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Antibiotic susceptible bacteria can develop resistance to antibiotics through different genetic pathways. Among the most important are mutations occurring within the genome, and the acquisition through horizontal genetic transfer (HGT) of additional genes that can reduce susceptibility to antibiotics, located in mobile genetic elements such as plasmids. The discovery of pathogenic strains of Escherichia coli and Klebsiella pneumoniae that have a chromosome with at least 20% (> 1 Mb) of DNA originating from a foreign strain suggest that an alternative pathway remains unexplored: the conjugative transfer of large areas of chromosomal DNA, generating bacterial strains with hybrid chromosomes. The projects presented in this thesis focused on studying different aspects about the generation of chromosomal hybrids.  

We first designed and implemented a conjugation method that allows for the selection of bacteria with hybrid chromosomes from large populations and found that a large proportion of clinical strains of E. coli are capable of mobilizing their chromosome and can generate hybrids. Genome sequencing showed that several Mb of foreign DNA could be integrated into the recipient’s chromosome. Multiple resistance genes and alleles could be acquired simultaneously and without direct selection are maintained stably by the hybrid. Furthermore, we showed that any one conjugative mobile element, be it plasmid or ICE, was itself sufficient to mobilize the chromosome. 

In the second project, we studied interspecies hybrids of K. pneumoniae clinical isolates and E. coli laboratory strains. We found chromosomal hybrids to be stable in the absence of selective pressure and fit for growth. 

Third, we initiated a study to identify biological barriers that inhibit the formation of chromosomal hybrids in nature. We used both phenotypic selection and transposon generated mutants of the clinical E. coli strain ATCC25922 to identify genes which, when inactivated, lower the conjugation barrier to the formation of hybrids.  

Finally, we explored whether E. coli could maintain prototrophy in the absence of HGT by acquiring compensatory mutations within its genome. We found that compensatory bypass mechanisms in mutants with gene deletions causing auxotrophy were accessible only to a handful of pathways for amino acid synthesis. 

These results highlight the importance of HGT in bacterial survival and evolution.