Assessment of bacterial superficial contamination in classical or ritually slaughtered cattle using metagenetics and microbiological analysis

The aim of this study was to investigate the influence of the slaughter technique (Halal vs Classical slaughter) on the superficial contamination of cattle carcasses, by using traditional microbiological procedures and 16S rDNA metagenetics. The purpose was also to investigate the neck area to identify bacteria originating from the digestive or the respiratory tract. Twenty bovine carcasses (10 from each group) were swabbed at the slaughterhouse, where both slaughtering methods are practiced. Two swabbing areas were chosen: one “legal” zone of 1600 cm2 (composed of zones from rump, flank, brisket and forelimb) and locally on the neck area (200 cm2). Samples were submitted to classical microbiology for aerobic Total Viable Counts (TVC) at 30 °C and Enterobacteriaceae counts, while metagenetic analysis was performed on the same samples. The classical microbiological results revealed no significant differences between both slaughtering practices; with values between 3.95 and 4.87 log CFU/100 cm2 and 0.49 and 1.94 log CFU/100 cm2, for TVC and Enterobacteriaceae respectively. Analysis of pyrosequencing data showed that differences in the bacterial population abundance between slaughtering methods were mainly observed in the “legal” swabbing zone compared to the neck area. Bacterial genera belonging to the Actinobacteria phylum were more abundant in the “legal” swabbing zone in “Halal” samples, while Brevibacterium and Corynebacterium were encountered more in “Halal” samples, in all swabbing areas. This was also the case for Firmicutes bacterial populations (families of Aerococcaceae, Planococcaceae). Except for Planococcoceae, the analysis of Operational Taxonomic Unit (OTU) abundances of bacteria from the digestive or respiratory tract revealed no differences between groups. In conclusion, the slaughtering method does not influence the superficial microbiological pattern in terms of specific microbiological markers of the digestive or respiratory tract. However, precise analysis of taxonomy at the genus level taxonomy highlights differences between swabbing areas. Although not clearly proven in this study, differences in hygiene practices used during both slaughtering protocols could explain the differences in contamination between carcasses from both slaughtering groups.