Supplemental Materials for E. Coli Antimicrobial Resistance Research

1. Genetic Capitalism and Stabilizing Selection of Antimicrobial Resistance Genotypes in Escherichia coli

Authors	Paper	Citation	Figures
Colby T. Ford, Ph.D. Gabriel Lopez Zenarosa, Ph.D. Kevin Smith David Brown John Williams Daniel Janies, Ph.D.	https://onlinelibrary.wiley.com/doi/abs/10.1111/cla.12421	@article{doi:10.1111/cla.12421,<br>author = {Ford, Colby T. and Zenarosa, Gabriel Lopez and Smith, Kevin B. and Brown, David C. and Williams, John and Janies, Daniel},<br>title = {Genetic capitalism and stabilizing selection of antimicrobial resistance genotypes in Escherichia coli},<br>journal = {Cladistics},<br>year = {2020},<br>doi = {10.1111/cla.12421},<br>url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cla.12421},<br>eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cla.12421}<br>}	Tableau Viz

Abstract

Antimicrobial resistance (AMR) in pathogenic strains of bacteria, such as Escherichia coli (E. coli), adversely impact personal and public health. In this study, we examine competing hypotheses for the evolution of AMR including: 1) “genetic capitalism” in which genotypes that confer antibiotic resistance are gained and not often lost in lineages, and 2) “stabilizing selection” in which genotypes that confer antibiotic resistance are gained and lost often. To test these hypotheses, we assembled a dataset that includes annotations for 409 AMR genotypes and a phylogenetic tree based on genome-wide single nucleotide polymorphisms from 29,255 isolates of E. coli. We used phylogenetic methods to count the times each AMR genotype was gained and lost across the tree and used model-based clustering of the genotypes with respect to their gain and loss rates. We demonstrate that many genotypes cluster to support the hypothesis for genetic capitalism while a few cluster to support the hypothesis for stabilizing selection. Comparing the sets of genotypes that fall under each of the hypotheses, we found a statistically significant difference in the breakdown of resistance mechanisms through which the AMR genotypes function. The result that many AMR genotypes cluster under genetic capitalism reflects that strong positive selective forces, primarily induced by human industrialization of antibiotics, outweigh the potential fitness costs to the bacterial lineages for carrying the AMR genotypes. We expect genetic capitalism to further drive bacterial lineages to resist antibiotics. We find that antibiotics that function via replacement and efflux tend to behave under stabilizing selection and thus may be valuable in an antibiotic cycling strategy.

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2. Multidrug Resistance Genes Associated with Colistin Resistance

Authors	Paper	Citation
Gabriel Lopez Zenarosa, Ph.D. Colby T. Ford, Ph.D. David Brown Kevin Smith Daniel Janies, Ph.D.	Coming Soon	Coming Soon