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

Hua, Guan Jie, Hung, Che Lun, Tang, Chuan Yi and Zheng, Huiru (2016) A simple algorithm for identifying integrons and gene cassettes in bacteria on next generation sequencing data. International Journal of Data Mining and Bioinformatics, 14 (1). p. 40. [Journal article]

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URL: http://dx.doi.org/10.1504/IJDMB.2016.073345

DOI: doi:10.1504/IJDMB.2016.073345

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.

Item Type:Journal article
Keywords:drug resistance, integrons, gene cassettes, next generation sequencing, bacteria, bioinformatics, antibiotic resistance, antibiotics, integron identification, case study, resistance genes, Acinetobacter baumannii, TYTH-1
Faculties and Schools:Faculty of Computing & Engineering
Faculty of Computing & Engineering > School of Computing and Mathematics
Research Institutes and Groups:Computer Science Research Institute > Smart Environments
Computer Science Research Institute
ID Code:33167
Deposited By: Dr Huiru Zheng
Deposited On:09 Mar 2016 14:25
Last Modified:09 Mar 2016 14:25

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