Environmental antibiotic resistome: selection of HAE-1 efflux pumps in early stages of plant root development

Natural environments are known to be reservoirs for antibiotic resistance genes (ARGs) and human pathogens. Thus, the One Health approach is necessary to fully understand their origin, spread and evolution. Among environments, the rhizosphere - i.e. the volume of soil in contact with plant roots - is of particular interest as it is both a hotspot of bacterial biomass and activity, and ARGs. In this study we investigated the role of the rhizosphere in the selection of antibiotic resistance in its associated bacterial community. We compared the abundance and expression levels of ARGs in seven metagenomes obtained after isotope labeling (DNA-SIP) and eighteen metatranscriptomes of soil and rhizosphere of Avena fatua from six to nine weeks old. ARGs were identified using the CARD database and an in-house HAE-1 (Hydrophobe Amphiphile Efflux-1) efflux pumps database. Our results showed that genes encoding the HAE-1 efflux pumps are enriched in the rhizosphere of six- and nine-week-old plants among the bacteria metabolizing the root exudates, and significantly overexpressed in the rhizosphere of nine-week-old plants. Additionnally, the diversity of HAE-1 pumps expressed in the rhizosphere was observed to be considerable, encompassing the full range of known diversity of these pumps in Gram-negative bacteria. We demonstrated that the environmental conditions in the rhizosphere directly selects for the HAE-1 pumps that is a major multidrug resistance factor in Gram-negative human pathogens. Studying the resistome of the rhizosphere is thus important to understand the emergence of multidrug resistance in human opportunistic pathogens.