Metagenomic analysis of effluents from broiler slaughterhouses as a surveillance action from the One Health perspective

• Grant number: 23/00969-3
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: June 01, 2023
• End date: February 28, 2027
• Field of knowledge: Agronomical Sciences - Veterinary Medicine - Preventive Veterinary Medicine
• Principal Investigator: João Pessoa Araújo Junior
• Grantee: Evelyn Cristine da Silva
• Host Institution: Instituto de Biotecnologia (IBTEC). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil

Abstract

Brazilian poultry farming is one of the most important sectors for the country's economy today and poultry production has increased in recent years. Linked to the high level of production, and inherent to the poultry slaughter process, there is the formation of large volumes of industrial effluents. These effluents can contain a wide range of pathogenic microorganisms, characterizing a health risk, and antibiotic resistant genes (ARGs), which are considered emerging pollutants and of importance for threatening animal production, public health and ecological security. In this sense, the study of slaughterhouse effluents is important as a surveillance action in an integrative approach of the One Health. Thus, the objective of the study is to analyze the complete metagenomics of effluents from broiler slaughterhouses created in two different production systems (conventional and antibiotic-free), using molecular genetics in the research of the microbiome, resistome and virome. The experimental design of the study is based on the collection of 16 samples of effluents from broiler slaughterhouses from two different production systems, conventional and antibiotic-free, in four different periods of the year during two years. Genomic material will be extracted using an in-house protocol with magnetic beads and the MagMAX" Viral/Pathogen Nucleic Acid Isolation kit (Thermo Fisher Scientific®). To prepare the libraries, the kits Illumina DNA Prep and Illumina RNA Prep with Enrichment will be used. Sequencing will be performed on the NextSeq platform (Illumina, San Diego, CA) using a 300-cycle flow cell cartridge and the data will be analyzed with updated bioinformatics platforms. Studies like this are important as a surveillance action in One Health using omics tools to determine the microorganisms present, their composition and diversity, their pathogenic potential and which antibiotic resistance genes (ARGs) are exploited in these environments that are sometimes neglected in the poultry production chain and in health surveillance.