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

Guan Jie Hua, Che Lun Hung*, Chuan Yi Tang, Huiru Zheng

*Corresponding author for this work

Research output: Contribution to journalJournal Article peer-review

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 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.

Original languageEnglish
Pages (from-to)40-50
Number of pages11
JournalInternational Journal of Data Mining and Bioinformatics
Volume14
Issue number1
DOIs
StatePublished - 2016
Externally publishedYes

Bibliographical note

Publisher Copyright:
Copyright © 2016 Inderscience Enterprises Ltd.

Keywords

  • Bacteria
  • Drug resistance
  • Gene cassettes
  • Integron
  • Next generation sequencing

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