Escherichia coli strain O55 contains two cryptic plasmids that depend on each other to replicate

Plasmids are fundamental to molecular biology and biotechnology, playing a crucial role in bacterial evolution. Some plasmids are linked to complex cellular dynamics, including pathogenicity islands, antibiotic resistance, and gene mobilization. This study reports the isolation and sequencing of two cryptic plasmids with different electrophoretic mobilities from the Escherichia coli clinical isolate O55. This strain was isolated based on its capacity to bind mannoses on the surface of yeast cells, a property that could be counteracted with methyl α-d-mannoside, a feature used to characterize yeast cell agglutination and, more recently, to assess virulence in Entamoeba histolytica. The strain exhibited no growth differences compared to the laboratory strain E. coli BW25113. Attempts to transform the plasmids independently were unsuccessful; however, they remained stable when the cells were co-transformed. Sequence analysis revealed that both plasmids have conserved counterparts in GenBank (over 100 sequences in Enterobacteriaceae) and can be classified into two distinct groups, regardless of host strain or species. Additionally, in E. coli and Klebsiella pneumoniae isolates, the smaller plasmid was identified as an integrated copy into the genome, aligning with the observation that the plasmids cannot be maintained separately. ORF content analysis identified only putative proteins except for two, one associated with the resistance to aminoglycosides (a functional aminoglycoside O-phosphotransferase), a putative sulfonamide resistance gene, and another associated with a replication protein, suggesting that one plasmid regulates the replication of the other based on AlphaFold3 DNA–protein models. Our findings underscore the importance of further analyzing plasmids in next-generation sequencing data from clinical samples to enhance our understanding of plasmid biology and their impact on the dissemination of pathogenesis-related traits in bacteria.