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Identification and Discrimination of Chlamydia trachomatis Ocular and Urogenital Strains and Major Phylogenetic Lineages by CtGEM Typing, A Double-Locus Genotyping Method.

Holt DC, Andersson P, Buckley C, Whiley DM, Giffard PM.

Methods Mol Biol. 2019;2042:87-122. doi: 10.1007/978-1-4939-9694-0_8.


Author Correction: Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics.

Davies MR, McIntyre L, Mutreja A, Lacey JA, Lees JA, Towers RJ, Duchêne S, Smeesters PR, Frost HR, Price DJ, Holden MTG, David S, Giffard PM, Worthing KA, Seale AC, Berkley JA, Harris SR, Rivera-Hernandez T, Berking O, Cork AJ, Torres RSLA, Lithgow T, Strugnell RA, Bergmann R, Nitsche-Schmitz P, Chhatwal GS, Bentley SD, Fraser JD, Moreland NJ, Carapetis JR, Steer AC, Parkhill J, Saul A, Williamson DA, Currie BJ, Tong SYC, Dougan G, Walker MJ.

Nat Genet. 2019 Aug;51(8):1295. doi: 10.1038/s41588-019-0482-z.


Concerns for efficacy of a 30-valent M-protein-based Streptococcus pyogenes vaccine in regions with high rates of rheumatic heart disease.

Giffard PM, Tong SYC, Holt DC, Ralph AP, Currie BJ.

PLoS Negl Trop Dis. 2019 Jul 3;13(7):e0007511. doi: 10.1371/journal.pntd.0007511. eCollection 2019 Jul.


Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics.

Davies MR, McIntyre L, Mutreja A, Lacey JA, Lees JA, Towers RJ, Duchêne S, Smeesters PR, Frost HR, Price DJ, Holden MTG, David S, Giffard PM, Worthing KA, Seale AC, Berkley JA, Harris SR, Rivera-Hernandez T, Berking O, Cork AJ, Torres RSLA, Lithgow T, Strugnell RA, Bergmann R, Nitsche-Schmitz P, Chhatwal GS, Bentley SD, Fraser JD, Moreland NJ, Carapetis JR, Steer AC, Parkhill J, Saul A, Williamson DA, Currie BJ, Tong SYC, Dougan G, Walker MJ.

Nat Genet. 2019 Jun;51(6):1035-1043. doi: 10.1038/s41588-019-0417-8. Epub 2019 May 27. Erratum in: Nat Genet. 2019 Jul 19;:.


Global Scale Dissemination of ST93: A Divergent Staphylococcus aureus Epidemic Lineage That Has Recently Emerged From Remote Northern Australia.

van Hal SJ, Steinig EJ, Andersson P, Holden MTG, Harris SR, Nimmo GR, Williamson DA, Heffernan H, Ritchie SR, Kearns AM, Ellington MJ, Dickson E, de Lencastre H, Coombs GW, Bentley SD, Parkhill J, Holt DC, Giffard PM, Tong SYC.

Front Microbiol. 2018 Jul 9;9:1453. doi: 10.3389/fmicb.2018.01453. eCollection 2018.


Investigation of trimethoprim/sulfamethoxazole resistance in an emerging sequence type 5 methicillin-resistant Staphylococcus aureus clone reveals discrepant resistance reporting.

Harris TM, Bowen AC, Holt DC, Sarovich DS, Stevens K, Currie BJ, Howden BP, Carapetis JR, Giffard PM, Tong SYC.

Clin Microbiol Infect. 2018 Sep;24(9):1027-1029. doi: 10.1016/j.cmi.2018.04.020. Epub 2018 May 1. No abstract available.


CtGEM typing: Discrimination of Chlamydia trachomatis ocular and urogenital strains and major evolutionary lineages by high resolution melting analysis of two amplified DNA fragments.

Giffard PM, Andersson P, Wilson J, Buckley C, Lilliebridge R, Harris TM, Kleinecke M, O'Grady KF, Huston WM, Lambert SB, Whiley DM, Holt DC.

PLoS One. 2018 Apr 10;13(4):e0195454. doi: 10.1371/journal.pone.0195454. eCollection 2018.


Primary health clinic toilet/bathroom surface swab sampling can indicate community profile of sexually transmitted infections.

Giffard PM, Su JY, Andersson P, Holt DC.

PeerJ. 2017 Jun 22;5:e3487. doi: 10.7717/peerj.3487. eCollection 2017.


Contaminated fingers: a potential cause of Chlamydia trachomatis-positive urine specimens.

Giffard PM, Lilliebridge RA, Wilson J, Murray G, Phillips S, Tabrizi SN, Garland SM, Martin L, Singh G, Tong SYC, Holt DC, Andersson P.

Sex Transm Infect. 2018 Feb;94(1):32-36. doi: 10.1136/sextrans-2016-053081. Epub 2017 Jun 9.


Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion.

Hadfield J, Harris SR, Seth-Smith HMB, Parmar S, Andersson P, Giffard PM, Schachter J, Moncada J, Ellison L, Vaulet MLG, Fermepin MR, Radebe F, Mendoza S, Ouburg S, Morré SA, Sachse K, Puolakkainen M, Korhonen SJ, Sonnex C, Wiggins R, Jalal H, Brunelli T, Casprini P, Pitt R, Ison C, Savicheva A, Shipitsyna E, Hadad R, Kari L, Burton MJ, Mabey D, Solomon AW, Lewis D, Marsh P, Unemo M, Clarke IN, Parkhill J, Thomson NR.

Genome Res. 2017 Jul;27(7):1220-1229. doi: 10.1101/gr.212647.116. Epub 2017 Jun 6.


Whole genome sequencing to investigate a putative outbreak of the virulent community-associated methicillin-resistant Staphylococcus aureus ST93 clone in a remote Indigenous community.

Meumann EM, Andersson P, Yeaman F, Oldfield S, Lilliebridge R, Bentley SD, Krause V, Beaman M, Currie BJ, Holt DC, Giffard PM, Tong SYC.

Microb Genom. 2016 Dec 12;2(12):e000098. doi: 10.1099/mgen.0.000098. eCollection 2016 Dec.


What does Chlamydia trachomatis detection in a urogenital specimen from a young child mean?

Giffard PM, Singh G, Garland SM.

Sex Transm Infect. 2017 Jun;93(4):236-237. doi: 10.1136/sextrans-2015-052473. Epub 2016 Apr 15. No abstract available.


Chlamydia trachomatis from Australian Aboriginal people with trachoma are polyphyletic composed of multiple distinctive lineages.

Andersson P, Harris SR, Smith HMBS, Hadfield J, O'Neill C, Cutcliffe LT, Douglas FP, Asche LV, Mathews JD, Hutton SI, Sarovich DS, Tong SYC, Clarke IN, Thomson NR, Giffard PM.

Nat Commun. 2016 Feb 25;7:10688. doi: 10.1038/ncomms10688.


Whole genome sequencing reveals extensive community-level transmission of group A Streptococcus in remote communities.

Bowen AC, Harris T, Holt DC, Giffard PM, Carapetis JR, Campbell PT, McVERNON J, Tong SY.

Epidemiol Infect. 2016 Jul;144(9):1991-8. doi: 10.1017/S095026881500326X. Epub 2016 Feb 1.


Differing epidemiology of two major healthcare-associated meticillin-resistant Staphylococcus aureus clones.

Jeremiah CJ, Kandiah JP, Spelman DW, Giffard PM, Coombs GW, Jenney AW, Tong SY.

J Hosp Infect. 2016 Feb;92(2):183-90. doi: 10.1016/j.jhin.2015.10.023. Epub 2015 Nov 21.


Chlamydia trachomatis genotypes in a cross-sectional study of urogenital samples from remote Northern and Central Australia.

Giffard PM, Brenner NC, Tabrizi SN, Garland SM, Holt DC, Andersson P, Lilliebridge RA, Tong SY, Karimi M, Boylan P, Ryder N, Johns T, Singh G.

BMJ Open. 2016 Jan 6;6(1):e009624. doi: 10.1136/bmjopen-2015-009624.


Invasive Staphylococcus aureus Infections in Children in Tropical Northern Australia.

Engelman D, Hofer A, Davis JS, Carapetis JR, Baird RW, Giffard PM, Holt DC, Tong SY.

J Pediatric Infect Dis Soc. 2014 Dec;3(4):304-11. doi: 10.1093/jpids/piu013. Epub 2014 Mar 26.


Multisite Direct Determination of the Potential for Environmental Contamination of Urine Samples Used for Diagnosis of Sexually Transmitted Infections.

Andersson P, Tong SY, Lilliebridge RA, Brenner NC, Martin LM, Spencer E, Delima J, Singh G, McCann F, Hudson C, Johns T, Giffard PM.

J Pediatric Infect Dis Soc. 2014 Sep;3(3):189-96. doi: 10.1093/jpids/pit085. Epub 2013 Dec 19.


Progressive increase in community-associated methicillin-resistant Staphylococcus aureus in Indigenous populations in northern Australia from 1993 to 2012.

Tong SY, Varrone L, Chatfield MD, Beaman M, Giffard PM.

Epidemiol Infect. 2015 May;143(7):1519-23. doi: 10.1017/S0950268814002611. Epub 2014 Oct 10.


Novel staphylococcal species that form part of a Staphylococcus aureus-related complex: the non-pigmented Staphylococcus argenteus sp. nov. and the non-human primate-associated Staphylococcus schweitzeri sp. nov.

Tong SY, Schaumburg F, Ellington MJ, Corander J, Pichon B, Leendertz F, Bentley SD, Parkhill J, Holt DC, Peters G, Giffard PM.

Int J Syst Evol Microbiol. 2015 Jan;65(Pt 1):15-22. doi: 10.1099/ijs.0.062752-0. Epub 2014 Sep 30.


DNA concentration can specify DNA melting point in a high-resolution melting analysis master mix.

Ng JW, Holt DC, Andersson P, Giffard PM.

Clin Chem. 2014 Feb;60(2):414-6. doi: 10.1373/clinchem.2013.215582. Epub 2013 Dec 9. No abstract available.


Burkholderia pseudomallei isolates from Sarawak, Malaysian Borneo, are predominantly susceptible to aminoglycosides and macrolides.

Podin Y, Sarovich DS, Price EP, Kaestli M, Mayo M, Hii K, Ngian H, Wong S, Wong I, Wong J, Mohan A, Ooi M, Fam T, Wong J, Tuanyok A, Keim P, Giffard PM, Currie BJ.

Antimicrob Agents Chemother. 2014;58(1):162-6. doi: 10.1128/AAC.01842-13. Epub 2013 Oct 21.


Extensive diversity of Streptococcus pyogenes in a remote human population reflects global-scale transmission rather than localised diversification.

Towers RJ, Carapetis JR, Currie BJ, Davies MR, Walker MJ, Dougan G, Giffard PM.

PLoS One. 2013 Sep 16;8(9):e73851. doi: 10.1371/journal.pone.0073851. eCollection 2013.


Sequences of multiple bacterial genomes and a Chlamydia trachomatis genotype from direct sequencing of DNA derived from a vaginal swab diagnostic specimen.

Andersson P, Klein M, Lilliebridge RA, Giffard PM.

Clin Microbiol Infect. 2013 Sep;19(9):E405-8. doi: 10.1111/1469-0691.12237. Epub 2013 May 7.


Virulence of endemic nonpigmented northern Australian Staphylococcus aureus clone (clonal complex 75, S. argenteus) is not augmented by staphyloxanthin.

Tong SY, Sharma-Kuinkel BK, Thaden JT, Whitney AR, Yang SJ, Mishra NN, Rude T, Lilliebridge RA, Selim MA, Ahn SH, Holt DC, Giffard PM, Bayer AS, Deleo FR, Fowler VG Jr.

J Infect Dis. 2013 Aug 1;208(3):520-7. doi: 10.1093/infdis/jit173. Epub 2013 Apr 18.


Community-associated meticillin-resistant Staphylococcus aureus carriage in hospitalized patients in tropical northern Australia.

Brennan L, Lilliebridge RA, Cheng AC, Giffard PM, Currie BJ, Tong SY.

J Hosp Infect. 2013 Mar;83(3):205-11. doi: 10.1016/j.jhin.2012.10.014. Epub 2013 Jan 15.


Microbiological applications of high-resolution melting analysis.

Tong SY, Giffard PM.

J Clin Microbiol. 2012 Nov;50(11):3418-21. doi: 10.1128/JCM.01709-12. Epub 2012 Aug 8. Review.


Guidelines for reporting novel mecA gene homologues.

Ito T, Hiramatsu K, Tomasz A, de Lencastre H, Perreten V, Holden MT, Coleman DC, Goering R, Giffard PM, Skov RL, Zhang K, Westh H, O'Brien F, Tenover FC, Oliveira DC, Boyle-Vavra S, Laurent F, Kearns AM, Kreiswirth B, Ko KS, Grundmann H, Sollid JE, John JF Jr, Daum R, Soderquist B, Buist G; International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements (IWG-SCC).

Antimicrob Agents Chemother. 2012 Oct;56(10):4997-9. Epub 2012 Aug 6. No abstract available.


Minim typing--a rapid and low cost MLST based typing tool for Klebsiella pneumoniae.

Andersson P, Tong SY, Bell JM, Turnidge JD, Giffard PM.

PLoS One. 2012;7(3):e33530. doi: 10.1371/journal.pone.0033530. Epub 2012 Mar 12.


High-resolution melting genotyping of Enterococcus faecium based on multilocus sequence typing derived single nucleotide polymorphisms.

Tong SY, Xie S, Richardson LJ, Ballard SA, Dakh F, Grabsch EA, Grayson ML, Howden BP, Johnson PD, Giffard PM.

PLoS One. 2011;6(12):e29189. doi: 10.1371/journal.pone.0029189. Epub 2011 Dec 16.


A very early-branching Staphylococcus aureus lineage lacking the carotenoid pigment staphyloxanthin.

Holt DC, Holden MT, Tong SY, Castillo-Ramirez S, Clarke L, Quail MA, Currie BJ, Parkhill J, Bentley SD, Feil EJ, Giffard PM.

Genome Biol Evol. 2011;3:881-95. doi: 10.1093/gbe/evr078. Epub 2011 Aug 2.


Rapid detection of the H275Y oseltamivir resistance mutation in influenza A/H1N1 2009 by single base pair RT-PCR and high-resolution melting.

Tong SY, Dakh F, Hurt AC, Deng YM, Freeman K, Fagan PK, Barr IG, Giffard PM.

PLoS One. 2011;6(6):e21446. doi: 10.1371/journal.pone.0021446. Epub 2011 Jun 24.


The utility of high-resolution melting analysis of SNP nucleated PCR amplicons--an MLST based Staphylococcus aureus typing scheme.

Lilliebridge RA, Tong SY, Giffard PM, Holt DC.

PLoS One. 2011;6(6):e19749. doi: 10.1371/journal.pone.0019749. Epub 2011 Jun 22.


Preliminary validation of a novel high-resolution melt-based typing method based on the multilocus sequence typing scheme of Streptococcus pyogenes.

Richardson LJ, Tong SY, Towers RJ, Huygens F, McGregor K, Fagan PK, Currie BJ, Carapetis JR, Giffard PM.

Clin Microbiol Infect. 2011 Sep;17(9):1426-34. doi: 10.1111/j.1469-0691.2010.03433.x. Epub 2011 Feb 25.


Diversity of emm sequence types in group A beta-haemolytic streptococci in two remote Northern Territory Indigenous communities: implications for vaccine development.

Richardson LJ, Towers RJ, Cheng AC, Currie BJ, Carapetis JR, Giffard PM, McDonald MI.

Vaccine. 2010 Jul 19;28(32):5301-5.


Clinical correlates of Panton-Valentine leukocidin (PVL), PVL isoforms, and clonal complex in the Staphylococcus aureus population of Northern Australia.

Tong SY, Lilliebridge RA, Bishop EJ, Cheng AC, Holt DC, McDonald MI, Giffard PM, Currie BJ, Boutlis CS.

J Infect Dis. 2010 Sep 1;202(5):760-9. doi: 10.1086/655396.


Rapid detection of H and R Panton-Valentine leukocidin isoforms in Staphylococcus aureus by high-resolution melting analysis.

Tong SY, Lilliebridge RA, Holt DC, Coombs GW, Currie BJ, Giffard PM.

Diagn Microbiol Infect Dis. 2010 Aug;67(4):399-401. doi: 10.1016/j.diagmicrobio.2010.03.015.


Campylobacter jejuni and Campylobacter coli genotyping by high-resolution melting analysis of a flaA fragment.

Merchant-Patel S, Blackall PJ, Templeton J, Price EP, Tong SY, Huygens F, Giffard PM.

Appl Environ Microbiol. 2010 Jan;76(2):493-9. doi: 10.1128/AEM.01164-09. Epub 2009 Nov 20.


Plasmid-borne blaSHV genes in Klebsiella pneumoniae are associated with strong promoters.

Turner MS, Andersson P, Bell JM, Turnidge JD, Harris T, Giffard PM.

J Antimicrob Chemother. 2009 Nov;64(5):960-4. doi: 10.1093/jac/dkp338. Epub 2009 Sep 12.


Phylogenetically distinct Staphylococcus aureus lineage prevalent among indigenous communities in northern Australia.

Ng JW, Holt DC, Lilliebridge RA, Stephens AJ, Huygens F, Tong SY, Currie BJ, Giffard PM.

J Clin Microbiol. 2009 Jul;47(7):2295-300. doi: 10.1128/JCM.00122-09. Epub 2009 May 6.


High-resolution melting analysis of the spa locus reveals significant diversity within sequence type 93 methicillin-resistant Staphylococcus aureus from northern Australia.

Tong SY, Lilliebridge RA, Holt DC, McDonald MI, Currie BJ, Giffard PM.

Clin Microbiol Infect. 2009 Dec;15(12):1126-31. doi: 10.1111/j.1469-0691.2009.02732.x. Epub 2009 Apr 15.


Community-associated strains of methicillin-resistant Staphylococcus aureus and methicillin-susceptible S. aureus in indigenous Northern Australia: epidemiology and outcomes.

Tong SY, Bishop EJ, Lilliebridge RA, Cheng AC, Spasova-Penkova Z, Holt DC, Giffard PM, McDonald MI, Currie BJ, Boutlis CS.

J Infect Dis. 2009 May 15;199(10):1461-70. doi: 10.1086/598218.


Analysis of bla(SHV) codon 238 and 240 allele mixtures using Sybr green high-resolution melting analysis.

Andersson P, Harris T, Tong SY, Giffard PM.

Antimicrob Agents Chemother. 2009 Jun;53(6):2679-83. doi: 10.1128/AAC.00063-09. Epub 2009 Apr 6.


Cystathionine gamma-lyase is a component of cystine-mediated oxidative defense in Lactobacillus reuteri BR11.

Lo R, Turner MS, Barry DG, Sreekumar R, Walsh TP, Giffard PM.

J Bacteriol. 2009 Mar;191(6):1827-37. doi: 10.1128/JB.01553-08. Epub 2009 Jan 5.


Random mutagenesis identifies novel genes involved in the secretion of antimicrobial, cell wall-lytic enzymes by Lactococcus lactis.

Tan YP, Giffard PM, Barry DG, Huston WM, Turner MS.

Appl Environ Microbiol. 2008 Dec;74(24):7490-6. doi: 10.1128/AEM.00767-08. Epub 2008 Oct 17.


Characterisation of chicken Campylobacter jejuni isolates using resolution optimised single nucleotide polymorphisms and binary gene markers.

Merchant-Patel S, Blackall PJ, Templeton J, Price EP, Miflin JK, Huygens F, Giffard PM.

Int J Food Microbiol. 2008 Dec 10;128(2):304-8. doi: 10.1016/j.ijfoodmicro.2008.09.002. Epub 2008 Sep 9.


Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

Honsa E, Fricke T, Stephens AJ, Ko D, Kong F, Gilbert GL, Huygens F, Giffard PM.

BMC Microbiol. 2008 Aug 19;8:140. doi: 10.1186/1471-2180-8-140.


High-resolution melting analysis of the spa repeat region of Staphylococcus aureus.

Stephens AJ, Inman-Bamber J, Giffard PM, Huygens F.

Clin Chem. 2008 Feb;54(2):432-6. doi: 10.1373/clinchem.2007.093658.


Selection of SHV extended-spectrum-beta-lactamase-dependent cefotaxime and ceftazidime resistance in Klebsiella pneumoniae requires a plasmid-borne blaSHV gene.

Hammond DS, Harris T, Bell J, Turnidge J, Giffard PM.

Antimicrob Agents Chemother. 2008 Feb;52(2):441-5. Epub 2007 Nov 12.


Inactivation of an iron transporter in Lactococcus lactis results in resistance to tellurite and oxidative stress.

Turner MS, Tan YP, Giffard PM.

Appl Environ Microbiol. 2007 Oct;73(19):6144-9. Epub 2007 Aug 3.

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