Abstract
Tracking trouble: sources, persistence, and risk factors of antimicrobial-resistant Escherichia spp in freshwater fish farms of north-west france
Antimicrobial resistance (AMR) represents a growing threat to human health, environmental integrity and animal populations. Its impact on aquaculture may be particularly alarming, given the essential role this sector plays in global food security through sustainable protein production. As it depends on surface water, fish farming is particularly exposed to microbial contamination from wastewater effluents and agricultural runoff, despite regulations. Climate events further complicate this issue, altering pollutant dynamics and amplifying the risk of AMR spread. In aquaculture environments, resistant bacteria can be introduced through multiple pathways, including contaminated water and interactions between fecal and aquatic microbial communities.
This study explores how antimicrobial-resistant Escherichia spp. could be introduced and persist in freshwater fish farms located in France. We sampled both external sources (water and feed) and potential reservoirs inside farm environment (sediment and biofilm). Particular focus was on E. coli and E. marmotae , indicators of fecal livestock, poultry, and human contamination, and recognized as AMR sentinels
This observational longitudinal study was carried out in four fish farms: two flow-through systems (Farm C & D) and two recirculating aquaculture systems (Farm A & B). For each system type, one farm was located downstream from a wastewater treatment plant (Farm B & D), offering a high-risk scenario for AMR exposure. Samples were collected seasonally, following an established protocol (Novais et al., 2018).In total, 452 samples were obtained. Escherichia isolates were identified using MALDI-TOF mass spectrometry, and all confirmed isolates (243) were tested for antimicrobial susceptibility by broth microdilution against a panel of 15 antibiotics. Complementary surveys gathered data on farm management practices, biosecurity, local antibiotic use, and surrounding land use.
Escherichia spp. were most frequently detected in water (83.4%) and biofilms (84.7%), while their presence was lower in sediment (25%) and minimal in feed (3.3%). Epidemiological resistance was detected against several antibiotics, including ciprofloxacin (n = 16), cefotaxime (n = 13), meropenem (n = 2), and amikacin (n = 1), with several strains showing multidrug resistance. In one farm (Farm D), we observed a recurring resistance pattern across two consecutive sampling periods (T3 ; 2 strains – T4 ; 11 strains), suggesting the persistence or local spread of specific resistant clones.
Statistical analysis is ongoing to assess the impact of different factors on AMR occurrence. These findings highlight aquaculture environments—particularly water and biofilms—as important AMR reservoirs and reinforce the value of integrated surveillance strategies within a One Health framework.