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Items: 1 to 50 of 124

1.

Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae.

Lam MMC, Wyres KL, Judd LM, Wick RR, Jenney A, Brisse S, Holt KE.

Genome Med. 2018 Oct 29;10(1):77. doi: 10.1186/s13073-018-0587-5.

2.

Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation.

Brynildsrud OB, Pepperell CS, Suffys P, Grandjean L, Monteserin J, Debech N, Bohlin J, Alfsnes K, Pettersson JO, Kirkeleite I, Fandinho F, da Silva MA, Perdigao J, Portugal I, Viveiros M, Clark T, Caws M, Dunstan S, Thai PVK, Lopez B, Ritacco V, Kitchen A, Brown TS, van Soolingen D, O'Neill MB, Holt KE, Feil EJ, Mathema B, Balloux F, Eldholm V.

Sci Adv. 2018 Oct 17;4(10):eaat5869. doi: 10.1126/sciadv.aat5869. eCollection 2018 Oct.

3.

Trajectories of childhood immune development and respiratory health relevant to asthma and allergy.

Tang HH, Teo SM, Belgrave DC, Evans MD, Jackson DJ, Brozynska M, Kusel MM, Johnston SL, Gern JE, Lemanske RF, Simpson A, Custovic A, Sly PD, Holt PG, Holt KE, Inouye M.

Elife. 2018 Oct 15;7. pii: e35856. doi: 10.7554/eLife.35856.

4.

Airway Microbiota Dynamics Uncover a Critical Window for Interplay of Pathogenic Bacteria and Allergy in Childhood Respiratory Disease.

Teo SM, Tang HHF, Mok D, Judd LM, Watts SC, Pham K, Holt BJ, Kusel M, Serralha M, Troy N, Bochkov YA, Grindle K, Lemanske RF Jr, Johnston SL, Gern JE, Sly PD, Holt PG, Holt KE, Inouye M.

Cell Host Microbe. 2018 Sep 12;24(3):341-352.e5. doi: 10.1016/j.chom.2018.08.005.

PMID:
30212648
5.

FastSpar: Rapid and scalable correlation estimation for compositional data.

Watts SC, Ritchie SC, Inouye M, Holt KE.

Bioinformatics. 2018 Aug 29. doi: 10.1093/bioinformatics/bty734. [Epub ahead of print]

PMID:
30169561
6.

Dynamics of antimicrobial resistance in intestinal Escherichia coli from children in community settings in South Asia and sub-Saharan Africa.

Ingle DJ, Levine MM, Kotloff KL, Holt KE, Robins-Browne RM.

Nat Microbiol. 2018 Sep;3(9):1063-1073. doi: 10.1038/s41564-018-0217-4. Epub 2018 Aug 20.

7.

Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating.

Mostowy RJ, Holt KE.

Trends Microbiol. 2018 Jul 20. pii: S0966-842X(18)30141-0. doi: 10.1016/j.tim.2018.06.006. [Epub ahead of print] Review.

8.

Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination.

Lam MMC, Wyres KL, Duchêne S, Wick RR, Judd LM, Gan YH, Hoh CH, Archuleta S, Molton JS, Kalimuddin S, Koh TH, Passet V, Brisse S, Holt KE.

Nat Commun. 2018 Jul 13;9(1):2703. doi: 10.1038/s41467-018-05114-7.

9.

Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations.

Lam MMC, Wick RR, Wyres KL, Gorrie CL, Judd LM, Jenney AWJ, Brisse S, Holt KE.

Microb Genom. 2018 Sep;4(9). doi: 10.1099/mgen.0.000196. Epub 2018 Jul 9.

10.

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.

11.

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.

12.

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
13.

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
14.

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.

15.

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.

16.

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.

17.

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]

18.

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 Jul;52(1):14-21. doi: 10.1016/j.ijantimicag.2018.02.019. Epub 2018 Feb 28.

PMID:
29501823
19.

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.

20.

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.

21.

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
22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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
36.

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.

37.

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
38.

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
39.

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
40.

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.

41.

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
42.

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.

43.

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
44.

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
45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

50.

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.

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