Strict relationship between class 1 integrons and resistance to sulfamethoxazole in Escherichia coli

Antibiotic resistance is a health concern. Class 1 integrons (Int1) are genetic elements that contribute to the problem, as they carry different antibiotic resistance genes in their variable region, frequently dfrA (resistance to trimethoprim) and, in their conserved region, the sul1 gene (resistance to sulfonamides, e.g. sulfamethoxazole). These are synthetic antibiotics that work by blocking two enzymes in the folic acid synthesis pathway. In the clinic, the combination of trimethoprim (TMP) and sulfamethoxazole (SMX), called co-trimoxazole (SXT), is widely used. A collection of 230 uropathogenic Escherichia coli strains was studied with three objectives: i) to analyze their phenotype of susceptibility to antifolate antibiotics, ii) to determine the genetic basis of their resistance to SMX, and iii) to correlate the phenotypic and genotypic data with the presence of Int1. The prevalence of resistance to SMX, TMP, and SXT was 54%, 45%, and 41%, respectively. The mobile genes sul1, sul2 and sul3, which confer resistance to sulfonamides, were PCR-surveyed: all sulfa-resistant strains were found to contain at least one of these genes, with the exception of three strains. For these latter, the possibility of being target folP mutants could be ruled out, pointing to the existence of a still unknown mechanism of resistance to SMX in E. coli. All 50 strains previously cataloged as positive for Int1 (because they had an intI1 gene for the integrase) were resistant to SMX: most had sul1, alone or with sul2 or sul3, others only had sul2, and one lacked every sul gene. In addition, 16 sul1⁺intI1^- strains were found to contain other typical integron sequences. That is, in no case was the sul1 gene detected independently of other Int1 sequences. Therefore, we propose that the sul1 gene would be a good marker for the presence of Int1, as well as the intI1 gene. Following this criterion, the prevalence of Int1 in our collection increased from 22% (50 intI1⁺) to 29% (66 intI1⁺ and/or sul1⁺). Of these 66 Int1⁺ strains, 63 were resistant to TMP. The main conclusion in this work is that the presence of a class 1 integron would always require a sulfamethoxazole resistant cellular context. In more general terms, these integrons appear to be closely related to resistance to antifolate compounds.