A workflow for the detection of antibiotic residues, measurement of water chemistry and preservation of hospital sink drain samples for metagenomic sequencing

G Rodger; K Chau; P Aranega-Bou; A Roohi; G Moore; K L Hopkins; S Hopkins; A S Walker; N Stoesser

doi:10.1016/j.jhin.2023.11.021

A workflow for the detection of antibiotic residues, measurement of water chemistry and preservation of hospital sink drain samples for metagenomic sequencing

J Hosp Infect. 2024 Feb:144:128-136. doi: 10.1016/j.jhin.2023.11.021. Epub 2023 Dec 23.

Authors

G Rodger¹, K Chau¹, P Aranega-Bou², A Roohi¹, G Moore², K L Hopkins³, S Hopkins³, A S Walker⁴, N Stoesser⁵

Affiliations

¹ Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Unit in Antimicrobial Resistance and Healthcare-associated Infection, University of Oxford, Oxford, UK.
² Biosafety, Air and Water Microbiology Group, UK Health Security Agency, Porton Down, UK.
³ UK Health Security Agency, Colindale, UK.
⁴ Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Unit in Antimicrobial Resistance and Healthcare-associated Infection, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.
⁵ Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Unit in Antimicrobial Resistance and Healthcare-associated Infection, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK. Electronic address: nicole.stoesser@ndm.ox.ac.uk.

PMID: 38145816
DOI: 10.1016/j.jhin.2023.11.021

Abstract

Background: Hospital sinks are environmental reservoirs that harbour healthcare-associated (HCA) pathogens. Selective pressures in sink environments, such as antibiotic residues, nutrient waste and hardness ions, may promote antibiotic resistance gene (ARG) exchange between bacteria. However, cheap and accurate sampling methods to characterize these factors are lacking.

Aims: To validate a workflow to detect antibiotic residues and evaluate water chemistry using dipsticks. Secondarily, to validate boric acid to preserve the taxonomic and ARG ('resistome') composition of sink trap samples for metagenomic sequencing.

Methods: Antibiotic residue dipsticks were validated against serial dilutions of ampicillin, doxycycline, sulfamethoxazole and ciprofloxacin, and water chemistry dipsticks against serial dilutions of chemical calibration standards. Sink trap aspirates were used for a 'real-world' pilot evaluation of dipsticks. To assess boric acid as a preservative of microbial diversity, the impact of incubation with and without boric acid at ∼22 °C on metagenomic sequencing outputs was evaluated at Day 2 and Day 5 compared with baseline (Day 0).

Findings: The limits of detection for each antibiotic were: 3 μg/L (ampicillin), 10 μg/L (doxycycline), 20 μg/L (sulfamethoxazole) and 8 μg/L (ciprofloxacin). The best performing water chemistry dipstick correctly characterized 34/40 (85%) standards in a concentration-dependent manner. One trap sample tested positive for the presence of tetracyclines and sulphonamides. Taxonomic and resistome composition were largely maintained after storage with boric acid at ∼22 °C for up to five days.

Conclusions: Dipsticks can be used to detect antibiotic residues and characterize water chemistry in sink trap samples. Boric acid was an effective preservative of trap sample composition, representing a low-cost alternative to cold-chain transport.

Keywords: Antibiotic residues; Antimicrobial resistance; Hospital sinks; Water chemistry.

MeSH terms

Ampicillin
Anti-Bacterial Agents* / pharmacology
Boric Acids*
Ciprofloxacin
Doxycycline
Hospitals
Humans
Sulfamethoxazole
Water*
Workflow

Substances

Anti-Bacterial Agents
Water
boric acid
Doxycycline
Sulfamethoxazole
Ampicillin
Ciprofloxacin
Boric Acids