Related Experiment Video
Updated: May 30, 2026
13:06
Pyrosequencing: A Simple Method for Accurate Genotyping
Published on: January 8, 2008
Single nucleotide polymorphism (SNP)-based differentiation of Shigella isolates by pyrosequencing.
Alice E Hayford1, Mark K Mammel, David W Lacher
1Division of Molecular Biology, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Laurel, MD 20708, USA. alice.hayford@fda.hhs.gov
Summary
This study introduces a novel method using 24 single nucleotide polymorphisms (SNPs) to rapidly differentiate Shigella serogroups and strains. This genetic tool enhances the identification of Shigella, crucial for public health surveillance.
Area of Science:
- Microbiology
- Genetics
- Molecular Biology
Background:
- Single nucleotide polymorphisms (SNPs) are valuable genetic markers for strain differentiation.
- Accurate identification of Shigella serogroups and strains is critical for epidemiological studies and outbreak investigations.
Purpose of the Study:
- To develop and validate a SNP-based typing scheme for distinguishing Shigella serogroups (Boydii, Dysenteriae, Flexneri, Sonnei) and individual strains.
- To identify novel SNPs from housekeeping and other genes for enhanced Shigella discrimination.
Main Methods:
- Selection of 24 SNPs from nine genes, including housekeeping genes (gapA, thrB) and genes identified through in silico genome analysis (lpxC, sanA, yaaH, ybaP, ygaZ, yhbO, ynhA).
- Analysis of 118 Shigella strains representing all four serogroups using the developed SNP typing scheme.
- Utilizing PCR amplification and rapid sequencing for SNP analysis.
Main Results:
- The 24-SNP scheme successfully identified 26 distinct SNP genotypes across the four Shigella serogroups.
- The method provided discriminatory resolution among individual strains within the same serogroup.
- The identified SNPs are suitable for rapid identification and typing of Shigella.
Conclusions:
- The developed SNP typing scheme is an effective tool for rapid and accurate identification of Shigella serogroups and strains.
- This genetic approach offers improved molecular markers for differentiating closely related Shigella isolates.
- The findings support the utility of these SNPs for future Shigella surveillance and research using PCR and sequencing.
Related Concept Videos
01:05Single Nucleotide Polymorphisms-SNPs
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
01:57Sanger Sequencing
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
01:29Modern Molecular Taxonomy
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
03:00Next-generation Sequencing
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
02:26Comparing Copy Number Variations and SNPs
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
03:21RNA-seq
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...