Int. J. of Data Mining and Bioinformatics   »   2016 Vol.14, No.1



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


Authors: Guan-Jie Hua; Che-Lun Hung; Chuan Yi Tang; Huiru Zheng


Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
Department of Computer Science and Communication Engineering, Providence University, Taichung, Taiwan
Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
School of Computing and Mathematics, University of Ulster, Newtownabbey, UK


Abstract: 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 antibiotic resistance. Meanwhile, integrons has been reported that it could play an important role in transfer of resistance to multiple drugs. In this paper, we propose a simple and efficient method to identify integrons from raw reads produced by next generation sequencing technology and detect the drug-resistant gene 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.


Keywords: drug resistance; integrons; gene cassettes; next generation sequencing; bacteria; bioinformatics; antibiotic resistance; antibiotics; integron identification; case study; resistance genes; Acinetobacter baumannii; TYTH-1.


DOI: 10.1504/IJDMB.2016.073345


Int. J. of Data Mining and Bioinformatics, 2016 Vol.14, No.1, pp.40 - 50


Submission date: 25 Feb 2015
Date of acceptance: 25 Feb 2015
Available online: 30 Nov 2015



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