Overexpression of the ABC transporter genes patA and patB confers efflux-mediated fluoroquinolone resistance in Streptococcus\npneumoniae and is also linked to pneumococcal stress responses. Although upregulation of patAB has been observed in many\nlaboratory mutants and clinical isolates, the regulatory mechanisms controlling expression of these genes are unknown. In this\nstudy, we aimed to identify the cause of high-level constitutive overexpression of patAB in M184, a multidrug-resistant mutant\nof S. pneumoniae R6. Using a whole-genome transformation and sequencing approach, we identified a novel duplication of a\n9.2-kb region of the M184 genome which included the patAB genes. This duplication did not affect growth and was semistable\nwith a low segregation rate. The expression levels of patAB in M184 were much higher than those that could be fully explained by\ndoubling of the gene dosage alone, and inactivation of the first copy of patA had no effect on multidrug resistance. Using a green\nfluorescent protein reporter system, increased patAB expression was ascribed to transcriptional read-through from a tRNA gene\nupstream of the second copy of patAB. This is the first report of a large genomic duplication causing antibiotic resistance in S.\npneumoniae and also of a genomic duplication causing antibiotic resistance by a promoter switching mechanism.
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