This study explores persistence mechanisms in the pandemic clones Escherichia coli ST131 and Pseudomonas aeruginosa clone C, focusing on survival in host environments during chronic infections through biofilm formation and stress tolerance, respectively. The exopolysaccharide cellulose, a key component of the biofilm extracellular matrix in Escherichia coli and Salmonella typhimurium, is often impaired in invasive isolates to enhance virulence. However, additional distinct cellulose biosynthesis gene clusters, mostly found on plasmids and classified into distinct phylogenetic groups, can be introduced into Escherichia coli. In this study, these horizontally transferred cellulose biosynthesis gene clusters are compared to clusters from non-Escherichia coli plasmids. Comparative phylogenetic and gene cluster analyses revealed cellulose synthase and co-located genes on plasmids harbored by other bacterial species to exhibit high similarity or distinctiveness to the Escherichia coli components. Word cloud analysis indicated Escherichia plasmids with a cellulose gene cluster to predominantly originate from distinct locations, host organisms, and isolation sources. Boxplot analysis demonstrated BcsA-encoding plasmids to be larger. To analyze biofilm development during chronic infection in Escherichia coli ST131, genomic DNA isolation methods were optimized to identify a protocol with superior performance, aiding accurate genome sequencing. In Pseudomonas aeruginosa clone C, molecular chaperones were screened for stress resistance, showing increased susceptibility in mutants, such as those in the two FtsH proteases, to green chemistry reagents. This comprehensive approach combined bioinformatic, and experimental methods to elucidate bacterial stress tolerance mechanisms, providing insights into pathogen adaptation and persistence in various environments and identifying potential targets for antimicrobial strategies.