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Computational disco...
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Boulund, Fredrik,1985Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper,CARe - Centrum för antibiotikaresistensforskning,Department of Mathematical Sciences,Centre for antibiotic resistance research, CARe
(författare)
Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets
- Artikel/kapitelEngelska2017
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2017-09-02
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Springer Science and Business Media LLC,2017
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electronicrdacarrier
Nummerbeteckningar
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LIBRIS-ID:oai:research.chalmers.se:cf9ec7b9-0925-41ac-bf52-7520e4b84ae1
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https://research.chalmers.se/publication/252050URI
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https://doi.org/10.1186/s12864-017-4064-0DOI
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https://gup.ub.gu.se/publication/257530URI
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Språk:engelska
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Sammanfattning på:engelska
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Ämneskategori:art swepub-publicationtype
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Ämneskategori:ref swepub-contenttype
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Background: Fluoroquinolones are broad-spectrum antibiotics used to prevent and treat a wide range of bacterial infections. Plasmid-mediated qnr genes provide resistance to fluoroquinolones in many bacterial species and are increasingly encountered in clinical settings. Over the last decade, several families of qnr genes have been discovered and characterized, but their true prevalence and diversity still remain unclear. In particular, environmental and host-associated bacterial communities have been hypothesized to maintain a large and unknown collection of qnr genes that could be mobilized into pathogens. Results: In this study we used computational methods to screen genomes and metagenomes for novel qnr genes. In contrast to previous studies, we analyzed an almost 20-fold larger dataset comprising almost 13 terabases of sequence data. In total, 362,843 potential qnr gene fragments were identified, from which 611 putative qnr genes were reconstructed. These gene sequences included all previously described plasmid-mediated qnr gene families. Fifty-two of the 611 identified qnr genes were reconstructed from metagenomes, and 20 of these were previously undescribed. All of the novel qnr genes were assembled from metagenomes associated with aquatic environments. Nine of the novel genes were selected for validation, and six of the tested genes conferred consistently decreased susceptibility to ciprofloxacin when expressed in Escherichia coli. Conclusions: The results presented in this study provide additional evidence for the ubiquitous presence of qnr genes in environmental microbial communities, expand the number of known qnr gene variants and further elucidate the diversity of this class of resistance genes. This study also strengthens the hypothesis that environmental bacterial communities act as sources of previously uncharacterized qnr genes.
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Berglund, Fanny,1988Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper,CARe - Centrum för antibiotikaresistensforskning,Department of Mathematical Sciences,Centre for antibiotic resistance research, CARe(Swepub:gu)xberfa
(författare)
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Flach, Carl-Fredrik,1977Gothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för infektionssjukdomar,CARe - Centrum för antibiotikaresistensforskning,Institute of Biomedicine, Department of Infectious Medicine,Centre for antibiotic resistance research, CARe(Swepub:gu)xflaca
(författare)
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Bengtsson-Palme, Johan,1985Gothenburg University,Göteborgs universitet,CARe - Centrum för antibiotikaresistensforskning,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Centre for antibiotic resistance research, CARe,Institute of Biomedicine, Department of Infectious Medicine(Swepub:gu)xbengg
(författare)
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Marathe, NachiketGothenburg University,Göteborgs universitet,CARe - Centrum för antibiotikaresistensforskning,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Centre for antibiotic resistance research, CARe,Institute of Biomedicine, Department of Infectious Medicine(Swepub:gu)xmarna
(författare)
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Larsson, D. G. Joakim,1969Gothenburg University,Göteborgs universitet,CARe - Centrum för antibiotikaresistensforskning,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Centre for antibiotic resistance research, CARe,Institute of Biomedicine, Department of Infectious Medicine(Swepub:gu)xlarjo
(författare)
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Kristiansson, Erik,1978Gothenburg University,Göteborgs universitet,CARe - Centrum för antibiotikaresistensforskning,Institutionen för matematiska vetenskaper,Centre for antibiotic resistance research, CARe,Department of Mathematical Sciences(Swepub:gu)xkrier
(författare)
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Göteborgs universitetInstitutionen för matematiska vetenskaper
(creator_code:org_t)
Sammanhörande titlar
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Ingår i:BMC Genomics: Springer Science and Business Media LLC18:1, s. Art 682-1471-2164
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