Novel approaches to monitoring antimicrobial resistance in aquatic environments

Abstract

Combined sewer overflows represent a poorly characterised but potentially significant pathway for the environmental dissemination of antimicrobial resistance (AMR), yet the monitoring tools currently used in riverine surveillance — principally streambed sediment sampling — are poorly suited to capturing the episodic, CSO-driven resistance signals most relevant to public health risk. This thesis addresses that limitation through an original empirical investigation of AMR dynamics in the Ballysally Blagh, a CSO-impacted peri-urban stream in Northern Ireland.

Using shotgun metagenomics across two contrasting seasons, three longitudinal sites, and four sampling matrices — natural sediments and three standardised surrogate substrates — the thesis demonstrates that surrogate substrates recover a substantially broader and more clinically informative resistome than sediment alone. Of 1,077 resistance genes identified across 269 ARG families, 30 CSO-proximal ARGs — including carbapenemases, sulfonamide resistance genes, and oxazolidinone resistance — were entirely absent from concurrent sediment samples. Matrix type was the sole significant determinant of resistome composition, and surrogate substrates detected 15 microbial taxa absent from sediment, including biogeographically anomalous organisms consistent with wastewater inputs from the Coleraine catchment.

Complementary conjugation experiments demonstrated that surface colonisation on granular activated carbon enhanced plasmid transfer in Enterococcus faecalis, and that sub-inhibitory rifampicin adsorbed to granular activated carbon modulated this transfer in a strain- and substrate-dependent manner, extending prior work on GAC-mediated conjugation by resolving the differential effects of specific adsorbed antibiotics across multiple donor-recipient pairings.

Together, these findings establish a new empirical and methodological basis for freshwater AMR surveillance and demonstrate the inadequacy of sediment-only monitoring for detecting clinically significant resistance in CSO-impacted systems.

Thesis embargoed until 30 June 2028

Date of Award	Jun 2026
Original language	English
Sponsors	Vice Chancellor's Research Scholarship (VCRS)
Supervisor	James Dooley (Supervisor) & Joerg Arnscheidt (Supervisor)