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

Addresses: 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

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

Received: 25 Feb 2015
Accepted: 25 Feb 2015
Published online: 30 Nov 2015 *

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