Secrets of the Hospital Underbelly: Patterns of Abundance of Antimicrobial Resistance Genes in Hospital Wastewater Vary by Specific Antimicrobial and Bacterial Family

Abstract

Background: Hospital wastewater is a major source of antimicrobial resistance (AMR) outflow into the environment. This study uses metagenomics to study how hospital clinical activity impacts antimicrobial resistance genes (ARGs) abundances in hospital wastewater.Methods: Sewage was collected over a 24-h period from multiple wastewater collection points (CPs) representing different specialties within a tertiary hospital site and simultaneously from community sewage works. High throughput shotgun sequencing was performed using Illumina HiSeq4000. ARG abundances were correlated to hospital antimicrobial usage (AMU), data on clinical activity and resistance prevalence in clinical isolates.Results: Microbiota and ARG composition varied between CPs and overall ARG abundance was higher in hospital wastewater than in community influent. ARG and microbiota compositions were correlated (Procrustes analysis, p=0.014). Total antimicrobial usage was not associated with higher ARG abundance in wastewater. However, there was a small positive association between resistance genes and antimicrobial usage matched to ARG phenotype (IRR 1.11, CI 1.06–1.16, p<0.001). Furthermore, analyzing carbapenem and vancomycin resistance separately indicated that counts of ARGs to these antimicrobials were positively associated with their increased usage [carbapenem rate ratio (RR) 1.91, 95% CI 1.01–3.72, p=0.07, and vancomycin RR 10.25, CI 2.32–49.10, p<0.01]. Overall, ARG abundance within hospital wastewater did not reflect resistance patterns in clinical isolates from concurrent hospital inpatients. However, for clinical isolates of the family Enterococcaceae and Staphylococcaceae, there was a positive relationship with wastewater ARG abundance [odds ratio (OR) 1.62, CI 1.33–2.00, p<0.001, and OR 1.65, CI 1.21–2.30, p=0.006 respectively].Conclusion: We found that the relationship between hospital wastewater ARGs and antimicrobial usage or clinical isolate resistance varies by specific antimicrobial and bacterial family studied. One explanation, we consider is that relationships observed from multiple departments within a single hospital site will be detectable only for ARGs against parenteral antimicrobials uniquely used in the hospital setting. Our work highlights that using metagenomics to identify the full range of ARGs in hospital wastewater is a useful surveillance tool to monitor hospital ARG carriage and outflow and guide environmental policy on AMR.

Wastewater surveillance of antibiotic-resistant bacterial pathogens: A systematic review

“…Healthcare settings such as hospitals and nursing homes can act as point sources of contamination of municipal sewerage systems with ARB and ARGs ( Rodriguez-mozaz et al, 2014 ; Khan et al, 2019 ; Perry et al, 2021 ). Greater quantities and different classes of antibiotics are being used in healthcare settings when compared to communities ( ECDC, 2020 ).…”

“…Hospital clinical reported data can be a source of reliable reference information for comparing with the WWS finding, but as mentioned earlier, hospital data represents only a fraction of the problem. Hospital wastewater is considered the next option, but also includes relatively more ARB from clinical isolates ( Perry et al, 2019 , 2021 ; Majlander et al, 2021 ; Hutinel et al, 2022 ). In addition, the geographical region of the sewerage network and hospital coverage area may not necessarily overlap ( Karkman et al, 2020 ; Tiwari et al, 2022d ).…”

Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics

“…Perry et al compared sewage samples from a hospital and the surrounding community sewage plants. The authors modeled the correlation between antimicrobial usage in the hospital and resistance gene abundances and showed that sewage from the hospital has a higher percentage of Antibiotic Resistance Genes (ARGs) compared to the communal sewage samples [ 136 ]. Another interesting function to study would be the microbial association network from microbiome data in order to capture the interactions between the various identified species.…”

Metagenomic Insight into Microbiome and Antibiotic Resistance Genes of High Clinical Concern in Urban and Rural Hospital Wastewater of Northern India Origin: a Major Reservoir of Antimicrobial Resistance

“…This, coupled with open drainage systems and inefficient wastewater treatment plants, can lead to the dissemination of HWW contents, including antimicrobial residues and MDR pathogens, into the local environment and community ( 9 ). Metagenomic surveillance of HWW using short-read next-generation sequencing data is an efficient approach for assessing the overall AMR burden in a given hospital ( 10 – 12 ). Unlike traditional culture- and PCR-based approaches, which are laborious and limited to selected taxa and ARGs, metagenomics can quantify thousands of species, ARGs, and virulence factors (VFs) from a single sample at a relatively low cost.…”