Unveiling Genomic Signatures for Source Tracking and Characterization of Virulence of Coagulase-Positive Staphylococci in the Canastra Minas Artisanal Cheese through Pangenome and Phylogenomic Analyses

• Grant number: 25/25313-9
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate (Direct)
• Start date: May 01, 2026
• End date: December 31, 2026
• Field of knowledge: Agronomical Sciences - Food Science and Technology - Food Science
• Principal Investigator: Bernadette Dora Gombossy de Melo Franco
• Grantee: Talita Gomes da Costa
• Supervisor: Fabiana Andrea Hoffmann Sarda
• Host Institution: Faculdade de Ciências Farmacêuticas (FCF). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Institution abroad: University of Limerick (UL), Ireland
• Associated to the scholarship: 22/16567-9 - Genomic signatures for tracking the source of contamination and characterizing the virulence of coagulase-positive Staphylococci in the artisanal minas Canastra cheese production chain, BP.DD

Abstract

The Canastra Minas Artisanal Cheese (CMAC) is a cultural and economic heritage of Brazil. However, its production using raw milk poses microbiological safety challenges, particularly due to coagulase-positive staphylococci (CoPS) capable of producing enterotoxins and carrying antimicrobial resistance genes. This project proposes an 8-month international research internship at the University of Limerick, supervised by Prof. Dr. Fabiana Sardá, to perform advanced bioinformatic analyses of 48 CoPS genomes previously sequenced from samples collected in milking and cheese-making environments of CMAC. Complementing the genomic characterization, a technical mission to Irish farms and cheese factories to observe management practices, mastitis control, hygiene protocols, antimicrobial use records, and regulatory standards will make it possible to compare two contrasting production systems: the Brazilian and the Irish. The genomic methodological framework integrates de novo genome assembly (SPAdes), functional annotation (Prokka), and targeted detection of virulence factors (VFDB), antimicrobial resistance genes (CARD via RGI/AMRFinderPlus), and mobile genetic elements (IslandViewer and others). Additional analyses include pangenome reconstruction (Panaroo/PPanGGOLiN), genotype-phenotype associations (PySEER, Scoary), and high-resolution phylogenomics (Snippy, Gubbins, IQ-TREE 2), with visualization through iTOL, Cytoscape, and heatmaps. Comparative analyses will incorporate publicly available European genomes and Irish collections to detect shared antimicrobial resistance (AMR) genes, plasmids, and prophages, and to assess potential epidemiological convergence. This will enable an operational comparison between the Brazilian (artisanal) and Irish (technified) systems, enriching the interpretation of genomic differences and convergences. Expected outcomes include the establishment of a public genomic database, the identification of critical markers of virulence and resistance, inference of contamination routes, training in bioinformatic workflows for whole-genome sequencing (WGS), and the generation of scientific and technical outputs, thereby strengthening Brazil-Ireland cooperation. (AU)