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2019

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

Davies, M. R., McIntyre, L., Mutreja, A., Lacey, J. A., Lees, J. A., Towers, R. J., Duchêne, S., Smeesters, P. R., Frost, H. R., Price, D. J., Holden, M. T. G., David, S., Giffard, P. M., Worthing, K. A., Seale, A. C., Berkley, J. A., Harris, S. R., Rivera-Hernandez, T., Berking, O., Cork, A. J. & 18 others, Torres, R. S. L. A., Lithgow, T., Strugnell, R. A., Bergmann, R., Nitsche-Schmitz, P., Chhatwal, G. S., Bentley, S. D., Fraser, J. D., Moreland, N. J., Carapetis, J. R., Steer, A. C., Parkhill, J., Saul, A., Williamson, D. A., Currie, B. J., Tong, S. Y. C., Dougan, G. & Walker, M. J., 1 Jun 2019, In : Nature Genetics. 51, 6, p. 1035-1043 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Streptococcal Vaccines
Atlases
Genomics
Vaccines
Antigens

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

Davies, M. R., McIntyre, L., Mutreja, A., Lacey, J. A., Lees, J. A., Towers, R. J., Duchêne, S., Smeesters, P. R., Frost, H. R., Price, D. J., Holden, M. T. G., David, S., Giffard, P. M., Worthing, K. A., Seale, A. C., Berkley, J. A., Harris, S. R., Rivera-Hernandez, T., Berking, O., Cork, A. J. & 18 others, Torres, R. S. L. A., Lithgow, T., Strugnell, R. A., Bergmann, R., Nitsche-Schmitz, P., Chhatwal, G. S., Bentley, S. D., Fraser, J. D., Moreland, N. J., Carapetis, J. R., Steer, A. C., Parkhill, J., Saul, A., Williamson, D. A., Currie, B. J., Tong, S. Y. C., Dougan, G. & Walker, M. J., Aug 2019, In : Nature Genetics. 51, 8, p. 1295-1295 1 p.

Research output: Contribution to journalComment/debateResearchpeer-review

Open Access
Streptococcal Vaccines
Atlases
Genomics
Alleles
Proteins
23 Downloads (Pure)

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

Giffard, P., Tong, S. Y. C., Holt, D., Ralph, A. & Currie, B., 3 Jul 2019, In : PLoS Neglected Tropical Diseases. 13, 7, p. 1-20 20 p., e0007511.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Rheumatic Heart Disease
Streptococcus pyogenes
Vaccines
Northern Territory
Proteins

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

Holt, D. C., Andersson, P., Buckley, C., Whiley, D. M. & Giffard, P. M., 6 Aug 2019, Methods in Molecular Biology. Humana Press Inc., p. 87-122 36 p. (Methods in Molecular Biology; vol. 2042).

Research output: Chapter in Book/Report/Conference proceedingChapterResearchpeer-review

Chlamydia trachomatis
Genotype
Genome
Phylogeny
Haplotypes
2018

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

Giffard, P. M., Lilliebridge, R. A., Wilson, J., Murray, G., Phillips, S., Tabrizi, S. N., Garland, S. M., Martin, L., Singh, G., Tong, S. Y. C., Holt, D. C. & Andersson, P., 18 Jan 2018, In : Sexually Transmitted Infections. 94, 1, p. 32-36 5 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
Chlamydia trachomatis
Fingers
Urine
Urine Specimen Collection
Sexually Transmitted Diseases
6 Downloads (Pure)

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, P. M., Andersson, P., Wilson, J., Buckley, C., Lilliebridge, R., Harris, T. M., Kleinecke, M., O’Grady, K. A. F., Huston, W. M., Lambert, S. B., Whiley, D. M. & Holt, D. C., 1 Apr 2018, In : PLoS One. 13, 4, p. 1-18 18 p., e0195454.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Chlamydia trachomatis
melting
Freezing
Melting
eyes
10 Downloads (Pure)

Global scale dissemination of ST93: A divergent staphylococcus aureus epidemic lineage that has recently emerged from remote northern Australia

van Hal, S. J., Steinig, E. J., Andersson, P., Holden, M. T. G., Harris, S. R., Nimmo, G. R., Williamson, D. A., Heffernan, H., Ritchie, S. R., Kearns, A. M., Ellington, M. J., Dickson, E., de Lencastre, H., Coombs, G. W., Bentley, S. D., Parkhill, J., Holt, D. C., Giffard, P. M. & Tong, S. Y. C., 9 Jul 2018, In : Frontiers in Microbiology. 9, July, p. 1-11 11 p., 1453.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Staphylococcus aureus
Methicillin-Resistant Staphylococcus aureus
Population
Genome
New Zealand

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

Harris, T. M., Bowen, A. C., Holt, D. C., Sarovich, D. S., Stevens, K., Currie, B. J., Howden, B. P., Carapetis, J. R., Giffard, P. M. & Tong, S. Y. C., Sep 2018, In : Clinical Microbiology and Infection. 24, 9, p. 1027-1029 3 p.

Research output: Contribution to journalLetterResearchpeer-review

Open Access
File
Trimethoprim Resistance
Sulfamethoxazole Drug Combination Trimethoprim
Methicillin-Resistant Staphylococcus aureus
Clone Cells
2017
1 Downloads (Pure)

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

Hadfield, J., Harris, S. R., Seth-Smith, H. M. B., Parmar, S., Andersson, P., Giffard, P. M., Schachter, J., Moncada, J., Ellison, L., Vaulet, M. L. G., Fermepin, M. R., Radebe, F., Mendoza, S., Ouburg, S., Morré, S. A., Sachse, K., Puolakkainen, M., Korhonen, S. J., Sonnex, C., Wiggins, R. & 18 others, Jalal, H., Brunelli, T., Casprini, P., Pitt, R., Ison, C., Savicheva, A., Shipitsyna, E., Hadad, R., Kari, L., Burton, M. J., Mabey, D., Solomon, A. W., Lewis, D., Marsh, P., Unemo, M., Clarke, I. N., Parkhill, J. & Thomson, N. R., Jul 2017, In : Genome Research. 27, 7, p. 1220-1229 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Chlamydia trachomatis
History
Genome
Ecotype
Blindness
2 Downloads (Pure)

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

Giffard, P. M., Su, J. Y., Andersson, P. & Holt, D. C., 22 Jun 2017, In : PEERJ. 2017, 5, p. 1-11 11 p., e3487.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Toilet Facilities
sexually transmitted diseases
Sexually Transmitted Diseases
Nucleic Acids
Health

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

Giffard, P., Singh, G. & Garland, S. M., 4 Jun 2017, In : Sexually Transmitted Infections. 93, 4, p. 236-237 2 p.

Research output: Contribution to journalEditorialResearch

Chlamydia trachomatis
2016
11 Downloads (Pure)

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

Andersson, P., Harris, S., Smith, H., Hadfield, J., O'Neill, C., Cutcliffe, LT., Douglas, F., Asche, LV., Seth-Smith, H. M. B., Hadfield, J., Colette E, ON., Lesley T, C., Fiona P, D., Asche, LV., Mathews, J., Hutton, S., Sarovich, D., Tong, S., Clarke, I., Thomson, N. & 1 others, Giffard, P., 2016, In : Nature Communications. 25, 7, p. 1-11 11 p., 10688.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Trachoma
genome
Chlamydia trachomatis
tropism
Genes
1 Downloads (Pure)

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

Giffard, P., Brenner, N., Tabrizi, S., Garland, S., Holt, D., Andersson, P., Gorie, R., Tong, S., Karimi, M., Boylan, P., Ryder, N., Johns, T. & Singh, G., 1 Jan 2016, In : BMJ Open. 6, p. 1-7 7 p., e009624.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Chlamydia trachomatis
Cross-Sectional Studies
Genotype
Northern Territory
Trachoma

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

Jeremiah, C., Kandiah, J. P., Spelman, D., Giffard, P., Coombs, G., Jenney, A. & Tong, S., 2016, In : Journal of Hospital Infection. 92, 2, p. 183-190 8 p.

Research output: Contribution to journalArticleResearchpeer-review

Methicillin
Staphylococcus aureus
Epidemiology
Clone Cells
Delivery of Health Care
2 Downloads (Pure)

Molecular epidemiology of methicillin-resistant Staphylococcus aureus isolated from Australian veterinarians

Groves, MD., Crouch, B., Coombs, G., Jordan, D., Pang, S., Barton, Giffard, P., Abraham, S. & Trott, 2016, In : PLoS One. 11, 1, p. 1-12 12 p., e0146034.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
molecular epidemiology
Methicillin
Molecular Epidemiology
Veterinarians
Methicillin-Resistant Staphylococcus aureus

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

Bowen, A., Harris, T., Holt, D., Giffard, P., Carapetis, J., Campbell, P. T. H., McVernon, J. & Tong, S., Jul 2016, In : Epidemiology and Infection. 144, 9, p. 1991-1998 8 p.

Research output: Contribution to journalArticleResearchpeer-review

Impetigo
Streptococcus
Genome
Streptococcus pyogenes
Single Nucleotide Polymorphism
2 Downloads (Pure)

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, E. M., Andersson, P., Yeaman, F., Oldfield, S., Lilliebridge, R. A., Bentley, S. D., Krause, V., Beaman, M., Currie, B., Holt, D., Giffard, P. & Tong, S., 2016, In : Microbial Genomics. 2, 12, p. 1-7 7 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Methicillin-Resistant Staphylococcus aureus
Disease Outbreaks
Clone Cells
Genome
Staphylococcus aureus
2015

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, S., Schaumburg, F., Ellington, M., Corander, J., Pichon, B., Leendertz, F., Bentley, S., Parkhill, J., Holt, D., Peters, G. & Giffard, P., 2015, In : International Journal of Systematic and Evolutionary Microbiology. 65, p. 15-22 8 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
Staphylococcus
primate
Primates
Staphylococcus aureus
new species

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

Tong, S., Varrone, L., Chatfield, M., Beaman, M. & Giffard, P., 2015, In : Epidemiology and Infection. 143, 7, p. 1519-1523 5 p.

Research output: Contribution to journalArticleResearchpeer-review

Methicillin-Resistant Staphylococcus aureus
Population Groups
Methicillin Resistance
Northern Territory
Macrolides
2014

Burkholderia pseudomallei Isolates from Sarawak, Malaysian Borneo, Are Predominantly Susceptible to Aminoglycosides and Macrolides

Podin, Y., Sarovich, D., Price, E., Kaestli, M., Mayo, M., Hii, K., Ngian, H., Wong, S-C., Wong, I., Wong, J., Mohan, A., Ooi, M., Fam, T., Wong, J., Tuanyok, A., Keim, P. S., Giffard, P. & Currie, B., 2014, In : Antimicrobial Agents and Chemotherapy. 58, 1, p. 162-166 5 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
Borneo
Burkholderia pseudomallei
Malaysia
Macrolides
Aminoglycosides

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

Ng, J., Holt, D., Andersson, P. & Giffard, P., 2014, In : Clinical Chemistry. 60, 2, p. 414-416 3 p.

Research output: Contribution to journalLetterResearchpeer-review

Open Access
Nucleic Acid Denaturation
Freezing
Melting point
Melting
DNA

Enhancement of the evidence base for the interpretation of positive diagnostic tests for sexually transmitted infection in children

Giffard, P., Andersson, P., Johns, T., Boylan, P., Ryder, N. & Singh, G., 2014

Research output: Other contributionOther types of outputsResearch

Invasive Staphylococcus aureus Infections in Children in Tropical Northern Australia

Engelman, D., Hofer, A., Davis, J., Carapetis, J., Baird, R., Giffard, P., Holt, D. & Tong, S., 1 Dec 2014, In : Journal of the Pediatric Infectious Diseases Society. 3, 4, p. 304-311 8 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
Staphylococcus aureus
Pediatrics
Methicillin-Resistant Staphylococcus aureus
Infection
Staphylococcal Skin Infections

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

Andersson, P., Tong, S., Gorie, R., Brenner, N., Martin, L., Spencer, E., Delima, J., Singh, G., McCann, F., Hudson, C., Johns, T. & Giffard, P., 1 Oct 2014, In : Journal of the Pediatric Infectious Diseases Society. 3, 3, p. 189-196 8 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
Sexually Transmitted Diseases
Urine
Toilet Facilities
Northern Territory
Nucleic Acids
2013

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

Brennan, L., Gorie, R., Cheng, A., Giffard, P., Currie, B. & Tong, S., 2013, In : Journal of Hospital Infection. 83, 3, p. 205-211 7 p.

Research output: Contribution to journalArticleResearchpeer-review

Methicillin
Methicillin-Resistant Staphylococcus aureus
Staphylococcus aureus
Inpatients
Delivery of Health Care
4 Downloads (Pure)

Extensive Diversity of Streptococcus pyogenes in a Remote Human Population Reflects Global-Scale Transmission Rather than Localised Diversification

Towers, R., Carapetis, J., Currie, B., Davies, M., Walker, M., Dougan, G. & Giffard, P., 2013, In : PLoS One. 8, 9, p. 1-6 6 p., e73851.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Northern Territory
Streptococcus pyogenes
Multilocus Sequence Typing
human population
Population

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, R. & Giffard, P., Sep 2013, In : Clinical Microbiology and Infection. 19, 9, p. E405-E408 4 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
Bacterial Genomes
Chlamydia trachomatis
DNA Sequence Analysis
Genotype
Genome

Virulence of Endemic Nonpigmented Northern Australian Staphylococcus aureus Clone (Clonal Complex 75, S. argenteus) Is Not Augmented by Staphyloxanthin

Tong, S., Sharma-Kuinkel, B., Thaden, J., Whitney, AR., Yang, S., Mishra, D., Rude, T., Gorie, R., Selim, M., Ahn, S., Holt, D., Giffard, P., Bayer, S., DeLeo, F. & Fowler Jr, V., 2013, In : Journal of Infectious Diseases. 208, 3, p. 520-527 8 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
Virulence
Staphylococcus aureus
Clone Cells
Oxidative Stress
Neutrophils
2012

Guidelines for Reporting Novel mecA Gene Homologues

Ito, T., Hiramatsu, K., Tomasz, A., de Lencastre, H., Perreten, V., Holden, M., Coleman, D., Goering, R., Giffard, P., Skov, R., Zhang, K., Westh, H., O'Brien, F., Tenover, F., Oliveria, D., Boyle-Vavra, S., Laurent, F., Kearns, A., Kreiswirth, B., Soo Ko, K. & 6 others, Grundmann, H., Sollid, J., John, J., Daum, R., Soderquist, B. & Buist, G., 2012, In : Antimicrobial Agents and Chemotherapy. 56, 10, p. 4997-4999 3 p.

Research output: Contribution to journalComment/debateResearch

Open Access
Guidelines
Genes

Microbiological Applications of High-Resolution Melting Analysis

Tong, S. & Giffard, P., Nov 2012, In : Journal of Clinical Microbiology. 50, 11, p. 3418-3421 4 p.

Research output: Contribution to journalShort surveyResearchpeer-review

Open Access
Freezing
Real-Time Polymerase Chain Reaction
Technology
Costs and Cost Analysis
3 Downloads (Pure)

Minim typing - A Rapid and Low Cost MLST Based Typing Tool for Klebsiella pneumoniae

Andersson, P., Tong, S., Bell, J., Turnidge, J. & Giffard, P., 2012, In : PLoS One. 7, 3, p. 1-7 7 p., e33530.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Multilocus Sequence Typing
Klebsiella pneumoniae
melting
Melting
Freezing
2011
2 Downloads (Pure)

A Very Early-Branching Staphylococcus aureus Lineage Lacking the Carotenoid Pigment Staphyloxanthin

Holt, D., Holden, M., Tong, S., Castillo-Ramirez, S., Clarke, L., Quail, M., Currie, B., Parkhill, J., Bentley, S., Feil, E. & Giffard, P., 2011, In : Genome Biology and Evolution. 3, p. 881-895 15 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Carotenoids
carotenoid
Staphylococcus aureus
branching
pigment

Carriage of methicillin-resistant Staphylococcus aureus by veterinarians in Australia

Jordon, D., Simon, J., Fury, S., Moss, S., Giffard, P., Maiwald, M., Southwell, P., Barton, Axon, Morris & Trott, 2011, In : Australian Veterinary Journal. 89, 5, p. 152-159 8 p.

Research output: Contribution to journalArticleResearchpeer-review

Veterinarians
Methicillin-Resistant Staphylococcus aureus
veterinarians
Horses
horses

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

Tong, S., Xie, S., Richardson, L. J., Ballard, S., Dakh, F., Grabsch, E., Grayson, L., Howden, B., Johnson, P. & Giffard, P., 2011, In : PLoS One. 6, 12, p. 1-8 8 p., e29189.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Multilocus Sequence Typing
Enterococcus faecium
Polymorphism
melting
Freezing

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

Richardson, L. J., Tong, S., Towers, R., Huygens, F., McGregor, K., Fagan, P., Currie, B., Carapetis, J. & Giffard, P., 2011, In : Clinical Microbiology and Infection. 17, p. 1426-1434 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
Multilocus Sequence Typing
Streptococcus pyogenes
Base Composition
Databases
Freezing
1 Downloads (Pure)

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

Tong, S., Dakh, F., Hurt, A., Deng, Y-M., Freeman, K., Fagan, P., Barr, I. & Giffard, P., 2011, In : PLoS One. 6, 6, p. 1-5 5 p., e21446.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Oseltamivir
melting
Base Pairing
influenza
Human Influenza
10 Downloads (Pure)

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

Lilliebridge, R. A., Tong, S., Giffard, P. & Holt, D., 2011, In : PLoS One. 6, 6, p. 1-11 11 p., e19749.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Polymorphism
melting
Freezing
single nucleotide polymorphism
Single Nucleotide Polymorphism