Integrons and gene cassettes in clinical isolates of co-trimoxazole-resistant Gram-negative bacteria

Despite a trend of declining consumption, resistance to co-trimoxazole has increased during a 12-year period in Stockholm. The molecular background to this surprising development was investigated by using PCR to screen for integrons and specific resistance genes, followed by sequence analysis of selected integrons, in 105 clinical urinary isolates of Gram-negative bacteria selected partly for trimethoprim resistance. Sixty-five integrons of class 1 or 2 were detected in a subset of 59 isolates, and of these positive isolates, all but one were resistant to trimethoprim. However, 11 isolates were resistant to trimethoprim, but negative for integrons. Isolates positive for integrons were resistant to an average of 4.2 antibiotics, compared with 1.9 antibiotics for integron-negative isolates. Despite this, the only gene cassettes identified in 19 class 1 integrons analysed were dfr and aadA cassettes. Thus, only resistance to trimethoprim, streptomycin, spectinomycin and sulphonamides could be explained by the presence of integrons in these isolates. A new dfr gene, named dfrA22, was discovered as a single gene cassette in a class 1 integron. In addition, sulphonamide resistance in many isolates was caused by carriage of sul2, which has no known association with integrons. Resistance to co-trimoxazole and many other antibiotics was thus not accounted for fully by the presence of integrons in these isolates.