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

PLoS ONE

Volumn 6, Issue 6, 2011, Pages

  Lilliebridge, Rachael A ^a   Tong, Steven Y C ^a   Giffard, Philip M ^a   Holt, Deborah C ^a  

^a MENZIES SCHOOL OF HEALTH RESEARCH   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT;

ALLELE; AMPLICON; ARTICLE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; COMPUTER MODEL; COMPUTER PREDICTION; CONTROLLED STUDY; DATA ANALYSIS; DNA BASE COMPOSITION; GENETIC DATABASE; GENETIC VARIABILITY; GENOTYPE; HIGH RESOLUTION MELTING ANALYSIS; MOLECULAR CLONING; MOLECULAR SIZE; MULTILOCUS SEQUENCE TYPING; NONHUMAN; OPTICAL RESOLUTION; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; STAPHYLOCOCCUS AUREUS; CLASSIFICATION; CLUSTER ANALYSIS; DNA DENATURATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; REPRODUCIBILITY; SPECIES DIFFERENCE;

BACTERIA (MICROORGANISMS); STAPHYLOCOCCUS AUREUS;

BACTERIAL TYPING TECHNIQUES; BASE SEQUENCE; CLUSTER ANALYSIS; DATABASES, GENETIC; GENOTYPE; MOLECULAR SEQUENCE DATA; MULTILOCUS SEQUENCE TYPING; NUCLEIC ACID DENATURATION; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SPECIES SPECIFICITY; STAPHYLOCOCCUS AUREUS;

EID: 79959464855     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0019749     Document Type: Article

References (23)

1. Robertson GA, Thiruvenkataswamy V, Shilling H, Price EP, Huygens F, et al. (2004) Identification and interrogation of highly informative single nucleotide polymorphism sets defined by bacterial multilocus sequence typing databases. J Med Microbiol 53: 35-45.
2. Price EP, Thiruvenkataswamy V, Mickan L, Unicomb L, Rios RE, et al. (2006) Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing. J Med Microbiol 55: 1061-1070.
3. Huygens F, Inman-Bamber J, Nimmo GR, Munckhof W, Schooneveldt J, et al. (2006) Staphylococcus aureus genotyping using novel real-time PCR formats. J Clin Microbiol 44: 3712-3719.
4. Honsa E, Fricke T, Stephens AJ, Ko D, Kong F, et al. (2008) Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms. BMC Microbiol 8: 140.
5. Stephens AJ, Huygens F, Inman-Bamber J, Price EP, Nimmo GR, et al. (2006) Methicillin-resistant Staphylococcus aureus genotyping using a small set of polymorphisms. J Med Microbiol 55: 43-51.
6. Keim P, Van Ert MN, Pearson T, Vogler AJ, Huynh LY, et al. (2004) Anthrax molecular epidemiology and forensics: using the appropriate marker for different evolutionary scales. Infect Genet Evol 4: 205-213.
7. Filliol I, Motiwala AS, Cavatore M, Qi W, Hazbon MH, et al. (2006) Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set. J Bacteriol 188: 759-772.
8. Richardson LJ, Tong SYC, Towers RJ, Huygens F, McGregor K, et al. (2010) Preliminary validation of a novel high resolution melt-based typing method based on the multilocus sequence typing scheme of Streptococcus pyogenes. Clin Microbiol Infect (in press) doi:10.1111/j.1469-0691.2010.03433.x.
9. Kibbe WA, (2007) OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Res 35: W43-46.
10. Schildkraut C, (1965) Dependence of the melting temperature of DNA on salt concentration. Biopolymers 3: 195-208.
11. Tong SY, Bishop EJ, Lilliebridge RA, Cheng AC, Spasova-Penkova Z, et al. (2009) Community-associated strains of methicillin-resistant Staphylococcus aureus and methicillin-susceptible S. aureus in Indigenous northern Australia: epidemiology and outcomes. J Infect Dis 199: 1461-1470.
12. Coombs GW, Monecke S, Ehricht R, Slickers P, Pearson JC, et al. (2010) Differentiation of clonal complex 59 community-associated methicillin-resistant Staphylococcus aureus in Western Australia. Antimicrob Agents Chemother 54: 1914-1921.
13. Pearson T, Giffard P, Beckstrom-Sternberg S, Auerbach R, Hornstra H, et al. (2009) Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. BMC Biol 7: 78.
14. Hall TA, Sampath R, Blyn LB, Ranken R, Ivy C, et al. (2009) Rapid molecular genotyping and clonal complex assignment of Staphylococcus aureus isolates by PCR coupled to electrospray ionization-mass spectrometry. J Clin Microbiol 47: 1733-1741.
15. Shopsin B, Gomez M, Montgomery SO, Smith DH, Waddington M, et al. (1999) Evaluation of protein A gene polymorphic region DNA sequencing for typing of Staphylococcus aureus strains. J Clin Microbiol 37: 3556-3563.
16. Tong SY, Lilliebridge RA, Holt DC, McDonald MI, Currie BJ, et al. (2009) High-resolution melting analysis of the spa locus reveals significant diversity within sequence type 93 methicillin-resistant Staphylococcus aureus from northern Australia. Clin Microbiol Infect 15: 1126-1131.
17. Ng JW, Holt DC, Lilliebridge RA, Stephens AJ, Huygens F, et al. (2009) Phylogenetically distinct Staphylococcus aureus lineage prevalent among indigenous communities in northern Australia. J Clin Microbiol 47: 2295-2300.
18. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
19. Price EP, Inman-Bamber J, Thiruvenkataswamy V, Huygens F, Giffard PM, (2007) Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants. BMC Bioinformatics 8: 278.
20. Tong SY, Lilliebridge RA, Bishop EJ, Cheng AC, Holt DC, et al. (2010) Clinical correlates of Panton-Valentine leukocidin (PVL), PVL isoforms, and clonal complex in the Staphylococcus aureus population of Northern Australia. J Infect Dis 202: 760-769.
21. Enright MC, Day NP, Davies CE, Peacock SJ, Spratt BG, (2000) Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus. J Clin Microbiol 38: 1008-1015.
22. Carrico JA, Silva-Costa C, Melo-Cristino J, Pinto FR, de Lencastre H, et al. (2006) Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes. J Clin Microbiol 44: 2524-2532.
23. Feil EJ, Li BC, Aanensen DM, Hanage WP, Spratt BG, (2004) eBURST: Inferring Patterns of Evolutionary Descent among Clusters of Related Bacterial Genotypes from Multilocus Sequence Typing Data. J Bacteriol 186: 1518-1530.