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Items: 1 to 50 of 140

1.

Corrigendum: Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1.

Holt KE, Kenyon JJ, Hamidian M, Schultz MB, Pickard DJ, Dougan G, Hall RM.

Microb Genom. 2019 Jul;5(7). doi: 10.1099/mgen.0.000280. No abstract available.

2.

Performance of neural network basecalling tools for Oxford Nanopore sequencing.

Wick RR, Judd LM, Holt KE.

Genome Biol. 2019 Jun 24;20(1):129. doi: 10.1186/s13059-019-1727-y.

3.

Empirical ways to identify novel Bedaquiline resistance mutations in AtpE.

Karmakar M, Rodrigues CHM, Holt KE, Dunstan SJ, Denholm J, Ascher DB.

PLoS One. 2019 May 29;14(5):e0217169. doi: 10.1371/journal.pone.0217169. eCollection 2019.

4.

Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198.

Hawkey J, Le Hello S, Doublet B, Granier SA, Hendriksen RS, Fricke WF, Ceyssens PJ, Gomart C, Billman-Jacobe H, Holt KE, Weill FX.

Microb Genom. 2019 Jul;5(7). doi: 10.1099/mgen.0.000269. Epub 2019 May 20.

5.

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae.

Wyres KL, Wick RR, Judd LM, Froumine R, Tokolyi A, Gorrie CL, Lam MMC, Duchêne S, Jenney A, Holt KE.

PLoS Genet. 2019 Apr 15;15(4):e1008114. doi: 10.1371/journal.pgen.1008114. eCollection 2019 Apr.

6.

hicap: In Silico Serotyping of the Haemophilus influenzae Capsule Locus.

Watts SC, Holt KE.

J Clin Microbiol. 2019 May 24;57(6). pii: e00190-19. doi: 10.1128/JCM.00190-19. Print 2019 Jun.

7.

Convergence of virulence and MDR in a single plasmid vector in MDR Klebsiella pneumoniae ST15.

Lam MMC, Wyres KL, Wick RR, Judd LM, Fostervold A, Holt KE, Löhr IH.

J Antimicrob Chemother. 2019 Feb 15. pii: dkz028. doi: 10.1093/jac/dkz028. [Epub ahead of print]

8.

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.

9.

Evolution of a clade of Acinetobacter baumannii global clone 1, lineage 1 via acquisition of carbapenem- and aminoglycoside-resistance genes and dispersion of ISAba1.

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

Microb Genom. 2019 Jan;5(1). doi: 10.1099/mgen.0.000242. Epub 2019 Jan 16.

10.

Co-circulation of multidrug-resistant Shigella among men who have sex with men, Australia.

Ingle DJ, Easton M, Valcanis M, Seemann T, Kwong JC, Stephens N, Carter GP, Gonçalves da Silva A, Adamopoulos J, Baines SL, Holt KE, Chow EPF, Fairley CK, Chen MY, Kirk M, Howden BP, Williamson DA.

Clin Infect Dis. 2019 Jan 7. doi: 10.1093/cid/ciz005. [Epub ahead of print]

PMID:
30615105
11.

Small IncQ1 and Col-Like Plasmids Harboring bla KPC-2 and Non-Tn4401 Elements (NTEKPC-IId) in High-Risk Lineages of Klebsiella pneumoniae CG258.

Cerdeira LT, Lam MMC, Wyres KL, Wick RR, Judd LM, Lopes R, Ribas RM, Morais MM, Holt KE, Lincopan N.

Antimicrob Agents Chemother. 2019 Feb 26;63(3). pii: e02140-18. doi: 10.1128/AAC.02140-18. Print 2019 Mar. No abstract available.

PMID:
30602517
12.

Complete Genome Sequence of WM99c, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 2 (GC2) Strain Representing an Australian GC2 Lineage.

Nigro SJ, Wick R, Holt KE, Hall RM.

Microbiol Resour Announc. 2018 Dec 6;7(22). pii: e01199-18. doi: 10.1128/MRA.01199-18. eCollection 2018 Dec.

13.

Comment on: CG258 Klebsiella pneumoniae isolates without β-lactam resistance at the onset of the carbapenem-resistant Enterobacteriaceae epidemic in New York City.

Wyres KL, Lam MMC, Holt KE.

J Antimicrob Chemother. 2019 Mar 1;74(3):831-833. doi: 10.1093/jac/dky472. No abstract available.

14.

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa.

Park SE, Pham DT, Boinett C, Wong VK, Pak GD, Panzner U, Espinoza LMC, von Kalckreuth V, Im J, Schütt-Gerowitt H, Crump JA, Breiman RF, Adu-Sarkodie Y, Owusu-Dabo E, Rakotozandrindrainy R, Soura AB, Aseffa A, Gasmelseed N, Keddy KH, May J, Sow AG, Aaby P, Biggs HM, Hertz JT, Montgomery JM, Cosmas L, Olack B, Fields B, Sarpong N, Razafindrabe TJL, Raminosoa TM, Kabore LP, Sampo E, Teferi M, Yeshitela B, El Tayeb MA, Sooka A, Meyer CG, Krumkamp R, Dekker DM, Jaeger A, Poppert S, Tall A, Niang A, Bjerregaard-Andersen M, Løfberg SV, Seo HJ, Jeon HJ, Deerin JF, Park J, Konings F, Ali M, Clemens JD, Hughes P, Sendagala JN, Vudriko T, Downing R, Ikumapayi UN, Mackenzie GA, Obaro S, Argimon S, Aanensen DM, Page A, Keane JA, Duchene S, Dyson Z, Holt KE, Dougan G, Marks F, Baker S.

Nat Commun. 2018 Nov 30;9(1):5094. doi: 10.1038/s41467-018-07370-z.

15.

Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307.

Wyres KL, Hawkey J, Hetland MAK, Fostervold A, Wick RR, Judd LM, Hamidian M, Howden BP, Löhr IH, Holt KE.

J Antimicrob Chemother. 2019 Mar 1;74(3):577-581. doi: 10.1093/jac/dky492.

16.

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks.

Wick RR, Judd LM, Holt KE.

PLoS Comput Biol. 2018 Nov 20;14(11):e1006583. doi: 10.1371/journal.pcbi.1006583. eCollection 2018 Nov.

17.

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.

18.

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.

19.

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.

20.

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
21.

FastSpar: rapid and scalable correlation estimation for compositional data.

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

Bioinformatics. 2019 Mar 15;35(6):1064-1066. doi: 10.1093/bioinformatics/bty734.

22.

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.

23.

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

Mostowy RJ, Holt KE.

Trends Microbiol. 2018 Dec;26(12):1008-1021. doi: 10.1016/j.tim.2018.06.006. Epub 2018 Jul 20. Review.

24.

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.

25.

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.

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.

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.

28.

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.

29.

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.

30.

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

Wyres KL, Holt KE.

Curr Opin Microbiol. 2018 Oct;45:131-139. doi: 10.1016/j.mib.2018.04.004. Epub 2018 May 1. Review.

31.

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.

32.

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.

33.

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;4(3). doi: 10.1099/mgen.0.000165. Epub 2018 Mar 16.

34.

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
35.

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.

36.

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.

37.

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
38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

50.

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.

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