WGS for routine Mycobacterium bovis epidemiology Northern Ireland
We mapped 2,108 home-bred animal isolate locations of the common MLVA type 1.140 over the years 2000-2022.  We also mapped the locations of 148 whole-genome sequenced down-sampled isolates from this lineage, collected over the same period and similar geographic range, stratifying by SNP relatedness cut-offs of 15 SNPs.  We determined a putative core range for the 1.140 MLVA type and single nucleotide polymorphism (SNP)-defined sequence clusters using a 50% kernel density estimate approach. We also interrogated cattle location and movement data to inform on the likely source of whole-genome sequenced isolates found outside of their estimated core range.  Finally, we applied Bayesian phylogenetic methods to investigate the substitution rate, past population history and reproductive number of the 1.140 M. bovis lineage.