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Items: 1 to 50 of 586

1.

Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii.

Boinett CJ, Cain AK, Hawkey J, Do Hoang NT, Khanh NNT, Thanh DP, Dordel J, Campbell JI, Lan NPH, Mayho M, Langridge GC, Hadfield J, Chau NVV, Thwaites GE, Parkhill J, Thomson NR, Holt KE, Baker S.

Microb Genom. 2019 Feb 5. doi: 10.1099/mgen.0.000246. [Epub ahead of print]

2.

'Candidatus Ornithobacterium hominis': insights gained from draft genomes obtained from nasopharyngeal swabs.

Salter SJ, Scott P, Page AJ, Tracey A, de Goffau MC, Cormie C, Ochoa-Montaño B, Ling CL, Tangmanakit J, Turner P, Parkhill J.

Microb Genom. 2019 Feb 5. doi: 10.1099/mgen.0.000247. [Epub ahead of print]

3.

Prospective genomic surveillance of methicillin-resistant Staphylococcus aureus (MRSA) associated with bloodstream infection, England, 1 October 2012 to 30 September 2013.

Toleman MS, Reuter S, Jamrozy D, Wilson HJ, Blane B, Harrison EM, Coll F, Hope RJ, Kearns A, Parkhill J, Peacock SJ, Török ME.

Euro Surveill. 2019 Jan;24(4). doi: 10.2807/1560-7917.ES.2019.24.4.1800215.

4.

One Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock.

Ludden C, Raven KE, Jamrozy D, Gouliouris T, Blane B, Coll F, de Goffau M, Naydenova P, Horner C, Hernandez-Garcia J, Wood P, Hadjirin N, Radakovic M, Brown NM, Holmes M, Parkhill J, Peacock SJ.

MBio. 2019 Jan 22;10(1). pii: e02693-18. doi: 10.1128/mBio.02693-18.

5.

Separating Bacteria by Capsule Amount Using a Discontinuous Density Gradient.

Feltwell T, Dorman MJ, Goulding DA, Parkhill J, Short FL.

J Vis Exp. 2019 Jan 7;(143). doi: 10.3791/58679.

PMID:
30663644
6.

Molecular epidemiology and expression of capsular polysaccharides in Staphylococcus aureus clinical isolates in the United States.

Mohamed N, Timofeyeva Y, Jamrozy D, Rojas E, Hao L, Silmon de Monerri NC, Hawkins J, Singh G, Cai B, Liberator P, Sebastian S, Donald RGK, Scully IL, Jones CH, Creech CB, Thomsen I, Parkhill J, Peacock SJ, Jansen KU, Holden MTG, Anderson AS.

PLoS One. 2019 Jan 14;14(1):e0208356. doi: 10.1371/journal.pone.0208356. eCollection 2019.

7.

Limited contribution of non-intensive chicken farming to ESBL-producing Escherichia coli colonization in humans in Vietnam: an epidemiological and genomic analysis.

Nguyen VT, Jamrozy D, Matamoros S, Carrique-Mas JJ, Ho HM, Thai QH, Nguyen TNM, Wagenaar JA, Thwaites G, Parkhill J, Schultsz C, Ngo TH.

J Antimicrob Chemother. 2019 Mar 1;74(3):561-570. doi: 10.1093/jac/dky506.

PMID:
30629197
8.

On the border between localization and delocalization: tris(iminoxolene)titanium(iv).

Marshall-Roth T, Yao K, Parkhill JA, Brown SN.

Dalton Trans. 2019 Jan 22;48(4):1427-1435. doi: 10.1039/c8dt04528c.

PMID:
30628607
9.

A mecC allotype, mecC3, in the CoNS Staphylococcus caeli, encoded within a variant SCCmecC.

MacFadyen AC, Harrison EM, Drigo I, Parkhill J, Holmes MA, Paterson GK.

J Antimicrob Chemother. 2019 Mar 1;74(3):547-552. doi: 10.1093/jac/dky502.

PMID:
30590583
10.

O-antigen dependent colicin insensitivity of uropathogenic Escherichia coli.

Sharp C, Boinett C, Cain A, Housden N, Kumar S, Turner K, Parkhill J, Kleanthous C.

J Bacteriol. 2018 Dec 3. pii: JB.00545-18. doi: 10.1128/JB.00545-18. [Epub ahead of print]

11.

The Capsule Regulatory Network of Klebsiella pneumoniae Defined by density-TraDISort.

Dorman MJ, Feltwell T, Goulding DA, Parkhill J, Short FL.

MBio. 2018 Nov 20;9(6). pii: e01863-18. doi: 10.1128/mBio.01863-18.

12.

Staphylococcus caeli sp. nov., isolated from air sampling in an industrial rabbit holding.

MacFadyen AC, Drigo I, Harrison EM, Parkhill J, Holmes MA, Paterson GK.

Int J Syst Evol Microbiol. 2019 Jan;69(1):82-86. doi: 10.1099/ijsem.0.003098. Epub 2018 Nov 14.

PMID:
30427304
13.

Whole Genome Sequencing for Determining the Source of Mycobacterium bovis Infections in Livestock Herds and Wildlife in New Zealand.

Price-Carter M, Brauning R, de Lisle GW, Livingstone P, Neill M, Sinclair J, Paterson B, Atkinson G, Knowles G, Crews K, Crispell J, Kao R, Robbe-Austerman S, Stuber T, Parkhill J, Wood J, Harris S, Collins DM.

Front Vet Sci. 2018 Oct 30;5:272. doi: 10.3389/fvets.2018.00272. eCollection 2018.

14.

Nasal carriage of Staphylococcus pseudintermedius in patients with granulomatosis with polyangiitis.

Kronbichler A, Blane B, Holmes MA, Wagner J, Parkhill J, Peacock SJ, Jayne DRW, Harrison EM.

Rheumatology (Oxford). 2018 Nov 8. doi: 10.1093/rheumatology/key317. [Epub ahead of print] No abstract available.

PMID:
30412252
15.

Genomic Surveillance of Enterococcus faecium Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom.

Gouliouris T, Raven KE, Ludden C, Blane B, Corander J, Horner CS, Hernandez-Garcia J, Wood P, Hadjirin NF, Radakovic M, Holmes MA, de Goffau M, Brown NM, Parkhill J, Peacock SJ.

MBio. 2018 Nov 6;9(6). pii: e01780-18. doi: 10.1128/mBio.01780-18.

16.

A global genomic approach uncovers novel components for twitching motility-mediated biofilm expansion in Pseudomonas aeruginosa.

Nolan LM, Whitchurch CB, Barquist L, Katrib M, Boinett CJ, Mayho M, Goulding D, Charles IG, Filloux A, Parkhill J, Cain AK.

Microb Genom. 2018 Nov;4(11). doi: 10.1099/mgen.0.000229. Epub 2018 Nov 1.

17.

Correction to: Detecting eukaryotic microbiota with single-cell sensitivity in human tissue.

Lager S, de Goffau MC, Sovio U, Peacock SJ, Parkhill J, Stephen Charnock-Jones D, Smith GCS.

Microbiome. 2018 Oct 20;6(1):188. doi: 10.1186/s40168-018-0576-3.

18.

Mutations in the MAB_2299c TetR Regulator Confer Cross-Resistance to Clofazimine and Bedaquiline in Mycobacterium abscessus.

Richard M, Gutiérrez AV, Viljoen A, Rodriguez-Rincon D, Roquet-Baneres F, Blaise M, Everall I, Parkhill J, Floto RA, Kremer L.

Antimicrob Agents Chemother. 2018 Dec 21;63(1). pii: e01316-18. doi: 10.1128/AAC.01316-18. Print 2019 Jan.

PMID:
30323043
19.

Spatial structuring of a Legionella pneumophila population within the water system of a large occupational building.

David S, Mentasti M, Lai S, Vaghji L, Ready D, Chalker VJ, Parkhill J.

Microb Genom. 2018 Oct;4(10). doi: 10.1099/mgen.0.000226. Epub 2018 Oct 12.

20.

Streptococcus suis contains multiple phase-variable methyltransferases that show a discrete lineage distribution.

Atack JM, Weinert LA, Tucker AW, Husna AU, Wileman TM, F Hadjirin N, Hoa NT, Parkhill J, Maskell DJ, Blackall PJ, Jennings MP.

Nucleic Acids Res. 2018 Nov 30;46(21):11466-11476. doi: 10.1093/nar/gky913.

21.

Impact of carbohydrate substrate complexity on the diversity of the human colonic microbiota.

Chung WSF, Walker AW, Vermeiren J, Sheridan PO, Bosscher D, Garcia-Campayo V, Parkhill J, Flint HJ, Duncan SH.

FEMS Microbiol Ecol. 2019 Jan 1;95(1). doi: 10.1093/femsec/fiy201.

PMID:
30304332
22.

Comparative genomics of Czech vaccine strains of Bordetella pertussis.

Dienstbier A, Pouchnik D, Wildung M, Amman F, Hofacker IL, Parkhill J, Holubova J, Sebo P, Vecerek B.

Pathog Dis. 2018 Oct 1;76(7). doi: 10.1093/femspd/fty071.

PMID:
30184175
23.

New Variant of Multidrug-Resistant Salmonella enterica Serovar Typhimurium Associated with Invasive Disease in Immunocompromised Patients in Vietnam.

Mather AE, Phuong TLT, Gao Y, Clare S, Mukhopadhyay S, Goulding DA, Hoang NTD, Tuyen HT, Lan NPH, Thompson CN, Trang NHT, Carrique-Mas J, Tue NT, Campbell JI, Rabaa MA, Thanh DP, Harcourt K, Hoa NT, Trung NV, Schultsz C, Perron GG, Coia JE, Brown DJ, Okoro C, Parkhill J, Thomson NR, Chau NVV, Thwaites GE, Maskell DJ, Dougan G, Kenney LJ, Baker S.

MBio. 2018 Sep 4;9(5). pii: e01056-18. doi: 10.1128/mBio.01056-18.

24.

Detecting eukaryotic microbiota with single-cell sensitivity in human tissue.

Lager S, de Goffau MC, Sovio U, Peacock SJ, Parkhill J, Charnock-Jones DS, Smith GCS.

Microbiome. 2018 Sep 1;6(1):151. doi: 10.1186/s40168-018-0529-x. Erratum in: Microbiome. 2018 Oct 20;6(1):188.

25.

A highly conserved mecC-encoding SCCmec type XI in a bovine isolate of methicillin-resistant Staphylococcus xylosus.

MacFadyen AC, Harrison EM, Ellington MJ, Parkhill J, Holmes MA, Paterson GK.

J Antimicrob Chemother. 2018 Dec 1;73(12):3516-3518. doi: 10.1093/jac/dky333. No abstract available.

PMID:
30165441
26.

Arginine-deprivation-induced oxidative damage sterilizes Mycobacterium tuberculosis.

Tiwari S, van Tonder AJ, Vilchèze C, Mendes V, Thomas SE, Malek A, Chen B, Chen M, Kim J, Blundell TL, Parkhill J, Weinrick B, Berney M, Jacobs WR Jr.

Proc Natl Acad Sci U S A. 2018 Sep 25;115(39):9779-9784. doi: 10.1073/pnas.1808874115. Epub 2018 Aug 24.

PMID:
30143580
27.

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.

28.

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.

29.

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.

30.

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 Aug 1;10(8):2102-2109. doi: 10.1093/gbe/evy152.

31.

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.

32.

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

Peacock SJ, Parkhill J, Brown NM.

Microbiology. 2018 Oct;164(10):1213-1219. doi: 10.1099/mic.0.000700. Epub 2018 Jul 27.

33.

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.

34.

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
35.

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.

36.

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.

37.

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 Sep;2(9):1468-1478. doi: 10.1038/s41559-018-0617-0. Epub 2018 Jul 23.

PMID:
30038246
38.

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
39.

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.

40.

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.

41.

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.

42.

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 Oct;179(4):951-958. doi: 10.1111/bjd.16722. Epub 2018 Jul 24.

43.

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.

44.

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
45.

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]

46.

Low genomic diversity of Legionella pneumophila within clinical specimens.

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

Clin Microbiol Infect. 2018 Sep;24(9):1020.e1-1020.e4. doi: 10.1016/j.cmi.2018.03.004. Epub 2018 Mar 13.

47.

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]

48.

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
49.

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.

50.

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;:.

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