Comparative sequence analysis elucidates the evolutionary patterns of Yersinia pestis in New Mexico over thirty-two
Mary E Warren1, Brett E Pickett1, Byron J Adams2,3
1Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States.
Background:
Yersinia pestis, a Gram-negative bacterium, is the causative agent of plague. Y. pestis 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 Y. pestis 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 Yscp 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 sapA, fliC, and argD. Phylogenetic analyses point to a single introduction of Y. pestis 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.
Insights
Genomic analysis of Yersinia pestis in the southwestern US reveals a single introduction event and identifies key genes under selection. This study enhances understanding of plague
Area of Science:
- Microbiology
- Evolutionary Biology
- Genomics
Background:
- Yersinia pestis is a Gram-negative bacterium responsible for plague.
- This zoonotic pathogen became endemic in the western United States in 1899.
- The bacterium occasionally infects humans, posing a public health risk.
Purpose of the Study:
- To investigate the evolutionary history of Yersinia pestis in the southwestern United States.
- To identify genetic variations and selection pressures within Y. pestis populations.
- To determine the introduction and dissemination patterns of Y. pestis in the region.
Main Methods:
- Sequencing and analysis of 22 novel Yersinia pestis genomes from New Mexico.
- Bioinformatic analyses including sequence alignment, phylogenetic tree reconstruction, and selection pressure analysis.
- Genotype-phenotype correlation and examination of nucleotide site variations over time.
Main Results:
- Identified four genes, including Yscp and YPO3944, with codons under negative selection.
- Observed 42 nucleotide sites with significant residue distribution skew correlated with isolation year.
- Phylogenetic analysis indicated a single introduction of Y. pestis to the US and two independent movements into New Mexico.
Conclusions:
- The study elucidates the evolutionary trajectory of Yersinia pestis in the southwestern US.
- Confirmed a single origin and introduction of the pathogen into North America.
- Highlighted specific genes (sapA, fliC, argD) associated with significant evolutionary variations.
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