Application of different computational approaches for characterization of the resistome and mobilome in WHO critical and high priority pathogens from the soil-plant interface

• Grant number: 25/07066-4
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• Start date: November 01, 2025
• End date: April 30, 2026
• Field of knowledge: Biological Sciences - Microbiology - Applied Microbiology
• Principal Investigator: Eliana Guedes Stehling
• Grantee: Micaela Santana Ramos
• Supervisor: Christina Boucher
• Host Institution: Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• Institution abroad: University of Florida, Gainesville (UF), United States
• Associated to the scholarship: 23/04555-9 - Isolation and genomic characterization of WHO critical priority pathogens in soils and vegetables, BP.DR

Abstract

Antimicrobial resistance (AMR) poses a major threat to human health, with significant global implications. The spread and control of AMR are multifactorial, fitting into the concept of One Health, which highlights the role of the environment, plants, humans, and other animals. In addition, the presence of AMR determinants in vegetable cultivation areas has been shown to pose a significant food security risk. However, with the advent of bacterial genomic analysis, it is now possible to characterize antimicrobial-resistant strains rapidly, comprehensively, and with high precision using diverse computational tools. Therefore, this study proposes to use different computational approaches to characterize the resistome and mobilome of reference bacterial genomes from the soil-plant interface. All publicly available bacterial genomes of Escherichia spp., Klebsiella spp., Enterobacter spp., Citrobacter spp., Acinetobacter baumannii, and Pseudomonas aeruginosa from the National Center for Biotechnology Information (NCBI), Pathogen Detection Database will be selected. The genomes will be analyzed by three computational methods: TELCoMB (Bravo et al., 2024), KARGVA (Marini et al., 2023), and Meta-MARC (Lakin et al., 2019) for characterization of the resistome and mobilome, which will detect acquired antimicrobial resistance genes, mutations associated with AMR, and prediction of genes that have not been detected in existing databases, respectively. Moreover, comparative genomic analyses will be carried out to compare the computational tools and bacterial strains according to their region, isolation year, and species. At the end of the project, it is expected to obtain a general overview of AMR in soil-plant interface and to acquire theoretical and practical learning related to the computational tools used for application in the strains obtained during the candidate's PhD project.