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NOVEL INSIGHTS INTO SELECTION FOR ANTIBIOTIC RESISTANCE IN COMPLEX MICROBIAL COMMUNITIES

By Aimee K. Murray, Lihong Zhang, Xiaole Yin, Tong Zhang, Angus Buckling, Jason Snape, William H. Gaze

Posted 16 May 2018
bioRxiv DOI: 10.1101/323634 (published DOI: 10.1128/mBio.00969-18)

Recent research has demonstrated selection for antibiotic resistance occurs at very low antibiotic concentrations in single species experiments, but the relevance of these findings when species are embedded in complex microbial communities is unclear. We show the strength of selection for naturally occurring resistance alleles in a complex community remains constant from low sub-inhibitory to above clinically relevant concentrations. Selection increases with antibiotic concentration before reaching a plateau where selection remains constant over a two order magnitude concentration range. This is likely to be due to cross-protection of the susceptible bacteria in the community following rapid extracellular antibiotic degradation by the resistant population, shown experimentally through a combination of chemical quantification and bacterial growth experiments. Metagenome and 16S rRNA analyses on sewage-derived bacterial communities evolved under cefotaxime exposure show preferential enrichment for blaCTX-M genes over all other beta-lactamase genes, as well as positive selection and co-selection for antibiotic resistant, opportunistic pathogens. These findings have far reaching implications for our understanding of the evolution of antibiotic resistance, by challenging the long-standing assumption that selection occurs in a dose-dependent manner.

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