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

    Research output: Contribution to journalArticle

    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.
    LanguageEnglish
    Pages40
    JournalInternational Journal of Data Mining and Bioinformatics
    Volume14
    Issue number1
    DOIs
    Publication statusPublished - 2016

    Fingerprint

    Integrons
    sound storage medium
    Bacteria
    Genes
    Antibiotics
    Microbial Drug Resistance
    Anti-Bacterial Agents
    drug
    Public health
    Acinetobacter baumannii
    Pharmaceutical Preparations
    Medicine
    Multiple Drug Resistance
    DNA
    public health
    Genetic Recombination
    medicine
    threat
    Public Health
    Technology

    Keywords

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

    Cite this

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    title = "A simple algorithm for identifying integrons and gene cassettes in bacteria on next generation sequencing data",
    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.",
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    author = "Hua, {Guan Jie} and Hung, {Che Lun} and Tang, {Chuan Yi} and Huiru Zheng",
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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; Zheng, Huiru.

    In: International Journal of Data Mining and Bioinformatics, Vol. 14, No. 1, 2016, p. 40.

    Research output: Contribution to journalArticle

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    AU - Hung, Che Lun

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