Man-made microbial resistances in built environments

Abstract

Antimicrobial resistance is a serious threat to global public health, but little is known about the effects of microbial control on the microbiota and its associated resistome. Here we compare the microbiota present on surfaces of clinical settings with other built environments. Using state-of-the-art metagenomics approaches and genome and plasmid reconstruction, we show that increased confinement and cleaning is associated with a loss of microbial diversity and a shift from Gram-positive bacteria, such as Actinobacteria and Firmicutes, to Gram-negative such as Proteobacteria. Moreover, the microbiome of highly maintained built environments has a different resistome when compared to other built environments, as well as a higher diversity in resistance genes. Our results highlight that the loss of microbial diversity correlates with an increase in resistance, and the need for implementing strategies to restore bacterial diversity in certain built environments.

Fig. 1

Microbial diversity estimates. Calculations were executed in MEGAN according to the results of the BLASTx searches against NCBInr. Data of single reads were filtered (unassigned reads were removed) and normalized (randomly and repeatedly subsampled to the smallest sample size). Violin plots showing the kernel probability density of the data, including a box with the median and the interquartile range, were created in R. a Significant differences of Shannon diversity estimates of microbial communities on species level in CB (confined) and UB (unrestricted built environments). b Similar Shannon diversity estimates of microbial functions on highest SEED levels (individual functional gene levels, level 5) in CB (confined) and UB (unrestricted built environments)

Fig. 2

Connection between different built environment types. UPGMA tree (Unweighted Pair Group Method with Arithmetic Mean tree) of sampled built environments based on different microbial communities resolved to species level. Calculations were executed with MEGAN according to the results of the BLASTx searches against NCBInr. Data of single reads were filtered (unassigned reads were removed) and normalized (randomly and repeatedly subsampled to the smallest sample size). Color code for column environment: blue (cleanroom facility); red (intensive care unit); dark green (public buildings); light green (public houses); yellow (private houses)

Fig. 3

Environmental variables associated with the microbiome of sampled built environments. NMDS of 16S rRNA gene amplicons based on Bray–Curtis distances with superimposed vectors representing Spearman correlations of measured environmental variables (bioenv) based on Eucledian distances. Color code for column environment: blue (cleanroom facility); red (intensive care unit); dark green (public buildings); light green (public houses); yellow (private houses)

Fig. 4

An overview of reconstructed genomes. High-quality binned genomes clustered by average nucleotide identity (ANI), resolved to highest taxonomic levels, respective built environment origins, and respective replication rates (activity). Color code for column environment: blue (cleanroom facility); red (intensive care unit); dark green (public buildings); light green (public houses); yellow (private houses)

Fig. 5

Diversity estimates of detected resistance features. Significant differences in Shannon diversity estimates of different resistance features (highest levels, level 3) of the CARD database inside CB (confined) and UB (unrestricted built environments) as well as on binned genomes and plasmids. Data were normalized (rarefied). CARD, Comprehensive Antibiotic Resistance Database

Fig. 6

Resistance network of genomes and plasmids. Potentially transferred (edge-connected) resistance genes (CARD database) according to their presence/absence in binned genomes and plasmids inside the same built environment. Edge-weighted spring-embedded algorithms implemented in Cytoscape were used for visualizations. Filled circles represent genomes and empty circles, plasmids. Most abundant resistance genes were used for labeling and correlated to circle sizes. Colors are defined by respective built environments: blue (cleanroom facility); red (intensive care unit); dark green (public buildings); light green (public houses); yellow (private houses). CARD, Comprehensive Antibiotic Resistance Database

Fig. 7

Proportion of CARD categories and drug classes. a Higher categories of the resistome according to CARD per environment (CB and UB), nucleotide structure (binned genomes and plasmids), and for individual binned genomes (referring to individual species). b Drug classes and their conferred resistance to them according to CARD per environment (CB and UB), nucleotide structure (binned genomes and plasmids), and for individual binned genomes (referring to individual species). CARD, Comprehensive Antibiotic Resistance Database