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Items: 1 to 50 of 633

1.

Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei.

Chewapreecha C, Mather AE, Harris SR, Hunt M, Holden MTG, Chaichana C, Wuthiekanun V, Dougan G, Day NPJ, Limmathurotsakul D, Parkhill J, Peacock SJ.

Commun Biol. 2019 Nov 22;2(1):428. doi: 10.1038/s42003-019-0678-x.

PMID:
31925232
2.

Sound Measurement in Patient-Specific 3D Printed Bench Models of Venous Pulsatile Tinnitus.

Valluru K, Parkhill J, Gautam A, Haraldsson H, Kao E, Leach J, Wright A, Ballweber M, Meisel K, Saloner D, Amans M.

Otol Neurotol. 2020 Jan;41(1):e7-e14. doi: 10.1097/MAO.0000000000002452.

PMID:
31834183
3.

Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei.

Chewapreecha C, Mather AE, Harris SR, Hunt M, Holden MTG, Chaichana C, Wuthiekanun V, Dougan G, Day NPJ, Limmathurotsakul D, Parkhill J, Peacock SJ.

Commun Biol. 2019 Nov 22;2:428. doi: 10.1038/s42003-019-0678-x. eCollection 2019.

4.

Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent.

Steinig EJ, Duchene S, Robinson DA, Monecke S, Yokoyama M, Laabei M, Slickers P, Andersson P, Williamson D, Kearns A, Goering RV, Dickson E, Ehricht R, Ip M, O'Sullivan MVN, Coombs GW, Petersen A, Brennan G, Shore AC, Coleman DC, Pantosti A, de Lencastre H, Westh H, Kobayashi N, Heffernan H, Strommenger B, Layer F, Weber S, Aamot HV, Skakni L, Peacock SJ, Sarovich D, Harris S, Parkhill J, Massey RC, Holden MTG, Bentley SD, Tong SYC.

mBio. 2019 Nov 26;10(6). pii: e01105-19. doi: 10.1128/mBio.01105-19.

5.

Publisher Correction: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis.

Weinert LA, Chaudhuri RR, Wang J, Peters SE, Corander J, Jombart T, Baig A, Howell KJ, Vehkala M, Välimäki N, Harris D, Chieu TTB, Van Vinh Chau N, Campbell J, Schultsz C, Parkhill J, Bentley SD, Langford PR, Rycroft AN, Wren BW, Farrar J, Baker S, Hoa NT, Holden MTG, Tucker AW, Maskell DJ; BRaDP1T Consortium.

Nat Commun. 2019 Nov 22;10(1):5326. doi: 10.1038/s41467-019-13138-w.

6.

Engineering bacteriocin-mediated resistance against the plant pathogen Pseudomonas syringae.

Rooney WM, Grinter RW, Correia A, Parkhill J, Walker DC, Milner JJ.

Plant Biotechnol J. 2019 Nov 9. doi: 10.1111/pbi.13294. [Epub ahead of print]

7.

Whole-Genome Sequences of Five Strains of Kocuria rosea, NCTC2676, NCTC7514, NCTC7512, NCTC7528, and NCTC7511.

Turnbull JD, Russell JE, Fazal MA, Grayson NE, Deheer-Graham A, Oliver K, Holroyd N, Parkhill J, Alexander S.

Microbiol Resour Announc. 2019 Oct 31;8(44). pii: e00256-19. doi: 10.1128/MRA.00256-19.

8.

Transient Silencing of Antibiotic Resistance by Mutation Represents a Significant Potential Source of Unanticipated Therapeutic Failure.

Kime L, Randall CP, Banda FI, Coll F, Wright J, Richardson J, Empel J, Parkhill J, O'Neill AJ.

mBio. 2019 Oct 29;10(5). pii: e01755-19. doi: 10.1128/mBio.01755-19.

9.

The composition and functional protein subsystems of the human nasal microbiome in granulomatosis with polyangiitis: a pilot study.

Wagner J, Harrison EM, Martinez Del Pero M, Blane B, Mayer G, Leierer J, Gopaluni S, Holmes MA, Parkhill J, Peacock SJ, Jayne DRW, Kronbichler A.

Microbiome. 2019 Oct 22;7(1):137. doi: 10.1186/s40168-019-0753-z.

10.

Genetic variation regulates the activation and specificity of Restriction-Modification systems in Neisseria gonorrhoeae.

Sánchez-Busó L, Golparian D, Parkhill J, Unemo M, Harris SR.

Sci Rep. 2019 Oct 11;9(1):14685. doi: 10.1038/s41598-019-51102-2.

11.

Complete Genome Sequence of Pseudomonas aeruginosa Reference Strain PAK.

Cain AK, Nolan LM, Sullivan GJ, Whitchurch CB, Filloux A, Parkhill J.

Microbiol Resour Announc. 2019 Oct 10;8(41). pii: e00865-19. doi: 10.1128/MRA.00865-19.

12.

Improved characterisation of MRSA transmission using within-host bacterial sequence diversity.

Hall MD, Holden MT, Srisomang P, Mahavanakul W, Wuthiekanun V, Limmathurotsakul D, Fountain K, Parkhill J, Nickerson EK, Peacock SJ, Fraser C.

Elife. 2019 Oct 8;8. pii: e46402. doi: 10.7554/eLife.46402.

13.

Author Correction: Human placenta has no microbiome but can contain potential pathogens.

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

Nature. 2019 Oct;574(7778):E15. doi: 10.1038/s41586-019-1628-y.

PMID:
31570886
14.

Genomic characterization of novel Neisseria species.

Diallo K, MacLennan J, Harrison OB, Msefula C, Sow SO, Daugla DM, Johnson E, Trotter C, MacLennan CA, Parkhill J, Borrow R, Greenwood BM, Maiden MCJ.

Sci Rep. 2019 Sep 24;9(1):13742. doi: 10.1038/s41598-019-50203-2.

15.

A dual transacylation mechanism for polyketide synthase chain release in enacyloxin antibiotic biosynthesis.

Masschelein J, Sydor PK, Hobson C, Howe R, Jones C, Roberts DM, Ling Yap Z, Parkhill J, Mahenthiralingam E, Challis GL.

Nat Chem. 2019 Oct;11(10):906-912. doi: 10.1038/s41557-019-0309-7. Epub 2019 Sep 23.

PMID:
31548673
16.

A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages.

Ajawatanawong P, Yanai H, Smittipat N, Disratthakit A, Yamada N, Miyahara R, Nedsuwan S, Imasanguan W, Kantipong P, Chaiyasirinroje B, Wongyai J, Plitphonganphim S, Tantivitayakul P, Phelan J, Parkhill J, Clark TG, Hibberd ML, Ruangchai W, Palittapongarnpim P, Juthayothin T, Thawornwattana Y, Viratyosin W, Tongsima S, Mahasirimongkol S, Tokunaga K, Palittapongarnpim P.

Sci Rep. 2019 Sep 23;9(1):13718. doi: 10.1038/s41598-019-50078-3.

17.

Emergence of dominant toxigenic M1T1 Streptococcus pyogenes clone during increased scarlet fever activity in England: a population-based molecular epidemiological study.

Lynskey NN, Jauneikaite E, Li HK, Zhi X, Turner CE, Mosavie M, Pearson M, Asai M, Lobkowicz L, Chow JY, Parkhill J, Lamagni T, Chalker VJ, Sriskandan S.

Lancet Infect Dis. 2019 Nov;19(11):1209-1218. doi: 10.1016/S1473-3099(19)30446-3. Epub 2019 Sep 10.

18.

Genome-wide mutational biases fuel transcriptional diversity in the Mycobacterium tuberculosis complex.

Chiner-Oms Á, Berney M, Boinett C, González-Candelas F, Young DB, Gagneux S, Jacobs WR Jr, Parkhill J, Cortes T, Comas I.

Nat Commun. 2019 Sep 5;10(1):3994. doi: 10.1038/s41467-019-11948-6.

19.

Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center.

Ellington MJ, Heinz E, Wailan AM, Dorman MJ, de Goffau M, Cain AK, Henson SP, Gleadall N, Boinett CJ, Dougan G, Brown NM, Woodford N, Parkhill J, Török ME, Peacock SJ, Thomson NR.

Genome Biol. 2019 Sep 2;20(1):184. doi: 10.1186/s13059-019-1785-1.

20.

Compressing physics with an autoencoder: Creating an atomic species representation to improve machine learning models in the chemical sciences.

Herr JE, Koh K, Yao K, Parkhill J.

J Chem Phys. 2019 Aug 28;151(8):084103. doi: 10.1063/1.5108803.

PMID:
31470722
21.

Pilot Evaluation of a Fully Automated Bioinformatics System for Analysis of Methicillin-Resistant Staphylococcus aureus Genomes and Detection of Outbreaks.

Brown NM, Blane B, Raven KE, Kumar N, Leek D, Bragin E, Rhodes PA, Enoch DA, Thaxter R, Parkhill J, Peacock SJ.

J Clin Microbiol. 2019 Oct 23;57(11). pii: e00858-19. doi: 10.1128/JCM.00858-19. Print 2019 Nov.

22.

The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential.

Webster G, Mullins AJ, Bettridge AS, Jones C, Cunningham-Oakes E, Connor TR, Parkhill J, Mahenthiralingam E.

Microbiol Resour Announc. 2019 Aug 22;8(34). pii: e00778-19. doi: 10.1128/MRA.00778-19.

23.

Human placenta has no microbiome but can contain potential pathogens.

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

Nature. 2019 Aug;572(7769):329-334. doi: 10.1038/s41586-019-1451-5. Epub 2019 Jul 31. Erratum in: Nature. 2019 Oct;574(7778):E15.

PMID:
31367035
24.

Genome-wide epistasis and co-selection study using mutual information.

Pensar J, Puranen S, Arnold B, MacAlasdair N, Kuronen J, Tonkin-Hill G, Pesonen M, Xu Y, Sipola A, Sánchez-Busó L, Lees JA, Chewapreecha C, Bentley SD, Harris SR, Parkhill J, Croucher NJ, Corander J.

Nucleic Acids Res. 2019 Oct 10;47(18):e112. doi: 10.1093/nar/gkz656.

25.

The impact of antimicrobials on gonococcal evolution.

Sánchez-Busó L, Golparian D, Corander J, Grad YH, Ohnishi M, Flemming R, Parkhill J, Bentley SD, Unemo M, Harris SR.

Nat Microbiol. 2019 Nov;4(11):1941-1950. doi: 10.1038/s41564-019-0501-y. Epub 2019 Jul 29.

PMID:
31358980
26.

The speciation and hybridization history of the genus Salmonella.

Criscuolo A, Issenhuth-Jeanjean S, Didelot X, Thorell K, Hale J, Parkhill J, Thomson NR, Weill FX, Falush D, Brisse S.

Microb Genom. 2019 Aug;5(8). doi: 10.1099/mgen.0.000284. Epub 2019 Jul 26.

27.

Author Correction: Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics.

Davies MR, McIntyre L, Mutreja A, Lacey JA, Lees JA, Towers RJ, Duchêne S, Smeesters PR, Frost HR, Price DJ, Holden MTG, David S, Giffard PM, Worthing KA, Seale AC, Berkley JA, Harris SR, Rivera-Hernandez T, Berking O, Cork AJ, Torres RSLA, Lithgow T, Strugnell RA, Bergmann R, Nitsche-Schmitz P, Chhatwal GS, Bentley SD, Fraser JD, Moreland NJ, Carapetis JR, Steer AC, Parkhill J, Saul A, Williamson DA, Currie BJ, Tong SYC, Dougan G, Walker MJ.

Nat Genet. 2019 Aug;51(8):1295. doi: 10.1038/s41588-019-0482-z.

PMID:
31324894
28.

Draft genome sequence of a multidrug-resistant caprine isolate of Staphylococcus cohnii subsp. urealyticus from Tanzania encoding ermB, tet(K), dfrG, fusF and fosD.

Seni J, Mshana SE, Msigwa F, Iddi S, Mazigo H, Parkhill J, Holmes MA, Paterson GK.

J Glob Antimicrob Resist. 2019 Sep;18:163-165. doi: 10.1016/j.jgar.2019.07.006. Epub 2019 Jul 16.

PMID:
31323428
29.

Identification and Characterization of Genetic Determinants of Isoniazid and Rifampicin Resistance in Mycobacterium tuberculosis in Southern India.

Munir A, Kumar N, Ramalingam SB, Tamilzhalagan S, Shanmugam SK, Palaniappan AN, Nair D, Priyadarshini P, Natarajan M, Tripathy S, Ranganathan UD, Peacock SJ, Parkhill J, Blundell TL, Malhotra S.

Sci Rep. 2019 Jul 16;9(1):10283. doi: 10.1038/s41598-019-46756-x.

30.

Domestication of Campylobacter jejuni NCTC 11168.

Pascoe B, Williams LK, Calland JK, Meric G, Hitchings MD, Dyer M, Ryder J, Shaw S, Lopes BS, Chintoan-Uta C, Allan E, Vidal A, Fearnley C, Everest P, Pachebat JA, Cogan TA, Stevens MP, Humphrey TJ, Wilkinson TS, Cody AJ, Colles FM, Jolley KA, Maiden MCJ, Strachan N, Pearson BM, Linton D, Wren BW, Parkhill J, Kelly DJ, van Vliet AHM, Forbes KJ, Sheppard SK.

Microb Genom. 2019 Jul;5(7). doi: 10.1099/mgen.0.000279. Epub 2019 Jul 16.

31.

An unusual Burkholderia gladioli double chain-initiating nonribosomal peptide synthetase assembles 'fungal' icosalide antibiotics.

Jenner M, Jian X, Dashti Y, Masschelein J, Hobson C, Roberts DM, Jones C, Harris S, Parkhill J, Raja HA, Oberlies NH, Pearce CJ, Mahenthiralingam E, Challis GL.

Chem Sci. 2019 Apr 25;10(21):5489-5494. doi: 10.1039/c8sc04897e. eCollection 2019 Jun 7.

32.

Complete Whole-Genome Sequences of Two Raoultella terrigena Strains, NCTC 13097 and NCTC 13098, Isolated from Human Cases.

Fazal MA, Alexander S, Grayson NE, Deheer-Graham A, Oliver K, Holroyd N, Parkhill J, Russell JE.

Microbiol Resour Announc. 2019 Jul 3;8(27). pii: e00239-19. doi: 10.1128/MRA.00239-19.

33.

Genomic identification of cryptic susceptibility to penicillins and β-lactamase inhibitors in methicillin-resistant Staphylococcus aureus.

Harrison EM, Ba X, Coll F, Blane B, Restif O, Carvell H, Köser CU, Jamrozy D, Reuter S, Lovering A, Gleadall N, Bellis KL, Uhlemann AC, Lowy FD, Massey RC, Grilo IR, Sobral R, Larsen J, Rhod Larsen A, Vingsbo Lundberg C, Parkhill J, Paterson GK, Holden MTG, Peacock SJ, Holmes MA.

Nat Microbiol. 2019 Oct;4(10):1680-1691. doi: 10.1038/s41564-019-0471-0. Epub 2019 Jun 24.

PMID:
31235959
34.

Staphylococcus pseudoxylosus sp. nov., isolated from bovine mastitis.

MacFadyen AC, Leroy S, Harrison EM, Parkhill J, Holmes MA, Paterson GK.

Int J Syst Evol Microbiol. 2019 Aug;69(8):2208-2213. doi: 10.1099/ijsem.0.003416. Epub 2019 Jun 21.

PMID:
31225789
35.

Complete Whole-Genome Sequence of Haemophilus haemolyticus NCTC 10839.

Fazal MA, Alexander S, Grayson NE, Deheer-Graham A, Oliver K, Holroyd N, Parkhill J, Russell JE.

Microbiol Resour Announc. 2019 Jun 20;8(25). pii: e00232-19. doi: 10.1128/MRA.00232-19.

36.

Multi-Compartment Profiling of Bacterial and Host Metabolites Identifies Intestinal Dysbiosis and Its Functional Consequences in the Critically Ill Child.

Wijeyesekera A, Wagner J, De Goffau M, Thurston S, Rodrigues Sabino A, Zaher S, White D, Ridout J, Peters MJ, Ramnarayan P, Branco RG, Torok ME, Valla F, Meyer R, Klein N, Frost G, Parkhill J, Holmes E, Pathan N.

Crit Care Med. 2019 Sep;47(9):e727-e734. doi: 10.1097/CCM.0000000000003841.

37.

Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics.

Davies MR, McIntyre L, Mutreja A, Lacey JA, Lees JA, Towers RJ, Duchêne S, Smeesters PR, Frost HR, Price DJ, Holden MTG, David S, Giffard PM, Worthing KA, Seale AC, Berkley JA, Harris SR, Rivera-Hernandez T, Berking O, Cork AJ, Torres RSLA, Lithgow T, Strugnell RA, Bergmann R, Nitsche-Schmitz P, Chhatwal GS, Bentley SD, Fraser JD, Moreland NJ, Carapetis JR, Steer AC, Parkhill J, Saul A, Williamson DA, Currie BJ, Tong SYC, Dougan G, Walker MJ.

Nat Genet. 2019 Jun;51(6):1035-1043. doi: 10.1038/s41588-019-0417-8. Epub 2019 May 27. Erratum in: Nat Genet. 2019 Jul 19;:.

38.

Genomic surveillance of Escherichia coli in municipal wastewater treatment plants as an indicator of clinically relevant pathogens and their resistance genes.

Raven KE, Ludden C, Gouliouris T, Blane B, Naydenova P, Brown NM, Parkhill J, Peacock SJ.

Microb Genom. 2019 May;5(5). doi: 10.1099/mgen.0.000267. Epub 2019 May 20.

39.

Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis.

Lees JA, Ferwerda B, Kremer PHC, Wheeler NE, Serón MV, Croucher NJ, Gladstone RA, Bootsma HJ, Rots NY, Wijmega-Monsuur AJ, Sanders EAM, Trzciński K, Wyllie AL, Zwinderman AH, van den Berg LH, van Rheenen W, Veldink JH, Harboe ZB, Lundbo LF, de Groot LCPGM, van Schoor NM, van der Velde N, Ängquist LH, Sørensen TIA, Nohr EA, Mentzer AJ, Mills TC, Knight JC, du Plessis M, Nzenze S, Weiser JN, Parkhill J, Madhi S, Benfield T, von Gottberg A, van der Ende A, Brouwer MC, Barrett JC, Bentley SD, van de Beek D.

Nat Commun. 2019 May 15;10(1):2176. doi: 10.1038/s41467-019-09976-3.

40.

Complete Assembly of Escherichia coli Sequence Type 131 Genomes Using Long Reads Demonstrates Antibiotic Resistance Gene Variation within Diverse Plasmid and Chromosomal Contexts.

Decano AG, Ludden C, Feltwell T, Judge K, Parkhill J, Downing T.

mSphere. 2019 May 8;4(3). pii: e00130-19. doi: 10.1128/mSphere.00130-19.

41.

Rapid sequencing of MRSA direct from clinical plates in a routine microbiology laboratory.

Blane B, Raven KE, Leek D, Brown N, Parkhill J, Peacock SJ.

J Antimicrob Chemother. 2019 Aug 1;74(8):2153-2156. doi: 10.1093/jac/dkz170.

42.

Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection.

McNally A, Kallonen T, Connor C, Abudahab K, Aanensen DM, Horner C, Peacock SJ, Parkhill J, Croucher NJ, Corander J.

mBio. 2019 Apr 23;10(2). pii: e00644-19. doi: 10.1128/mBio.00644-19.

43.

Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment.

Gouliouris T, Raven KE, Moradigaravand D, Ludden C, Coll F, Blane B, Naydenova P, Horner C, Brown NM, Corander J, Limmathurotsakul D, Parkhill J, Peacock SJ.

Genome Res. 2019 Apr;29(4):626-634. doi: 10.1101/gr.232629.117. Epub 2019 Mar 21.

44.

Methodology for Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Isolates in a Routine Hospital Microbiology Laboratory.

Raven KE, Blane B, Leek D, Churcher C, Kokko-Gonzales P, Pugazhendhi D, Fraser L, Betley J, Parkhill J, Peacock SJ.

J Clin Microbiol. 2019 May 24;57(6). pii: e00180-19. doi: 10.1128/JCM.00180-19. Print 2019 Jun.

45.

A One Health Study of the Genetic Relatedness of Klebsiella pneumoniae and Their Mobile Elements in the East of England.

Ludden C, Moradigaravand D, Jamrozy D, Gouliouris T, Blane B, Naydenova P, Hernandez-Garcia J, Wood P, Hadjirin N, Radakovic M, Crawley C, Brown NM, Holmes M, Parkhill J, Peacock SJ.

Clin Infect Dis. 2020 Jan 2;70(2):219-226. doi: 10.1093/cid/ciz174.

46.

Genome mining identifies cepacin as a plant-protective metabolite of the biopesticidal bacterium Burkholderia ambifaria.

Mullins AJ, Murray JAH, Bull MJ, Jenner M, Jones C, Webster G, Green AE, Neill DR, Connor TR, Parkhill J, Challis GL, Mahenthiralingam E.

Nat Microbiol. 2019 Jun;4(6):996-1005. doi: 10.1038/s41564-019-0383-z. Epub 2019 Mar 4.

47.

Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana.

Otchere ID, van Tonder AJ, Asante-Poku A, Sánchez-Busó L, Coscollá M, Osei-Wusu S, Asare P, Aboagye SY, Ekuban SA, Yahayah AI, Forson A, Baddoo A, Laryea C, Parkhill J, Harris SR, Gagneux S, Yeboah-Manu D.

PLoS One. 2019 Mar 4;14(3):e0209395. doi: 10.1371/journal.pone.0209395. eCollection 2019.

48.

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(2). doi: 10.1099/mgen.0.000246. Epub 2019 Feb 5.

49.

'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(2). doi: 10.1099/mgen.0.000247. Epub 2019 Feb 5.

50.

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.

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