The Univeristy of Melbourne The Royal Melbourne Hopspital

A joint venture between The University of Melbourne and The Royal Melbourne Hospital

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.

Evidence for a new paradigm of gonorrhoea transmission: cross-sectional analysis of Neisseria gonorrhoeae infections by anatomical site in both partners in 60 male couples.
Cornelisse VJ, Williamson D, Zhang L, Chen MY, Bradshaw C, Hocking JS, Hoy J, Howden BP, Chow EPF, Fairley CK.
Sex Transm Infect. 2019 Apr 17. pii: sextrans-2018-053803. doi: 10.1136/sextrans-2018-053803. [Epub ahead of print]

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.

Utilizing genomic analyses to investigate the first outbreak of vanA vancomycin-resistant Enterococcus in Australia with emergence of daptomycin non-susceptibility.​​​​​​​
Douglas AP, Marshall C, Baines SL, Ritchie D, Szer J, Madigan V, Chan HT, Ballard SA, Howden BP, Buising K, Slavin MA.
J Med Microbiol. 2019 Mar;68(3):303-308. doi: 10.1099/jmm.0.000916. Epub 2019 Jan 21.

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.

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]

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.

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.

Low incidence of recurrent Buruli ulcers in treated Australian patients living in an endemic region
Wynne JW, Stinear TP, Athan E, Michalski WP, O'Brien DP.
PLoS Negl Trop Dis. 2018 Aug 13;12(8):e0006724. doi: 10.1371/journal.pntd.0006724. eCollection 2018 Aug.

Bilateral osteomyelitis and liver abscess caused by hypervirulent Klebsiella pneumoniae- a rare clinical manifestation (case report)
Sturm E, Tai A, Lin B, Kwong J, Athan E, Howden BP, Angliss RD, Asaid R, Pollard J.
BMC Infect Dis. 2018 Aug 7;18(1):380. doi: 10.1186/s12879-018-3277-4.

Primary prevention of rheumatic fever in the 21st century: evaluation of a national programme
Jack SJ, Williamson DA, Galloway Y, Pierse N, Zhang J, Oliver J, Milne RJ, Mackereth G, Jackson CM, Steer AC, Carapetis JR, Baker MG.
Int J Epidemiol. 2018 Jul 27. doi: 10.1093/ije/dyy150.

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.

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

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 CF, Bates J, Glass K, Williamson DA, Sintchenko V, Howden BP, Kirk MD.
Foodborne pathogens and disease. 2018;15(5):285-92.

Daptomycin selects for genetic and phenotypic adaptations leading to antibiotic tolerance in MRSA
Berti AD, Shukla N, Rottier AD, McCrone JS, Turner HM, Monk IR, Baines SL, Howden BP, Proctor RA, Rose WE.
J Antimicrob Chemother. 2018 Apr 21. doi:10.1093/jac/dky148

Complete Genome Sequence of a New Zealand Isolate of the Bovine Pathogen Streptococcus uberis
Taiaroa G, Harbison-Price N, Ferguson SA, Carter GP, Williamson DA, Macknight RC, Cook GM, Heikal A.
Genome Announc. 2018 Mar 1;6(9). pii: e00119-18. doi: 10.1128/genomeA.00119-18.

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.

Comparative genomics shows Mycobacterium ulcerans migration and expansion has preceded the rise of Buruli ulcer in south-eastern 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 Feb 9. pii: AEM.02612-17. doi: 10.1128/AEM.02612-17.

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.

Topical Antibiotic Use Coselects for the Carriage of Mobile Genetic Elements Conferring Resistance to Unrelated Antimicrobials in Staphylococcus aureus
Carter GP, Schultz MB, Baines SL, Gonçalves da Silva A, Heffernan H, Tiong A, Pham PH, Monk IR, Stinear TP, Howden BP, Williamson DA.
Antimicrob Agents Chemother. 2018 Jan 25;62(2). pii: e02000-17. doi: 10.1128/AAC.02000-17. Print 2018 Feb.

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.

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 Jan 16. doi: 10.1089/fpd.2017.2352.

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.

A supervised statistical learning approach for accurate Legionalla 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.

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.

Current and Emerging Topical Antibacterials and Antiseptics: Agents, Action, and Resistance Patterns
Williamson DA, Carter GP, Howden BP.
Clin Microbiol Rev. 2017 Jul;30(3):827-860. doi: 10.1128/CMR.00112-16. Review.

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.

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.

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.

Genomic analysis of ST88 community-acquired methicillin resistant Staphylococcus aureus in Ghana
Kpeli G, Buultjens AH, Giulieri S, Owusu-Mireku E, Aboagye SY, Baines SL, Seemann T, Bulach D, Gonçalves da Silva A, Monk IR, Howden BP, Pluschke G, Yeboah-Manu D, Stinear T. 
PeerJ. 2017 Feb 28;5:e3047. doi: 10.7717/peerj.3047. eCollection 2017.

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.

Genomic Insights into a Sustained National Outbreak of Yersinia pseudotuberculosis
Williamson DA, Baines SL, Carter GP, da Silva AG, Ren X, Sherwood J, Dufour M, Schultz MB, French NP, Seemann T, Stinear TP, Howden BP.
Genome Biol Evol. 2016 Dec 1;8(12):3806-3814. doi: 10.1093/gbe/evw285.

Emergence of endemic MLST non-typeable vancomycin-resistant Enterococcus faecium
Carter GP, Buultjens AH, Ballard SA, Baines SL, Tomita T, Strachan J, Johnson PD, Ferguson JK, Seemann T, Stinear TP, Howden BP.
J Antimicrob Chemother. 2016 Dec;71(12):3367-3371. Epub 2016 Aug 15.

Use of bacterial whole-genome sequencing to understand and improve the management of invasive Staphylococcus aureus infections.
Giulieri SG, Holmes NE, Stinear TP, Howden BP.
Expert Rev Anti Infect Ther. 2016 Nov;14(11):1023-1036. Epub 2016 Sep 21.

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.

Sharing Is Caring: International Sharing of Data Enhances Genomic Surveillance of Listeria monocytogenes
Kwong JC, Stafford R, Strain E, Stinear TP, Seemann T, Howden BP.
Clin Infect Dis. 2016 Sep 15;63(6):846-8. doi: 10.1093/cid/ciw359. Epub 2016 Jun 9.

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.

A Phenotypically Silent vanB2 Operon Carried on a Tn1549-Like Element in Clostridium difficile
Knight DR, Androga GO, Ballard SA, Howden BP, Riley TV.
mSphere. 2016 Aug 10;1(4). pii: e00177-16. doi: 10.1128/mSphere.00177-16. eCollection 2016 Jul-Aug.

Possible healthcare-associated transmission as a cause of secondary infection and population structure of Staphylococcus aureus isolates from two wound treatment centres in Ghana
Kpeli G, Darko Otchere I, Lamelas A, Buultjens AL, Bulach D, Baines SL, Seemann T, Giulieri S, Nakobu Z, Aboagye SY, Owusu-Mireku E, Pluschke G, Stinear TP, Yeboah-Manu D
New Microbes New Infect. 2016 Jul 12;13:92-101. doi: 10.1016/j.nmni.2016.07.001. eCollection 2016 Sep.

Rapid Emergence and Evolution of Staphylococcus aureus Clones Harboring fusC-Containing Staphylococcal Cassette Chromosome Elements
Baines SL, Howden BP, Heffernan H, Stinear TP, Carter GP, Seemann T, Kwong JC, Ritchie SR, Williamson DA
Antimicrob Agents Chemother. 2016 Mar 25;60(4):2359-65. doi: 10.1128/AAC.03020-15

Prospective Whole-Genome Sequencing Enhances National Surveillance of Listeria monocytogenes
Kwong JC, Mercoulia K, Tomita T, Easton M, Li HY, Bulach DM, Stinear TP, Seemann T, Howden BP
Clin Microbiol. 2016 Feb;54(2):333-42. doi: 10.1128/JCM.02344-15

Genome sequence comparisons of serial multi-drug-resistant Mycobacterium tuberculosis isolates over 21 years of infection in a single patient
Kwong JC, Mercoulia K, Tomita T, Easton M, Li HY, Bulach DM, Stinear TP, Seemann T, Howden BP
Microb Genom. 2015 Nov 26;1(5):e000037. doi: 10.1099/mgen.0.000037