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

•A biofilm remover consistently reduced the bacterial load on environmental surfaces.•An acid cleaner significantly altered the fungal microbiota on environmental surfaces.•Biofilm formation and stress resistance genes were identified in metagenomes. 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