A Study of Vancomycin-Resistant Enterococci Derived From Wastewater Treatment Plants

Abstract

Antimicrobial resistance (AMR) is a growing public health problem and a threat to the sustainability of the global healthcare system. It is not only detected in the clinical setting but also other environments including wastewater treatment plants (WWTPs) which are potential targets for surveillance and points of control for the environmental dissemination of AMR. Vancomycin-resistant enterococci (VRE) are potential candidates as indicator organisms for AMR in water environments. Identification methods for Enterococcus were compared and the groESL locus was the most accurate method. The enterococci/VRE from two WWTPs, a biological aerated filter (BAF) and a conventional activated sludge (CAS) system, from the same municipality collected over 2 years were characterized through quantification, speciation, antimicrobial susceptibility testing, and genomic analysis. The primary effluents (PE) of the two WWTPs were similar in the quantity, species composition, and frequency of AMR of enterococci. VRE were not selectively removed by either WWTP and the BAF system removed enterococci most effectively. Presumptive VRE isolated from the CAS final effluent (FE) included more E. faecium and had increased prevalence of nitrofurantoin resistance and decreased quinupristin/dalfopristin resistance compared to the CAS PE isolates. The BAF FE had a higher proportion of E. faecalis than the CAS FE and a decrease in levofloxacin resistance. The AMR profiles of the isolates after treatment differed from the pre-treatment isolates. Enterococcus isolates (n = 39) were sequenced and were compared with additional genomes from other sources. For E. faecium, wastewater genomes cluster separately from the clinical genomes while, for E. faecalis, wastewater genomes cluster with either clinical or agricultural genomes. Multiple multidrug efflux pumps were detected in the wastewater enterococcal genomes. The majority of virulence genes detected were associated with adhesion, biofilm formation, and capsule formation. Variation in genome size was correlated with the amount of genes associated with the mobilome in E. faecium and E. faecalis. The mobile genetic elements detected were shared among Enterococcus spp. Bacteriophage belonged to Siphoviridae and Myoviridae. Type II CRISPR-Cas arrays were detected in E. faecalis. Understanding the dynamics and characteristics of VRE in wastewater can improve environmental AMR risk assessment frameworks and migitation efforts.