Superbug Arsenal: Antimicrobial Resistance in Hospital and Wastewater Environments

Abstract

Background: Antimicrobial resistance (AMR) is a serious problem with growing threats to the health situation of societies. AMR is particularly important in hospital environments and is a major cause of death in nosocomial (hospital-acquired) infections. Similarly, wastewater is a hotspot for AMR with high bacterial diversity and stress exerted by pollutants, such as antibiotics and heavy metals. Objectives: We sought to get a better insight of AMR in these two environments. Methods: In 30 high-throughput sequenced metagenomes from both environments, we assessed AMR using the open reading frames, called from the assembled contigs, via Resistance Gene Identifier. Taxonomy of the sequences for which AMR could be detected was also determined. Results: Taxonomy generally agreed between both environments for the most abundant families, namely, Enterobacteriaceae, Moraxellaceae, and Pseudomonadaceae. However, for other less abundant families, each environment showed unique distribution. On the genus level, Moraxellaceae and Pseudomonadaceae were mainly dominated by Acinetobacter and Pseudomonas, respectively, which are notorious superbugs. Assessment of AMR identified 1,652 AMR genes belonging to 156 gene families. Tetracycline occupied the top of the list of drug classes for which resistance was detected in both environments, followed by fluoroquinolones in hospital samples and macrolides in wastewater samples. Top resistance mechanisms detected in both environments were efflux pumps and antibiotic inactivation. Accordingly, gene families manifested this pattern of resistance mechanisms with the top three gene families being Resistance-Nodulation-Division (RND) efflux pumps, Major Facilitator Superfamily (MFS) efflux pumps, and OXA-beta-lactamases. Conclusions: Taken together, we shed light on AMR in two particularly important environments, emphasizing the significance of wastewater as a reservoir of resistance.