Academic Journal

Identification and reconstruction of novel antibiotic resistance genes from metagenomes

التفاصيل البيبلوغرافية
العنوان: Identification and reconstruction of novel antibiotic resistance genes from metagenomes
المؤلفون: Fanny Berglund, Tobias Österlund, Fredrik Boulund, Nachiket P. Marathe, D. G. Joakim Larsson, Erik Kristiansson
المصدر: Microbiome, Vol 7, Iss 1, Pp 1-14 (2019)
بيانات النشر: BMC, 2019.
سنة النشر: 2019
المجموعة: LCC:Microbial ecology
مصطلحات موضوعية: Antibiotic resistance, Resistome, Environmental sequencing, Gene assembly, Microbiome, Beta-lactamases, Microbial ecology, QR100-130
الوصف: Abstract Background Environmental and commensal bacteria maintain a diverse and largely unknown collection of antibiotic resistance genes (ARGs) that, over time, may be mobilized and transferred to pathogens. Metagenomics enables cultivation-independent characterization of bacterial communities but the resulting data is noisy and highly fragmented, severely hampering the identification of previously undescribed ARGs. We have therefore developed fARGene, a method for identification and reconstruction of ARGs directly from shotgun metagenomic data. Results fARGene uses optimized gene models and can therefore with high accuracy identify previously uncharacterized resistance genes, even if their sequence similarity to known ARGs is low. By performing the analysis directly on the metagenomic fragments, fARGene also circumvents the need for a high-quality assembly. To demonstrate the applicability of fARGene, we reconstructed β-lactamases from five billion metagenomic reads, resulting in 221 ARGs, of which 58 were previously not reported. Based on 38 ARGs reconstructed by fARGene, experimental verification showed that 81% provided a resistance phenotype in Escherichia coli. Compared to other methods for detecting ARGs in metagenomic data, fARGene has superior sensitivity and the ability to reconstruct previously unknown genes directly from the sequence reads. Conclusions We conclude that fARGene provides an efficient and reliable way to explore the unknown resistome in bacterial communities. The method is applicable to any type of ARGs and is freely available via GitHub under the MIT license.
نوع الوثيقة: article
وصف الملف: electronic resource
اللغة: English
تدمد: 2049-2618
Relation: http://link.springer.com/article/10.1186/s40168-019-0670-1; https://doaj.org/toc/2049-2618
DOI: 10.1186/s40168-019-0670-1
URL الوصول: https://doaj.org/article/766b724af9364dd683b3f3b846b0d214
رقم الانضمام: edsdoj.766b724af9364dd683b3f3b846b0d214
قاعدة البيانات: Directory of Open Access Journals
الوصف
تدمد:20492618
DOI:10.1186/s40168-019-0670-1