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Updated: Mar 28, 2026
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Published on: June 24, 2025
Novel Single Nucleotide Polymorphism-Based Assay for Genotyping Mycobacterium avium subsp. paratuberculosis
Célia Leão1, Robert J Goldstone2, Josephine Bryant3
1Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom Unidade Estratégica de Investigação e Serviços em Produção e Saúde Animal, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), Lisbon, Portugal celia.leao@iniav.pt j.inacio@brighton.ac.uk.
A new single nucleotide polymorphism (SNP) assay offers a powerful method for typing Mycobacterium avium subspecies paratuberculosis. This approach provides higher discriminatory power than traditional methods for global epidemiological studies.
Area of Science:
- Microbiology
- Genetics
- Epidemiology
Background:
- Mycobacterium avium subspecies paratuberculosis (MAP) strains are genetically similar, making traditional typing methods challenging.
- Whole-genome sequencing offers advanced characterization and phylogenetic insights for MAP.
Purpose of the Study:
- To develop a novel single nucleotide polymorphism (SNP) assay for high-resolution typing of MAP.
- To assess the discriminatory power of the SNP assay compared to existing methods.
Main Methods:
- Developed a SNP assay using PCR and restriction enzyme digestion or sequencing.
- Analyzed genome data from 133 MAP isolates from diverse hosts and geographic regions.
- Employed a sequential SNP detection approach with a decision tree.
Main Results:
- Identified 28,402 SNPs across all isolates.
- Determined that 93 SNPs could distinguish all 133 genomes.
- Characterized MAP isolates into 14 phylogenetic groups using 14 SNPs, exceeding the discriminatory power of other methods.
Conclusions:
- The novel SNP assay is a simple, reproducible, and highly discriminative method for large-scale global typing of MAP.
- The assay requires basic laboratory equipment, facilitating widespread use.
- Continuous genome sequencing updates are essential for refining phylogenetic characterization.
