Determining Hosts of Antibiotic Resistance Genes: A Review of Methodological Advances

Advancing environmental research on antibiotic resistance will require developing better databases of not only the occurrences of antibiotic resistance genes (ARGs) in the environment but also which microorganisms host those ARGs, as hosts are critical to determining risk to human health. This brief review critically evaluates methods that link ARGs with their hosts, including correlation analysis, metagenomics, fluorescence-activated cell sorting, single-cell fusion polymerase chain reaction, and genomic cross-linking. Existing data sets that have identified host–ARG relationships in wastewater, livestock waste, freshwater sediments, landfills, and human gut microbiomes have been compiled and summarized. Data aggregation allowed us to identify dominant hosts of ARGs across all studies and also revealed an immense diversity in the types of ARGs and their hosts. The process also exposed a clear need for more data on ARG hosts across different environments, more resolved phylogenetic identification of ARG hosts, and standardized metadata collection. With the emergence of culture-independent methods that directly link ARGs and hosts, dominant environmental reservoirs of ARGs and a priority list of high-risk ARG hosts can be identified and subsequently used to design interventions to reduce the spread of ARGs to pathogenic bacteria.