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Items: 1 to 50 of 146

1.

Correction for Kennan et al., "Genomic Evidence for a Globally Distributed, Bimodal Population in the Ovine Footrot Pathogen Dichelobacter nodosus".

Kennan RM, Gilhuus M, Frosth S, Seemann T, Dhungyel OP, Whittington RJ, Boyce JD, Powell DR, Aspán A, Jørgensen HJ, Bulach DM, Rood JI.

MBio. 2019 Oct 29;10(5). pii: e02560-19. doi: 10.1128/mBio.02560-19. No abstract available.

2.

Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software.

Georgeson P, Syme A, Sloggett C, Chung J, Dashnow H, Milton M, Lonsdale A, Powell D, Seemann T, Pope B.

Gigascience. 2019 Sep 1;8(9). pii: giz109. doi: 10.1093/gigascience/giz109.

3.

Unstable chromosome rearrangements in Staphylococcus aureus cause phenotype switching associated with persistent infections.

Guérillot R, Kostoulias X, Donovan L, Li L, Carter GP, Hachani A, Vandelannoote K, Giulieri S, Monk IR, Kunimoto M, Starrs L, Burgio G, Seemann T, Peleg AY, Stinear TP, Howden BP.

Proc Natl Acad Sci U S A. 2019 Oct 1;116(40):20135-20140. doi: 10.1073/pnas.1904861116. Epub 2019 Sep 16.

4.

Bridging of Neisseria gonorrhoeae lineages across sexual networks in the HIV pre-exposure prophylaxis era.

Williamson DA, Chow EPF, Gorrie CL, Seemann T, Ingle DJ, Higgins N, Easton M, Taiaroa G, Grad YH, Kwong JC, Fairley CK, Chen MY, Howden BP.

Nat Commun. 2019 Sep 5;10(1):3988. doi: 10.1038/s41467-019-12053-4.

5.

Genomic investigation of Staphylococcus aureus recovered from Gambian women and newborns following an oral dose of intra-partum azithromycin.

Bojang A, Baines SL, Donovan L, Guerillot R, Stevens K, Higgs C, Bottomley C, Secka O, Schultz MB, Gonçalves da Silva A, Seemann T, Stinear TP, Roca A, Howden BP.

J Antimicrob Chemother. 2019 Nov 1;74(11):3170-3178. doi: 10.1093/jac/dkz341.

6.

A nonclonal outbreak of vancomycin-sensitive Enterococcus faecalis bacteremia in a neonatal intensive care unit.

Kotsanas D, Tan K, Scott C, Baade B, Cheng MHL, Tan ZV, Taylor JE, Kwong JC, Seemann T, Coombs GW, Howden BP, Stuart RL.

Infect Control Hosp Epidemiol. 2019 Oct;40(10):1116-1122. doi: 10.1017/ice.2019.202. Epub 2019 Aug 5.

PMID:
31379308
7.

Genomics for Molecular Epidemiology and Detecting Transmission of Carbapenemase-Producing Enterobacterales in Victoria, Australia, 2012 to 2016.

Sherry NL, Lane CR, Kwong JC, Schultz M, Sait M, Stevens K, Ballard S, Gonçalves da Silva A, Seemann T, Gorrie CL, Stinear TP, Williamson DA, Brett J, van Diemen A, Easton M, Howden BP.

J Clin Microbiol. 2019 Aug 26;57(9). pii: e00573-19. doi: 10.1128/JCM.00573-19. Print 2019 Sep.

8.

Zinc-binding to the cytoplasmic PAS domain regulates the essential WalK histidine kinase of Staphylococcus aureus.

Monk IR, Shaikh N, Begg SL, Gajdiss M, Sharkey LKR, Lee JYH, Pidot SJ, Seemann T, Kuiper M, Winnen B, Hvorup R, Collins BM, Bierbaum G, Udagedara SR, Morey JR, Pulyani N, Howden BP, Maher MJ, McDevitt CA, King GF, Stinear TP.

Nat Commun. 2019 Jul 11;10(1):3067. doi: 10.1038/s41467-019-10932-4.

9.

Emergence and divergence of major lineages of Shiga-toxin-producing Escherichia coli in Australia.

Ingle DJ, Gonçalves da Silva A, Valcanis M, Ballard SA, Seemann T, Jennison AV, Bastian I, Wise R, Kirk MD, Howden BP, Williamson DA.

Microb Genom. 2019 May;5(5). doi: 10.1099/mgen.0.000268. Epub 2019 May 20.

10.

Wave 2 strains of atypical Vibrio cholerae El Tor caused the 2009-2011 cholera outbreak in Papua New Guinea.

Greenhill AR, Mutreja A, Bulach D, Belousoff MJ, Jonduo MH, Collins DA, Kas MP, Wapling J, Seemann T, Lafana A, Dougan G, Brown MV, Horwood PF.

Microb Genom. 2019 Mar;5(3). doi: 10.1099/mgen.0.000256. Epub 2019 Feb 27.

11.

Remodeling of pSK1 Family Plasmids and Enhanced Chlorhexidine Tolerance in a Dominant Hospital Lineage of Methicillin-Resistant Staphylococcus aureus.

Baines SL, Jensen SO, Firth N, Gonçalves da Silva A, Seemann T, Carter GP, Williamson DA, Howden BP, Stinear TP.

Antimicrob Agents Chemother. 2019 Apr 25;63(5). pii: e02356-18. doi: 10.1128/AAC.02356-18. Print 2019 May.

12.

Biosynthesis and Ether-Bridge Formation in Nargenicin Macrolides.

Pidot SJ, Herisse M, Sharkey L, Atkin L, Porter JL, Seemann T, Howden BP, Rizzacasa MA, Stinear TP.

Angew Chem Int Ed Engl. 2019 Mar 18;58(12):3996-4001. doi: 10.1002/anie.201900290. Epub 2019 Feb 11.

PMID:
30677204
13.

Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing.

Mu A, Kwong JC, Isles NS, Gonçalves da Silva A, Schultz MB, Ballard SA, Lane CR, Carter GP, Williamson DA, Seemann T, Stinear TP, Howden BP.

mSphere. 2019 Jan 16;4(1). pii: e00529-18. doi: 10.1128/mSphere.00529-18.

14.

Capacity To Utilize Raffinose Dictates Pneumococcal Disease Phenotype.

Minhas V, Harvey RM, McAllister LJ, Seemann T, Syme AE, Baines SL, Paton JC, Trappetti C.

MBio. 2019 Jan 15;10(1). pii: e02596-18. doi: 10.1128/mBio.02596-18.

15.

Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in 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 MD, Howden BP, Williamson DA.

Clin Infect Dis. 2019 Oct 15;69(9):1535-1544. doi: 10.1093/cid/ciz005.

PMID:
30615105
16.

Urinary proteomics to diagnose chronic active antibody-mediated rejection in pediatric kidney transplantation - a pilot study.

Kanzelmeyer NK, Zürbig P, Mischak H, Metzger J, Fichtner A, Ruszai KH, Seemann T, Hansen M, Wygoda S, Krupka K, Tönshoff B, Melk A, Pape L.

Transpl Int. 2019 Jan;32(1):28-37. doi: 10.1111/tri.13363. Epub 2018 Nov 12.

PMID:
30357927
17.

The changing landscape of vancomycin-resistant Enterococcus faecium in Australia: a population-level genomic study.

Lee RS, Gonçalves da Silva A, Baines SL, Strachan J, Ballard S, Carter GP, Kwong JC, Schultz MB, Bulach DM, Seemann T, Stinear TP, Howden BP.

J Antimicrob Chemother. 2018 Dec 1;73(12):3268-3278. doi: 10.1093/jac/dky331.

PMID:
30189014
18.

Global spread of three multidrug-resistant lineages of Staphylococcus epidermidis.

Lee JYH, Monk IR, Gonçalves da Silva A, Seemann T, Chua KYL, Kearns A, Hill R, Woodford N, Bartels MD, Strommenger B, Laurent F, Dodémont M, Deplano A, Patel R, Larsen AR, Korman TM, Stinear TP, Howden BP.

Nat Microbiol. 2018 Oct;3(10):1175-1185. doi: 10.1038/s41564-018-0230-7. Epub 2018 Sep 3.

19.

Comprehensive antibiotic-linked mutation assessment by resistance mutation sequencing (RM-seq).

Guérillot R, Li L, Baines S, Howden B, Schultz MB, Seemann T, Monk I, Pidot SJ, Gao W, Giulieri S, Gonçalves da Silva A, D'Agata A, Tomita T, Peleg AY, Stinear TP, Howden BP.

Genome Med. 2018 Aug 31;10(1):63. doi: 10.1186/s13073-018-0572-z.

20.

Best practice data life cycle approaches for the life sciences.

Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WWH, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider MV.

Version 2. F1000Res. 2017 Aug 31 [revised 2018 Jan 1];6:1618. doi: 10.12688/f1000research.12344.2. eCollection 2017.

21.

Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia.

Giulieri SG, Baines SL, Guerillot R, Seemann T, Gonçalves da Silva A, Schultz M, Massey RC, Holmes NE, Stinear TP, Howden BP.

Genome Med. 2018 Aug 23;10(1):65. doi: 10.1186/s13073-018-0574-x.

22.

Increasing tolerance of hospital Enterococcus faecium to handwash alcohols.

Pidot SJ, Gao W, Buultjens AH, Monk IR, Guerillot R, Carter GP, Lee JYH, Lam MMC, Grayson ML, Ballard SA, Mahony AA, Grabsch EA, Kotsanas D, Korman TM, Coombs GW, Robinson JO, Gonçalves da Silva A, Seemann T, Howden BP, Johnson PDR, Stinear TP.

Sci Transl Med. 2018 Aug 1;10(452). pii: eaar6115. doi: 10.1126/scitranslmed.aar6115.

PMID:
30068573
23.

The First Isolation and Whole Genome Sequencing of Murray Valley Encephalitis Virus from Cerebrospinal Fluid of a Patient with Encephalitis.

Russell JS, Caly L, Kostecki R, McGuinness SL, Carter G, Bulach D, Seemann T, Stinear TP, Baird R, Catton M, Druce J.

Viruses. 2018 Jun 11;10(6). pii: E319. doi: 10.3390/v10060319.

24.

Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens.

Lacey JA, Allnutt TR, Vezina B, Van TTH, Stent T, Han X, Rood JI, Wade B, Keyburn AL, Seemann T, Chen H, Haring V, Johanesen PA, Lyras D, Moore RJ.

BMC Genomics. 2018 May 22;19(1):379. doi: 10.1186/s12864-018-4771-1.

25.

The ΦBT1 large serine recombinase catalyzes DNA integration at pseudo-attB sites in the genus Nocardia.

Herisse M, Porter JL, Guerillot R, Tomita T, Goncalves Da Silva A, Seemann T, Howden BP, Stinear TP, Pidot SJ.

PeerJ. 2018 May 4;6:e4784. doi: 10.7717/peerj.4784. eCollection 2018.

26.

Emergence of High-Level Colistin Resistance in an Acinetobacter baumannii Clinical Isolate Mediated by Inactivation of the Global Regulator H-NS.

Deveson Lucas D, Crane B, Wright A, Han ML, Moffatt J, Bulach D, Gladman SL, Powell D, Aranda J, Seemann T, Machado D, Pacheco T, Marques T, Viveiros M, Nation R, Li J, Harper M, Boyce JD.

Antimicrob Agents Chemother. 2018 Jun 26;62(7). pii: e02442-17. doi: 10.1128/AAC.02442-17. Print 2018 Jul.

27.

Seven Salmonella Typhimurium Outbreaks in Australia Linked by Trace-Back and Whole Genome Sequencing.

Ford L, Wang Q, Stafford R, Ressler KA, Norton S, Shadbolt C, Hope K, Franklin N, Krsteski R, Carswell A, Carter GP, Seemann T, Howard P, Valcanis M, Castillo CFS, Bates J, Glass K, Williamson DA, Sintchenko V, Howden BP, Kirk MD.

Foodborne Pathog Dis. 2018 May;15(5):285-292. doi: 10.1089/fpd.2017.2353. Epub 2018 Mar 20.

PMID:
29638170
28.

Vancomycin-resistant Enterococcus faecium sequence type 796 - rapid international dissemination of a new epidemic clone.

Mahony AA, Buultjens AH, Ballard SA, Grabsch EA, Xie S, Seemann T, Stuart RL, Kotsanas D, Cheng A, Heffernan H, Roberts SA, Coombs GW, Bak N, Ferguson JK, Carter GC, Howden BP, Stinear TP, Johnson PDR.

Antimicrob Resist Infect Control. 2018 Mar 22;7:44. doi: 10.1186/s13756-018-0335-z. eCollection 2018.

29.

Concurrent training protocol for men with androgen deficiency in the aging male: a randomized clinical trial.

Vieira MCS, Leitão AE, Vieira G, Moratelli J, Boing L, Seemann T, Guimarães ACA.

Aging Male. 2018 Sep;21(3):149-157. doi: 10.1080/13685538.2018.1454421. Epub 2018 Mar 25.

PMID:
29575951
30.

Mobile phones and computer keyboards: unlikely reservoirs of multidrug-resistant organisms in the tertiary intensive care unit.

Smibert OC, Aung AK, Woolnough E, Carter GP, Schultz MB, Howden BP, Seemann T, Spelman D, McGloughlin S, Peleg AY.

J Hosp Infect. 2018 Jul;99(3):295-298. doi: 10.1016/j.jhin.2018.02.013. Epub 2018 Mar 2.

PMID:
29501730
31.

Determination of the small RNA GcvB regulon in the Gram-negative bacterial pathogen Pasteurella multocida and identification of the GcvB seed binding region.

Gulliver EL, Wright A, Lucas DD, Mégroz M, Kleifeld O, Schittenhelm RB, Powell DR, Seemann T, Bulitta JB, Harper M, Boyce JD.

RNA. 2018 May;24(5):704-720. doi: 10.1261/rna.063248.117. Epub 2018 Feb 12.

32.

Comparative Genomics Shows That Mycobacterium ulcerans Migration and Expansion Preceded the Rise of Buruli Ulcer in Southeastern Australia.

Buultjens AH, Vandelannoote K, Meehan CJ, Eddyani M, de Jong BC, Fyfe JAM, Globan M, Tobias NJ, Porter JL, Tomita T, Tay EL, Seemann T, Howden BP, Johnson PDR, Stinear TP.

Appl Environ Microbiol. 2018 Apr 2;84(8). pii: e02612-17. doi: 10.1128/AEM.02612-17. Print 2018 Apr 15.

33.

Human blood MAIT cell subsets defined using MR1 tetramers.

Gherardin NA, Souter MN, Koay HF, Mangas KM, Seemann T, Stinear TP, Eckle SB, Berzins SP, d'Udekem Y, Konstantinov IE, Fairlie DP, Ritchie DS, Neeson PJ, Pellicci DG, Uldrich AP, McCluskey J, Godfrey DI.

Immunol Cell Biol. 2018 May;96(5):507-525. doi: 10.1111/imcb.12021. Epub 2018 Mar 25.

34.

Convergent Evolution Driven by Rifampin Exacerbates the Global Burden of Drug-Resistant Staphylococcus aureus.

Guérillot R, Gonçalves da Silva A, Monk I, Giulieri S, Tomita T, Alison E, Porter J, Pidot S, Gao W, Peleg AY, Seemann T, Stinear TP, Howden BP.

mSphere. 2018 Jan 24;3(1). pii: e00550-17. doi: 10.1128/mSphere.00550-17. eCollection 2018 Jan-Feb.

35.

Structure, Function, and Biosynthetic Origin of Octapeptin Antibiotics Active against Extensively Drug-Resistant Gram-Negative Bacteria.

Velkov T, Gallardo-Godoy A, Swarbrick JD, Blaskovich MAT, Elliott AG, Han M, Thompson PE, Roberts KD, Huang JX, Becker B, Butler MS, Lash LH, Henriques ST, Nation RL, Sivanesan S, Sani MA, Separovic F, Mertens H, Bulach D, Seemann T, Owen J, Li J, Cooper MA.

Cell Chem Biol. 2018 Apr 19;25(4):380-391.e5. doi: 10.1016/j.chembiol.2018.01.005. Epub 2018 Feb 3.

36.

Incorporating Whole-Genome Sequencing into Public Health Surveillance: Lessons from Prospective Sequencing of Salmonella Typhimurium in Australia.

Ford L, Carter GP, Wang Q, Seemann T, Sintchenko V, Glass K, Williamson DA, Howard P, Valcanis M, Castillo CFS, Sait M, Howden BP, Kirk MD.

Foodborne Pathog Dis. 2018 Mar;15(3):161-167. doi: 10.1089/fpd.2017.2352. Epub 2018 Jan 16.

PMID:
29336594
37.

Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak.

Kwong JC, Lane CR, Romanes F, Gonçalves da Silva A, Easton M, Cronin K, Waters MJ, Tomita T, Stevens K, Schultz MB, Baines SL, Sherry NL, Carter GP, Mu A, Sait M, Ballard SA, Seemann T, Stinear TP, Howden BP.

PeerJ. 2018 Jan 3;6:e4210. doi: 10.7717/peerj.4210. eCollection 2018.

38.

Whole-genome sequencing reveals transmission of gonococcal antibiotic resistance among men who have sex with men: an observational study.

Kwong JC, Chow EPF, Stevens K, Stinear TP, Seemann T, Fairley CK, Chen MY, Howden BP.

Sex Transm Infect. 2018 Mar;94(2):151-157. doi: 10.1136/sextrans-2017-053287. Epub 2017 Dec 15.

39.

Genomic epidemiology and antimicrobial resistance of Neisseria gonorrhoeae in New Zealand.

Lee RS, Seemann T, Heffernan H, Kwong JC, Gonçalves da Silva A, Carter GP, Woodhouse R, Dyet KH, Bulach DM, Stinear TP, Howden BP, Williamson DA.

J Antimicrob Chemother. 2018 Feb 1;73(2):353-364. doi: 10.1093/jac/dkx405.

40.

Methicillin Resistant Staphylococcus aureus Transmission in a Ghanaian Burn Unit: The Importance of Active Surveillance in Resource-Limited Settings.

Amissah NA, Buultjens AH, Ablordey A, van Dam L, Opoku-Ware A, Baines SL, Bulach D, Tetteh CS, Prah I, van der Werf TS, Friedrich AW, Seemann T, van Dijl JM, Stienstra Y, Stinear TP, Rossen JW.

Front Microbiol. 2017 Oct 6;8:1906. doi: 10.3389/fmicb.2017.01906. eCollection 2017.

41.

Comparison of classical multi-locus sequence typing software for next-generation sequencing data.

Page AJ, Alikhan NF, Carleton HA, Seemann T, Keane JA, Katz LS.

Microb Genom. 2017 Jul 4;3(8):e000124. doi: 10.1099/mgen.0.000124. eCollection 2017 Aug. Review.

42.

Draft Genome Sequences of Two Strains of a Newly Described Species, Sphingobacterium cellulitidis.

Seemann T, Bulach DM, Carter G, Albert MJ.

Genome Announc. 2017 Sep 21;5(38). pii: e00956-17. doi: 10.1128/genomeA.00956-17.

43.

De novo transcriptome assembly for the spiny mouse (Acomys cahirinus).

Mamrot J, Legaie R, Ellery SJ, Wilson T, Seemann T, Powell DR, Gardner DK, Walker DW, Temple-Smith P, Papenfuss AT, Dickinson H.

Sci Rep. 2017 Aug 21;7(1):8996. doi: 10.1038/s41598-017-09334-7.

44.

A Supervised Statistical Learning Approach for Accurate Legionella pneumophila Source Attribution during Outbreaks.

Buultjens AH, Chua KYL, Baines SL, Kwong J, Gao W, Cutcher Z, Adcock S, Ballard S, Schultz MB, Tomita T, Subasinghe N, Carter GP, Pidot SJ, Franklin L, Seemann T, Gonçalves Da Silva A, Howden BP, Stinear TP.

Appl Environ Microbiol. 2017 Oct 17;83(21). pii: e01482-17. doi: 10.1128/AEM.01482-17. Print 2017 Nov 1.

45.

Functional analysis of the first complete genome sequence of a multidrug resistant sequence type 2 Staphylococcus epidermidis.

Lee JYH, Monk IR, Pidot SJ, Singh S, Chua KYL, Seemann T, Stinear TP, Howden BP.

Microb Genom. 2016 Sep 20;2(9):e000077. doi: 10.1099/mgen.0.000077. eCollection 2016 Sep.

46.

Emergence of multidrug resistance in locally-acquired human infections with Salmonella Typhimurium in Australia owing to a new clade harbouring blaCTX-M-9.

Sparham SJ, Kwong JC, Valcanis M, Easton M, Trott DJ, Seemann T, Stinear TP, Howden BP.

Int J Antimicrob Agents. 2017 Jul;50(1):101-105. doi: 10.1016/j.ijantimicag.2017.02.014. Epub 2017 May 2.

PMID:
28476613
47.

Target-Specific Assay for Rapid and Quantitative Detection of Mycobacterium chimaera DNA.

Zozaya-Valdés E, Porter JL, Coventry J, Fyfe JAM, Carter GP, Gonçalves da Silva A, Schultz MB, Seemann T, Johnson PDR, Stewardson AJ, Bastian I, Roberts SA, Howden BP, Williamson DA, Stinear TP.

J Clin Microbiol. 2017 Jun;55(6):1847-1856. doi: 10.1128/JCM.00197-17. Epub 2017 Apr 5.

48.

A phylogenomic framework for assessing the global emergence and evolution of clonal complex 398 methicillin-resistant Staphylococcus aureus.

Gonçalves da Silva A, Baines SL, Carter GP, Heffernan H, French NP, Ren X, Seemann T, Bulach D, Kwong J, Stinear TP, Howden BP, Williamson DA.

Microb Genom. 2017 Jan 31;3(1):e000105. doi: 10.1099/mgen.0.000105. eCollection 2017 Jan.

49.

NGMASTER:in silico multi-antigen sequence typing for Neisseria gonorrhoeae.

Kwong JC, Gonçalves da Silva A, Dyet K, Williamson DA, Stinear TP, Howden BP, Seemann T.

Microb Genom. 2016 Aug 25;2(8):e000076. doi: 10.1099/mgen.0.000076. eCollection 2016 Aug.

50.

SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments.

Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T, Keane JA, Harris SR.

Microb Genom. 2016 Apr 29;2(4):e000056. doi: 10.1099/mgen.0.000056. eCollection 2016 Apr.

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