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Whole genome investigation of a divergent clade of the pathogen Streptococcus suis.

Baig A, Weinert LA, Peters SE, Howell KJ, Chaudhuri RR, Wang J, Holden MT, Parkhill J, Langford PR, Rycroft AN, Wren BW, Tucker AW, Maskell DJ.

Front Microbiol. 2015 Nov 4;6:1191. eCollection 2015.


Nonadiabatic Dynamics for Electrons at Second-Order: Real-Time TDDFT and OSCF2.

Nguyen TS, Parkhill J.

J Chem Theory Comput. 2015 Jul 14;11(7):2918-24. doi: 10.1021/acs.jctc.5b00262. Epub 2015 Jun 24.


Erratum for Kulohoma et al., Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core Genome.

Kulohoma BW, Cornick JE, Chaguza C, Yalcin F, Harris SR, Gray KJ, Kiran AM, Molyneux E, French N, Parkhill J, Faragher BE, Everett DB, Bentley SD, Heyderman RS.

Infect Immun. 2015 Dec;83(12):4896. doi: 10.1128/IAI.01156-15. No abstract available.


Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention.

Cuthbertson L, Rogers GB, Walker AW, Oliver A, Green LE, Daniels TW, Carroll MP, Parkhill J, Bruce KD, van der Gast CJ.

ISME J. 2015 Nov 10. doi: 10.1038/ismej.2015.198. [Epub ahead of print]


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.


Genomic epidemiology of age-associated meningococcal lineages in national surveillance: an observational cohort study.

Hill DM, Lucidarme J, Gray SJ, Newbold LS, Ure R, Brehony C, Harrison OB, Bray JE, Jolley KA, Bratcher HB, Parkhill J, Tang CM, Borrow R, Maiden MC.

Lancet Infect Dis. 2015 Oct 26. pii: S1473-3099(15)00267-4. doi: 10.1016/S1473-3099(15)00267-4. [Epub ahead of print]


Development of a Multiplex PCR Assay for Rapid Molecular Serotyping of Haemophilus parasuis.

Howell KJ, Peters SE, Wang J, Hernandez-Garcia J, Weinert LA, Luan SL, Chaudhuri RR, Angen Ø, Aragon V, Williamson SM, Parkhill J, Langford PR, Rycroft AN, Wren BW, Maskell DJ, Tucker AW.

J Clin Microbiol. 2015 Dec;53(12):3812-21. doi: 10.1128/JCM.01991-15. Epub 2015 Sep 30.


Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera.

Sun Z, Harris HM, McCann A, Guo C, Argimón S, Zhang W, Yang X, Jeffery IB, Cooney JC, Kagawa TF, Liu W, Song Y, Salvetti E, Wrobel A, Rasinkangas P, Parkhill J, Rea MC, O'Sullivan O, Ritari J, Douillard FP, Paul Ross R, Yang R, Briner AE, Felis GE, de Vos WM, Barrangou R, Klaenhammer TR, Caufield PW, Cui Y, Zhang H, O'Toole PW.

Nat Commun. 2015 Sep 29;6:8322. doi: 10.1038/ncomms9322.


The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource.

Baker KS, Burnett E, McGregor H, Deheer-Graham A, Boinett C, Langridge GC, Wailan AM, Cain AK, Thomson NR, Russell JE, Parkhill J.

Genome Med. 2015 Sep 28;7(1):97. doi: 10.1186/s13073-015-0222-7.


Old Drugs To Treat Resistant Bugs: Methicillin-Resistant Staphylococcus aureus Isolates with mecC Are Susceptible to a Combination of Penicillin and Clavulanic Acid.

Ba X, Harrison EM, Lovering AL, Gleadall N, Zadoks R, Parkhill J, Peacock SJ, Holden MT, Paterson GK, Holmes MA.

Antimicrob Agents Chemother. 2015 Dec;59(12):7396-404. doi: 10.1128/AAC.01469-15. Epub 2015 Sep 21.


Variable alterations of the microbiota, without metabolic or immunological change, following faecal microbiota transplantation in patients with chronic pouchitis.

Landy J, Walker AW, Li JV, Al-Hassi HO, Ronde E, English NR, Mann ER, Bernardo D, McLaughlin SD, Parkhill J, Ciclitira PJ, Clark SK, Knight SC, Hart AL.

Sci Rep. 2015 Aug 12;5:12955. doi: 10.1038/srep12955.


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

Kulohoma BW, Cornick JE, Chaguza C, Yalcin F, Harris SR, Gray KJ, Kiran AM, Molyneux E, French N, Parkhill J, Faragher BE, Everett DB, Bentley SD, Heyderman RS.

Infect Immun. 2015 Oct;83(10):4165-73. doi: 10.1128/IAI.00814-15. Epub 2015 Aug 10. Erratum in: Infect Immun. 2015 Dec;83(12):4896.


Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri.

Connor TR, Barker CR, Baker KS, Weill FX, Talukder KA, Smith AM, Baker S, Gouali M, Pham Thanh D, Jahan Azmi I, Dias da Silveira W, Semmler T, Wieler LH, Jenkins C, Cravioto A, Faruque SM, Parkhill J, Wook Kim D, Keddy KH, Thomson NR.

Elife. 2015 Aug 4;4:e07335. doi: 10.7554/eLife.07335.


Essential roles of methionine and S-adenosylmethionine in the autarkic lifestyle of Mycobacterium tuberculosis.

Berney M, Berney-Meyer L, Wong KW, Chen B, Chen M, Kim J, Wang J, Harris D, Parkhill J, Chan J, Wang F, Jacobs WR Jr.

Proc Natl Acad Sci U S A. 2015 Aug 11;112(32):10008-13. doi: 10.1073/pnas.1513033112. Epub 2015 Jul 28.


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, Peacock SJ.

J Antimicrob Chemother. 2015 Oct;70(10):2775-8. doi: 10.1093/jac/dkv206. Epub 2015 Jul 28.


Roary: rapid large-scale prokaryote pan genome analysis.

Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, Fookes M, Falush D, Keane JA, Parkhill J.

Bioinformatics. 2015 Nov 15;31(22):3691-3. doi: 10.1093/bioinformatics/btv421. Epub 2015 Jul 20.


Erratum for Boinett et al., Complete Genome Sequence of Bordetella pertussis D420.

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

Genome Announc. 2015 Jul 16;3(4). pii: e00842-15. doi: 10.1128/genomeA.00842-15. No abstract available.


Whole Genome Sequencing Shows a Low Proportion of Tuberculosis Disease Is Attributable to Known Close Contacts in Rural Malawi.

Glynn JR, Guerra-Assunção JA, Houben RM, Sichali L, Mzembe T, Mwaungulu LK, Mwaungulu JN, McNerney R, Khan P, Parkhill J, Crampin AC, Clark TG.

PLoS One. 2015 Jul 16;10(7):e0132840. doi: 10.1371/journal.pone.0132840. eCollection 2015.


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, Parkhill J, Holden MT, Waller AS.

Genome Res. 2015 Sep;25(9):1360-71. doi: 10.1101/gr.189803.115. Epub 2015 Jul 9.


16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice.

Walker AW, Martin JC, Scott P, Parkhill J, Flint HJ, Scott KP.

Microbiome. 2015 Jun 22;3:26. doi: 10.1186/s40168-015-0087-4. eCollection 2015.

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