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Items: 1 to 50 of 249

1.

Isolation of five Enterobacteriaceae species harbouring blaNDM-1 and mcr-1 plasmids from a single paediatric patient.

Martino F, Tijet N, Melano R, Petroni A, Heinz E, De Belder D, Faccone D, Rapoport M, Biondi E, Rodrigo V, Vazquez M, Pasteran F, Thomson NR, Corso A, Gomez SA.

PLoS One. 2019 Sep 9;14(9):e0221960. doi: 10.1371/journal.pone.0221960. eCollection 2019.

2.

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.

3.

Corrigendum: Genetic and Phenotypic Characterization of the Etiological Agent of Canine Orchiepididymitis Smooth Brucella sp. BCCN84.3.

Guzmán-Verri C, Suárez-Esquivel M, Ruíz-Villalobos N, Zygmunt MS, Gonnet M, Campos E, Víquez-Ruiz E, Chacón-Díaz C, Aragón-Aranda B, Conde-Álvarez R, Moriyón I, Blasco JM, Muñoz PM, Baker KS, Thomson NR, Cloeckaert A, Moreno E.

Front Vet Sci. 2019 Aug 2;6:253. doi: 10.3389/fvets.2019.00253. eCollection 2019.

4.

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.

5.

Genomic epidemiology of syphilis reveals independent emergence of macrolide resistance across multiple circulating lineages.

Beale MA, Marks M, Sahi SK, Tantalo LC, Nori AV, French P, Lukehart SA, Marra CM, Thomson NR.

Nat Commun. 2019 Jul 22;10(1):3255. doi: 10.1038/s41467-019-11216-7.

6.

Determining antimicrobial susceptibility in Salmonella enterica serovar Typhimurium through whole genome sequencing: a comparison against multiple phenotypic susceptibility testing methods.

Mensah N, Tang Y, Cawthraw S, AbuOun M, Fenner J, Thomson NR, Mather AE, Petrovska-Holmes L.

BMC Microbiol. 2019 Jul 2;19(1):148. doi: 10.1186/s12866-019-1520-9.

7.

Genetic and Phenotypic Characterization of the Etiological Agent of Canine Orchiepididymitis Smooth Brucella sp. BCCN84.3.

Guzmán-Verri C, Suárez-Esquivel M, Ruíz-Villalobos N, Zygmunt MS, Gonnet M, Campos E, Víquez-Ruiz E, Chacón-Díaz C, Aragón-Aranda B, Conde-Álvarez R, Moriyón I, Blasco JM, Muñoz PM, Baker KS, Thomson NR, Cloeckaert A, Moreno E.

Front Vet Sci. 2019 Jun 7;6:175. doi: 10.3389/fvets.2019.00175. eCollection 2019. Erratum in: Front Vet Sci. 2019 Aug 02;6:253.

8.

Response of sulfate-reducing bacteria and supporting microbial community to persulfate exposure in a continuous flow system.

Bartlett CK, Slawson RM, Thomson NR.

Environ Sci Process Impacts. 2019 Jul 17;21(7):1193-1203. doi: 10.1039/c9em00094a.

PMID:
31204424
9.

Caribbean multi-centre study of Klebsiella pneumoniae: whole-genome sequencing, antimicrobial resistance and virulence factors.

Heinz E, Brindle R, Morgan-McCalla A, Peters K, Thomson NR.

Microb Genom. 2019 May;5(5). doi: 10.1099/mgen.0.000266. Epub 2019 Apr 29.

10.

Antimicrobial Resistance Diversity Suggestive of Distinct Salmonella Typhimurium Sources or Selective Pressures in Food-Production Animals.

Mellor KC, Petrovska L, Thomson NR, Harris K, Reid SWJ, Mather AE.

Front Microbiol. 2019 Apr 12;10:708. doi: 10.3389/fmicb.2019.00708. eCollection 2019.

11.

High quality reference genomes for toxigenic and non-toxigenic Vibrio cholerae serogroup O139.

Dorman MJ, Domman D, Uddin MI, Sharmin S, Afrad MH, Begum YA, Qadri F, Thomson NR.

Sci Rep. 2019 Apr 10;9(1):5865. doi: 10.1038/s41598-019-41883-x.

12.

The history, genome and biology of NCTC 30: a non-pandemic Vibrio cholerae isolate from World War One.

Dorman MJ, Kane L, Domman D, Turnbull JD, Cormie C, Fazal MA, Goulding DA, Russell JE, Alexander S, Thomson NR.

Proc Biol Sci. 2019 Apr 10;286(1900):20182025. doi: 10.1098/rspb.2018.2025.

13.

rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree.

Wailan AM, Coll F, Heinz E, Tonkin-Hill G, Corander J, Feasey NA, Thomson NR.

Microb Genom. 2019 Apr;5(4). doi: 10.1099/mgen.0.000264. Epub 2019 Mar 28.

14.

Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages.

Musicha P, Msefula CL, Mather AE, Chaguza C, Cain AK, Peno C, Kallonen T, Khonga M, Denis B, Gray KJ, Heyderman RS, Thomson NR, Everett DB, Feasey NA.

J Antimicrob Chemother. 2019 May 1;74(5):1223-1232. doi: 10.1093/jac/dkz032.

15.

Publisher Correction: Genomic insights into the 2016-2017 cholera epidemic in Yemen.

Weill FX, Domman D, Njamkepo E, Almesbahi AA, Naji M, Nasher SS, Rakesh A, Assiri AM, Sharma NC, Kariuki S, Pourshafie MR, Rauzier J, Abubakar A, Carter JY, Wamala JF, Seguin C, Bouchier C, Malliavin T, Bakhshi B, Abulmaali HHN, Kumar D, Njoroge SM, Malik MR, Kiiru J, Luquero FJ, Azman AS, Ramamurthy T, Thomson NR, Quilici ML.

Nature. 2019 Feb;566(7745):E14. doi: 10.1038/s41586-019-0966-0.

PMID:
30755740
16.

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.

17.

Retrospective application of transposon-directed insertion-site sequencing to investigate niche-specific virulence of Salmonella Typhimurium in cattle.

Vohra P, Chaudhuri RR, Mayho M, Vrettou C, Chintoan-Uta C, Thomson NR, Hope JC, Hopkins J, Stevens MP.

BMC Genomics. 2019 Jan 8;20(1):20. doi: 10.1186/s12864-018-5319-0.

18.

Genomic insights into the 2016-2017 cholera epidemic in Yemen.

Weill FX, Domman D, Njamkepo E, Almesbahi AA, Naji M, Nasher SS, Rakesh A, Assiri AM, Sharma NC, Kariuki S, Pourshafie MR, Rauzier J, Abubakar A, Carter JY, Wamala JF, Seguin C, Bouchier C, Malliavin T, Bakhshi B, Abulmaali HHN, Kumar D, Njoroge SM, Malik MR, Kiiru J, Luquero FJ, Azman AS, Ramamurthy T, Thomson NR, Quilici ML.

Nature. 2019 Jan;565(7738):230-233. doi: 10.1038/s41586-018-0818-3. Epub 2019 Jan 2. Erratum in: Nature. 2019 Feb;566(7745):E14.

19.

Intra-NAPL diffusion and dissolution of a MGP NAPL exposed to persulfate in a flow-through system.

Shafieiyoun S, Thomson NR.

J Hazard Mater. 2019 Mar 5;365:366-374. doi: 10.1016/j.jhazmat.2018.10.096. Epub 2018 Nov 1.

PMID:
30448549
20.

Complement Susceptibility in Relation to Genome Sequence of Recent Klebsiella pneumoniae Isolates from Thai Hospitals.

Loraine J, Heinz E, De Sousa Almeida J, Milevskyy O, Voravuthikunchai SP, Srimanote P, Kiratisin P, Thomson NR, Taylor PW.

mSphere. 2018 Nov 7;3(6). pii: e00537-18. doi: 10.1128/mSphere.00537-18.

21.

Targeted nanoparticle binding & detection in petroleum hydrocarbon impacted porous media.

Linley S, Holmes A, Leshuk T, Nafo W, Thomson NR, Al-Mayah A, McVey K, Sra K, Gu FX.

Chemosphere. 2019 Jan;215:353-361. doi: 10.1016/j.chemosphere.2018.10.046. Epub 2018 Oct 8.

PMID:
30326441
22.

Realistic expectations for the treatment of FMGP residuals by chemical oxidants.

Shafieiyoun S, Thomson NR, Brey AP, Gasinski CM, Pence W, Marley M.

J Contam Hydrol. 2018 Dec;219:1-17. doi: 10.1016/j.jconhyd.2018.08.007. Epub 2018 Sep 4.

PMID:
30314848
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.

SLING: a tool to search for linked genes in bacterial datasets.

Horesh G, Harms A, Fino C, Parts L, Gerdes K, Heinz E, Thomson NR.

Nucleic Acids Res. 2018 Nov 30;46(21):e128. doi: 10.1093/nar/gky738.

25.

Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia.

Zhou Z, Lundstrøm I, Tran-Dien A, Duchêne S, Alikhan NF, Sergeant MJ, Langridge G, Fotakis AK, Nair S, Stenøien HK, Hamre SS, Casjens S, Christophersen A, Quince C, Thomson NR, Weill FX, Ho SYW, Gilbert MTP, Achtman M.

Curr Biol. 2018 Aug 6;28(15):2420-2428.e10. doi: 10.1016/j.cub.2018.05.058. Epub 2018 Jul 19.

26.

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.

27.

Defining endemic cholera at three levels of spatiotemporal resolution within Bangladesh.

Domman D, Chowdhury F, Khan AI, Dorman MJ, Mutreja A, Uddin MI, Paul A, Begum YA, Charles RC, Calderwood SB, Bhuiyan TR, Harris JB, LaRocque RC, Ryan ET, Qadri F, Thomson NR.

Nat Genet. 2018 Jul;50(7):951-955. doi: 10.1038/s41588-018-0150-8. Epub 2018 Jun 25.

28.

Microevolution and Patterns of Transmission of Shigella sonnei within Cyclic Outbreaks Shigellosis, Israel.

Behar A, Baker KS, Bassal R, Ezernitchi A, Valinsky L, Thomson NR, Cohen D.

Emerg Infect Dis. 2018 Jul;24(7):1335-1339. doi: 10.3201/eid2407.171313.

29.

An outbreak of a rare Shiga-toxin-producing Escherichia coli serotype (O117:H7) among men who have sex with men.

Baker KS, Dallman TJ, Thomson NR, Jenkins C.

Microb Genom. 2018 Jul;4(7). doi: 10.1099/mgen.0.000181. Epub 2018 May 21.

30.

The role of intra-NAPL diffusion on mass transfer from MGP residuals.

Shafieiyoun S, Thomson NR.

J Contam Hydrol. 2018 Jun;213:49-61. doi: 10.1016/j.jconhyd.2018.04.002. Epub 2018 Apr 24.

PMID:
29776661
31.

Genomic evidence that the live Chlamydia abortus vaccine strain 1B is not attenuated and has the potential to cause disease.

Longbottom D, Sait M, Livingstone M, Laroucau K, Sachse K, Harris SR, Thomson NR, Seth-Smith HMB.

Vaccine. 2018 Jun 14;36(25):3593-3598. doi: 10.1016/j.vaccine.2018.05.042.

32.

The Chlamydia muridarum plasmid revisited : new insights into growth kinetics.

Skilton RJ, Wang Y, O'Neill C, Filardo S, Marsh P, Bénard A, Thomson NR, Ramsey KH, Clarke IN.

Wellcome Open Res. 2018 Mar 8;3:25. doi: 10.12688/wellcomeopenres.13905.1. eCollection 2018.

33.

Whole-genome sequencing revealed concurrent outbreaks of shigellosis in the English Orthodox Jewish Community caused by multiple importations of Shigella sonnei from Israel.

Rew V, Mook P, Trienekens S, Baker KS, Dallman TJ, Jenkins C, Crook PD, Thomson NR.

Microb Genom. 2018 Mar;4(3). doi: 10.1099/mgen.0.000170. Epub 2018 Mar 27.

34.

Direct Whole-Genome Sequencing of Cutaneous Strains of Haemophilus ducreyi.

Marks M, Fookes M, Wagner J, Ghinai R, Sokana O, Sarkodie YA, Solomon AW, Mabey DCW, Thomson NR.

Emerg Infect Dis. 2018 Apr;24(4):786-789. doi: 10.3201/eid2404.171726.

35.

PlasmidTron: assembling the cause of phenotypes and genotypes from NGS data.

Page AJ, Wailan A, Shao Y, Judge K, Dougan G, Klemm EJ, Thomson NR, Keane JA.

Microb Genom. 2018 Mar;4(3). doi: 10.1099/mgen.0.000164. Epub 2018 Mar 12.

36.

Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity.

Last AR, Pickering H, Roberts CH, Coll F, Phelan J, Burr SE, Cassama E, Nabicassa M, Seth-Smith HMB, Hadfield J, Cutcliffe LT, Clarke IN, Mabey DCW, Bailey RL, Clark TG, Thomson NR, Holland MJ.

Genome Med. 2018 Feb 26;10(1):15. doi: 10.1186/s13073-018-0521-x.

37.

Antimicrobial-Resistant Klebsiella pneumoniae Carriage and Infection in Specialized Geriatric Care Wards Linked to Acquisition in the Referring Hospital.

Gorrie CL, Mirceta M, Wick RR, Judd LM, Wyres KL, Thomson NR, Strugnell RA, Pratt NF, Garlick JS, Watson KM, Hunter PC, McGloughlin SA, Spelman DW, Jenney AWJ, Holt KE.

Clin Infect Dis. 2018 Jul 2;67(2):161-170. doi: 10.1093/cid/ciy027.

38.

Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure.

Fookes MC, Hadfield J, Harris S, Parmar S, Unemo M, Jensen JS, Thomson NR.

BMC Genomics. 2017 Dec 28;18(1):993. doi: 10.1186/s12864-017-4399-6.

39.

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
40.

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
41.

An untypeable enterotoxigenic Escherichia coli represents one of the dominant types causing human disease.

Iguchi A, von Mentzer A, Kikuchi T, Thomson NR.

Microb Genom. 2017 Jul 3;3(9):e000121. doi: 10.1099/mgen.0.000121. eCollection 2017 Sep.

42.

Brucella Genetic Variability in Wildlife Marine Mammals Populations Relates to Host Preference and Ocean Distribution.

Suárez-Esquivel M, Baker KS, Ruiz-Villalobos N, Hernández-Mora G, Barquero-Calvo E, González-Barrientos R, Castillo-Zeledón A, Jiménez-Rojas C, Chacón-Díaz C, Cloeckaert A, Chaves-Olarte E, Thomson NR, Moreno E, Guzmán-Verri C.

Genome Biol Evol. 2017 Jul 1;9(7):1901-1912. doi: 10.1093/gbe/evx137.

43.

Genome-wide profiling of humoral immunity and pathogen genes under selection identifies immune evasion tactics of Chlamydia trachomatis during ocular infection.

Pickering H, Teng A, Faal N, Joof H, Makalo P, Cassama E, Nabicassa M, Last AR, Burr SE, Rowland-Jones SL, Thomson NR, Roberts CH, Mabey DCW, Bailey RL, Hayward RD, de la Maza LM, Holland MJ.

Sci Rep. 2017 Aug 29;7(1):9634. doi: 10.1038/s41598-017-09193-2.

44.

Transcriptome and proteome analysis of Salmonella enterica serovar Typhimurium systemic infection of wild type and immune-deficient mice.

Oshota O, Conway M, Fookes M, Schreiber F, Chaudhuri RR, Yu L, Morgan FJE, Clare S, Choudhary J, Thomson NR, Lio P, Maskell DJ, Mastroeni P, Grant AJ.

PLoS One. 2017 Aug 10;12(8):e0181365. doi: 10.1371/journal.pone.0181365. eCollection 2017.

45.

Molecular epidemiology of Klebsiella pneumoniae invasive infections over a decade at Kilifi County Hospital in Kenya.

Henson SP, Boinett CJ, Ellington MJ, Kagia N, Mwarumba S, Nyongesa S, Mturi N, Kariuki S, Scott JAG, Thomson NR, Morpeth SC.

Int J Med Microbiol. 2017 Oct;307(7):422-429. doi: 10.1016/j.ijmm.2017.07.006. Epub 2017 Jul 22.

46.

Assessing gut microbiota perturbations during the early phase of infectious diarrhea in Vietnamese children.

The HC, Florez de Sessions P, Jie S, Pham Thanh D, Thompson CN, Nguyen Ngoc Minh C, Chu CW, Tran TA, Thomson NR, Thwaites GE, Rabaa MA, Hibberd M, Baker S.

Gut Microbes. 2018 Jan 2;9(1):38-54. doi: 10.1080/19490976.2017.1361093. Epub 2017 Aug 24.

47.

Minimal genetic change in Vibrio cholerae in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing.

Garrine M, Mandomando I, Vubil D, Nhampossa T, Acacio S, Li S, Paulson JN, Almeida M, Domman D, Thomson NR, Alonso P, Stine OC.

PLoS Negl Trop Dis. 2017 Jun 16;11(6):e0005671. doi: 10.1371/journal.pntd.0005671. eCollection 2017 Jun.

48.

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.

49.

Brucella neotomae Infection in Humans, Costa Rica.

Suárez-Esquivel M, Ruiz-Villalobos N, Jiménez-Rojas C, Barquero-Calvo E, Chacón-Díaz C, Víquez-Ruiz E, Rojas-Campos N, Baker KS, Oviedo-Sánchez G, Amuy E, Chaves-Olarte E, Thomson NR, Moreno E, Guzmán-Verri C.

Emerg Infect Dis. 2017 Jun;23(6):997-1000. doi: 10.3201/eid2306.162018. Erratum in: Emerg Infect Dis. 2017 Aug;23(8):1435.

50.

European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures.

Seth-Smith HMB, Busó LS, Livingstone M, Sait M, Harris SR, Aitchison KD, Vretou E, Siarkou VI, Laroucau K, Sachse K, Longbottom D, Thomson NR.

BMC Genomics. 2017 May 4;18(1):344. doi: 10.1186/s12864-017-3657-y.

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