Abstract
BackgroundIntegrons, especially the class 1 integrons, are major contributors to the acquisition and dissemination of antibiotic resistance genes (ARGs). However, comprehensive knowledge of the types, content, and distribution of integrons in bacterial taxa is lacking to evaluate their contribution.ResultsWe have constructed a new integrase database and developed a pipeline that provides comprehensive recovery of class 1 integrons. Previous PCR-based techniques might only detect one fourth of the integron-integrases and integrons recovered in this study. By exploring the class 1 integrons in over 73,000 currently available complete and draft bacterial genomes, the contribution of class 1 integrons in spreading and acquiring ARGs was evaluated. Firstly, the host species of class 1 integrons are highly conserved within (96%) in class Gammaproteobacteria, dominated by four pathogenic species of “ESKAPE.” Secondly, more than half of class 1 integrons are embedded in chromosomes with less potential for horizontal gene transfer. Finally, ARGs that have been acquired by these integrons only cover 11% of all the ARG genotypes detected in bacterial genomes.ConclusionsThe above observations indicated that there are both biological and ecological limitations to class 1 integrons in acquiring and spreading ARGs across different classes of the domain Bacteria.
Highlights
Integrons, especially the class 1 integrons, are major contributors to the acquisition and dissemination of antibiotic resistance genes (ARGs)
Integrons are the major contributors to the acquisition and dissemination of antibiotic resistance genes (ARGs) [1, 2], and class 1 integrons are the central agents
whole genome database (WGD) collected in this study contains 73,655 complete and draft (≥ 50% completeness on May 11, 2018) genomes (Additional file 1: Table S3)
Summary
Especially the class 1 integrons, are major contributors to the acquisition and dissemination of antibiotic resistance genes (ARGs). Integrons are the major contributors to the acquisition and dissemination of antibiotic resistance genes (ARGs) [1, 2], and class 1 integrons are the central agents. They have been so successful at spreading into diverse clinically relevant taxa that they have been likened to invasive species [3]. A program targeting whole integrons, the IntegronFinder [12], was
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