BIOMAT Database Logo BIOMAT Database Logo

Preliminary validation of a novel high-resolution melt-based typing method based on the multilocus sequence typing scheme of Streptococcus pyogenes. 2011

L J Richardson, and S Y C Tong, and R J Towers, and F Huygens, and K McGregor, and P K Fagan, and B J Currie, and J R Carapetis, and P M Giffard
Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia.

The major limitation of current typing methods for Streptococcus pyogenes, such as emm sequence typing and T typing, is that these are based on regions subject to considerable selective pressure. Multilocus sequence typing (MLST) is a better indicator of the genetic backbone of a strain but is not widely used due to high costs. The objective of this study was to develop a robust and cost-effective alternative to S. pyogenes MLST. A 10-member single nucleotide polymorphism (SNP) set that provides a Simpson's Index of Diversity (D) of 0.99 with respect to the S. pyogenes MLST database was derived. A typing format involving high-resolution melting (HRM) analysis of small fragments nucleated by each of the resolution-optimized SNPs was developed. The fragments were 59-119 bp in size and, based on differences in G+C content, were predicted to generate three to six resolvable HRM curves. The combination of curves across each of the 10 fragments can be used to generate a melt type (MelT) for each sequence type (ST). The 525 STs currently in the S. pyogenes MLST database are predicted to resolve into 298 distinct MelTs and the method is calculated to provide a D of 0.996 against the MLST database. The MelTs are concordant with the S. pyogenes population structure. To validate the method we examined clinical isolates of S. pyogenes of 70 STs. Curves were generated as predicted by G+C content discriminating the 70 STs into 65 distinct MelTs.

UI MeSH Term Description Entries
D004269 DNA, Bacterial Deoxyribonucleic acid that makes up the genetic material of bacteria. Bacterial DNA
D005838 Genotype The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS. Genogroup,Genogroups,Genotypes
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D001482 Base Composition The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid. Base Ratio,G+C Composition,Guanine + Cytosine Composition,G+C Content,GC Composition,GC Content,Guanine + Cytosine Content,Base Compositions,Base Ratios,Composition, Base,Composition, G+C,Composition, GC,Compositions, Base,Compositions, G+C,Compositions, GC,Content, G+C,Content, GC,Contents, G+C,Contents, GC,G+C Compositions,G+C Contents,GC Compositions,GC Contents,Ratio, Base,Ratios, Base
D013290 Streptococcal Infections Infections with bacteria of the genus STREPTOCOCCUS. Group A Strep Infection,Group A Streptococcal Infection,Group A Streptococcal Infections,Group B Strep Infection,Group B Streptococcal Infection,Group B Streptococcal Infections,Infections, Streptococcal,Infection, Streptococcal,Streptococcal Infection
D013297 Streptococcus pyogenes A species of gram-positive, coccoid bacteria isolated from skin lesions, blood, inflammatory exudates, and the upper respiratory tract of humans. It is a group A hemolytic Streptococcus that can cause SCARLET FEVER and RHEUMATIC FEVER. Flesh-Eating Bacteria,Streptococcus Group A,Bacteria, Flesh-Eating
D015203 Reproducibility of Results The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results. Reliability and Validity,Reliability of Result,Reproducibility Of Result,Reproducibility of Finding,Validity of Result,Validity of Results,Face Validity,Reliability (Epidemiology),Reliability of Results,Reproducibility of Findings,Test-Retest Reliability,Validity (Epidemiology),Finding Reproducibilities,Finding Reproducibility,Of Result, Reproducibility,Of Results, Reproducibility,Reliabilities, Test-Retest,Reliability, Test-Retest,Result Reliabilities,Result Reliability,Result Validities,Result Validity,Result, Reproducibility Of,Results, Reproducibility Of,Test Retest Reliability,Validity and Reliability,Validity, Face
D058885 Multilocus Sequence Typing Direct nucleotide sequencing of gene fragments from multiple housekeeping genes for the purpose of phylogenetic analysis, organism identification, and typing of species, strain, serovar, or other distinguishable phylogenetic level. Multilocus Sequence Analysis,Analyses, Multilocus Sequence,Analysis, Multilocus Sequence,Multilocus Sequence Analyses,Sequence Analyses, Multilocus,Sequence Analysis, Multilocus,Sequence Typing, Multilocus,Typing, Multilocus Sequence
D019295 Computational Biology A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets. Bioinformatics,Molecular Biology, Computational,Bio-Informatics,Biology, Computational,Computational Molecular Biology,Bio Informatics,Bio-Informatic,Bioinformatic,Biologies, Computational Molecular,Biology, Computational Molecular,Computational Molecular Biologies,Molecular Biologies, Computational
D020641 Polymorphism, Single Nucleotide A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population. SNPs,Single Nucleotide Polymorphism,Nucleotide Polymorphism, Single,Nucleotide Polymorphisms, Single,Polymorphisms, Single Nucleotide,Single Nucleotide Polymorphisms

Related Publications

L J Richardson, and S Y C Tong, and R J Towers, and F Huygens, and K McGregor, and P K Fagan, and B J Currie, and J R Carapetis, and P M Giffard
Annotated Whole-Genome Multilocus Sequence Typing Schema for Scalable High-Resolution Typing of Streptococcus pyogenes.
June 2022, Journal of clinical microbiology,
L J Richardson, and S Y C Tong, and R J Towers, and F Huygens, and K McGregor, and P K Fagan, and B J Currie, and J R Carapetis, and P M Giffard
A core-genome multilocus sequence typing scheme for the detection of genetically related Streptococcus pyogenes clusters.
November 2023, Journal of clinical microbiology,
L J Richardson, and S Y C Tong, and R J Towers, and F Huygens, and K McGregor, and P K Fagan, and B J Currie, and J R Carapetis, and P M Giffard
Core Genome Multilocus Sequence Typing Scheme for High- Resolution Typing of Enterococcus faecium.
December 2015, Journal of clinical microbiology,
L J Richardson, and S Y C Tong, and R J Towers, and F Huygens, and K McGregor, and P K Fagan, and B J Currie, and J R Carapetis, and P M Giffard
Development of a multilocus sequence typing scheme for Streptococcus gallolyticus.
January 2014, Microbiology (Reading, England),
L J Richardson, and S Y C Tong, and R J Towers, and F Huygens, and K McGregor, and P K Fagan, and B J Currie, and J R Carapetis, and P M Giffard
A Core Genome Multilocus Sequence Typing Scheme for Streptococcus mutans.
July 2020, mSphere,
L J Richardson, and S Y C Tong, and R J Towers, and F Huygens, and K McGregor, and P K Fagan, and B J Currie, and J R Carapetis, and P M Giffard
Multilocus sequence typing of Streptococcus pyogenes and the relationships between emm type and clone.
April 2001, Infection and immunity,
L J Richardson, and S Y C Tong, and R J Towers, and F Huygens, and K McGregor, and P K Fagan, and B J Currie, and J R Carapetis, and P M Giffard
A rapid typing method for Listeria monocytogenes based on high-throughput multilocus sequence typing (Hi-MLST).
February 2017, International journal of food microbiology,
L J Richardson, and S Y C Tong, and R J Towers, and F Huygens, and K McGregor, and P K Fagan, and B J Currie, and J R Carapetis, and P M Giffard
Development and application of a multilocus sequence typing scheme for Streptococcus gallolyticus subsp. gallolyticus.
July 2014, Journal of clinical microbiology,
L J Richardson, and S Y C Tong, and R J Towers, and F Huygens, and K McGregor, and P K Fagan, and B J Currie, and J R Carapetis, and P M Giffard
Multilocus sequence typing scheme for Enterococcus faecium.
June 2002, Journal of clinical microbiology,
L J Richardson, and S Y C Tong, and R J Towers, and F Huygens, and K McGregor, and P K Fagan, and B J Currie, and J R Carapetis, and P M Giffard
[A novel typing method and scheme for Streptococcus pneumoniae].
July 2013, Epidemiologie, mikrobiologie, imunologie : casopis Spolecnosti pro epidemiologii a mikrobiologii Ceske lekarske spolecnosti J.E. Purkyne,
Copied contents to your clipboard!