Comparative metagenomics of controlled and uncontrolled built environments.

Antimicrobial resistance is an increasingly serious threat to global public health, but less is known how microbial control in health care or cleanroom facilities modifies the in-house microbiota and its associated resistome. To understand these human interventions, we compared the microbiota present in abiotic surfaces of clinical settings and other built environments. State-of-the-art metagenomic assembly and binning strategies as well as genome and plasmid reconstructions allowed us to determine that increased confinement and cleaning was associated with a loss of microbial diversity and a shift from Gram-positive (Actinobacteria, Firmicutes) to Gram-negative (Proteobacteria) bacteria as well as within genomes (Acinetobacter). Moreover, the microbiome of highly maintained built environments showed a completely different resistome and present a higher diversity of resistance genes than naturally unrestricted buildings. Our results highlight that the loss of microbial diversity correlates with an increase of resistances and indicate the need of implementing strategies to restore diversity to counteract propagation of resistances in the future.