Host-associated microbiomes act as reservoirs of antimicrobial resistance in Mediterranean coastal waters

Introduction Understanding how host-associated microbiomes contribute to the environmental ecology of antimicrobial resistance (AMR) remains a major challenge for coastal One Health surveillance. We compared seawater, commercially farmed Mediterranean mussels ( Mytilus galloprovincialis ), and the invasive ascidian Styela plicata to assess differences in microbiome composition, resistomes, mobilomes, and putative pathobiomes across interconnected coastal compartments. Methods Samples collected from Mediterranean coastal environments were analysed using 16S rRNA gene sequencing and high-throughput quantitative PCR targeting 71 AMR determinants, including antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). Results Host-associated microbiomes were consistently distinct from surrounding seawater and remained comparatively stable across sampling periods. Seawater exhibited greater richness of AMR determinants, whereas mussels and ascidians harboured higher relative abundances of ARGs, MGEs, and several clinically relevant resistance determinants. AMR profile composition differed significantly among biotypes but only partially mirrored microbiome structure, indicating that bacterial community composition alone does not explain resistance gene organization. Putative pathogenic bacterial communities also differed among biotypes, with mussels enriched in several human-associated genera whose abundances positively correlated with ARGs. Discussion Although these associations do not demonstrate genetic linkage or pathogenicity, they identify host-associated microbiomes as ecologically relevant compartments where clinically relevant resistance determinants, mobile genetic elements, and bacterial genera containing recognized human-associated or opportunistic pathogens coexist. Our findings demonstrate that marine invertebrates complement seawater for environmental AMR surveillance and support their inclusion in integrated coastal One Health monitoring strategies.