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Class 1 integrons are an important vector for the spread of antibiotic resistance. The core of this genetic element is highly conserved in all class 1 integrons recovered from clinical contexts. Recently, bacteria containing more divergent class 1 integrons have been isolated from environmental samples, suggesting undiscovered diversity in these elements. We performed a culture-independent survey of the class 1 integron-integrase gene ( intI1) from environmental DNA, assessing sequence variation using capillary electrophoresis single-strand conformation polymorphism. This analysis allowed informed selection of environments for further investigation based on the diversity of intI1 targets that were present. IntI1 was common in environmental samples and exhibited previously unsuspected sequence diversity. The method allowed discrimination between clinical and environmental variants of intI1. [ABSTRACT FROM AUTHOR]

Integrons are bacterial genetic elements capable of capturing and expressing potentially adaptive genetic material. Class 1 integrons constitute the most intensely studied group of these elements to date, mainly due to their well-established role in the acquisition and dissemination of antibiotic resistance genes in clinical environments. However, virtually nothing is known about the distribution or abundance of class 1 integrons outside of the clinical context. Here we develop a SYBR Green-based real-time quantitative PCR assay capable of quantifying the abundance of class 1 integrons in environmental samples. It was shown that the abundance of the intI1 gene in creek sediment correlates with ecological condition, implying that class 1 integrons provide selective advantages relevant to environmental pressures other than the use of antibiotics. By comparing the quantities of intI1 and 16S rRNA gene in each sample, it was demonstrated that ∼2.7% of cells potentially harbour a class 1 integron. These findings suggest that class 1 integrons are widespread in natural environments removed from clinical settings and occur in a broader range of host organisms than had previously been assumed on the basis of culture-dependent estimates. [ABSTRACT FROM AUTHOR]