The scope of antimicrobial resistance in residential aged care facilities determined through analysis of
Escherichia coli
and the total wastewater resistome
Authors: Sapula Sylvia A. , Amsalu Anteneh , Whittall Jon J. , Hart Bradley J. , Siderius Naomi L. , Nguyen Lynn , Gerber Cobus , Turnidge John , Venter Henrietta 
Published: October 2023

High and often inappropriate antibiotic use has been documented for residential aged care facilities (RACFs). As a result, RACFs represent selective environments favoring the development of antimicrobial resistance (AMR). However, surveillance of the prevalence and scope of AMR in RACFs is limited. Here, wastewater-based epidemiology encompassing culture-based methods in combination with whole genome sequencing and metagenomics allowed for the in-depth analysis of the prevalence of antimicrobial-resistant
Escherichia coli
in two RACFs and one retirement facility. Wastewater was collected at five different time points over 18 months. From these,
E. coli
were isolated and assessed for phenotypic and genotypic resistance. The antimicrobial resistome of each wastewater sample was also determined. A comparison of facilities revealed a higher prevalence of AMR and multidrug-resistant
E. coli
observed in one RACF. The international high-risk
E. coli
clone, ST131, carrying CTX-M-like extended-spectrum beta-lactamases was exclusively isolated from this facility. A high proportion of these isolates were classified as belonging to phylogroups B2 and D, associated with virulent extra-intestinal
E. coli
infections. The resistome of this facility also revealed a higher prevalence of mobile resistance genes such as
sul1
and
sul2
, conferring sulfamethoxazole resistance, the plasmid-mediated quinolone-resistance gene
qnrS
, and
qacEdelta1
that confers biocide resistance. High fluoroquinolone resistance rates were observed in all three sample sites despite measures in place limiting the use of this class of antibiotics. The findings of this study illustrate that RACFs are highly selective environments that require measures to limit AMR development, potentially through antimicrobial stewardship.

IMPORTANCE

Antimicrobial resistance (AMR) is a global threat that imposes a heavy burden on our health and economy. Residential aged care facilities (RACFs), where frequent inappropriate antibiotic use creates a selective environment that promotes the development of bacterial resistance, significantly contribute to this problem. We used wastewater-based epidemiology to provide a holistic whole-facility assessment and comparison of antimicrobial resistance in two RACFs and a retirement village. Resistant
Escherichia coli
, a common and oftentimes problematic pathogen within RACFs, was isolated from the wastewater, and the phenotypic and genotypic AMR was determined for all isolates. We observed a high prevalence of an international high-risk clone, carrying an extended-spectrum beta-lactamase in one facility. Analysis of the entire resistome also revealed a greater number of mobile resistance genes in this facility. Finally, both facilities displayed high fluoroquinolone resistance rates—a worrying trend seen globally despite measures in place aimed at limiting their use.