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Antimicrobial peptides, or AMPs, are cationic oligopeptides present across a wide range of organisms, from bacteria to mammals, as part of their natural defense against microbes. The diverse functions and structures of AMPs have attracted considerable attention over the past few decades as possible alternatives to conventional antibiotics. However, there have been some concerns over bacterial resistance to AMPs as much is still unknown about the rates and mechanisms of AMP resistance. Here, we sequenced the genomes of several experimentally evolved Pseudomonas fluorescens populations resistant to high concentrations of pexiganan, a synthetically modified AMP, to investigate the genetic pathways involved in AMP resistance. Our analysis of the sequence data revealed very poor alignment of the pexiganan resistant genomes to the ancestral reference genome. In order to identify possible large structural genetic variants that might explain the poor alignment, de novo assembly and multiple alignment of the genomes were conducted with limited success. Visual inspection of the reference alignments revealed a high number of variants and gaps across the genome, prompting us to suspect possible contamination. A metagenomic analysis of our sequences revealed close alignment to the genome of another Pseudomonas strain closely related to the the ancestral genome of our P. fluorescens populations, suggesting either genome convergence or, most likely, contamination during the original selection experiment. Due to the nature of our findings, we suggest an investigation into previous studies that have utilized these Pseudomonas populations in order to identify the source of contamination and a reevaluation of the results reported in these studies.
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Shrestha, Shailab Darshan, "Identifying candidate mutations responsible for antimicrobial peptide resistance in experimentally evolved Pseudomonas fluorescens." (2016). Senior Projects Spring 2016. 121.