EOHA ASM 2026

Abstract

Background

Antimicrobial resistance (AMR) is an escalating One Health threat driven by antimicrobial use and environmental dissemination of resistance determinants. Coastal zones are key sentinels because they integrate human and agricultural wastewater inputs with exposure via recreation and seafood consumption.

Objectives

The aim was to profile the resistome —including clinically relevant ARGs (antibiotic resistance genes) and host–ARG associations—along a wastewater-to-beach gradient on Ireland’s west coast.

Methods

We generated 60 shotgun metagenomes (triplicates) from 1-L surface-water samples collected at four sites on six dates in spring and winter 2021: seawater at a raw effluent discharge point (B), seawater from two beaches flanking the discharge (A, C), and an adjacent freshwater stream (F). Quality-filtered reads were taxonomically classified (Kraken2/Bracken) and annotated for ARGs (AMR++) using stringent thresholds. Reads were also screened against a curated panel of clinically relevant ARGs (CARPDM) to distinguish priority signals from background resistomes.

Results

Host–ARG relationships followed a clear spatial gradient (B > F > A/C). A shared core was dominated by Alpha-, Gamma- and Epsilonproteobacteria linked to MLS (Macrolides-Lincosamides-Streptogramins) resistance. Beaches (A, C) also showed Actinomycetes and Alpha-/Betaproteobacteria associated with aminoglycosides, elfamycins, tetracyclines, fluoroquinolones and rifampin. Location B was dominated by Gammaproteobacteria linked to β-lactam, multi-metal and drug/biocide resistance, whereas location F was characterised by drug/biocide resistance across Proteobacteria and prominent Betaproteobacteria–fluoroquinolone/rifampin associations. Clinically relevant ARGs were detected only at locations B and F, dominated by tetracycline and MLS resistance determinants (tet(O), tet(T), tet(X3–X4), mphE/msrE, erm), with additional OXA-type β-lactamase, sul1/sul2, dfr and qac signals mapping mainly to Enterobacterales and other pathogenic genera, including ESKAPE members.

Conclusions

AMR was pervasive across the system, but clinically relevant ARGs were restricted to effluent and freshwater sites and were not detected at beaches, supporting targeted mitigation and routine surveillance at discharge points and upstream sources.