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Items: 1 to 50 of 542

1.

Are commercial providers a viable option for clinical bacterial sequencing?

Raven K, Blane B, Churcher C, Parkhill J, Peacock SJ.

Microb Genom. 2018 Apr 5. doi: 10.1099/mgen.0.000173. [Epub ahead of print]

2.

Low genomic diversity of Legionella pneumophila within clinical specimens.

David S, Mentasti M, Parkhill J, Chalker VJ.

Clin Microbiol Infect. 2018 Mar 13. pii: S1198-743X(18)30210-6. doi: 10.1016/j.cmi.2018.03.004. [Epub ahead of print]

3.

Genomic survey of Clostridium difficile reservoirs in the East of England implicates environmental contamination of wastewater treatment plants by clinical lineages.

Moradigaravand D, Gouliouris T, Ludden C, Reuter S, Jamrozy D, Blane B, Naydenova P, Judge K, H Aliyu S, F Hadjirin N, A Holmes M, Török E, M Brown N, Parkhill J, Peacock S.

Microb Genom. 2018 Mar 2. doi: 10.1099/mgen.0.000162. [Epub ahead of print]

4.

The Impact of NOD2 Variants on Fecal Microbiota in Crohn's Disease and Controls Without Gastrointestinal Disease.

Kennedy NA, Lamb CA, Berry SH, Walker AW, Mansfield J, Parkes M, Simpkins R, Tremelling M, Nutland S; UK IBD Genetics Consortium, Parkhill J, Probert C, Hold GL, Lees CW.

Inflamm Bowel Dis. 2018 Feb 15;24(3):583-592. doi: 10.1093/ibd/izx061.

PMID:
29462388
5.

Gut microbiota trajectory in early life may predict development of celiac disease.

Olivares M, Walker AW, Capilla A, Benítez-Páez A, Palau F, Parkhill J, Castillejo G, Sanz Y.

Microbiome. 2018 Feb 20;6(1):36. doi: 10.1186/s40168-018-0415-6.

6.

Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis.

Coll F, Phelan J, Hill-Cawthorne GA, Nair MB, Mallard K, Ali S, Abdallah AM, Alghamdi S, Alsomali M, Ahmed AO, Portelli S, Oppong Y, Alves A, Bessa TB, Campino S, Caws M, Chatterjee A, Crampin AC, Dheda K, Furnham N, Glynn JR, Grandjean L, Minh Ha D, Hasan R, Hasan Z, Hibberd ML, Joloba M, Jones-López EC, Matsumoto T, Miranda A, Moore DJ, Mocillo N, Panaiotov S, Parkhill J, Penha C, Perdigão J, Portugal I, Rchiad Z, Robledo J, Sheen P, Shesha NT, Sirgel FA, Sola C, Oliveira Sousa E, Streicher EM, Helden PV, Viveiros M, Warren RM, McNerney R, Pain A, Clark TG.

Nat Genet. 2018 Feb;50(2):307-316. doi: 10.1038/s41588-017-0029-0. Epub 2018 Jan 22.

PMID:
29358649
7.

Within-host evolution of Enterococcus faecium during longitudinal carriage and transition to bloodstream infection in immunocompromised patients.

Moradigaravand D, Gouliouris T, Blane B, Naydenova P, Ludden C, Crawley C, Brown NM, Török ME, Parkhill J, Peacock SJ.

Genome Med. 2017 Dec 27;9(1):119. doi: 10.1186/s13073-017-0507-0.

8.

Convergent evolution and topologically disruptive polymorphisms among multidrug-resistant tuberculosis in Peru.

Grandjean L, Gilman RH, Iwamoto T, Köser CU, Coronel J, Zimic M, Török ME, Ayabina D, Kendall M, Fraser C, Harris S, Parkhill J, Peacock SJ, Moore DAJ, Colijn C.

PLoS One. 2017 Dec 27;12(12):e0189838. doi: 10.1371/journal.pone.0189838. eCollection 2017.

9.

Genome-Based Analysis of Enterococcus faecium Bacteremia Associated with Recurrent and Mixed-Strain Infection.

Raven KE, Gouliouris T, Parkhill J, Peacock SJ.

J Clin Microbiol. 2018 Feb 22;56(3). pii: e01520-17. doi: 10.1128/JCM.01520-17. Print 2018 Mar.

10.

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.

11.

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.

12.

Limited Impact of Adolescent Meningococcal ACWY Vaccination on Neisseria meningitidis Serogroup W Carriage in University Students.

Oldfield NJ, Green LR, Parkhill J, Bayliss CD, Turner DPJ.

J Infect Dis. 2018 Jan 30;217(4):608-616. doi: 10.1093/infdis/jix596.

PMID:
29155998
13.

What Is Resistance? Impact of Phenotypic versus Molecular Drug Resistance Testing on Therapy for Multi- and Extensively Drug-Resistant Tuberculosis.

Heyckendorf J, Andres S, Köser CU, Olaru ID, Schön T, Sturegård E, Beckert P, Schleusener V, Kohl TA, Hillemann D, Moradigaravand D, Parkhill J, Peacock SJ, Niemann S, Lange C, Merker M.

Antimicrob Agents Chemother. 2018 Jan 25;62(2). pii: e01550-17. doi: 10.1128/AAC.01550-17. Print 2018 Feb.

14.

Integrated view of Vibrio cholerae in the Americas.

Domman D, Quilici ML, Dorman MJ, Njamkepo E, Mutreja A, Mather AE, Delgado G, Morales-Espinosa R, Grimont PAD, Lizárraga-Partida ML, Bouchier C, Aanensen DM, Kuri-Morales P, Tarr CL, Dougan G, Parkhill J, Campos J, Cravioto A, Weill FX, Thomson NR.

Science. 2017 Nov 10;358(6364):789-793. doi: 10.1126/science.aao2136.

PMID:
29123068
15.

Genomic history of the seventh pandemic of cholera in Africa.

Weill FX, Domman D, Njamkepo E, Tarr C, Rauzier J, Fawal N, Keddy KH, Salje H, Moore S, Mukhopadhyay AK, Bercion R, Luquero FJ, Ngandjio A, Dosso M, Monakhova E, Garin B, Bouchier C, Pazzani C, Mutreja A, Grunow R, Sidikou F, Bonte L, Breurec S, Damian M, Njanpop-Lafourcade BM, Sapriel G, Page AL, Hamze M, Henkens M, Chowdhury G, Mengel M, Koeck JL, Fournier JM, Dougan G, Grimont PAD, Parkhill J, Holt KE, Piarroux R, Ramamurthy T, Quilici ML, Thomson NR.

Science. 2017 Nov 10;358(6364):785-789. doi: 10.1126/science.aad5901.

PMID:
29123067
16.

Streptococcus bovimastitidis sp. nov., isolated from a dairy cow with mastitis.

de Vries SPW, Hadjirin NF, Lay EM, Zadoks RN, Peacock SJ, Parkhill J, Grant AJ, McDougall S, Holmes MA.

Int J Syst Evol Microbiol. 2018 Jan;68(1):21-27. doi: 10.1099/ijsem.0.002321. Epub 2017 Nov 3.

PMID:
29099353
17.

Investigation of a Cluster of Sequence Type 22 Methicillin-Resistant Staphylococcus aureus Transmission in a Community Setting.

Toleman MS, Watkins ER, Williams T, Blane B, Sadler B, Harrison EM, Coll F, Parkhill J, Nazareth B, Brown NM, Peacock SJ.

Clin Infect Dis. 2017 Nov 29;65(12):2069-2077. doi: 10.1093/cid/cix539.

18.

Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community.

Coll F, Harrison EM, Toleman MS, Reuter S, Raven KE, Blane B, Palmer B, Kappeler ARM, Brown NM, Török ME, Parkhill J, Peacock SJ.

Sci Transl Med. 2017 Oct 25;9(413). pii: eaak9745. doi: 10.1126/scitranslmed.aak9745. Epub 2017 Oct 25.

PMID:
29070701
19.

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.

20.

Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing.

Ludden C, Reuter S, Judge K, Gouliouris T, Blane B, Coll F, Naydenova P, Hunt M, Tracey A, Hopkins KL, Brown NM, Woodford N, Parkhill J, Peacock SJ.

Microb Genom. 2017 Jul 4;3(7):e000114. doi: 10.1099/mgen.0.000114. eCollection 2017 Jul.

21.

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.

22.

Role of Alanine Racemase Mutations in Mycobacterium tuberculosis d-Cycloserine Resistance.

Nakatani Y, Opel-Reading HK, Merker M, Machado D, Andres S, Kumar SS, Moradigaravand D, Coll F, Perdigão J, Portugal I, Schön T, Nair D, Devi KRU, Kohl TA, Beckert P, Clark TG, Maphalala G, Khumalo D, Diel R, Klaos K, Aung HL, Cook GM, Parkhill J, Peacock SJ, Swaminathan S, Viveiros M, Niemann S, Krause KL, Köser CU.

Antimicrob Agents Chemother. 2017 Nov 22;61(12). pii: e01575-17. doi: 10.1128/AAC.01575-17. Print 2017 Dec.

23.

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.

24.

The Microevolution and Epidemiology of Staphylococcus aureus Colonization during Atopic Eczema Disease Flare.

Harkins CP, Pettigrew KA, Oravcová K, Gardner J, Hearn RMR, Rice D, Mather AE, Parkhill J, Brown SJ, Proby CM, Holden MTG.

J Invest Dermatol. 2018 Feb;138(2):336-343. doi: 10.1016/j.jid.2017.09.023. Epub 2017 Sep 23.

25.

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.

26.

Whole genome sequencing of ESBL-producing Escherichia coli isolated from patients, farm waste and canals in Thailand.

Runcharoen C, Raven KE, Reuter S, Kallonen T, Paksanont S, Thammachote J, Anun S, Blane B, Parkhill J, Peacock SJ, Chantratita N.

Genome Med. 2017 Sep 6;9(1):81. doi: 10.1186/s13073-017-0471-8.

27.

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.

28.

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.

29.

Community outbreaks of group A Streptococcus revealed by genome sequencing.

Turner CE, Bedford L, Brown NM, Judge K, Török ME, Parkhill J, Peacock SJ.

Sci Rep. 2017 Aug 17;7(1):8554. doi: 10.1038/s41598-017-08914-x.

30.

Genomic surveillance reveals low prevalence of livestock-associated methicillin-resistant Staphylococcus aureus in the East of England.

Harrison EM, Coll F, Toleman MS, Blane B, Brown NM, Török ME, Parkhill J, Peacock SJ.

Sci Rep. 2017 Aug 7;7(1):7406. doi: 10.1038/s41598-017-07662-2.

31.

Origin of the Size-Dependent Stokes Shift in CsPbBr3 Perovskite Nanocrystals.

Brennan MC, Herr JE, Nguyen-Beck TS, Zinna J, Draguta S, Rouvimov S, Parkhill J, Kuno M.

J Am Chem Soc. 2017 Sep 6;139(35):12201-12208. doi: 10.1021/jacs.7b05683. Epub 2017 Aug 23.

PMID:
28772067
32.

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.

33.

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.

34.

Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in a long-term care facility in the United Kingdom.

Brodrick HJ, Raven KE, Kallonen T, Jamrozy D, Blane B, Brown NM, Martin V, Török ME, Parkhill J, Peacock SJ.

Genome Med. 2017 Jul 25;9(1):70. doi: 10.1186/s13073-017-0457-6.

35.

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.

36.

Accelerating Realtime TDDFT with Block-Orthogonalized Manby-Miller Embedding Theory.

Koh KJ, Nguyen-Beck TS, Parkhill J.

J Chem Theory Comput. 2017 Sep 12;13(9):4173-4178. doi: 10.1021/acs.jctc.7b00494. Epub 2017 Aug 4.

PMID:
28723221
37.

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]

38.

Evolution of the Staphylococcus argenteus ST2250 Clone in Northeastern Thailand Is Linked with the Acquisition of Livestock-Associated Staphylococcal Genes.

Moradigaravand D, Jamrozy D, Mostowy R, Anderson A, Nickerson EK, Thaipadungpanit J, Wuthiekanun V, Limmathurotsakul D, Tandhavanant S, Wikraiphat C, Wongsuvan G, Teerawattanasook N, Jutrakul Y, Srisurat N, Chaimanee P, Eoin West T, Blane B, Parkhill J, Chantratita N, Peacock SJ.

MBio. 2017 Jul 5;8(4). pii: e00802-17. doi: 10.1128/mBio.00802-17.

39.

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.

40.

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.

41.

Intrinsic Bond Energies from a Bonds-in-Molecules Neural Network.

Yao K, Herr JE, Brown SN, Parkhill J.

J Phys Chem Lett. 2017 Jun 15;8(12):2689-2694. doi: 10.1021/acs.jpclett.7b01072. Epub 2017 Jun 5.

PMID:
28573865
42.

Defining the ABC of gene essentiality in streptococci.

Charbonneau ARL, Forman OP, Cain AK, Newland G, Robinson C, Boursnell M, Parkhill J, Leigh JA, Maskell DJ, Waller AS.

BMC Genomics. 2017 May 31;18(1):426. doi: 10.1186/s12864-017-3794-3.

43.

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.

44.

MRSA Transmission Dynamics Among Interconnected Acute, Intermediate-Term, and Long-Term Healthcare Facilities in Singapore.

Chow A, Lim VW, Khan A, Pettigrew K, Lye DCB, Kanagasabai K, Phua K, Krishnan P, Ang B, Marimuthu K, Hon PY, Koh J, Leong I, Parkhill J, Hsu LY, Holden MTG.

Clin Infect Dis. 2017 May 15;64(suppl_2):S76-S81. doi: 10.1093/cid/cix072.

PMID:
28475785
45.

Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex.

Loveridge EJ, Jones C, Bull MJ, Moody SC, Kahl MW, Khan Z, Neilson L, Tomeva M, Adams SE, Wood AC, Rodriguez-Martin D, Pinel I, Parkhill J, Mahenthiralingam E, Crosby J.

J Bacteriol. 2017 Jun 13;199(13). pii: e00125-17. doi: 10.1128/JB.00125-17. Print 2017 Jul 1.

46.

A non-endoscopic device to sample the oesophageal microbiota: a case-control study.

Elliott DRF, Walker AW, O'Donovan M, Parkhill J, Fitzgerald RC.

Lancet Gastroenterol Hepatol. 2017 Jan;2(1):32-42. doi: 10.1016/S2468-1253(16)30086-3. Epub 2016 Nov 12.

47.

The Influence of HIV on the Evolution of Mycobacterium tuberculosis.

Koch AS, Brites D, Stucki D, Evans JC, Seldon R, Heekes A, Mulder N, Nicol M, Oni T, Mizrahi V, Warner DF, Parkhill J, Gagneux S, Martin DP, Wilkinson RJ.

Mol Biol Evol. 2017 Jul 1;34(7):1654-1668. doi: 10.1093/molbev/msx107.

48.

Complex Routes of Nosocomial Vancomycin-Resistant Enterococcus faecium Transmission Revealed by Genome Sequencing.

Raven KE, Gouliouris T, Brodrick H, Coll F, Brown NM, Reynolds R, Reuter S, Török ME, Parkhill J, Peacock SJ.

Clin Infect Dis. 2017 Apr 1;64(7):886-893. doi: 10.1093/cid/ciw872.

49.

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.

PMID:
28358127
50.

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.

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