Antibiotic resistance gene analyses in microbial communities: challenges and opportunities

Culture-independent antibiotic resistance gene analyses enable broad explorations of microbial communities but often fail to link such genes to bacterial hosts and genetic contexts. This makes assessing prevalence of resistant pathogens and likelihood of further transmission or resistance evolution uncertain. There is an increasing interest in studying antibiotic resistance genes in microbial communities, however, there is no unified way to identify them in metagenomics datasets or to interpret the risks associated with them. In this Comment, the authors discuss current technical challenges and how to mitigate them.