Surveillance of Enterococcus spp. reveals distinct species and antimicrobial resistance diversity across a One-Health continuum

Abstract

for a one-Health investigation of antimicrobial resistance (AMR) in Enterococcus spp., isolates from humans and beef cattle along with abattoirs, manured fields, natural streams, and wastewater from both urban and cattle feedlot sources were collected over two years. Species identification of Enterococcus revealed distinct associations across the continuum. Of the 8430 isolates collected, Enterococcus faecium and Enterococcus faecalis were the main species in urban wastewater (90%) and clinical human isolates (99%); Enterococcus hirae predominated in cattle (92%) and feedlot catch-basins (60%), whereas natural streams harbored environmental Enterococcus spp. Wholegenome sequencing of E. faecalis (n = 366 isolates) and E. faecium (n = 342 isolates), revealed source clustering of isolates, indicative of distinct adaptation to their respective environments. phenotypic resistance to tetracyclines and macrolides encoded by tet(M) and erm(B) respectively, was prevalent among Enterococcus spp. regardless of source. for E. faecium from cattle, resistance to β-lactams and quinolones was observed among 3% and 8% of isolates respectively, compared to 76% and 70% of human clinical isolates. clinical vancomycin-resistant E. faecium exhibited high rates of multi-drug resistance, with resistance to all β-lactam, macrolides, and quinolones tested. Differences in the AMR profiles among isolates reflected antimicrobial use practices in each sector of the One-Health continuum. Public concern for antimicrobial use (AMU) and resistance (AMR) in livestock is increasing, as is continuing pressure for industries and governments to address these concerns. Science-based and epidemiologically sound research is critical to drive policy, communication, legislation, and inform consumer choices. To effectively investigate the current state of antimicrobial resistance, holistic One Health approaches are required to determine correlation between AMU and AMR across the human-agriculture-environment continuum. The genus Enterococcus is ubiquitous in nature and member species can be found in a range of habitats including soils, sediments, freshwater, marine water, beach sand, and a variety of plants 1,2. Enterococcus spp. are also common members of the normal gastrointestinal (GI) flora of both livestock and humans 3 , with their concentrations in human and animal feces typically ranging from 10 3-10 7 cells per gram 4-6. Enterococcus spp. are also commonly isolated from water contaminated by sewage or fecal wastes, and are widely used as bacteriological

Antimicrobial Resistance Gene Detection and Plasmid Typing Among Multidrug Resistant Enterococci Isolated from Freshwater Environment

“…Three streptomycin-resistant isolates were tested for the presence of the two commonly detected streptomycin resistance genes, but only one isolate carried ant(6)-Ia. The high prevalence of ant(6)-Ia was also observed in other studies, not only for human and animals but also for environmental water [4,13,30,32,33].…”

A One Health Comparative Assessment of Antimicrobial Resistance in Generic and Extended-Spectrum Cephalosporin-Resistant Escherichia coli from Beef Production, Sewage and Clinical Settings

“…Descriptive analysis comparing the distributions of resistance (R), intermediate (I) and susceptible (S) E. coli , MDR and ESBL-resistant phenotypes as well as β-lactamase genotypes was performed with PROC FREQ (SAS software, version 9.4 SAS Institute, Cary, North Carolina, USA). Isolates were categorized as MDR if they showed resistance to antimicrobial agents in ≥2 different antimicrobial classes [ 49 , 50 ]. To compare the effect of isolate source on AMR in both ESC r and generic E. coli sub-populations, univariate multinomial logistic regression models were fitted to the data using the SAS GLIMMIX procedure [ 13 , 51 ].…”

Enterococci, from Harmless Bacteria to a Pathogen

“…Until 1984, the enterococci were considered as part of the genus Streptococcus , but they have constituted a unique taxonomic entity since the mid-1980s [ 4 , 5 ]. Today, over 50 different species of enterococci have been described, of which E. faecium and E. faecalis are the most common in the human gastrointestinal tract, whereas, among farm animals E. faecium together with E. cecorum , E. faecalis and, to some extent, E. hirae predominate, while E. mundtii and E. casseliflavus are commonly found in plant sources [ 6 , 7 ]. Moreover, ecology and epidemiological studies have reported E. faecalis and E. faecium as frequently isolated from food products (cheese, fish, sausages, minced beef, and pork) and the environment (sewage, soil, and water) [ 8 ].…”