Diversity of class 1 integrons in an aquatic ecosystem

The emergence and rapid dissemination of antibiotic resistance is a most striking example of evolution in action, driven by lateral gene transfer. Lateral movement of genetic information is largely mediated by mobile genetic elements such as plasmids, transposons, integrons and genomic islands. These elements are able to move within or between genomes, conferring adaptive phenotypes on bacterial recipients. Integrons are genetic elements that have a central role in the dissemination of antibiotic resistance. They are found in diverse lineages of environmental and pathogenic bacteria. Integrons possess a site specific recombination system that captures and expresses genes as a part of mobile gene cassettes. Class 1 integrons are of most clinical importance, being largely responsible for the transmission and ongoing acquisition of new antibiotic resistance genes. The aim of this study was to investigate the evolutionary history of class 1 integrons. I also examined the potential for transmission of class 1 integrons with new gene cassettes into human pathogens and commensals and the potential for exchange of gene cassettes among different classes of integrons. Bacteria were isolated from digestive tracts of uncooked prawns, and screened for the presence of integrons. Most prawns tested were positive for class 1 integrons. A class 1 integron recovered from a Pseudomonas sp. resident in the gut flora of a wild prawn had an unusual structure, and was worthy of detailed characterization. This integron was unusual, firstly in that it contained a functional Tn402-like transposition module, and secondly, that it had two gene cassettes, neither of which encoded antibiotic resistance. One gene cassette was identical to a cassette previously recorded in a chromosomal class 3 integron. This structure represents an example of a key intermediate in the evolution of the clinical class 1 integron, which was previously predicted but never observed. The recovery of such an integron from a natural environment helps confirm our ideas on the likely origin of the integrons and resistance cassettes that are currently in such high abundance in clinical situations. Another unusual class 1 integron was found in an Acinetobacter species isolated from the digestive flora of wild prawn. It possessed features typical of a Tn402-like class 1 integron, in that it contained a 3'-Conserved segment, a cassette array containing a typical aadA2 gene cassette, and an integrase gene with 100% identity to those found in clinical contexts. These features identified it as originating from a clinical source, most likely making its way into the environment via a human waste stream. However, after its release into the natural environment, its structure had been modified by replacement of the Tn402 terminal repeats with miniature inverted-repeat transposable elements (MITEs). It had also acquired a novel gene cassette, msr, that encoded methionine sulfoxide reductases. This is a function and a cassette that had not previously been recorded in any integrons. Further work discovered multiple independent examples of this unusual class 1 integron, present in diverse Acinetobacter species (Acinetobacter johnsonii, Acinetobacter lwoffii and an unnamed Acinetobacter sp.), each of which consisted of multiple clonal lines. PCR mapping of the integron and flanking regions showed that the integron was probably part of a much larger DNA segment that was being mobilized between diverse Acinetobacter strains and species.This demonstrates lateral transfer of this genetic element within and between various species of Acinetobacter in a marine ecosystem. Our observations suggest the potential for rapid dissemination of class 1 integrons among various bacterial strains in aquatic environments, from where they might spread back into human pathogens and commensals. This work also shows that Tn402-like class 1 integrons are recruiting new gene cassettes when they are released into the environment, and that these encode phenotypes unrelated to the neutralization of antibiotics. The msr gene cassette, in particular, may have the potential to enhance bacterial colonization and pathogenicity because it encodes enzymes that repair oxidative damage to proteins. The novel class 1 integrons characterized in this thesis were isolated from opportunistic pathogens (Acinetobacter sp. and Pseudomonas sp.), resident in the gut flora of prawns, which are an important food source and are consumed after only light cooking. This provides a clear pathway for these integrons to make their way back into the human commensal flora, along with any novel genes they might carry. Consequently, we should begin to think about the potential second wave of bacterial adaptation that will result from acquisition of pathogenicity and virulence factors via lateral transfer. These phenotypes will add to the considerable arsenal of resistance genes that are already present in pathogens, and will have unknown consequences for human health and welfare.