Culture-independent analysis of abattoir samples using metagenomic sequencing reveals the presence of bacteria of public health importance

Livestock slaughterhouses and processing plants, known as abattoirs, can become breeding grounds for microorganisms, creating potential health risks for animals and humans through foodborne and environmental contamination. All animal wastes are heavily laden with toxic chemicals, pathogenic microorganisms, etc. and these eventually make our environment unsafe. Samples from abattoir slaughter slabs, tables, and soil were collected from abattoirs in 2 towns from the 3 senatorial districts in Osun state, Nigeria. The samples were processed and genomic DNA was extracted. A full-length 16s RNA gene sequencing was carried out on the extracted DNA. The raw subreads were processed through the SMRTlink (v11.0) Circular Consensus Sequences (CCS) algorithm. Length of sequence, mean, standard deviation, frequencies and percentages of the nucleotide and GC were produced. Taxonomic information was determined based on QIIME2. The sequence lengths of 40, 987, 31, 055, and 24, 449, and a G+C of between 54.1, 54.1, and 33.3% were obtained for Osun east (SD1), Osun west (SD2), and Osun central (SD3) senatorial districts respectively. Taxonomic profiling showed a high presence of Enterococcus in all locations followed by Escherichia. Lysinibacillus, Prevotella, Staphylococcus, Aeromonas and Exiguobacterium were only isolated from SD1; Rikenellaceae_RC9_gut_group, Faecalibacterium, UCG, and Veillonella were only isolated from SD2 while Mycobacterium, Kurthia, Alcaligenes and Vagococcus occurred only in SD3 The detection of these bacteria in various abattoir samples highlights the critical need for proper animal handling during slaughter to minimize meat contamination with these pathogenic bacteria, which could potentially lead to infections in humans who consume the contaminated meat.