SNP-based typing: a useful tool to study Bordetella pertussis populations

Area of Science:

• Microbiology
• Epidemiology
• Genetics

Background:

• Bordetella pertussis surveillance relies on Pulsed-Field Gel Electrophoresis (PFGE) and Multiple-Locus Variable-Number Tandem Repeat Analysis (MLVA).
• Limitations exist in the discriminatory power and phylogenetic accuracy of current typing methods for B. pertussis.

Purpose of the Study:

• To develop and evaluate a novel single nucleotide polymorphism (SNP) typing method for B. pertussis.
• To compare the efficacy of SNP typing against PFGE and MLVA for epidemiological surveillance.
• To investigate the evolutionary dynamics of ptxP3 B. pertussis strains using SNP typing.

Main Methods:

• Development of an 87-SNP typing assay for B. pertussis.
• Comparative analysis of SNP typing, PFGE, and MLVA discriminatory indices.
• Phylogenetic analysis using SNP data as the gold standard.
• Application of SNP typing to global ptxP3 B. pertussis strains.

Main Results:

• SNP typing demonstrated a high discriminatory index (0.85), comparable to PFGE (0.95) and superior to MLVA (0.83).
• Phylogenetic analyses revealed inaccuracies in PFGE and MLVA trees, with SNP typing providing a more accurate evolutionary depiction.
• SNP typing identified a monophyletic origin for ptxP3 strains, showing recent divergence from ptxP1 strains and revealing two predominant worldwide types.
• The method correlated root-to-tip distance with isolation year, unlike PFGE and MLVA.

Conclusions:

• SNP typing is a phylogenetically informative and highly discriminative method for B. pertussis surveillance.
• SNP typing offers standardization for interlaboratory comparisons, overcoming limitations of PFGE.
• The study elucidates the recent global spread and evolutionary trajectory of ptxP3 B. pertussis strains, enhancing epidemiological understanding.