Dataset Information

Rapid and simple SNP genotyping for Bordetella pertussis epidemic strain MT27 based on a multiplexed single-base extension assay.

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.

SUBMITTER: Kamachi K

PROVIDER: S-EPMC7921669 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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Rapid and simple SNP genotyping for Bordetella pertussis epidemic strain MT27 based on a multiplexed single-base extension assay.

Kamachi Kazunari K Yao Shu-Man SM Chiang Chuen-Sheue CS Koide Kentaro K Otsuka Nao N Shibayama Keigo K

Scientific reports 20210301 1

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 199 ...[more]

PMID: 33649512

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Project description:Bordetella pertussis causes whooping cough, a severe respiratory disease. B. pertussis is a highly genetically homogenous species with only minor levels of genetic variation. It has been shown that single nucleotide polymorphism (SNP) cluster I containing the dominant pertussis toxin promoter allele, ptxP3 has overtaken the previously dominant SNP cluster II (ptxP1) strains. Studies comparing cluster I and cluster II strains have identified changes that may relate to the increased dominance of the cluster I strains however these studies were performed on planktonic cells. Recent studies have demonstrated the ability of B. pertussis to form biofilms. Bacteria within biofilms have been shown to be phenotypically distinct from their planktonic counterparts. Therefore, this study compared the biofilm formation capabilities of representative strains of cluster I and cluster II using confocal laser scanning microscopy. It was found that the cluster I strain has a more densely packed biofilm structure. Differences in protein expression of the biofilm cells were then compared using Tandem Mass Tagging (TMT) mass spectrometry. In total, there were 1453 proteins identified of which 40 proteins had significant differential expression between the two strains in biofilm conditions. Of particular interest was a large increase in expression of cytochrome proteins PetABC and BP3650 and a decrease in the alcaligin synthesis protein, AlcC in the cluster I strain. These changes were not identified when a previous study compared these strains in planktonic conditions suggesting they are under the control of a biofilm specific regulator. To identify whether these differences are cluster specific, high resolution multiple reaction monitoring (MRM-hr) mass spectrometry was performed on a subset of 9 of the differentially regulated proteins on an additional 6 strains from each SNP cluster. The major changes in protein expression identified between the two representative strains were not reflected by the additional strains. However, there was a large variation in the expression of the proteins between the different strains from each cluster. These findings suggest that there are large levels of individual proteomic diversity between B. pertussis strains in biofilm conditions despite the highly conserved genome of the species.

Dataset Information

Rapid and simple SNP genotyping for Bordetella pertussis epidemic strain MT27 based on a multiplexed single-base extension assay.

Publications

Rapid and simple SNP genotyping for Bordetella pertussis epidemic strain MT27 based on a multiplexed single-base extension assay.

Similar Datasets

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