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Items: 1 to 50 of 114

1.

Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods.

Duchene S, Duchene DA, Geoghegan JL, Dyson ZA, Hawkey J, Holt KE.

BMC Evol Biol. 2018 Jun 19;18(1):95. doi: 10.1186/s12862-018-1210-5.

2.

Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam.

Holt KE, McAdam P, Thai PVK, Thuong NTT, Ha DTM, Lan NN, Lan NH, Nhu NTQ, Hai HT, Ha VTN, Thwaites G, Edwards DJ, Nath AP, Pham K, Ascher DB, Farrar J, Khor CC, Teo YY, Inouye M, Caws M, Dunstan SJ.

Nat Genet. 2018 Jun;50(6):849-856. doi: 10.1038/s41588-018-0117-9. Epub 2018 May 21.

PMID:
29785015
3.

Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens.

Baker S, Thomson N, Weill FX, Holt KE.

Science. 2018 May 18;360(6390):733-738. doi: 10.1126/science.aar3777. Review.

PMID:
29773743
4.

Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria.

Wyres KL, Holt KE.

Curr Opin Microbiol. 2018 Apr 30;45:131-139. doi: 10.1016/j.mib.2018.04.004. [Epub ahead of print] Review.

5.

Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: Antimicrobial resistance and implications for vaccine policy.

Britto CD, Dyson ZA, Duchene S, Carter MJ, Gurung M, Kelly DF, Murdoch DR, Ansari I, Thorson S, Shrestha S, Adhikari N, Dougan G, Holt KE, Pollard AJ.

PLoS Negl Trop Dis. 2018 Apr 23;12(4):e0006408. doi: 10.1371/journal.pntd.0006408. eCollection 2018 Apr.

6.

Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes.

Wick RR, Heinz E, Holt KE, Wyres KL.

J Clin Microbiol. 2018 May 25;56(6). pii: e00197-18. doi: 10.1128/JCM.00197-18. Print 2018 Jun.

7.

Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection.

Hawkey J, Ascher DB, Judd LM, Wick RR, Kostoulias X, Cleland H, Spelman DW, Padiglione A, Peleg AY, Holt KE.

Microb Genom. 2018 Mar 16. doi: 10.1099/mgen.0.000165. [Epub ahead of print]

8.

Multidrug-resistant Shigella sonnei carrying the plasmid-mediated mcr-1 gene in China.

Ma Q, Huang Y, Wang J, Xu X, Hawkey J, Yang C, Liang B, Hu X, Wu F, Yang X, Wang J, Li R, Li P, Xie J, Jia L, Wang L, Hao R, Tong Y, Holt KE, Qiu S, Sun Y, Song H.

Int J Antimicrob Agents. 2018 Feb 28. pii: S0924-8579(18)30057-8. doi: 10.1016/j.ijantimicag.2018.02.019. [Epub ahead of print]

PMID:
29501823
9.

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 Jan 11. doi: 10.1093/cid/ciy027. [Epub ahead of print]

PMID:
29340588
10.

Completing bacterial genome assemblies with multiplex MinION sequencing.

Wick RR, Judd LM, Gorrie CL, Holt KE.

Microb Genom. 2017 Sep 14;3(10):e000132. doi: 10.1099/mgen.0.000132. eCollection 2017 Oct.

11.

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
12.

Corrigendum: In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages.

Ingle DJ, Valcanis M, Kuzevski A, Tauschek M, Inouye M, Stinear T, Levine MM, Robins-Browne RM, Holt KE.

Microb Genom. 2017 Aug 1;3(7):e000109. doi: 10.1099/mgen.0.000109. eCollection 2017 Jul.

13.

A novel genetic variant of Streptococcus pneumoniae serotype 11A discovered in Fiji.

Manna S, Ortika BD, Dunne EM, Holt KE, Kama M, Russell FM, Hinds J, Satzke C.

Clin Microbiol Infect. 2018 Apr;24(4):428.e1-428.e7. doi: 10.1016/j.cmi.2017.06.031. Epub 2017 Jul 20.

14.

The STRATAA study protocol: a programme to assess the burden of enteric fever in Bangladesh, Malawi and Nepal using prospective population census, passive surveillance, serological studies and healthcare utilisation surveys.

Darton TC, Meiring JE, Tonks S, Khan MA, Khanam F, Shakya M, Thindwa D, Baker S, Basnyat B, Clemens JD, Dougan G, Dolecek C, Dunstan SJ, Gordon MA, Heyderman RS, Holt KE, Pitzer VE, Qadri F, Zaman K, Pollard AJ; STRATAA Study Consortium.

BMJ Open. 2017 Jul 2;7(6):e016283. doi: 10.1136/bmjopen-2017-016283.

15.

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.

Wick RR, Judd LM, Gorrie CL, Holt KE.

PLoS Comput Biol. 2017 Jun 8;13(6):e1005595. doi: 10.1371/journal.pcbi.1005595. eCollection 2017 Jun.

16.

Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain.

Perrin A, Larsonneur E, Nicholson AC, Edwards DJ, Gundlach KM, Whitney AM, Gulvik CA, Bell ME, Rendueles O, Cury J, Hugon P, Clermont D, Enouf V, Loparev V, Juieng P, Monson T, Warshauer D, Elbadawi LI, Walters MS, Crist MB, Noble-Wang J, Borlaug G, Rocha EPC, Criscuolo A, Touchon M, Davis JP, Holt KE, McQuiston JR, Brisse S.

Nat Commun. 2017 May 24;8:15483. doi: 10.1038/ncomms15483.

17.

Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients.

Gorrie CL, Mirceta M, Wick RR, Edwards DJ, Thomson NR, Strugnell RA, Pratt NF, Garlick JS, Watson KM, Pilcher DV, McGloughlin SA, Spelman DW, Jenney AWJ, Holt KE.

Clin Infect Dis. 2017 Jul 15;65(2):208-215. doi: 10.1093/cid/cix270.

18.

The diversity of Klebsiella pneumoniae surface polysaccharides.

Follador R, Heinz E, Wyres KL, Ellington MJ, Kowarik M, Holt KE, Thomson NR.

Microb Genom. 2016 Aug 25;2(8):e000073. doi: 10.1099/mgen.0.000073. eCollection 2016 Aug.

19.

In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages.

Ingle DJ, Valcanis M, Kuzevski A, Tauschek M, Inouye M, Stinear T, Levine MM, Robins-Browne RM, Holt KE.

Microb Genom. 2016 Jul 11;2(7):e000064. doi: 10.1099/mgen.0.000064. eCollection 2016 Jul. Erratum in: Microb Genom. 2017 Aug 01;3(7):e000109.

20.

Repeated local emergence of carbapenem-resistant Acinetobacter baumannii in a single hospital ward.

Schultz MB, Pham Thanh D, Tran Do Hoan N, Wick RR, Ingle DJ, Hawkey J, Edwards DJ, Kenyon JJ, Phu Huong Lan N, Campbell JI, Thwaites G, Thi Khanh Nhu N, Hall RM, Fournier-Level A, Baker S, Holt KE.

Microb Genom. 2016 Mar 2;2(3):e000050. doi: 10.1099/mgen.0.000050. eCollection 2016 Mar.

21.

Identification of Klebsiella capsule synthesis loci from whole genome data.

Wyres KL, Wick RR, Gorrie C, Jenney A, Follador R, Thomson NR, Holt KE.

Microb Genom. 2016 Dec 12;2(12):e000102. doi: 10.1099/mgen.0.000102. eCollection 2016 Dec.

22.

Genome-scale rates of evolutionary change in bacteria.

Duchêne S, Holt KE, Weill FX, Le Hello S, Hawkey J, Edwards DJ, Fourment M, Holmes EC.

Microb Genom. 2016 Nov 30;2(11):e000094. doi: 10.1099/mgen.0.000094. eCollection 2016 Nov.

23.

Variants of AbGRI3 carrying the armA gene in extensively antibiotic-resistant Acinetobacter baumannii from Singapore.

Blackwell GA, Holt KE, Bentley SD, Hsu LY, Hall RM.

J Antimicrob Chemother. 2017 Apr 1;72(4):1031-1039. doi: 10.1093/jac/dkw542.

24.

Whole Genome Sequence Analysis of Salmonella Typhi Isolated in Thailand before and after the Introduction of a National Immunization Program.

Dyson ZA, Thanh DP, Bodhidatta L, Mason CJ, Srijan A, Rabaa MA, Vinh PV, Thanh TH, Thwaites GE, Baker S, Holt KE.

PLoS Negl Trop Dis. 2017 Jan 6;11(1):e0005274. doi: 10.1371/journal.pntd.0005274. eCollection 2017 Jan.

25.

Prediction of antibiotic resistance from antibiotic resistance genes detected in antibiotic-resistant commensal Escherichia coli using PCR or WGS.

Moran RA, Anantham S, Holt KE, Hall RM.

J Antimicrob Chemother. 2017 Mar 1;72(3):700-704. doi: 10.1093/jac/dkw511.

PMID:
28039273
26.

Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?

Robins-Browne RM, Holt KE, Ingle DJ, Hocking DM, Yang J, Tauschek M.

Front Cell Infect Microbiol. 2016 Nov 18;6:141. eCollection 2016. Review.

27.

Erratum: Global phylogeography and evolutionary history of Shigella dysenteriae type 1.

Njamkepo E, Fawal N, Tran-Dien A, Hawkey J, Strockbine N, Jenkins C, Talukder KA, Bercion R, Kuleshov K, Kolínská R, Russell JE, Kaftyreva L, Accou-Demartin M, Karas A, Vandenberg O, Mather AE, Mason CJ, Page AJ, Ramamurthy T, Bizet C, Gamian A, Carle I, Sow AG, Bouchier C, Wester AL, Lejay-Collin M, Fonkoua MC, Le Hello S, Blaser MJ, Jernberg C, Ruckly C, Mérens A, Page AL, Aslett M, Roggentin P, Fruth A, Denamur E, Venkatesan M, Bercovier H, Bodhidatta L, Chiou CS, Clermont D, Colonna B, Egorova S, Pazhani GP, Ezernitchi AV, Guigon G, Harris SR, Izumiya H, Korzeniowska-Kowal A, Lutyńska A, Gouali M, Grimont F, Langendorf C, Marejková M, Peterson LA, Perez-Perez G, Ngandjio A, Podkolzin A, Souche E, Makarova M, Shipulin GA, Ye C, Žemličková H, Herpay M, Grimont PA, Parkhill J, Sansonetti P, Holt KE, Brisse S, Thomson NR, Weill FX.

Nat Microbiol. 2016 Oct 3;1(11):16209. doi: 10.1038/nmicrobiol.2016.209. No abstract available.

PMID:
27694821
28.

Klebsiella pneumoniae Population Genomics and Antimicrobial-Resistant Clones.

Wyres KL, Holt KE.

Trends Microbiol. 2016 Dec;24(12):944-956. doi: 10.1016/j.tim.2016.09.007. Epub 2016 Oct 11. Review.

PMID:
27742466
29.

Vitamin D over the first decade and susceptibility to childhood allergy and asthma.

Hollams EM, Teo SM, Kusel M, Holt BJ, Holt KE, Inouye M, De Klerk NH, Zhang G, Sly PD, Hart PH, Holt PG.

J Allergy Clin Immunol. 2017 Feb;139(2):472-481.e9. doi: 10.1016/j.jaci.2016.07.032. Epub 2016 Oct 7.

PMID:
27726947
30.

An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid.

Wong VK, Baker S, Connor TR, Pickard D, Page AJ, Dave J, Murphy N, Holliman R, Sefton A, Millar M, Dyson ZA, Dougan G, Holt KE; International Typhoid Consortium.

Nat Commun. 2016 Oct 5;7:12827. doi: 10.1038/ncomms12827.

31.

Microbial mercury methylation in Antarctic sea ice.

Gionfriddo CM, Tate MT, Wick RR, Schultz MB, Zemla A, Thelen MP, Schofield R, Krabbenhoft DP, Holt KE, Moreau JW.

Nat Microbiol. 2016 Aug 1;1(10):16127. doi: 10.1038/nmicrobiol.2016.127.

PMID:
27670112
32.

Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa.

International Typhoid Consortium, Wong VK, Holt KE, Okoro C, Baker S, Pickard DJ, Marks F, Page AJ, Olanipekun G, Munir H, Alter R, Fey PD, Feasey NA, Weill FX, Le Hello S, Hart PJ, Kariuki S, Breiman RF, Gordon MA, Heyderman RS, Jacobs J, Lunguya O, Msefula C, MacLennan CA, Keddy KH, Smith AM, Onsare RS, De Pinna E, Nair S, Amos B, Dougan G, Obaro S.

PLoS Negl Trop Dis. 2016 Sep 22;10(9):e0004781. doi: 10.1371/journal.pntd.0004781. eCollection 2016 Sep.

33.

Global phylogeography and evolutionary history of Shigella dysenteriae type 1.

Njamkepo E, Fawal N, Tran-Dien A, Hawkey J, Strockbine N, Jenkins C, Talukder KA, Bercion R, Kuleshov K, Kolínská R, Russell JE, Kaftyreva L, Accou-Demartin M, Karas A, Vandenberg O, Mather AE, Mason CJ, Page AJ, Ramamurthy T, Bizet C, Gamian A, Carle I, Sow AG, Bouchier C, Wester AL, Lejay-Collin M, Fonkoua MC, Le Hello S, Blaser MJ, Jernberg C, Ruckly C, Mérens A, Page AL, Aslett M, Roggentin P, Fruth A, Denamur E, Venkatesan M, Bercovier H, Bodhidatta L, Chiou CS, Clermont D, Colonna B, Egorova S, Pazhani GP, Ezernitchi AV, Guigon G, Harris SR, Izumiya H, Korzeniowska-Kowal A, Lutyńska A, Gouali M, Grimont F, Langendorf C, Marejková M, Peterson LA, Perez-Perez G, Ngandjio A, Podkolzin A, Souche E, Makarova M, Shipulin GA, Ye C, Žemličková H, Herpay M, Grimont PA, Parkhill J, Sansonetti P, Holt KE, Brisse S, Thomson NR, Weill FX.

Nat Microbiol. 2016 Mar 21;1:16027. doi: 10.1038/nmicrobiol.2016.27. Erratum in: Nat Microbiol. 2016 Oct 03;1(11):16209.

PMID:
27572446
34.

Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants.

Ingle DJ, Tauschek M, Edwards DJ, Hocking DM, Pickard DJ, Azzopardi KI, Amarasena T, Bennett-Wood V, Pearson JS, Tamboura B, Antonio M, Ochieng JB, Oundo J, Mandomando I, Qureshi S, Ramamurthy T, Hossain A, Kotloff KL, Nataro JP, Dougan G, Levine MM, Robins-Browne RM, Holt KE.

Nat Microbiol. 2016 Jan 18;1:15010. doi: 10.1038/nmicrobiol.2015.10.

PMID:
27571974
35.

South Asia as a Reservoir for the Global Spread of Ciprofloxacin-Resistant Shigella sonnei: A Cross-Sectional Study.

Chung The H, Rabaa MA, Pham Thanh D, De Lappe N, Cormican M, Valcanis M, Howden BP, Wangchuk S, Bodhidatta L, Mason CJ, Nguyen Thi Nguyen T, Vu Thuy D, Thompson CN, Phu Huong Lan N, Voong Vinh P, Ha Thanh T, Turner P, Sar P, Thwaites G, Thomson NR, Holt KE, Baker S.

PLoS Med. 2016 Aug 2;13(8):e1002055. doi: 10.1371/journal.pmed.1002055. eCollection 2016 Aug.

36.

A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets.

Ritchie SC, Watts S, Fearnley LG, Holt KE, Abraham G, Inouye M.

Cell Syst. 2016 Jul;3(1):71-82. doi: 10.1016/j.cels.2016.06.012.

37.

Differential host susceptibility and bacterial virulence factors driving Klebsiella liver abscess in an ethnically diverse population.

Lee IR, Molton JS, Wyres KL, Gorrie C, Wong J, Hoh CH, Teo J, Kalimuddin S, Lye DC, Archuleta S, Holt KE, Gan YH.

Sci Rep. 2016 Jul 13;6:29316. doi: 10.1038/srep29316.

38.

The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia.

Pham Thanh D, Thompson CN, Rabaa MA, Sona S, Sopheary S, Kumar V, Moore C, Tran Vu Thieu N, Wijedoru L, Holt KE, Wong V, Pickard D, Thwaites GE, Day N, Dougan G, Turner P, Parry CM, Baker S.

PLoS Negl Trop Dis. 2016 Jun 22;10(6):e0004785. doi: 10.1371/journal.pntd.0004785. eCollection 2016 Jun.

39.

Inducible colistin resistance via a disrupted plasmid-borne mcr-1 gene in a 2008 Vietnamese Shigella sonnei isolate.

Pham Thanh D, Thanh Tuyen H, Nguyen Thi Nguyen T, Chung The H, Wick RR, Thwaites GE, Baker S, Holt KE.

J Antimicrob Chemother. 2016 Aug;71(8):2314-7. doi: 10.1093/jac/dkw173. Epub 2016 May 30.

40.

Cross-validation to select Bayesian hierarchical models in phylogenetics.

Duchêne S, Duchêne DA, Di Giallonardo F, Eden JS, Geoghegan JL, Holt KE, Ho SY, Holmes EC.

BMC Evol Biol. 2016 May 26;16(1):115. doi: 10.1186/s12862-016-0688-y.

41.

Comparative genomics of Crohn's disease-associated adherent-invasive Escherichia coli.

O'Brien CL, Bringer MA, Holt KE, Gordon DM, Dubois AL, Barnich N, Darfeuille-Michaud A, Pavli P.

Gut. 2017 Aug;66(8):1382-1389. doi: 10.1136/gutjnl-2015-311059. Epub 2016 Apr 20.

42.

A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure.

Pham Thanh D, Karkey A, Dongol S, Ho Thi N, Thompson CN, Rabaa MA, Arjyal A, Holt KE, Wong V, Tran Vu Thieu N, Voong Vinh P, Ha Thanh T, Pradhan A, Shrestha SK, Gajurel D, Pickard D, Parry CM, Dougan G, Wolbers M, Dolecek C, Thwaites GE, Basnyat B, Baker S.

Elife. 2016 Mar 11;5:e14003. doi: 10.7554/eLife.14003.

43.

The genomic signatures of Shigella evolution, adaptation and geographical spread.

The HC, Thanh DP, Holt KE, Thomson NR, Baker S.

Nat Rev Microbiol. 2016 Apr;14(4):235-50. doi: 10.1038/nrmicro.2016.10. Epub 2016 Feb 29. Review.

PMID:
26923111
44.

pCERC3 from a commensal ST95 Escherichia coli: A ColV virulence-multiresistance plasmid carrying a sul3-associated class 1 integron.

Moran RA, Holt KE, Hall RM.

Plasmid. 2016 Mar-May;84-85:11-9. doi: 10.1016/j.plasmid.2016.02.002. Epub 2016 Feb 18.

PMID:
26855083
45.

Introduction and establishment of fluoroquinolone-resistant Shigella sonnei into Bhutan.

Chung The H, Rabaa MA, Thanh DP, Ruekit S, Wangchuk S, Dorji T, Tshering KP, Nguyen TN, Vinh PV, Thanh TH, Minh CN, Turner P, Sar P, Thwaites G, Holt KE, Thomson NR, Bodhidatta L, Jeffries Mason C, Baker S.

Microb Genom. 2015 Dec 24;1(6):e000042. doi: 10.1099/mgen.0.000042. eCollection 2015 Dec.

46.

Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1.

Hamidian M, Hawkey J, Holt KE, Hall RM.

Genome Announc. 2015 Dec 17;3(6). pii: e01478-15. doi: 10.1128/genomeA.01478-15.

47.

Effect of Nocturnal Dialysis on Prognosis in Adult Patients: A Review of the Literature.

Bridge AB, Holt KE.

Nephrol Nurs J. 2015 Jul-Aug;42(4):375-9; quiz 380. Review.

PMID:
26462310
48.

Multiple Genetic Mutations Associated with Polymyxin Resistance in Acinetobacter baumannii.

Lim TP, Ong RT, Hon PY, Hawkey J, Holt KE, Koh TH, Leong ML, Teo JQ, Tan TY, Ng MM, Hsu LY.

Antimicrob Agents Chemother. 2015 Dec;59(12):7899-902. doi: 10.1128/AAC.01884-15. Epub 2015 Oct 5.

49.

A small Acinetobacter plasmid carrying the tet39 tetracycline resistance determinant.

Hamidian M, Holt KE, Pickard D, Hall RM.

J Antimicrob Chemother. 2016 Jan;71(1):269-71. doi: 10.1093/jac/dkv293. Epub 2015 Sep 27. No abstract available.

50.

Draft Genome Sequence of a Clinical Isolate of Serratia marcescens, Strain AH0650_Sm1.

Wan Y, Gorrie CL, Jenney A, Mirceta M, Holt KE.

Genome Announc. 2015 Sep 3;3(5). pii: e01007-15. doi: 10.1128/genomeA.01007-15.

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