Antibiotic treatment and stewardship in the era of microbiota-oriented diagnostics

Excerpt

Antibiotics are key to the battle against infectious diseases by their capacity to completely block or attenuate microbial growth. Their use is widely accepted and has saved many lives. Still, antibiotic treatment has obvious downsides. For instance, (severe) allergic reactions have been documented and most if not all antibiotics have toxic side effects [1]. Moreover, antibiotics do not specifically target single bacterial species, instead they may extinguish entire (mixed) populations of bacteria. Many of such populations are considered physiologically important. These so-called microbiota, inhabiting all niches in and on our body, are known to have clear and mostly beneficial health effects. Our microbiota, defined as the total ecological community of commensal, symbiotic, and pathogenic microorganisms that inhabit us, are most commonly composed of a mixture of Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Recent nucleic acid sequencing-based efforts have shown great progress in cataloguing this diversity of microbial species: this made us realize that until then, we had only been scratching the surface in identifying human-associated microbes, and had only been assured that many more species are still left to be discovered [2]. …