Genetic determinants of disinfectant and antibiotic resistance, and virulence factors in Enterococcus faecalis...

Blue swimming crab (Portunus pelagicus) is highly commercial Indonesian seafood commodity and exported in the form of pasteurized canned crab product. As a ready-to-eat food industry, the effectiveness of sanitization practices and the level of hygiene in the production environment are critical factors in ensuring food safety. These challenges are heightened by bacteria that form biofilms or carry resistance genes. This study aimed to identify resistance bacterial species and strain, identify disinfectants and antibiotic resistance genes, and virulence genes in the pasteurized crab production environment. Environmental samples were collected after sanitization process with 200 ppm chlorine and 30,000 ppm trypsin. Following collection, samples were cultured, DNA was extracted, and long-read sequencing was performed to assess strain and genes through Whole-genome Sequencing (WGS). Whole-genome Sequencing (WGS) analysis identified Enterococcus faecalis D32 as a bacterial strain that survived sanitization in a pasteurized crab canning environment. Genome annotation revealed the presence of disinfectant resistance gene emeA, associated with efflux-mediated tolerance, along with seven antibiotic resistance genes, including dfrE, vanTG, vanYB, efrA, efrB, emeA, and lsaA. In addition, 29 virulence genes related to adhesion, quorum sensing, anti-phagocytosis, and biofilm formation were detected, indicating a high capacity for biofilm-associated persistence. The coexistence of resistance determinants and biofilm-forming traits suggests that E. faecalis D32 possesses adaptive mechanisms that support tolerance to chlorine-based disinfection and enzymatic treatment with trypsin. These findings highlight the potential persistence of resistant and opportunistic bacteria following sanitization and emphasize the need for improved hygiene strategies in crab processing facilities.