Evidence for wastewaters as environments where mobile antibiotic resistance genes emerge

Abstract

The emergence and spread of mobile antibiotic resistance genes (ARGs) in pathogens have become a serious threat to global health. Still little is known about where ARGs gain mobility in the first place. Here, we aimed to collect evidence indicating where such initial mobilization events of clinically relevant ARGs may have occurred. We found that the majority of previously identified origin species did not carry the mobilizing elements that likely enabled intracellular mobility of the ARGs, suggesting a necessary interplay between different bacteria. Analyses of a broad range of metagenomes revealed that wastewaters and wastewater-impacted environments had by far the highest abundance of both origin species and corresponding mobilizing elements. Most origin species were only occasionally detected in other environments. Co-occurrence of origin species and corresponding mobilizing elements were rare in human microbiota. Our results identify wastewaters and wastewater-impacted environments as plausible arenas for the initial mobilization of resistance genes.

Fig. 1. Relative abundance and prevalence of 22 known origin species.

Average relative abundance of the 22 investigated origin species in different environments (2496 samples) normalized by each species’ highest relative abundance (a), and the prevalence of the 22 investigated origin species as fraction of samples with detectable levels of the corresponding species within each environment type (b). Some environments are excluded from the analysis in (b) due to too few identified bacterial fragments.

Fig. 2. Origin species’ genomes carrying IS elements associated with mobilization from the corresponding species.

Fraction of genomes (chromosome in (a) and plasmid in (b)) carrying any of the IS elements showed to have been involved in mobilization of an antibiotic resistance gene (ARG) from the studied origin species. A cross indicates that the IS has likely been involved in the mobilization of an ARG from the corresponding species. A gray color of the species name indicates that there were fewer than five genomes used in the analysis.

Fig. 3. Relative abundance of IS elements.

The average relative abundance of specific IS elements likely to have been involved in the mobilization of an antibiotic resistance gene (MISE) (a) and relative abundance of all IS elements (b). Boxplot: A box represents the first (Q1) and third (Q3) quartile (the 25–75th percentile), the centerline represents the median. The dots represent values larger or smaller than Q1−1.5 or Q3 + 1.5 times the inter-quartile range.

Fig. 4. Co-existing origin species and mobilizing IS elements.

Fractions of samples that contained both an origin species and an IS elements involved in mobilization (MISE) for the following subsets of data, (a) combined soil and water environments where no crAssphage was detected (n = 391), (b) combined soil and water environments with detectable levels of crAssphage (n = 22), (c) human stool (n = 384), (d) influent of wastewater treatment plants (n = 102).