2021
AusTrakka: Fast-tracking nationalized genomics surveillance in response to the COVID-19 pandemic
Hoang, T., da Silva, A.G., Jennison, A.V. et al. AusTrakka: Fast-tracking nationalized genomics surveillance in response to the COVID-19 pandemic. Nat Commun 13, 865 (2022). https://doi.org/10.1038/s41467-022-28529-9
Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia
Ingle, D.J., Ambrose, R.L., Baines, S.L. et al. Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia. Nat Commun 12, 4786 (2021). https://doi.org/10.1038/s41467-021-25073-w
An implementation science approach to evaluating pathogen whole genome sequencing in public health
Ferdinand, A.S., Kelaher, M., Lane, C.R. et al. An implementation science approach to evaluating pathogen whole genome sequencing in public health. Genome Med 13, 121 (2021). https://doi.org/10.1186/s13073-021-00934-7
Genomics-informed responses in the elimination of COVID-19 in Victoria, Australia: an observational, genomic epidemiological study
Courtney R Lane, Norelle L Sherry, Ashleigh F Porter, Sebastian Duchene, Kristy Horan, Patiyan Andersson, Mathilda Wilmot, Annabelle Turner, Sally Dougall, Sandra A Johnson, Michelle Sait, Anders Gonçalves da Silva, Susan A Ballard, Tuyet Hoang, Timothy P Stinear, Leon Caly, Vitali Sintchenko, Rikki Graham, Jamie McMahon, David Smith, Lex EX Leong, Ella M Meumann, Louise Cooley, Benjamin Schwessinger, William Rawlinson, Sebastiaan J van Hal, Nicola Stephens, Mike Catton, Clare Looker, Simon Crouch, Brett Sutton, Charles Alpren, Deborah A Williamson*, Torsten Seemann*, Benjamin P Howden*
Lancet Public Health. 2021 July 9. https://doi.org/10.1016/S2468-2667(21)00133-X
Surveillance for SARS-CoV-2 variants of concern in the Australian context
Andersson P, Sherry NL, Howden BP. Surveillance for SARS-CoV-2 variants of concern in the Australian context. Med J Aust 2021; https://www.mja.com.au/journal/2021/surveillance-sars-cov-2-variants-concern-australian-context [Preprint, 7 May 2021].
2020
Complete microbial genomes for public health in Australia and the Southwest Pacific
Baines, SL, Gonçalves da Silva, A, Carter, G, Jennison, AV, Rathnayake, I, Graham, RM, Sintchenko, V, Wang, Q, Rockett, RJ, Timms, VJ, Martinez, E, Ballard, S, Tomita, T, Isles, N, Horan, KA, Pitchers, W, Stinear, TP, Williamson, DA, Howden, BP & Seemann, T. Communicable Diseases Genomics Network.
bioRxiv. 2020 Nov 12. https://doi.org/10.1099/mgen.0.000471
Tracking the COVID-19 pandemic in Australia using genomics
Seemann T, Lane CR, Sherry NL, Duchene S, Gonçalves da Silva A, Caly L, Sait M, Ballard SA, Horan K, Schultz MB, Hoang T, Easton M, Dougall S, Stinear TP, Druce J, Catton M, Sutton B, van Diemen A, Alpren C, Williamson DA, Howden BP.
Nat Comm. 2020 Sep 1. doi: 10.1038/s41467-020-18314-x.
Molecular characterization of Campylobacter spp. recovered from beef, chicken, lamb and pork products at retail in Australia.
Wallace RL, Bulach DM, Jennison AV, Valcanis M, McLure A, Smith JJ, Graham T, Saputra T, Firestone S, Symes S, Waters N, Stylianopoulos A, Kirk MD, Glass K.
PLoS One. 2020 Jul 30;15(7):e0236889. doi: 10.1371/journal.pone.0236889. eCollection 2020.
Search and Contain: Impact of an integrated genomic and epidemiological surveillance and response program for control of carbapenemase-producing Enterobacterales.
Lane CR, Brett J, Schultz M, Gorrie CL, Stevens K, Cameron DRM, St George S, van Diemen A, Easton M, Stuart RL, Sait M, Peleg AY, Stewardson AJ, Cheng AC, Spelman DW, Waters MJ, Ballard SA, Sherry NL, Williamson DA, Romanes F, Sutton B, Kwong JC, Seemann T, Goncalves da Silva A, Stephens N, Howden BP.
Clin Infect Dis. 2020 Jul 14:ciaa972. doi: 10.1093/cid/ciaa972. Online ahead of print.
Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling.
Rockett RJ, Arnott A, Lam C, Sadsad R, Timms V, Gray KA, Eden JS, Chang S, Gall M, Draper J, Sim EM, Bachmann NL, Carter I, Basile K, Byun R, O'Sullivan MV, Chen SC, Maddocks S, Sorrell TC, Dwyer DE, Holmes EC, Kok J, Prokopenko M, Sintchenko V.
Nat Med. 2020 Jul 9. doi: 10.1038/s41591-020-1000-7. Online ahead of print.
Genomic surveillance enables suitability assessment of Salmonella gene targets used for culture-independent diagnostic testing.
Rockett RJ, Arnott A, Wang Q, Howard P, Sintchenko V.
J Clin Microbiol. 2020 Jun 24:JCM.00038-20. doi: 10.1128/JCM.00038-20. Online ahead of print.
Isolation and rapid sharing of the 2019 novel coronavirus (SARS-CoV-2) from the first patient diagnosed with COVID-19 in Australia.
Caly L, Druce J, Roberts J, Bond K, Tran T, Kostecki R, Yoga Y, Naughton W, Taiaroa G, Seemann T, Schultz MB, Howden BP, Korman TM, Lewin SR, Williamson DA, Catton MG.
Med J Aust. 2020 Jun;212(10):459-462. doi: 10.5694/mja2.50569. Epub 2020 Apr 1.
Incursions of Candida auris into Australia, 2018.
Lane CR, Seemann T, Worth LJ, Easton M, Pitchers W, Wong J, Cameron D, Azzato F, Bartolo R, Mateevici C, Marshall C, Slavin MA, Howden BP, Williamson DA.
Emerg Infect Dis. 2020 Jun;26(6):1326-1328. doi: 10.3201/eid2606.190936. Epub 2020 Jun 17.
Editorial: Pathogen Genomics: Empowering Infectious Disease Surveillance and Outbreak Investigations.
Struelens MJ, Sintchenko V.
Front Public Health. 2020 May 19;8:179. doi: 10.3389/fpubh.2020.00179. eCollection 2020
Genetic Heterogeneity of Australian Candida auris Isolates: Insights From a Nonoutbreak Setting Using Whole-Genome Sequencing.
Biswas C, Wang Q, van Hal SJ, Eyre DW, Hudson B, Halliday CL, Mazsewska K, Kizny Gordon A, Lee A, Irinyi L, Heath CH, Chakrabarti A, Govender NP, Meyer W, Sintchenko V, Chen SC.
Open Forum Infect Dis. 2020 May 7;7(5):ofaa158. doi: 10.1093/ofid/ofaa158. eCollection 2020 May.
Multilevel genome typing: genomics-guided scalable resolution typing of microbial pathogens.
Payne M, Kaur S, Wang Q, Hennessy D, Luo L, Octavia S, Tanaka MM, Sintchenko V, Lan R.
Euro Surveill. 2020 May;25(20):1900519. doi: 10.2807/1560-7917.ES.2020.25.20.1900519.
Genomic Investigation Reveals Contaminated Detergent as the Source of an Extended-Spectrum-β-Lactamase-Producing Klebsiella michiganensis Outbreak in a Neonatal Unit.
Chapman P, Forde BM, Roberts LW, Bergh H, Vesey D, Jennison AV, Moss S, Paterson DL, Beatson SA, Harris PNA.
J Clin Microbiol. 2020 Apr 23;58(5):e01980-19. doi: 10.1128/JCM.01980-19. Print 2020 Apr 23.
An emergent clade of SARS-CoV-2 linked to returned travellers from Iran.
Eden JS, Rockett R, Carter I, Rahman H, de Ligt J, Hadfield J, Storey M, Ren X, Tulloch R, Basile K, Wells J, Byun R, Gilroy N, O'Sullivan MV, Sintchenko V, Chen SC, Maddocks S, Sorrell TC, Holmes EC, Dwyer DE, Kok J; 2019-nCoV Study Group.
Virus Evol. 2020 Apr 10;6(1):veaa027. doi: 10.1093/ve/veaa027. eCollection 2020 Jan.
Genomic Characterization of Recent and Historic Meningococcal Serogroup E Invasive Disease in Australia: A Case Series.
Thangarajah D, Guglielmino CJD, Lambert SB, Khandaker G, Vasant BR, Malo JA, Smith HV, Jennison AV.
Clin Infect Dis. 2020 Apr 10;70(8):1761-1763. doi: 10.1093/cid/ciz767.
Optimization of sample preparation for culture-independent sequencing of Bordetella pertussis.
Fong W, Rockett R, Timms V, Sintchenko V.
Microb Genom. 2020 Mar;6(3):e000332. doi: 10.1099/mgen.0.000332.
J Clin Virol. 2020 Jan;122:104216. doi: 10.1016/j.jcv.2019.104216. Epub 2019 Nov 17.
Two carbapenemase-producing Enterobacteriaceae outbreaks detected retrospectively by whole-genome sequencing at an Australian tertiary hospital
Marmor A, Daveson K, Harley D, Coatsworth N, Kennedy K.
Infect Dis Health. 2020 Feb;25(1):30-33. doi: 10.1016/j.idh.2019.08.005. Epub 2019 Oct 11.
Key Transitions in the Evolution of Rapid and Slow Growing Mycobacteria Identified by Comparative Genomics.
Bachmann NL, Salamzade R, Manson AL, Whittington R, Sintchenko V, Earl AM, Marais BJ.
Front Microbiol. 2020 Jan 21;10:3019. doi: 10.3389/fmicb.2019.03019. eCollection 2019.
Genomic analysis of carbapenemase-producing Enterobacteriaceae in Queensland reveals widespread transmission of bla IMP-4 on an IncHI2 plasmid.
Roberts LW, Catchpoole E, Jennison AV, Bergh H, Hume A, Heney C, George N, Paterson DL, Schembri MA, Beatson SA, Harris PNA.
Microb Genom. 2020 Jan;6(1):e000321. doi: 10.1099/mgen.0.000321. Epub 2019 Dec 19.
Next generation sequencing of human enterovirus strains from an outbreak of enterovirus A71 shows applicability to outbreak investigations
Stelzer-Braid S, Wynn M, Chatoor R, Scotch M, Ramachandran V, Teoh HL, Farrar MA, Sampaio H, Andrews PI, Craig ME, MacIntyre CR, Varadhan H, Kesson A, Britton PN, Newcombe J, Rawlinson WD.
J Clin Virol. 2020 Jan;122:104216. doi: 10.1016/j.jcv.2019.104216. Epub 2019 Nov 17.
2019
Extensively Drug-Resistant Shigellosis in Australia among Men Who Have Sex with Men.
Williamson D, Ingle D, Howden B.
N Engl J Med. 2019 Dec 19;381(25):2477-2479. doi: 10.1056/NEJMc1910648.
Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.
Hunt M, Bradley P, Lapierre SG, Heys S, Thomsit M, Hall MB, Malone KM, Wintringer P, Walker TM, Cirillo DM, Comas I, Farhat MR, Fowler P, Gardy J, Ismail N, Kohl TA, Mathys V, Merker M, Niemann S, Omar SV, Sintchenko V, Smith G, van Soolingen D, Supply P, Tahseen S, Wilcox M, Arandjelovic I, Peto TEA, Crook DW, Iqbal Z.
Wellcome Open Res. 2019 Dec 2;4:191. doi: 10.12688/wellcomeopenres.15603.1. eCollection 2019.
Enhancing genomics-based outbreak detection of endemic Salmonella enterica serovar Typhimurium using dynamic thresholds.
Payne M, Octavia S, Luu LDW, Sotomayor-Castillo C, Wang Q, Tay ACY, Sintchenko V, Tanaka MM, Lan R.
Microb Genom. 2019 Nov 4. doi: 10.1099/mgen.0.000310. Online ahead of print.
Identification of an Unusual 16S rRNA Mutation in Neisseria gonorrhoeae.
Guglielmino CJD, Appleton S, Vohra R, Jennison AV.
J Clin Microbiol. 2019 Oct 23;57(11):e01337-19. doi: 10.1128/JCM.01337-19. Print 2019 Nov.
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.
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.
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.
Genome Sequences of Enteroinvasive Escherichia coli Sequence Type 6, 99, and 311 Strains Acquired in Asia Pacific.
Dhakal R, Wang Q, Howard P, Sintchenko V.
Microbiol Resour Announc. 2019 Sep 5;8(36):e00944-19. doi: 10.1128/MRA.00944-19.
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):e00573-19. doi: 10.1128/JCM.00573-19. Print 2019 Sep.
Rapid diagnosis of Capnocytophaga canimorsus septic shock in an immunocompetent individual using real-time Nanopore sequencing: a case report.
Bialasiewicz S, Duarte TPS, Nguyen SH, Sukumaran V, Stewart A, Appleton S, Pitt ME, Bainomugisa A, Jennison AV, Graham R, Coin LJM, Hajkowicz K.
BMC Infect Dis. 2019 Jul 24;19(1):660. doi: 10.1186/s12879-019-4173-2.
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):e000268. doi: 10.1099/mgen.0.000268. Epub 2019 May 20.
Vancomycin-resistant Enterococcus (VRE) outbreak in a neonatal intensive care unit and special care nursery at a tertiary-care hospital in Australia-A retrospective case-control study
Andersson P, Beckingham W, Gorrie CL, Kennedy K, Daveson K, Ballard SA, Chen M, Roper K, Coatsworth N.
Infect Control Hosp Epidemiol. 2019 May;40(5):551-558. doi: 10.1017/ice.2019.41. Epub 2019 Mar 14.
The importance of public health genomics for ensuring health security for Australia.
Williamson DA, Kirk MD, Sintchenko V, Howden BP.
Med J Aust. 2019 Apr;210(7):295-297.e1. doi: 10.5694/mja2.50063. Epub 2019 Mar 19.
Genetic characterisation of variants of the virulence plasmid, pSLT, in Salmonella enterica serovar Typhimurium provides evidence of a variety of evolutionary directions consistent with vertical rather than horizontal transmission.
Hiley L, Graham RMA, Jennison AV.
PLoS One. 2019 Apr 11;14(4):e0215207. doi: 10.1371/journal.pone.0215207. eCollection 2019.
Cross-Border Movement of Highly Drug-Resistant Mycobacterium tuberculosis from Papua New Guinea to Australia through Torres Strait Protected Zone, 2010-2015.
Bainomugisa A, Pandey S, Donnan E, Simpson G, Foster J, Lavu E, Hiasihri S, McBryde ES, Moke R, Vincent S, Sintchenko V, Marais BJ, Coin LJM, Coulter C.
Emerg Infect Dis. 2019 Mar;25(3):406-415. doi: 10.3201/eid2503.181003.
Genetic relatedness of ceftriaxone-resistant and high-level azithromycin resistant Neisseria gonorrhoeae cases, United Kingdom and Australia, February to April 2018.
Jennison AV, Whiley D, Lahra MM, Graham RM, Cole MJ, Hughes G, Fifer H, Andersson M, Edwards A, Eyre D.
Euro Surveill. 2019 Feb;24(8):1900118. doi: 10.2807/1560-7917.ES.2019.24.8.1900118.
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):e00529-18. doi: 10.1128/mSphere.00529-18.
2018
Whole-genome sequencing reveals genetic signature of bedaquiline resistance in a clinical isolate of Mycobacterium tuberculosis.
Chawla K, Martinez E, Kumar A, Shenoy VP, Sintchenko V.
J Glob Antimicrob Resist. 2018 Dec;15:103-104. doi: 10.1016/j.jgar.2018.09.006. Epub 2018 Sep 21.
Advances in Clinical Sample Preparation for Identification and Characterization of Bacterial Pathogens Using Metagenomics.
Bachmann NL, Rockett RJ, Timms VJ, Sintchenko V.
Front Public Health. 2018 Dec 12;6:363. doi: 10.3389/fpubh.2018.00363. eCollection 2018.
Whole Genome Sequencing of Australian Candida glabrata Isolates Reveals Genetic Diversity and Novel Sequence Types.
Biswas C, Marcelino VR, Van Hal S, Halliday C, Martinez E, Wang Q, Kidd S, Kennedy K, Marriott D, Morrissey CO, Arthur I, Weeks K, Slavin MA, Sorrell TC, Sintchenko V, Meyer W, Chen SC.
Front Microbiol. 2018 Dec 3;9:2946. doi: 10.3389/fmicb.2018.02946. eCollection 2018.
Genome-wide comparison of Corynebacterium diphtheriae isolates from Australia identifies differences in the Pan-genomes between respiratory and cutaneous strains.
Timms VJ, Nguyen T, Crighton T, Yuen M, Sintchenko V.
BMC Genomics. 2018 Dec 4;19(1):869. doi: 10.1186/s12864-018-5147-2.
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.
Genome-wide analysis of Streptococcus pneumoniae serogroup 19 in the decade after the introduction of pneumococcal conjugate vaccines in Australia.
Rockett RJ, Oftadeh S, Bachmann NL, Timms VJ, Kong F, Gilbert GL, Sintchenko V.
Sci Rep. 2018 Nov 16;8(1):16969. doi: 10.1038/s41598-018-35270-1.
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.
Mutations associated with in vitro resistance to bedaquiline in Mycobacterium tuberculosis isolates in Australia.
Martinez E, Hennessy D, Jelfs P, Crighton T, Chen SC, Sintchenko V.
Tuberculosis (Edinb). 2018 Jul;111:31-34. doi: 10.1016/j.tube.2018.04.007. Epub 2018 Apr 25.
Fulminant meningococcal sepsis due to non-groupable Neisseria meningitidis in a patient receiving eculizumab.
Hall V, Pai Mangalore R, He S, Stevens K, Trubiano JA, Holmes NE, Howden BP, Kwong JC.
Med J Aust. 2018 Jun 18;208(11):478-479.
Recurrence of tuberculosis in a low-incidence setting: a retrospective cross-sectional study augmented by whole genome sequencing.
Parvaresh L, Crighton T, Martinez E, Bustamante A, Chen S, Sintchenko V.
BMC Infect Dis. 2018 Jun 7;18(1):265. doi: 10.1186/s12879-018-3164-z.
Relentless spread and adaptation of non-typeable vanA vancomycin-resistant Enterococcus faecium: a genome-wide investigation.
van Hal SJ, Beukers AG, Timms VJ, Ellem JA, Taylor P, Maley MW, Newton PJ, Ferguson JK, Lee A, Chen SC, Sintchenko V.
J Antimicrob Chemother. 2018 Jun 1;73(6):1487-1491. doi: 10.1093/jac/dky074.
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.
Multidrug-Resistant Salmonella enterica 4,[5],12:i:- Sequence Type 34, New South Wales, Australia, 2016-2017.
Arnott A, Wang Q, Bachmann N, Sadsad R, Biswas C, Sotomayor C, Howard P, Rockett R, Wiklendt A, Iredell JR, Sintchenko V.
Emerg Infect Dis. 2018 Apr;24(4):751-753. doi: 10.3201/eid2404.171619.
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):e02612-17. doi: 10.1128/AEM.02612-17. Print 2018 Apr 15.
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.
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.
Genomic epidemiology and population structure of Neisseria gonorrhoeae from remote highly endemic Western Australian populations
Al Suwayyid BA, Coombs GW, Speers DJ, Pearson J, Wise MJ, Kahler CM.
BMC Genomics. 2018 Feb 27;19(1):165. doi: 10.1186/s12864-018-4557-5.
Genome Sequencing Links Persistent Outbreak of Legionellosis in Sydney (New South Wales, Australia) to an Emerging Clone of Legionella pneumophila Sequence Type 211.
Timms VJ, Rockett R, Bachmann NL, Martinez E, Wang Q, Chen SC, Jeoffreys N, Howard PJ, Smith A, Adamson S, Gilmour R, Sheppeard V, Sintchenko V.
Appl Environ Microbiol. 2018 Feb 14;84(5):e02020-17. doi: 10.1128/AEM.02020-17. Print 2018 Mar 1.
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.
Comparative genomics identifies distinct lineages of S. Enteritidis from Queensland, Australia.
Graham RMA, Hiley L, Rathnayake IU, Jennison AV.
PLoS One. 2018 Jan 16;13(1):e0191042. doi: 10.1371/journal.pone.0191042. eCollection 2018.
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.
2017
Whole Genome Sequencing of Candida glabrata for Detection of Markers of Antifungal Drug Resistance.
Biswas C, Chen SC, Halliday C, Martinez E, Rockett RJ, Wang Q, Timms VJ, Dhakal R, Sadsad R, Kennedy KJ, Playford G, Marriott DJ, Slavin MA, Sorrell TC, Sintchenko V.
J Vis Exp. 2017 Dec 28;(130):56714. doi: 10.3791/56714.
Detection of Spotted Fever Group Rickettsia DNA by Deep Sequencing.
Graham RMA, Donohue S, McMahon J, Jennison AV.
Emerg Infect Dis. 2017 Nov;23(11):1911-1913. doi: 10.3201/eid2311.170474.
Towards a Universal Molecular Microbiological Test.
Allcock RJN, Jennison AV, Warrilow D.
J Clin Microbiol. 2017 Nov;55(11):3175-3182. doi: 10.1128/JCM.01155-17. Epub 2017 Aug 23.
Mild Illness during Outbreak of Shiga Toxin-Producing Escherichia coli O157 Infections Associated with Agricultural Show, Australia.
Vasant BR, Stafford RJ, Jennison AV, Bennett SM, Bell RJ, Doyle CJ, Young JR, Vlack SA, Titmus P, El Saadi D, Jarvinen KAJ, Coward P, Barrett J, Staples M, Graham RMA, Smith HV, Lambert SB.
Emerg Infect Dis. 2017 Oct;23(10):1686-1689. doi: 10.3201/eid2310.161836.
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):e01482-17. doi: 10.1128/AEM.01482-17. Print 2017 Nov 1.
Identification of genetic markers of resistance to echinocandins, azoles and 5-fluorocytosine in Candida glabrata by next-generation sequencing: a feasibility study.
Biswas C, Chen SC, Halliday C, Kennedy K, Playford EG, Marriott DJ, Slavin MA, Sorrell TC, Sintchenko V.
Clin Microbiol Infect. 2017 Sep;23(9):676.e7-676.e10. doi: 10.1016/j.cmi.2017.03.014. Epub 2017 Mar 23.
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.
Epidemiology and whole genome sequencing of an ongoing point-source Salmonella Agona outbreak associated with sushi consumption in western Sydney, Australia 2015.
Thompson CK, Wang Q, Bag SK, Franklin N, Shadbolt CT, Howard P, Fearnley EJ, Quinn HE, Sintchenko V, Hope KG.
Epidemiol Infect. 2017 Jul;145(10):2062-2071. doi: 10.1017/S0950268817000693. Epub 2017 May 2.
Genetic characterization of a Neisseria meningitidis cluster in Queensland, Australia.
Abady NR, Guglielmino CJD, Graham RM, Adelskov J, Smith HV, Patel BKC, Jennison AV.
Can J Microbiol. 2017 Jul;63(7):644-647. doi: 10.1139/cjm-2017-0017. Epub 2017 May 1.
Characterisation of invasive clinical Haemophilus influenzae isolates in Queensland, Australia using whole-genome sequencing.
Staples M, Graham RMA, Jennison AV.
Epidemiol Infect. 2017 Jun;145(8):1727-1736. doi: 10.1017/S0950268817000450. Epub 2017 Mar 6.
Analysis of the Listeria monocytogenes Population Structure among Isolates from 1931 to 2015 in Australia.
Jennison AV, Masson JJ, Fang NX, Graham RM, Bradbury MI, Fegan N, Gobius KS, Graham TM, Guglielmino CJ, Brown JL, Fox EM.
Front Microbiol. 2017 Apr 6;8:603. doi: 10.3389/fmicb.2017.00603. eCollection 2017.
Mycobacterium chimaera Spread from Heating and Cooling Units in Heart Surgery.
Williamson D, Howden B, Stinear T.
N Engl J Med. 2017 Feb 9;376(6):600-602. doi: 10.1056/NEJMc1612023.
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.
Sequence Analysis of Toxin Gene-Bearing Corynebacterium diphtheriae Strains, Australia.
Doyle CJ, Mazins A, Graham RM, Fang NX, Smith HV, Jennison AV.
Emerg Infect Dis. 2017 Jan;23(1):105-107. doi: 10.3201/eid2301.160584.
2016
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.
A large outbreak of Campylobacter jejuni infection in a university college caused by chicken liver pâté, Australia, 2013.
Moffatt CR, Greig A, Valcanis M, Gao W, Seemann T, Howden BP, Kirk MD.
Epidemiol Infect. 2016 Oct;144(14):2971-2978. doi: 10.1017/S0950268816001187. Epub 2016 Jun 16.
Whole Genome Sequencing Demonstrates Limited Transmission within Identified Mycobacterium tuberculosis Clusters in New South Wales, Australia.
Gurjav U, Outhred AC, Jelfs P, McCallum N, Wang Q, Hill-Cawthorne GA, Marais BJ, Sintchenko V.
PLoS One. 2016 Oct 13;11(10):e0163612. doi: 10.1371/journal.pone.0163612. eCollection 2016.
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.
Whole genome sequencing of Salmonella Typhimurium illuminates distinct outbreaks caused by an endemic multi-locus variable number tandem repeat analysis type in Australia, 2014.
Phillips A, Sotomayor C, Wang Q, Holmes N, Furlong C, Ward K, Howard P, Octavia S, Lan R, Sintchenko V.
BMC Microbiol. 2016 Sep 15;16:211. doi: 10.1186/s12866-016-0831-3.
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.
Rising incidence of invasive meningococcal disease caused by Neisseria meningitidis serogroup W in Victoria.
Bond KA, Stevens K, Bulach D, Carville K, Ong KS, Howden BP.
Med J Aust. 2016 Apr 18;204(7):265-6. doi: 10.5694/mja15.01222.
Whole-genome sequencing of Mycobacterium tuberculosis for rapid diagnostics: feasibility of a decentralised model.
Martinez E, Bustamante A, Menon R, Wang Q, Jelfs P, Marais B, Chen SC, Sintchenko V.
Lancet Respir Med. 2016 Apr;4(4):e13-4. doi: 10.1016/S2213-2600(16)00092-8. Epub 2016 Apr 4.
2015
It Is Not All about Single Nucleotide Polymorphisms: Comparison of Mobile Genetic Elements and Deletions in Listeria monocytogenes Genomes Links Cases of Hospital-Acquired Listeriosis to the Environmental Source.
Wang Q, Holmes N, Martinez E, Howard P, Hill-Cawthorne G, Sintchenko V.
J Clin Microbiol. 2015 Nov;53(11):3492-500. doi: 10.1128/JCM.00202-15. Epub 2015 Aug 26.
Genomic Epidemiology of Clostridium botulinum Isolates from Temporally Related Cases of Infant Botulism in New South Wales, Australia.
McCallum N, Gray TJ, Wang Q, Ng J, Hicks L, Nguyen T, Yuen M, Hill-Cawthorne GA, Sintchenko V.
J Clin Microbiol. 2015 Sep;53(9):2846-53. doi: 10.1128/JCM.00143-15. Epub 2015 Jun 24.
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.
J Clin Microbiol. 2016 Feb;54(2):333-42. doi: 10.1128/JCM.02344-15. Epub 2015 Nov 25.