Genetic context and mobilization of class 1 integrons in Pseudomonas aeruginosa : are plasmids redundant?

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Antibiotic resistance is a global problem with some predicting a return to the pre antibiotic era where a bacterial infection was commonly fatal. Pseudomonas aeruginosa is one example of this problem. This bacterium is a major cause of infection especially in cystic fibrosis sufferers and in burns victims. The rising rates of adverse outcomes are partly a consequence of strains commonly displaying multi-drug resistance (MDR) profiles. MDR is driven by a number of intrinsic mechanisms in P. aeruginosa clinical isolates as well as by the capture of diverse resistance-mediating genes by Lateral Gene Transfer (LGT). LGT and intrinsic factors often act cooperatively to generate complex MDR phenotypes. While these complex interactions have been examined in a small number of isolates there has not been a comprehensive survey of strains on a global scale. Thus it is not clear what mechanisms and genes may be important in influencing the evolution of MDR at regional or global levels. Also, in some isolates, resistance profiles cannot always be explained by identifying the common resistance determining pathways, suggesting that additional mechanisms of resistance may be emerging in P. aeruginosa. The focus of this project was to comprehensively study the major mechanisms responsible for antibiotic resistance in P. aeruginosa strains from diverse geographical areas. Pathogenic P. aeruginosa isolates from four countries (Australia and three South American countries) were characterized by PCR to identify mobile elements and their genetic context. Also, quantitative expression analysis for activity of several pathways that influence antibiotic resistance was assessed and culture experiments were conducted to test how random movement of mobile elements during growth may influence resistance to some antibiotics. Data presented in this thesis indicated that, in most strains, antibiotic resistance was being driven by changes in multiple pathways (including overexpression of AmpC and two efflux pumps) and by the presence or absence of genes acquired by Lateral Gene Transfer (LGT). Class 1 integrons, elements important in the spread of antibiotic resistance genes in Gram-negative bacteria, were most frequently recovered in South American countries. Many class 1 integrons were mapped to a specific location within the genome. Regardless of country of origin all these mapped integrons were found to be in the chromosome, often in Genomic islands, and not on a plasmid despite data in the literature implying the opposite. The association of class 1 integrons with genomic islands may be an important mechanism driving LGT in P. aeruginosa. Also, a newly emerging mechanism involving the insertion sequence IS26 was identified that is capable of mobilizing resistance and other genes. This IS26-mediated mechanism may allow phenotype switching in clonal lines in a way that is likely to further exacerbate the treatment of infections mediated by P. aeruginosa. Data presented here suggested that P. aeruginosa strains are evolving to become multidrug resistant in increasingly complex ways. This is occurring by single strains acquiring changes in numerous known pathways as well as by newly emerging resistance mechanisms in this species.
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