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Items: 1 to 50 of 72

1.

Genomic epidemiology of penicillin-non-susceptible Streptococcus pneumoniae.

Dewé TCM, D'Aeth JC, Croucher NJ.

Microb Genom. 2019 Oct 14. doi: 10.1099/mgen.0.000305. [Epub ahead of print]

2.

Peptide Occurring in Enterobacteriaceae Triggers Streptococcus pneumoniae Cell Death.

Nasher F, Kwun MJ, Croucher NJ, Heller M, Hathaway LJ.

Front Cell Infect Microbiol. 2019 Sep 10;9:320. doi: 10.3389/fcimb.2019.00320. eCollection 2019.

3.

Synergistic Activity of Mobile Genetic Element Defences in Streptococcus pneumoniae.

Kwun MJ, Oggioni MR, Bentley SD, Fraser C, Croucher NJ.

Genes (Basel). 2019 Sep 13;10(9). pii: E707. doi: 10.3390/genes10090707.

4.

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 Oct 10;47(18):e112. doi: 10.1093/nar/gkz656.

5.

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.

6.

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.

7.

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.

8.

Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection.

McNally A, Kallonen T, Connor C, Abudahab K, Aanensen DM, Horner C, Peacock SJ, Parkhill J, Croucher NJ, Corander J.

MBio. 2019 Apr 23;10(2). pii: e00644-19. doi: 10.1128/mBio.00644-19.

9.

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.

10.

Genomic and Functional Analysis of Emerging Virulent and Multidrug-Resistant Escherichia coli Lineage Sequence Type 648.

Schaufler K, Semmler T, Wieler LH, Trott DJ, Pitout J, Peirano G, Bonnedahl J, Dolejska M, Literak I, Fuchs S, Ahmed N, Grobbel M, Torres C, McNally A, Pickard D, Ewers C, Croucher NJ, Corander J, Guenther S.

Antimicrob Agents Chemother. 2019 May 24;63(6). pii: e00243-19. doi: 10.1128/AAC.00243-19. Print 2019 Jun.

PMID:
30885899
11.

Population genomics of pneumococcal carriage in Massachusetts children following introduction of PCV-13.

Mitchell PK, Azarian T, Croucher NJ, Callendrello A, Thompson CM, Pelton SI, Lipsitch M, Hanage WP.

Microb Genom. 2019 Feb;5(2). doi: 10.1099/mgen.0.000252. Epub 2019 Feb 19.

12.

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.

13.

Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination.

Campo JJ, Le TQ, Pablo JV, Hung C, Teng AA, Tettelin H, Tate A, Hanage WP, Alderson MR, Liang X, Malley R, Lipsitch M, Croucher NJ.

Elife. 2018 Dec 28;7. pii: e37015. doi: 10.7554/eLife.37015.

14.

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.

15.

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.

16.

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
17.

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.

18.

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.

Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M, Bezemer D, Croucher NJ, Hall M, Hillebregt M, Ong SH, Ratmann O, Albert J, Bannert N, Fellay J, Fransen K, Gourlay A, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Cornelissen M, Kellam P, Reiss P, Fraser C; BEEHIVE Collaboration.

Virus Evol. 2018 May 18;4(1):vey007. doi: 10.1093/ve/vey007. eCollection 2018 Jan.

19.

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.

20.

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

Cremers AJH, Mobegi FM, van der Gaast-de Jongh C, van Weert M, van Opzeeland FJ, Vehkala M, Knol MJ, Bootsma HJ, Välimäki N, Croucher NJ, Meis JF, Bentley S, van Hijum SAFT, Corander J, Zomer AL, Ferwerda G, de Jonge MI.

Clin Infect Dis. 2019 Jan 1;68(1):61-69. doi: 10.1093/cid/ciy417.

PMID:
29788414
21.

Transformation asymmetry and the evolution of the bacterial accessory genome.

Apagyi KJ, Fraser C, Croucher NJ.

Mol Biol Evol. 2017 Dec 1. doi: 10.1093/molbev/msx309. [Epub ahead of print]

22.

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.

23.

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]

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations.

Mostowy R, Croucher NJ, Andam CP, Corander J, Hanage WP, Marttinen P.

Mol Biol Evol. 2017 May 1;34(5):1167-1182. doi: 10.1093/molbev/msx066.

30.

Evolution of antibiotic resistance is linked to any genetic mechanism affecting bacterial duration of carriage.

Lehtinen S, Blanquart F, Croucher NJ, Turner P, Lipsitch M, Fraser C.

Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):1075-1080. doi: 10.1073/pnas.1617849114. Epub 2017 Jan 17.

31.

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

Croucher NJ, Campo JJ, Le TQ, Liang X, Bentley SD, Hanage WP, Lipsitch M.

Proc Natl Acad Sci U S A. 2017 Jan 17;114(3):E357-E366. doi: 10.1073/pnas.1613937114. Epub 2017 Jan 4.

32.

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

Lees JA, Vehkala M, Välimäki N, Harris SR, Chewapreecha C, Croucher NJ, Marttinen P, Davies MR, Steer AC, Tong SY, Honkela A, Parkhill J, Bentley SD, Corander J.

Nat Commun. 2016 Sep 16;7:12797. doi: 10.1038/ncomms12797.

33.

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

Croucher NJ, Mostowy R, Wymant C, Turner P, Bentley SD, Fraser C.

PLoS Biol. 2016 Mar 2;14(3):e1002394. doi: 10.1371/journal.pbio.1002394. eCollection 2016 Mar.

34.

Recombination produces coherent bacterial species clusters in both core and accessory genomes.

Marttinen P, Croucher NJ, Gutmann MU, Corander J, Hanage WP.

Microb Genom. 2015 Nov 5;1(5):e000038. doi: 10.1099/mgen.0.000038. eCollection 2015 Nov.

35.

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

Croucher NJ, Finkelstein JA, Pelton SI, Parkhill J, Bentley SD, Lipsitch M, Hanage WP.

Sci Data. 2015 Oct 27;2:150058. doi: 10.1038/sdata.2015.58. eCollection 2015.

36.

Identification of pneumococcal colonization determinants in the stringent response pathway facilitated by genomic diversity.

Li Y, Croucher NJ, Thompson CM, Trzciński K, Hanage WP, Lipsitch M.

BMC Genomics. 2015 May 9;16:369. doi: 10.1186/s12864-015-1573-6.

37.

Stability of the pneumococcal population structure in Massachusetts as PCV13 was introduced.

Chang Q, Stevenson AE, Croucher NJ, Lee GM, Pelton SI, Lipsitch M, Finkelstein JA, Hanage WP.

BMC Infect Dis. 2015 Feb 18;15:68. doi: 10.1186/s12879-015-0797-z.

38.

Selective and genetic constraints on pneumococcal serotype switching.

Croucher NJ, Kagedan L, Thompson CM, Parkhill J, Bentley SD, Finkelstein JA, Lipsitch M, Hanage WP.

PLoS Genet. 2015 Mar 31;11(3):e1005095. doi: 10.1371/journal.pgen.1005095. eCollection 2015 Mar.

39.

The application of genomics to tracing bacterial pathogen transmission.

Croucher NJ, Didelot X.

Curr Opin Microbiol. 2015 Feb;23:62-7. doi: 10.1016/j.mib.2014.11.004. Epub 2014 Nov 22. Review.

PMID:
25461574
40.

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

Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA, Bentley SD, Parkhill J, Harris SR.

Nucleic Acids Res. 2015 Feb 18;43(3):e15. doi: 10.1093/nar/gku1196. Epub 2014 Nov 20.

41.

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

Croucher NJ, Coupland PG, Stevenson AE, Callendrello A, Bentley SD, Hanage WP.

Nat Commun. 2014 Nov 19;5:5471. doi: 10.1038/ncomms6471.

42.

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, Mather AE, Hanage WP, Goldblatt D, Nosten FH, Turner C, Turner P, Bentley SD, Parkhill J.

PLoS Genet. 2014 Aug 7;10(8):e1004547. doi: 10.1371/journal.pgen.1004547. eCollection 2014 Aug.

43.

The emergence of bacterial "hopeful monsters".

Croucher NJ, Klugman KP.

MBio. 2014 Jul 29;5(4):e01550-14. doi: 10.1128/mBio.01550-14.

44.

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

Croucher NJ, Hanage WP, Harris SR, McGee L, van der Linden M, de Lencastre H, Sá-Leão R, Song JH, Ko KS, Beall B, Klugman KP, Parkhill J, Tomasz A, Kristinsson KG, Bentley SD.

BMC Biol. 2014 Jun 23;12:49. doi: 10.1186/1741-7007-12-49.

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, van der Linden M, Song JH, Ko KS, de Lencastre H, Turner C, Yang F, Sá-Leão R, Beall B, Klugman KP, Parkhill J, Turner P, Bentley SD.

Genome Biol Evol. 2014 Jun 10;6(7):1589-602. doi: 10.1093/gbe/evu120.

46.

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

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

PLoS Genet. 2014 May 1;10(5):e1004300. doi: 10.1371/journal.pgen.1004300. eCollection 2014 May.

47.

Impact of 13-Valent Pneumococcal Conjugate Vaccination on Streptococcus pneumoniae Carriage in Young Children in Massachusetts.

Lee GM, Kleinman K, Pelton SI, Hanage W, Huang SS, Lakoma M, Dutta-Linn M, Croucher NJ, Stevenson A, Finkelstein JA.

J Pediatric Infect Dis Soc. 2014 Mar;3(1):23-32. doi: 10.1093/jpids/pit057. Epub 2013 Oct 3.

48.

Dense genomic sampling identifies highways of pneumococcal recombination.

Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P, Cheng L, Pessia A, Aanensen DM, Mather AE, Page AJ, Salter SJ, Harris D, Nosten F, Goldblatt D, Corander J, Parkhill J, Turner P, Bentley SD.

Nat Genet. 2014 Mar;46(3):305-309. doi: 10.1038/ng.2895. Epub 2014 Feb 9.

49.

RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006.

Wilf NM, Reid AJ, Ramsay JP, Williamson NR, Croucher NJ, Gatto L, Hester SS, Goulding D, Barquist L, Lilley KS, Kingsley RA, Dougan G, Salmond GP.

BMC Genomics. 2013 Nov 22;14:822. doi: 10.1186/1471-2164-14-822.

50.

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

Croucher NJ, Mitchell AM, Gould KA, Inverarity D, Barquist L, Feltwell T, Fookes MC, Harris SR, Dordel J, Salter SJ, Browall S, Zemlickova H, Parkhill J, Normark S, Henriques-Normark B, Hinds J, Mitchell TJ, Bentley SD.

PLoS Genet. 2013;9(10):e1003868. doi: 10.1371/journal.pgen.1003868. Epub 2013 Oct 10.

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