A comprehensive study on Salmonella enterica serovar Richmond in farmed fish Pangasianodon hypophthalmus: insights into zoonotic potential, virulence and antimicrobial resistance.

Salmonella enterica serovar Richmond is an emerging pathogen from contaminated animal food, posing a risk of global foodborne outbreaks. Few reports have documented this species in live aquatic organisms. In this study, Salmonella Richmond COFI-RLBCAU-I was isolated from live Pangasianodon hypophthalmus, and its pathogenicity was tested on the three most culturable fish species, P. hypophthalmus, Labeo rohita, and Oreochromis niloticus. The results showed that the bacteria are non-pathogenic to these three species. Techniques, including β-hemolytic activity, Gram staining, biochemical tests such as IMViC, nanopore-based whole-genome sequencing, and in silico serotyping, identified this strain as S. enterica subsp. enterica serovar Richmond. The de novo-assembled genome totalled 4,919,008 base pairs with a GC content of 52.06%. Phylogenomic analysis based on NCBI GenBank serotypes revealed that COFI-RLBCAU-I clusters closely with Salmonella Richmond CGA007471575. A protein-language model using PathogenFinder2 suggested that the strain may be potentially pathogenic to humans, with a score of 0.9637 out of 1. Gene ontology classification included 39 biological processes, 17 cellular components, and 8 molecular functions. The genome contains six prophage regions linked to bacteriophage. The study also identified 29 virulence genes and 2 antimicrobial resistance genes. Methylation analysis across the genome revealed methylated bases, including 4mC, 5mC, and 6 mA at various positions. This research presents the first comprehensive study on Salmonella Richmond isolated from farm-raised fish, emphasizing its potential as a zoonotic pathogen for humans.