Genomic signatures for tracking the source of contamination and characterizing the virulence of coagulase-positive Staphylococci in the artisanal minas Canastra cheese production chain

Abstract

Artisanal Minas Canastra Cheese (QMAC) is one of the best-known and most consumed artisanal cheeses in Brazil. The colonization of environments where raw milk is obtained, as well as the artisanal production environments at QMAC, by populations of Coagulase-Positive Staphylococci (ECP) is a notorious condition in this production system. Certain strains of ECP can potentially produce enterotoxins, indicating that QMAC contamination is a public health issue. Due to the potential compromise of product safety, ECP counts in milk and cheese must be kept within limits established by law, representing one of the greatest challenges for the production chain in question. This scenario highlights the importance of scientific research aimed at identifying the sources of contamination of QMAC by possible different strains of ECP, as well as the characterization of the enterotoxigenic potential of each one of them and their source tracking. In this context, this project aims to apply a modern technique based on third-generation genomic sequencing (Oxford Nanopore-rep-seq) for tracking the source tracking of QMAC by different ECP strains in milking and cheese production environments. Additionally, representatives of the ECP subtypes identified as contaminants of the QMAC will be submitted to comparative genomic analysis to characterize the diversity of virulence genes, antimicrobial resistance genes and mobile genetic elements. The experimental design involves four enterprises producing Artisanal Minas Canastra Cheese with different production capacities, duly registered by the local inspection body, with collections carried out in eight quarterly campaigns in order to verify possible seasonal variations. In each enterprise, 20 points considered as potential sources of ECP contamination will be sampled. The generated results will be used for the preparation of scientific articles and for the creation of a bank of ECP isolates, which can be used in subsequent projects. Furthermore, the results will also be presented to the association of producers of Artisanal Minas Cheese from Canastra as a way of supporting improvements in procedures for controlling microbiological contamination by ECP. (AU)