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Strain Resolution Revolution: Phylogenetic Reconstruction and Rapid SNP Assay Development for Mycobacterium bovis in Ireland

R Magee(1,2)

1:Queen's University Belfast; 2:Agri-Food and Biosciences Institute (AFBI)

Bovine Tuberculosis poses significant challenges to the livestock industry and wildlife in Ireland. Monitoring the strains of the causative, slow-evolving pathogen presents its own unique challenges. Here, we reconstruct the evolution of M. bovis in Ireland using Next-Generation Sequencing technologies (NGS) and exploit the genomic uniformity of the pathogen for potential epidemiological applications.

We employed a microbial variant calling pipeline on 992 Whole-Genome Sequences of Irish M. bovis samples. Hierarchical clade-defining Single-Nucleotide Polymorphisms (SNPs) were identified. We tested 30 SNPs from the phylogeny using LCG’s SNPline plate-based genotyping system on a diverse sample set. Additionally, 12 SNPs representing the MRCAs of multiple sub-clades were identified to confirm ancestry and control delineation errors.

Our method consistently and reliably identified sample lineage to the Most Recent Common Ancestor (MRCA) of specific sub-clades, while excluding descent from other sub-clades' MRCAs. Compared to current methods, hierarchical strain typing offers superior resolution, adaptability, speed, and scalability but without the homoplasy issues that can impede epidemiological investigations. The use of hierarchical clade-defining SNPs enhances strain-typing resolution to a level only comparable to WGS, but without the significant associated costs, promising significant improvements for track-and-trace systems in both the livestock industry and wildlife disease control.

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