Impact of Improved Sanitation Standard Operating Procedures on Microbial Populations at Three Tree Fruit Packing Facilities

Cleaning and sanitizing are of vital importance to control Listeria monocytogenes in food processing facilities. Here, we evaluated the effect of four cleaning and sanitation standard operating procedures (SSOPs; T1, T2, T3, T4) on the reduction of total aerobic mesophilic microorganisms, the occurrence of L. monocytogenes, and the microbiota composition in three tree fruit packing facilities (F1, F2, and F3) over two packing seasons (Y1 and Y2). Environmental samples were collected from non-food contact surfaces before and after the application of SSOPs. Total aerobic bacteria were quantified using a standard plate count method, and Listeria spp. and L. monocytogenes concentration was quantified using a Most Probable Number method. Amplicon sequencing was used to determine bacterial and fungal microbiota composition, and Nanopore sequencing was used to detect functional elements in the microbiota that could promote the survival and persistence of L. monocytogenes in the studied environments. The use of SSOPs reduced the total bacterial load by 0.27–2.48 log₁₀ CFU/swab (p ≤ 0.001). Among the treatments tested, the inclusion of a biofilm remover in T4 was most effective in significantly reducing the total Listeria spp. concentration by 1.57–1.27 log₁₀ MPN/swab (p < 0.02) and the frequency of L. monocytogenes, although the latter was not statistically significant. We observed inconsistent changes in the bacterial and fungal microbiota composition due to the application of cleaning and sanitizing SSOPs, which may be due to the presence of dead DNA after the treatment. Using Nanopore sequencing, we detected functional elements related to biofilm formation and stress resistance in the microbiomes of the studied environments. Overall, our study shows that the implementation of SSOPs improved the sanitation outcomes in tree fruit packing facilities. There is a need for the future work to focus on optimizing and validating the standard operating procedures, especially in the areas in which SSOPs were less effective, such as those covered with wax residues.