A simple algorithm for identifying integrons and gene cassettes in bacteria on next generation sequencing data

In 21st century, antibiotic resistance is a crucial phenomenon in contemporary medicine and has revealed the serious threat to public health. Integrons are mobile DNA units to capture and incorporate gene cassettes by site-specific recombination, particularly those responsible for antibioticresistance. Meanwhile, integrons has been reported that it could play an important role in transfer of resistance to multiple drugs. In this paper, wepropose a simple and efficient method to identify integrons from raw reads produced by next generation sequencing technology and detect the drugresistantgene from gene cassettes incorporated by the integrons. In the case study, it shows that the proposed method is able to identify the integron and find the resistance genes of Acinetobacter baumannii, TYTH-1.