Human microbiomes and antibiotic resistance

Human microbiomes are complex ecosystems involving bacteria, viruses, archaea or eukaryotes that are co-evolving in an environment subject to various selective pressures, such as antibiotic administration, diet and/or lifestyle. In this sympatric lifestyle, competition is hard and the synthesis of antibiotic molecules and/or antibiotic resistance genes (ARGs) is one solution that was developed by the organisms to survive. This environment becomes a large source of ARGs for pathogenic bacteria, leading to the risk of infection due to multidrug resistant bacteria. Culture and metagenomics are two complementary methods developed to study these microbiomes in order to better understand the type of bacteria and ARGs present in the human body, as well as the factors that modulate the abundance and variety of these ARGs. The objective of this review was to identify factors that influence the colonization and propagation of multidrug resistant bacteria and/or ARGs, and to define resistance genes and multidrug resistant bacteria that have already been isolated from the human microbiota using culturomics and metagenomics techniques.