The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology
Open accessAbstract
Antibiotic resistance is a dire clinical problem with important ecological dimensions. While antibiotic resistance in human pathogens continues to rise at alarming rates, the impact of environmental resistance on human health is still unclear. To investigate the relationship between human-associated and environmental resistomes, we analyzed functional metagenomic selections for resistance against 18 clinically relevant antibiotics from soil and human gut microbiota as well as a set of multidrug-resistant cultured soil isolates. These analyses were enabled by Resfams, a new curated database of protein families and associated highly precise and accurate profile hidden Markov models, confirmed for antibiotic resistance function and organized by ontology. We demonstrate that the antibiotic resistance functions that give rise to the resistance profiles observed in environmental and human-associated microbial communities significantly differ between ecologies. Antibiotic resistance functions that most discriminate between ecologies provide resistance to β-lactams and tetracyclines, two of the most widely used classes of antibiotics in the clinic and agriculture. We also analyzed the antibiotic resistance gene composition of over 6000 sequenced microbial genomes, revealing significant enrichment of resistance functions by both ecology and phylogeny. Together, our results indicate that environmental and human-associated microbial communities harbor distinct resistance genes, suggesting that antibiotic resistance functions are largely constrained by ecology.
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QIIME allows analysis of high-throughput community sequencing data
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Antibiotic resistance is ancient
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The shared antibiotic resistome of soil bacteria and human pathogens
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Self-citationFunctional characterization of the antibiotic resistance reservoir in the human microflora
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Self-citationTrends in antimicrobial drug development: Implications for the future
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Cited by
CARD 2020: Antibiotic Resistome Surveillance with the Comprehensive Antibiotic Resistance Database
Alcock, B. P., Raphenya, A. R., Lau, T. T. Y., Tsang, K. K., Bouchard, M., Edalatmand, A., Huynh, W., Nguyen, A.-L. V., Cheng, A. A., Liu, S., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz935 · Cited by 3,202
Shotgun metagenomics, from sampling to analysis
Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J., & Segata, N. (2017) · Nature Biotechnology · doi:10.1038/nbt.3935 · Cited by 2,202
Best practices for analysing microbiomes
Knight, R., Vrbanac, A., Taylor, B. C., Aksenov, A., Callewaert, C., Debelius, J., Gonzalez, A., Kosciolek, T., McCall, L.-I., McDonald, D., et al. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0029-9 · Cited by 2,030
Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer
von Wintersdorff, C. J. H., Penders, J., van Niekerk, J. M., Mills, N. D., Majumder, S., van Alphen, L. B., Savelkoul, P. H. M., & Wolffs, P. F. G. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00173 · Cited by 1,707
Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania
Smits, S. A., Leach, J., Sonnenburg, E. D., Gonzalez, C. G., Lichtman, J. S., Reid, G., Knight, R., Manjurano, A., Changalucha, J., Elias, J. E., et al. (2017) · Science · doi:10.1126/science.aan4834 · Cited by 886
Metadata
- Authors
- Gibson, M. K., Forsberg, K. J., & Dantas, G.
- Venue
- The ISME Journal
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-07-08
- Volume
- 9
- Issue
- 1
- Pages
- 207-216
- ISSN
- 1751-7362 (ISSN-L)
- 1751-7370
- OpenAlex
- W1964640602
- Cited by
- 653
- References
- 7
- FWCI
- 19.09
- Type
- journal article
- Language
- en
- Open access
- green
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