As persistent residents of planktonic bacterial cultures, small colony variants (SCVs) constitute a slow-growing subpopulation with atypical colony morphology and unusual biochemical characteristics that, in the case of clinical isolates, cause latent and recurrent infections. We propose a novel blueprint for the formation of E. coli SCVs through DNA microarray analysis, coupled with complete genome sequencing and verification by qRT-PCR. While others have used DNA microarrays to study quorum sensing in E. coli SCVs, our work represents the first proposal for a combination of novel mutations, amplified by a differential shift in expression of select gene groups that work in concert to establish and maintain the SCV phenotype. This combination of genetic and expression events fall under selective pressure, leading to unequal fitness in our strain, SCV IH9 versus its parental strain, BW7261 (a MG1655 descendant). We hypothesize that this combination of events would ordinarily be lethal for bacteria, but instead confers a survival advantage to SCV IH9 due to its slow growth and resistance to acidic and oxidative stress challenges.