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Updated: Nov 15, 2025
A Multi-detection Assay for Malaria Transmitting Mosquitoes
Published on: February 28, 2015
Rapid and simple SNP genotyping for Bordetella pertussis epidemic strain MT27 based on a multiplexed single-base
Kazunari Kamachi1, Shu-Man Yao2, Chuen-Sheue Chiang2
1Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan. kamachi@nih.go.jp.
Abstract:
Multilocus variable-number tandem repeat analysis (MLVA) is widely used for genotyping of Bordetella pertussis, the causative bacteria for pertussis. However, MLVA genotyping is losing its discriminate power because prevalence of the epidemic MT27 strain (MLVA-27) is increasing worldwide. To address this, we developed a single nucleotide polymorphism (SNP) genotyping method for MT27 based on multiplexed single-base extension (SBE) assay. A total of 237 MT27 isolates collected in Japan during 1999-2018 were genotyped and classified into ten SNP genotypes (SG1 to SG10) with a Simpson's diversity index (DI) of 0.79 (95% CI 0.76-0.82). Temporal trends showed a marked increase in the genotypic diversity in the 2010s: Simpson's DI was zero in 1999-2004, 0.16 in 2005-2009, 0.83 in 2010-2014, and 0.76 in 2015-2018. This indicates that the SNP genotyping is applicable to the recently circulating MT27 strain. Additionally, almost all outbreak-associated MT27 isolates were classified into the same SNP genotypes for each outbreak. Multiplexed SBE assay allows for rapid and simple genotyping, indicating that the SNP genotyping can potentially be a useful tool for subtyping the B. pertussis MT27 strain in routine surveillance and outbreak investigations.
Insights
New single nucleotide polymorphism (SNP) genotyping effectively subtypes the Bordetella pertussis MT27 strain, addressing limitations of MLVA. This method enhances surveillance and outbreak investigations for pertussis.
Area of Science:
- Microbiology
- Genetics
- Epidemiology
Background:
- Multilocus variable-number tandem repeat (MLVA) analysis is standard for Bordetella pertussis genotyping.
- Increasing prevalence of the MT27 strain has reduced MLVA's discriminatory power.
- A more refined genotyping method is needed for pertussis surveillance.
Purpose of the Study:
- To develop and evaluate a single nucleotide polymorphism (SNP) genotyping method for the Bordetella pertussis MT27 strain.
- To assess the method's ability to track genotypic diversity and outbreaks.
- To provide a tool for improved pertussis surveillance.
Main Methods:
- Development of a multiplexed single-base extension (SBE) assay for SNP genotyping.
- Genotyping of 237 MT27 isolates collected in Japan (1999-2018).
- Analysis of temporal trends and Simpson's diversity index (DI).
Main Results:
- Ten distinct SNP genotypes (SG1-SG10) were identified with a DI of 0.79.
- Genotypic diversity significantly increased in the 2010s.
- SNP genotyping correlated with specific outbreaks, demonstrating its utility.
Conclusions:
- SNP genotyping is effective for subtyping the circulating Bordetella pertussis MT27 strain.
- The method offers enhanced discriminatory power compared to MLVA.
- SNP genotyping is a valuable tool for routine surveillance and outbreak investigations of pertussis.
