Characterisation of plasmids in commensal Escherichia coli from healthy Australian adults

Abstract

Commensal Escherichia coli are thought to be an important reservoir of antibiotic resistance determinants, which are disseminated by the actions of translocatable genetic elements and plasmids that can transfer horizontally between cells. However, the plasmids of commensal E. coli and their role in the global spread of resistance genes have not been examined in detail. Here, 16 E. coli strains isolated from a single subject over a 700-day period were added to an existing, diverse collection of E. coli from healthy Australians. The complete collection contains 111 strains, with 51 resistant to one or more antibiotics. The plasmid content of the collection was examined using PCR and sequence-based approaches, revealing that plasmid replicons are far more diverse than previously appreciated. The presence of identical FII, FIB and several different I-complex replicons in unrelated strains from different subjects provided evidence for the dissemination of these types. Furthermore, several different plasmids were shown to have transferred between strains in the gastrointestinal tracts of healthy subjects in the absence of antibiotic selection. The complete sequences of plasmids of various types from this collection that contain antibiotic or heavy metal resistance genes were assembled. Their backbones were defined and used to query the GenBank database, revealing that most were also found in strains associated with infections, and that these plasmids are globally disseminated. The evolution of plasmid lineages via recombination and the actions of translocatable elements was traced, revealing how each lineage acquired and accumulated resistance determinants. This study has demonstrated that plasmids found in commensal E. coli are also found in strains that cause infections. The plasmids are acquiring antibiotic resistance genes and disseminating amongst strains, with the healthy human gastrointestinal tract an important site for their persistence and transfer.