Journal
GENOME BIOLOGY AND EVOLUTION
Volume 7, Issue 6, Pages 1743-1757Publisher
OXFORD UNIV PRESS
DOI: 10.1093/gbe/evv102
Keywords
antibiotic resistance; microbiome; metagenomics; allele frequencies
Categories
Funding
- ERC FP7 CIG grant [321780]
- BSF [2013463]
- Yigal Allon Fellowship - Israeli Council for Higher Education
- Robert J. Shillman Career Advancement Chair
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Antibiotic resistance poses a major threat to human health. It is therefore important to characterize the frequency of resistance within natural bacterial environments. Many studies have focused on characterizing the frequencies with which horizontally acquired resistance genes segregate within natural bacterial populations. Yet, very little is currently understood regarding the frequency of segregation of resistance alleles occurring within the housekeeping targets of antibiotics. We surveyed a large number of metagenomic datasets extracted from a large variety of host-associated and non host-associated environments for such alleles conferring resistance to three groups of broad spectrum antibiotics: streptomycin, rifamycins, and quinolones. We find notable segregation frequencies of resistance alleles occurring within the target genes of each of the three antibiotics, with quinolone resistance alleles being the most frequent and rifamycin resistance alleles being the least frequent. Resistance allele frequencies varied greatly between different phyla and as a function of environment. The frequency of quinolone resistance alleles was especially high within host-associated environments, where it averaged an alarming similar to 40%. Within host-associated environments, resistance to quinolones was most often conferred by a specific resistance allele. High frequencies of quinolone resistance alleles were also found within hosts that were not directly treated with antibiotics. Therefore, the high segregation frequency of quinolone resistance alleles occurring within the housekeeping targets of antibiotics inhost-associated environments does not seem to be the sole result of clinical antibiotic usage.
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