Antibiotic resistance poses a major threat to human health. It is therefore important to characterize the frequency of resistance within natural bacterial environments. Yet, very little is currently understood about how the frequency of resistance varies between various resistance alleles, different bacterial phyla and various environments. We surveyed a large number of metagenomic datasets extracted from a large variety of host-associated and non-host-associated environments for alleles conferring resistance to three groups of broad spectrum antibiotics: streptomycin, rifamycins, and quinolones. We find notable segregation frequencies of resistance alleles known to confer resistance to 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 ~40%. Within host-associated environments, resistance to quinolones was most often conferred by a specific resistance allele. Interestingly, we have previously found that this particular quinolone resistance allele conferrs a growth advantage on Escherichia coli cells grown in the absence of antibiotics under starvation in micro-colonies. 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 within host-associated environments does not seem to be the sole result of clinical antibiotic usage.
