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dc.contributor.authorBerglund, Fanny
dc.contributor.authorOsterlund, Tobias
dc.contributor.authorBoulund, Fredrik
dc.contributor.authorMarathe, Nachiket
dc.contributor.authorLarsson, D.G. Joakim
dc.contributor.authorKristiansson, Erik
dc.date.accessioned2020-01-17T09:04:31Z
dc.date.available2020-01-17T09:04:31Z
dc.date.created2019-08-01T16:46:39Z
dc.date.issued2019
dc.identifier.citationMicrobiome. 2019, 7 1-14.nb_NO
dc.identifier.issn2049-2618
dc.identifier.urihttp://hdl.handle.net/11250/2636772
dc.description.abstractBackground 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.nb_NO
dc.language.isoengnb_NO
dc.titleIdentification and reconstruction of novel antibiotic resistance genes from metagenomesnb_NO
dc.typeJournal articlenb_NO
dc.typePeer reviewednb_NO
dc.description.versionpublishedVersionnb_NO
dc.source.pagenumber1-14nb_NO
dc.source.volume7nb_NO
dc.source.journalMicrobiomenb_NO
dc.identifier.doi10.1186/s40168-019-0670-1
dc.identifier.cristin1713714
cristin.unitcode7431,33,0,0
cristin.unitnameFremmed- og smittestoff
cristin.ispublishedtrue
cristin.fulltextoriginal
cristin.qualitycode1


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