Parasitological and bacteriological survey on fish and shellfish from sea cages in Italy.

Sustainable aquaculture requires integrated approaches to safeguard animal health and welfare while minimizing antimicrobial use. This study, carried out on fish and shellfish sampled from three different farms along the Italian coasts, aimed to identify the main parasitological and bacteriological microorganisms and their potential involvement as etiological agent of health issues in the farming environments under study. Several marine species were investigated, combining parasitological and bacteriological monitoring together with biofilm assessment on different matrices, to provide a comprehensive framework of the health status and possible management strategies in Mediterranean aquaculture. Samplings involved gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax), meagre (Argyrosomus regius), mussels (Mytilus galloprovincialis), and oysters (Ostrea edulis and Crassostrea gigas) from cage-based farms located in Thyrrenian sea. Between January 2023 and August 2025, a total of 1.360 fish and 218 shellfish were collected during 35 sampling sessions from sea cages and an Integrated Multitrophic Aquaculture (IMTA) system. Fish were subjected to necropsy, parasitological and bacteriological exams, while shellfish and fish target organs were processed for histology. Bacterial isolates were identified phenotypically by MALDI-TOF and genotypically confirmed trough molecular methods; representative isolates were subjected to antibiotic susceptibility test (Kirby–Bauer, CLSI guidelines). Biofilms were sampled from cage substrates and ropes, disaggregated, and analyzed for bacterial composition. In vitro assays evaluated also biofilm formation by pathogenic bacteria under varying conditions. Parasitological analyses confirmed Sparicotyle chrysophrii as the most prevalent and pathogenic parasite in gilthead seabream. In flat oysters (O. edulis), severe infections by digenean trematodes (Prosorhynchoides sp.) were observed, causing severe damage to the gonads and digestive gland, resulting in loss of gonadal function in nearly half of the specimens. Mussels showed occasional, low-intensity infections by Nematopsis sp. and microsporidia. Bacteriological investigations identified Gram-negative pathogens such as Vibrio harveyi, Aeromonas veronii, and Photobacterium damselae subsp. piscicida, as well as emerging pathogens Lactococcus garvieae and Piscirickettsia sp. Antibiotic susceptibility test revealed overall sensitivity to authorized antimicrobials, although resistance was observed in A. veronii and L. garvieae, underscoring the need for alternative control strategies. Biofilm analyses detected multiple Vibrio spp. and P. damselae subsp. damselae on cage surfaces, some isolated also from the fish in the cage. In vitro assays confirmed strong biofilm-forming capacity of V. harveyi under optimal conditions and enhanced biofilm production by A. veronii at 25°C, particularly in seabass isolates. The obtained results highlight the importance of integrated health monitoring and pathogen surveillance taking into consideration the possible interaction between different biotic factors within sea cage farming systems. The detection of significant parasitic burdens and antimicrobial-resistant bacteria emphasizes the need for innovative, non-pharmacological approaches to maintain biosecurity and animal health in intensive farming systems.