Due to the decades of our massive use of antibiotics against human-, animal- and plant pathogens, we selected for resistant microorganisms. Typically, antimicrobial resistance is achieved by mutations in specific genes, or so-called Antimicrobial Resistance Genes (AMGs).
The AMGs can be further transferred to another microorganism which than aquires corresponding AMR. If several different AMRs are picked up by, for example new bacteria, they become multidrug-resistant. In a worst-case scenario, bacteria can become resistant to practically all known antibiotics.
Researchers are constantly searching for new antibiotics and new types of antimicrobials. However, as AMR develops quickly, this is a race against time. Many recent studies have been focused on spread of AMGs in sewage, wastewaters, freshwaters, soils, etc. Unfortunately, it seems that the AMGs are much more frequent in the environment than previously thought and, an urgent global action is needed to prevent further generation of AMR.
Microbiome analysis opens new possibilities to fight AMR. An increased immunization of humans and animals (for example by vaccinations) or improvement of microbiomes (see our other chapters on human, animal and plant microbiomes) can lead to better immunity and lower exposure to antimicrobials. Second, microbiomes can facilitate immunizations by vaccines. Finally, detection of antibiotic-degrading strains or enzymes in microbiomes can help to selectively remove antibiotic before AMR spreads in a given environment.