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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.


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.


PANINI: Pangenome Neighbour Identification for Bacterial Populations.

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

Microb Genom. 2018 Nov 22. doi: 10.1099/mgen.0.000220. [Epub ahead of print]


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.


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.


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.


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.


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 May 29. doi: 10.1099/mgen.0.000184. [Epub ahead of print]


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.


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]


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.


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]


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.


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.


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.


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

Lees JA, Kremer PH, 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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


The emergence of bacterial "hopeful monsters".

Croucher NJ, Klugman KP.

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


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.


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.


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.


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.


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.


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.


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.


Population genomics of post-vaccine changes in pneumococcal epidemiology.

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

Nat Genet. 2013 Jun;45(6):656-63. doi: 10.1038/ng.2625. Epub 2013 May 5.


Bacterial genomes in epidemiology--present and future.

Croucher NJ, Harris SR, Grad YH, Hanage WP.

Philos Trans R Soc Lond B Biol Sci. 2013 Feb 4;368(1614):20120202. doi: 10.1098/rstb.2012.0202. Print 2013 Mar 19. Review.


Pneumococcal capsular switching: a historical perspective.

Wyres KL, Lambertsen LM, Croucher NJ, McGee L, von Gottberg A, Liñares J, Jacobs MR, Kristinsson KG, Beall BW, Klugman KP, Parkhill J, Hakenbeck R, Bentley SD, Brueggemann AB.

J Infect Dis. 2013 Feb 1;207(3):439-49. doi: 10.1093/infdis/jis703. Epub 2012 Nov 21. Erratum in: J Infect Dis. 2013 Oct 1;208(7):1187.


The multidrug-resistant PMEN1 pneumococcus is a paradigm for genetic success.

Wyres KL, Lambertsen LM, Croucher NJ, McGee L, von Gottberg A, Liñares J, Jacobs MR, Kristinsson KG, Beall BW, Klugman KP, Parkhill J, Hakenbeck R, Bentley SD, Brueggemann AB.

Genome Biol. 2012 Nov 16;13(11):R103. doi: 10.1186/gb-2012-13-11-r103.


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

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

PLoS Pathog. 2012;8(6):e1002745. doi: 10.1371/journal.ppat.1002745. Epub 2012 Jun 14.


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

Köser CU, Holden MT, Ellington MJ, Cartwright EJ, Brown NM, Ogilvy-Stuart AL, Hsu LY, Chewapreecha C, Croucher NJ, Harris SR, Sanders M, Enright MC, Dougan G, Bentley SD, Parkhill J, Fraser LJ, Betley JR, Schulz-Trieglaff OB, Smith GP, Peacock SJ.

N Engl J Med. 2012 Jun 14;366(24):2267-75. doi: 10.1056/NEJMoa1109910.


Lineage-specific virulence determinants of Haemophilus influenzae biogroup aegyptius.

Strouts FR, Power P, Croucher NJ, Corton N, van Tonder A, Quail MA, Langford PR, Hudson MJ, Parkhill J, Kroll JS, Bentley SD.

Emerg Infect Dis. 2012 Mar;18(3):449-57. doi: 10.3201/eid1803.110728.


Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis.

Arnvig KB, Comas I, Thomson NR, Houghton J, Boshoff HI, Croucher NJ, Rose G, Perkins TT, Parkhill J, Dougan G, Young DB.

PLoS Pathog. 2011 Nov;7(11):e1002342. doi: 10.1371/journal.ppat.1002342. Epub 2011 Nov 3.


Detection of recombination events in bacterial genomes from large population samples.

Marttinen P, Hanage WP, Croucher NJ, Connor TR, Harris SR, Bentley SD, Corander J.

Nucleic Acids Res. 2012 Jan;40(1):e6. doi: 10.1093/nar/gkr928. Epub 2011 Nov 7.


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

Mutreja A, Kim DW, Thomson NR, Connor TR, Lee JH, Kariuki S, Croucher NJ, Choi SY, Harris SR, Lebens M, Niyogi SK, Kim EJ, Ramamurthy T, Chun J, Wood JL, Clemens JD, Czerkinsky C, Nair GB, Holmgren J, Parkhill J, Dougan G.

Nature. 2011 Aug 24;477(7365):462-5. doi: 10.1038/nature10392.


Identification, variation and transcription of pneumococcal repeat sequences.

Croucher NJ, Vernikos GS, Parkhill J, Bentley SD.

BMC Genomics. 2011 Feb 18;12:120. doi: 10.1186/1471-2164-12-120.

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