May 16. pii: ciz404. doi: 10.1093/cid/ciz404. [Epub ahead of print]

PMID:
31094423
9.

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

Lees JA, Ferwerda B, Kremer PHC, Wheeler NE, Serón MV, Croucher NJ, Gladstone RA, Bootsma HJ, Rots NY, Wijmega-Monsuur AJ, Sanders EAM, Trzciński K, Wyllie AL, Zwinderman AH, van den Berg LH, van Rheenen W, Veldink JH, Harboe ZB, Lundbo LF, de Groot LCPGM, van Schoor NM, van der Velde N, Ängquist LH, Sørensen TIA, Nohr EA, Mentzer AJ, Mills TC, Knight JC, du Plessis M, Nzenze S, Weiser JN, Parkhill J, Madhi S, Benfield T, von Gottberg A, van der Ende A, Brouwer MC, Barrett JC, Bentley SD, van de Beek D.

Nat Commun. 2019 May 15;10(1):2176. doi: 10.1038/s41467-019-09976-3.

10.

Recombination of the Phase-Variable spnIII Locus Is Independent of All Known Pneumococcal Site-Specific Recombinases.

De Ste Croix M, Chen KY, Vacca I, Manso AS, Johnston C, Polard P, Kwun MJ, Bentley SD, Croucher NJ, Bayliss CD, Haigh RD, Oggioni MR.

J Bacteriol. 2019 Jul 10;201(15). pii: e00233-19. doi: 10.1128/JB.00233-19. Print 2019 Aug 1.

11.

Fast hierarchical Bayesian analysis of population structure.

Tonkin-Hill G, Lees JA, Bentley SD, Frost SDW, Corander J.

Nucleic Acids Res. 2019 Jun 20;47(11):5539-5549. doi: 10.1093/nar/gkz361.

12.

International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact.

Gladstone RA, Lo SW, Lees JA, Croucher NJ, van Tonder AJ, Corander J, Page AJ, Marttinen P, Bentley LJ, Ochoa TJ, Ho PL, du Plessis M, Cornick JE, Kwambana-Adams B, Benisty R, Nzenze SA, Madhi SA, Hawkins PA, Everett DB, Antonio M, Dagan R, Klugman KP, von Gottberg A, McGee L, Breiman RF, Bentley SD; Global Pneumococcal Sequencing Consortium.

EBioMedicine. 2019 May;43:338-346. doi: 10.1016/j.ebiom.2019.04.021. Epub 2019 Apr 16.

13.

Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.

van Tonder AJ, Bray JE, Jolley KA, Jansen van Rensburg M, Quirk SJ, Haraldsson G, Maiden MCJ, Bentley SD, Haraldsson Á, Erlendsdóttir H, Kristinsson KG, Brueggemann AB.

Front Microbiol. 2019 Feb 25;10:317. doi: 10.3389/fmicb.2019.00317. eCollection 2019.

14.

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.

15.

Vaccination of Icelandic Children with the 10-Valent Pneumococcal Vaccine Leads to a Significant Herd Effect among Adults in Iceland.

Quirk SJ, Haraldsson G, Hjálmarsdóttir MÁ, van Tonder AJ, Hrafnkelsson B, Bentley SD, Haraldsson Á, Erlendsdóttir H, Brueggemann AB, Kristinsson KG.

J Clin Microbiol. 2019 Mar 28;57(4). pii: e01766-18. doi: 10.1128/JCM.01766-18. Print 2019 Apr.

16.

pyseer: a comprehensive tool for microbial pangenome-wide association studies.

Lees JA, Galardini M, Bentley SD, Weiser JN, Corander J.

Bioinformatics. 2018 Dec 15;34(24):4310-4312. doi: 10.1093/bioinformatics/bty539.

17.

Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci.

Azarian T, Mitchell PK, Georgieva M, Thompson CM, Ghouila A, Pollard AJ, von Gottberg A, du Plessis M, Antonio M, Kwambana-Adams BA, Clarke SC, Everett D, Cornick J, Sadowy E, Hryniewicz W, Skoczynska A, Moïsi JC, McGee L, Beall B, Metcalf BJ, Breiman RF, Ho PL, Reid R, O'Brien KL, Gladstone RA, Bentley SD, Hanage WP.

PLoS Pathog. 2018 Nov 26;14(11):e1007438. doi: 10.1371/journal.ppat.1007438. eCollection 2018 Nov.

18.

PANINI: Pangenome Neighbour Identification for Bacterial Populations.

Abudahab K, Prada JM, Yang Z, Bentley SD, Croucher NJ, Corander J, Aanensen DM.

Microb Genom. 2019 Apr;5(4). doi: 10.1099/mgen.0.000220. Epub 2018 Nov 22.

19.

A genomic infection control study for Staphylococcus aureus in two Ghanaian hospitals.

Donkor ES, Jamrozy D, Mills RO, Dankwah T, Amoo PK, Egyir B, Badoe EV, Twasam J, Bentley SD.

Infect Drug Resist. 2018 Oct 11;11:1757-1765. doi: 10.2147/IDR.S167639. eCollection 2018.

20.

RhierBAPS: An R implementation of the population clustering algorithm hierBAPS.

Tonkin-Hill G, Lees JA, Bentley SD, Frost SDW, Corander J.

Wellcome Open Res. 2018 Jul 30;3:93. doi: 10.12688/wellcomeopenres.14694.1. eCollection 2018.

21.

Excision-reintegration at a pneumococcal phase-variable restriction-modification locus drives within- and between-strain epigenetic differentiation and inhibits gene acquisition.

Kwun MJ, Oggioni MR, De Ste Croix M, Bentley SD, Croucher NJ.

Nucleic Acids Res. 2018 Nov 30;46(21):11438-11453. doi: 10.1093/nar/gky906.

22.

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

Quirk SJ, Haraldsson G, Erlendsdóttir H, Hjálmarsdóttir MÁ, van Tonder AJ, Hrafnkelsson B, Sigurdsson S, Bentley SD, Haraldsson Á, Brueggemann AB, Kristinsson KG.

J Clin Microbiol. 2018 Nov 27;56(12). pii: e01046-18. doi: 10.1128/JCM.01046-18. Print 2018 Dec.

23.

Pneumococcal Vaccines: Host Interactions, Population Dynamics, and Design Principles.

Croucher NJ, Løchen A, Bentley SD.

Annu Rev Microbiol. 2018 Sep 8;72:521-549. doi: 10.1146/annurev-micro-090817-062338.

PMID:
30200849
24.

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.

25.

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

Epping L, van Tonder AJ, Gladstone RA, Bentley SD, Page AJ, Keane JA; The Global Pneumococcal Sequencing Consortium.

Microb Genom. 2018 Aug;4(8). doi: 10.1099/mgen.0.000204. No abstract available.

26.

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.

27.

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.

28.

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

Epping L, van Tonder AJ, Gladstone RA, The Global Pneumococcal Sequencing Consortium, Bentley SD, Page AJ, Keane JA.

Microb Genom. 2018 Jul;4(7). doi: 10.1099/mgen.0.000186. Epub 2018 Jun 15. Erratum in: Microb Genom. 2018 Aug;4(8):.

29.

SuperDCA for genome-wide epistasis analysis.

Puranen S, Pesonen M, Pensar J, Xu YY, Lees JA, Bentley SD, Croucher NJ, Corander J.

Microb Genom. 2018 Jun;4(6). doi: 10.1099/mgen.0.000184. Epub 2018 May 29.

30.

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.

31.

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

Lo SW, Gladstone RA, van Tonder AJ, Hawkins PA, Kwambana-Adams B, Cornick JE, Madhi SA, Nzenze SA, du Plessis M, Kandasamy R, Carter PE, Eser ÖK, Ho PL, Elmdaghri N, Shakoor S, Clarke SC, Antonio M, Everett DB, von Gottberg A, Klugman KP, McGee L, Breiman RF, Bentley SD.

J Clin Microbiol. 2018 Jun 25;56(7). pii: e00228-18. doi: 10.1128/JCM.00228-18. Print 2018 Jul.

32.

The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome.

Azarian T, Grant LR, Arnold BJ, Hammitt LL, Reid R, Santosham M, Weatherholtz R, Goklish N, Thompson CM, Bentley SD, O'Brien KL, Hanage WP, Lipsitch M.

PLoS Pathog. 2018 Apr 4;14(4):e1006966. doi: 10.1371/journal.ppat.1006966. eCollection 2018 Apr.

33.

Frequency-dependent selection in vaccine-associated pneumococcal population dynamics.

Corander J, Fraser C, Gutmann MU, Arnold B, Hanage WP, Bentley SD, Lipsitch M, Croucher NJ.

Nat Ecol Evol. 2017 Dec;1(12):1950-1960. doi: 10.1038/s41559-017-0337-x. Epub 2017 Oct 16.

34.

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.

35.

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

Donker T, Reuter S, Scriberras J, Reynolds R, Brown NM, Török ME, James R, Network EOEMR, Aanensen DM, Bentley SD, Holden MTG, Parkhill J, Spratt BG, Peacock SJ, Feil EJ, Grundmann H.

Microb Genom. 2017 Jul 4;3(7):e000113. doi: 10.1099/mgen.0.000113. eCollection 2017 Jul.

36.

Pre-vaccine serotype composition within a lineage signposts its serotype replacement - a carriage study over 7 years following pneumococcal conjugate vaccine use in the UK.

Gladstone RA, Devine V, Jones J, Cleary D, Jefferies JM, Bentley SD, Faust SN, Clarke SC.

Microb Genom. 2017 Jun 9;3(6):e000119. doi: 10.1099/mgen.0.000119. eCollection 2017 Jun 30.

37.

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

Salter SJ, Turner C, Watthanaworawit W, de Goffau MC, Wagner J, Parkhill J, Bentley SD, Goldblatt D, Nosten F, Turner P.

PLoS Negl Trop Dis. 2017 Oct 2;11(10):e0005975. doi: 10.1371/journal.pntd.0005975. eCollection 2017 Oct.

38.

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

Reuter S, Török ME, Holden MTG, Reynolds R, Raven KE, Blane B, Donker T, Bentley SD, Aanensen DM, Grundmann H, Feil EJ, Spratt BG, Parkhill J, Peacock SJ.

Genome Res. 2017 Sep;27(9):1622. doi: 10.1101/gr.228155.117. No abstract available.

39.

Phase-variable methylation and epigenetic regulation by type I restriction-modification systems.

De Ste Croix M, Vacca I, Kwun MJ, Ralph JD, Bentley SD, Haigh R, Croucher NJ, Oggioni MR.

FEMS Microbiol Rev. 2017 Aug 1;41(Supp_1):S3-S15. doi: 10.1093/femsre/fux025. Review.

40.

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

Hawkins PA, Akpaka PE, Nurse-Lucas M, Gladstone R, Bentley SD, Breiman RF, McGee L, Swanston WH.

J Glob Antimicrob Resist. 2017 Dec;11:148-151. doi: 10.1016/j.jgar.2017.08.004. Epub 2017 Aug 14.

41.

Stronger together.

Lees JA, Tonkin-Hill G, Bentley SD.

Nat Rev Microbiol. 2017 Sep;15(9):516. doi: 10.1038/nrmicro.2017.95. Epub 2017 Aug 7. No abstract available.

PMID:
28781366
42.

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

Hawkins P, Mercado E, Chochua S, Castillo ME, Reyes I, Chaparro E, Gladstone R, Bentley SD, Breiman RF, Metcalf BJ, Beall B, Ochoa TJ, McGee L.

Int J Med Microbiol. 2017 Oct;307(7):415-421. doi: 10.1016/j.ijmm.2017.07.008. Epub 2017 Jul 22.

43.

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

Lees JA, Croucher NJ, Goldblatt D, Nosten F, Parkhill J, Turner C, Turner P, Bentley SD.

Elife. 2017 Jul 25;6. pii: e26255. doi: 10.7554/eLife.26255.

44.

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

Harkins CP, Pichon B, Doumith M, Parkhill J, Westh H, Tomasz A, de Lencastre H, Bentley SD, Kearns AM, Holden MTG.

Genome Biol. 2017 Jul 20;18(1):130. doi: 10.1186/s13059-017-1252-9.

45.

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

Chaguza C, Cornick JE, Andam CP, Gladstone RA, Alaerts M, Musicha P, Peno C, Bar-Zeev N, Kamng'ona AW, Kiran AM, Msefula CL, McGee L, Breiman RF, Kadioglu A, French N, Heyderman RS, Hanage WP, Bentley SD, Everett DB.

Vaccine. 2017 Aug 16;35(35 Pt B):4594-4602. doi: 10.1016/j.vaccine.2017.07.009. Epub 2017 Jul 12.

46.

Adaptation... that's what you need?

Chaguza C, Bentley SD.

Nat Rev Microbiol. 2017 Aug;15(8):452. doi: 10.1038/nrmicro.2017.78. Epub 2017 Jul 10. No abstract available.

PMID:
28690321
47.

Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination.

Mostowy RJ, Croucher NJ, De Maio N, Chewapreecha C, Salter SJ, Turner P, Aanensen DM, Bentley SD, Didelot X, Fraser C.

Mol Biol Evol. 2017 Oct 1;34(10):2537-2554. doi: 10.1093/molbev/msx173.

48.

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

Lees JA, Kremer PHC, Manso AS, Croucher NJ, Ferwerda B, Serón MV, Oggioni MR, Parkhill J, Brouwer MC, van der Ende A, van de Beek D, Bentley SD.

Microb Genom. 2017 Jan 31;3(1):e000103. doi: 10.1099/mgen.0.000103. eCollection 2017 Jan.

49.

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

Meumann EM, Andersson P, Yeaman F, Oldfield S, Lilliebridge R, Bentley SD, Krause V, Beaman M, Currie BJ, Holt DC, Giffard PM, Tong SYC.

Microb Genom. 2016 Dec 12;2(12):e000098. doi: 10.1099/mgen.0.000098. eCollection 2016 Dec.

50.

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

Lees JA, Brouwer M, van der Ende A, Parkhill J, van de Beek D, Bentley SD.

Infect Immun. 2017 Feb 23;85(3). pii: e01061-16. doi: 10.1128/IAI.01061-16. Print 2017 Mar. No abstract available.

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