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Items: 1 to 50 of 560

1.

Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data.

Sobkowiak B, Glynn JR, Houben RMGJ, Mallard K, Phelan JE, Guerra-Assunção JA, Banda L, Mzembe T, Viveiros M, McNerney R, Parkhill J, Crampin AC, Clark TG.

BMC Genomics. 2018 Aug 14;19(1):613. doi: 10.1186/s12864-018-4988-z.

2.

Investigating the Campylobacter jejuni Transcriptional Response to Host Intestinal Extracts Reveals the Involvement of a Widely Conserved Iron Uptake System.

Liu MM, Boinett CJ, Chan ACK, Parkhill J, Murphy MEP, Gaynor EC.

MBio. 2018 Aug 7;9(4). pii: e01347-18. doi: 10.1128/mBio.01347-18.

3.

Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates.

Palittapongarnpim P, Ajawatanawong P, Viratyosin W, Smittipat N, Disratthakit A, Mahasirimongkol S, Yanai H, Yamada N, Nedsuwan S, Imasanguan W, Kantipong P, Chaiyasirinroje B, Wongyai J, Toyo-Oka L, Phelan J, Parkhill J, Clark TG, Hibberd ML, Ruengchai W, Palittapongarnpim P, Juthayothin T, Tongsima S, Tokunaga K.

Sci Rep. 2018 Aug 2;8(1):11597. doi: 10.1038/s41598-018-29986-3.

4.

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 Jul 27. doi: 10.1093/gbe/evy152. [Epub ahead of print]

PMID:
30060167
5.

Reply to Dookie et al., "Whole-Genome Sequencing To Guide the Selection of Treatment for Drug-Resistant Tuberculosis".

Köser CU, Heyckendorf J, Andres S, 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 Jul 27;62(8). pii: e00616-18. doi: 10.1128/AAC.00616-18. Print 2018 Aug. No abstract available.

PMID:
30054377
6.

Changing the paradigm for hospital outbreak detection by leading with genomic surveillance of nosocomial pathogens.

Peacock SJ, Parkhill J, Brown NM.

Microbiology. 2018 Jul 27. doi: 10.1099/mic.0.000700. [Epub ahead of print]

PMID:
30052172
7.

Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches.

Otchere ID, Coscollá M, Sánchez-Busó L, Asante-Poku A, Brites D, Loiseau C, Meehan C, Osei-Wusu S, Forson A, Laryea C, Yahayah AI, Baddoo A, Ansa GA, Aboagye SY, Asare P, Borrell S, Gehre F, Beckert P, Kohl TA, N'dira S, Beisel C, Antonio M, Niemann S, de Jong BC, Parkhill J, Harris SR, Gagneux S, Yeboah-Manu D.

Sci Rep. 2018 Jul 26;8(1):11269. doi: 10.1038/s41598-018-29620-2.

8.

Recognizing the reagent microbiome.

de Goffau MC, Lager S, Salter SJ, Wagner J, Kronbichler A, Charnock-Jones DS, Peacock SJ, Smith GCS, Parkhill J.

Nat Microbiol. 2018 Aug;3(8):851-853. doi: 10.1038/s41564-018-0202-y. No abstract available.

PMID:
30046175
9.

Transposon Insertion Sequencing Elucidates Novel Gene Involvement in Susceptibility and Resistance to Phages T4 and T7 in Escherichia coli O157.

Cowley LA, Low AS, Pickard D, Boinett CJ, Dallman TJ, Day M, Perry N, Gally DL, Parkhill J, Jenkins C, Cain AK.

MBio. 2018 Jul 24;9(4). pii: e00705-18. doi: 10.1128/mBio.00705-18.

10.

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.

11.

Gene exchange drives the ecological success of a multi-host bacterial pathogen.

Richardson EJ, Bacigalupe R, Harrison EM, Weinert LA, Lycett S, Vrieling M, Robb K, Hoskisson PA, Holden MTG, Feil EJ, Paterson GK, Tong SYC, Shittu A, van Wamel W, Aanensen DM, Parkhill J, Peacock SJ, Corander J, Holmes M, Fitzgerald JR.

Nat Ecol Evol. 2018 Jul 23. doi: 10.1038/s41559-018-0617-0. [Epub ahead of print]

PMID:
30038246
12.

Metadynamics for training neural network model chemistries: A competitive assessment.

Herr JE, Yao K, McIntyre R, Toth DW, Parkhill J.

J Chem Phys. 2018 Jun 28;148(24):241710. doi: 10.1063/1.5020067.

PMID:
29960377
13.

Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin.

Cain AK, Boinett CJ, Barquist L, Dordel J, Fookes M, Mayho M, Ellington MJ, Goulding D, Pickard D, Wick RR, Holt KE, Parkhill J, Thomson NR.

Sci Rep. 2018 Jun 29;8(1):9868. doi: 10.1038/s41598-018-28199-y.

14.

Surveillance and Epidemiology of Drug Resistant Infections Consortium (SEDRIC): Supporting the transition from strategy to action.

Fukuda K, Limmathurotsakul D, Okeke IN, Shetty N, van Doorn R, Feasey NA, Chiara F, Zoubiane G, Jinks T, Parkhill J, Patel J, Reid SWJ, Holmes AH, Peacock SJ; Surveillance and Epidemiology of Drug Resistant Infections Consortium (SEDRIC).

Wellcome Open Res. 2018 May 16;3:59. doi: 10.12688/wellcomeopenres.14586.2. eCollection 2018.

15.

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.

16.

The widespread use of topical antimicrobials enriches for resistance in Staphylococcus aureus isolated from patients with atopic dermatitis.

Harkins CP, McAleer MA, Bennett D, McHugh M, Fleury OM, Pettigrew KA, Oravcová K, Parkhill J, Proby CM, Dawe RS, Geoghegan JA, Irvine AD, Holden MTG.

Br J Dermatol. 2018 May 5. doi: 10.1111/bjd.16722. [Epub ahead of print]

PMID:
29729180
17.

The TensorMol-0.1 model chemistry: a neural network augmented with long-range physics.

Yao K, Herr JE, Toth DW, Mckintyre R, Parkhill J.

Chem Sci. 2018 Jan 18;9(8):2261-2269. doi: 10.1039/c7sc04934j. eCollection 2018 Feb 28.

18.

Author Correction: 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, Ha DM, 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, Sousa EO, Streicher EM, Van Helden P, Viveiros M, Warren RM, McNerney R, Pain A, Clark TG.

Nat Genet. 2018 May;50(5):764. doi: 10.1038/s41588-018-0074-3.

PMID:
29674744
19.

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]

20.

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]

21.

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]

22.

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
23.

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.

24.

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. Erratum in: Nat Genet. 2018 Apr 19;:.

PMID:
29358649
25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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
31.

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.

32.

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
33.

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
34.

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
35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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
50.

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.

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