Journal Article

Comparative genomics of multidrug-resistant Enterococcus spp. isolated from wastewater treatment plants

Zaheer, Rahat, Brown, R. Stephen, McAllister, Tim A., Ortega-Polo, Rodrigo, Sanderson, Haley, Goji, Noriko, Liss, Steven N., Amoako, Kingsley K., Majury, Anna

2020

Overview

Background Wastewater treatment plants (WWTPs) are considered hotspots for the environmental dissemination of antimicrobial resistance (AMR) determinants. Vancomycin-Resistant Enterococcus (VRE) are candidates for gauging the degree of AMR bacteria in wastewater. Enterococcus faecalis and Enterococcus faecium are recognized indicators of fecal contamination in water. Comparative genomics of enterococci isolated from conventional activated sludge (CAS) and biological aerated filter (BAF) WWTPs was conducted. Results VRE isolates, including E. faecalis ( n  = 24), E. faecium ( n  = 11), E. casseliflavus (n = 2) and E. gallinarum (n = 2) were selected for sequencing based on WWTP source, species and AMR phenotype. The pangenomes of E. faecium and E. faecalis were both open. The genomic fraction related to the mobilome was positively correlated with genome size in E. faecium ( p  < 0.001) and E. faecalis ( p  < 0.001) and with the number of AMR genes in E. faecium ( p  = 0.005). Genes conferring vancomycin resistance, including van A and van M ( E. faecium ), van G ( E. faecalis ), and van C ( E. casseliflavus / E. gallinarum ), were detected in 20 genomes. The most prominent functional AMR genes were efflux pumps and transporters. A minimum of 16, 6, 5 and 3 virulence genes were detected in E. faecium , E. faecalis , E. casseliflavus and E. gallinarum, respectively. Virulence genes were more common in E. faecalis and E. faecium , than E. casseliflavus and E. gallinarum . A number of mobile genetic elements were shared among species. Functional CRISPR/Cas arrays were detected in 13 E. faecalis genomes, with all but one also containing a prophage. The lack of a functional CRISPR/Cas arrays was associated with multi-drug resistance in E. faecium . Phylogenetic analysis demonstrated differential clustering of isolates based on original source but not WWTP. Genes related to phage and CRISPR/Cas arrays could potentially serve as environmental biomarkers. Conclusions There was no discernible difference between enterococcal genomes from the CAS and BAF WWTPs. E. faecalis and E. faecium have smaller genomes and harbor more virulence, AMR, and mobile genetic elements than other Enterococcus spp .

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Activated sludge / Aeration / Antibiotic resistance / Antibiotics / Antimicrobial agents / Antimicrobial resistance / Arrays / Bacterial Proteins - genetics / Biological Microscopy / Biomarkers / Biomedical and Life Sciences / Biosynthesis / Cell division / Clustering / Comparative genomic hybridization / Contamination / CRISPR / Drug resistance / Drug Resistance, Multiple, Bacterial / Efflux / Enterococci / Enterococcus / Enterococcus faecium - genetics / Environmental aspects / Fecal coliforms / Food / Gaging / Genes / Genetic aspects / Genome Size / Genomes / Genomics / Genomics - methods / genomics and proteomics / Harbors / Infections / Interspersed Repetitive Sequences / Life Sciences / Metabolism / Metabolites / Methods / Microbial genetics / Microbiological research / Microbiology / Mobilome / Motility / Multidrug resistance / Multidrug resistant organisms / Multilocus Sequence Typing / Mycology / Observations / Parasitology / Phages / Phenotypes / Phylogeny / Research Article / Sewage disposal plants / Signal transduction / Vancomycin / Vancomycin Resistance / Vancomycin resistant Enterococcus (VRE) / Virology / Virulence / Virulence Factors - genetics / Wastewater - microbiology / Wastewater treatment / Wastewater treatment plants / Water pollution / Water treatment / Whole Genome Sequencing