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Items: 1 to 50 of 617

1.

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 Sep 10. pii: S1473-3099(19)30446-3. doi: 10.1016/S1473-3099(19)30446-3. [Epub ahead of print]

2.

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.

3.

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.

4.

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
5.

Pilot evaluation of a fully automated bioinformatics system for the analysis of MRSA 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 Aug 28. pii: JCM.00858-19. doi: 10.1128/JCM.00858-19. [Epub ahead of print]

6.

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.

7.

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.

PMID:
31367035
8.

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 Jul 30. pii: gkz656. doi: 10.1093/nar/gkz656. [Epub ahead of print]

PMID:
31361894
9.

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 Jul 29. doi: 10.1038/s41564-019-0501-y. [Epub ahead of print]

PMID:
31358980
10.

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.

11.

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
12.

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
13.

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.

14.

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.

15.

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.

16.

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.

17.

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 Jun 24. doi: 10.1038/s41564-019-0471-0. [Epub ahead of print]

PMID:
31235959
18.

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
19.

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.

20.

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.

21.

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;:.

PMID:
31133745
22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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. 2019 Mar 7. pii: ciz174. doi: 10.1093/cid/ciz174. [Epub ahead of print]

PMID:
30840764
30.

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.

31.

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.

32.

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.

33.

'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.

34.

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.

35.

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.

36.

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
37.

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.

38.

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.

39.

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
40.

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
41.

O-Antigen-Dependent Colicin Insensitivity of Uropathogenic Escherichia coli.

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

J Bacteriol. 2019 Jan 28;201(4). pii: e00545-18. doi: 10.1128/JB.00545-18. Print 2019 Feb 15.

42.

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.

43.

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
44.

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.

45.

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). 2019 Mar 1;58(3):548-550. doi: 10.1093/rheumatology/key317. No abstract available.

46.

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.

47.

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.

48.

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.

49.

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.

50.

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.

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