Identification and biocide susceptibility of dominant bacteria after cleaning and disinfection of broiler houses

Hygiene in animal production is key for both farm management and food safety. Cleaning and disinfection (C&D) of broiler houses is essential to manage farm hygiene. Still high levels of total aerobic flora after C&D in broiler houses are reported. However, little is known about the microbial composition after cleaning (AC) and after disinfection (AD). In addition, the question why some bacterial species/isolates are still present AD whereas others are killed remains. The study was carried out in 4 broiler houses. Sampling was performed AC and AD. The disinfectant was based on hydrogen peroxide and peracetic acid. Enumerations were carried out for total aerobic flora, Enterococcus spp. and Enterobacteriaceae. The dominant bacteria present was assessed by (GTG) 5 analysis and 16S rRNA gene sequence analysis. Moreover, minimum bactericidal concentration (MBC) tests were carried out on 18 selected isolates belonging to the Enterobacteriaceae family and 10 Enterococcus faecium isolates. A wide variety of bacteria were detected AC and AD. In total, 363 and 255 isolates were identified AC and AD, respectively, resulting in a total of 109 identified species. The most dominant bacteria belonged to Brevibacterium, Brachybacterium, and Staphylococcus AC and Bacillus, Brevibacterium, and Staphylococcus AD. At both sampling moments, Enterococcus faecium was dominant among the Enterococcus spp. isolates. On the selective medium for Enterobacteriaceae, the genera Enterobacter and Pantoea and Aeromonas (non Enterobacteriaceae) were dominant AC while Escherichia, Lelliottia, and Pantoea were dominant AD. In addition, species pathogenic to poultry and humans were identified not only AC but also AD. MBC results showed no trend in selection of less susceptible isolates for the used disinfectant AD compared to AC. Finally, the recommended concentration of the disinfectant (i.e., 0.5% commercial solution of hydrogen peroxide and peracetic acid) seemed too low to kill Enterobacteriaceae.