Slicing of animal origin food affects the final quality of products and potentially transfers pathogenic microorganisms as it occurs after microorganism control and elimination steps, such as cooking and pasteurization. Therefore, the food industry needs to ensure the safety of food products to reduce the incidence of foodborne diseases. This requires an understanding of the dangers involved in each stage of production, along with the microorganisms transferred during processing. In this study, we aimed to understand the impact of industrial slicing on mozzarella cheese and ham by investigating the quality indicator microorganisms, aerobic mesophiles, psychrotrophs, total coliforms, Staphylococcus aureus, and pathogens, such as Escherichia coli, Salmonella spp., and Listeria monocytogenes. Samples were collected from pieces (20) and slices (20) of mozzarella cheese and ham. The number of mesophilic aerobes differed significantly before and after slicing (P < 0.05) for mozzarella. However, no difference was observed in the psychrotrophic microorganism counts during slicing. The counts of total coliforms and S. aureus increased after slicing (P > 0.05). In total, 844 isolates were analyzed for pathogenic genes, and Salmonella spp. were identified in 40% of the piece and 20% of the sliced mozzarella cheese samples and in 30% of the piece and 50% of the sliced ham samples. Furthermore, S. aureus genes with the potential to produce enterotoxins C and D were identified in two sliced mozzarella cheese samples. Slicing of ready-to-eat food is an important step in food microbiology. Our results highlight the importance of maintaining hygienic practices during processing and demonstrate that the microbiological quality of the slicing sample affects the quality and safety of the sliced product.

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