Comparative sequence analysis elucidates the evolutionary patterns of in New Mexico over thirty-two years.

Background: , a Gram-negative bacterium, is the causative agent of plague. is a zoonotic pathogen that occasionally infects humans and became endemic in the western United States after spreading from California in 1899.

Methods: To better understand evolutionary patterns in from the southwestern United States, we sequenced and analyzed 22 novel genomes from New Mexico. Analytical methods included, assembly, multiple sequences alignment, phylogenetic tree reconstruction, genotype-phenotype correlation, and selection pressure.

Results: We identified four genes, including and locus tag YPO3944, which contained codons undergoing negative selection. We also observed 42 nucleotide sites displaying a statistically significant skew in the observed residue distribution based on the year of isolation. Overall, the three genes with the most statistically significant variations that associated with metadata for these isolates were , , and . Phylogenetic analyses point to a single introduction of into the United States with two subsequent, independent movements into New Mexico. Taken together, these analyses shed light on the evolutionary history of this pathogen in the southwestern US over a focused time range and confirm a single origin and introduction into North America.