Molecular epidemiology of clinical important antimicrobial-resistant Escherichia coli isolated from opossums (Didelphis spp.) rescued in a wildlife management center in the city of São Paulo

• Grant number: 24/17243-8
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: May 01, 2025
• End date: April 30, 2029
• Field of knowledge: Agronomical Sciences - Veterinary Medicine - Preventive Veterinary Medicine
• Principal Investigator: Marcos Bryan Heinemann
• Grantee: Gabriel Siqueira dos Santos
• Host Institution: Faculdade de Medicina Veterinária e Zootecnia (FMVZ). Universidade de São Paulo (USP). São Paulo , SP, Brazil

Abstract

The threat of bacterial resistance to antimicrobials (AMR) poses serious impacts in public health and the global economy. Wild synanthropic animals, such as opossums (Didelphis spp.), can act as reservoirs and disseminators of multidrug-resistant bacteria, especially in anthropomorphized environments. This project aims to phenotypically and genotypically characterize Escherichia coli strains isolated from opossums in São Paulo City regarding susceptibility to antimicrobials, as well as performing phylogenomic analyses and georeferencing the resistant isolates. Swabs from pseudocloaca and fecal samples will be collected from opossums rescued and attended by the São Paulo City Wildlife Management and Conservation Center (CEMACAS) for culture, isolation and identification of Escherichia coli strains at the Laboratory of Bacterial Zoonoses of the School of Veterinary Medicine and Animal Sciences of the University of São Paulo. The strains will be analyzed for antimicrobial susceptibility by disk-diffusion and broth microdilution, and resistance mechanisms encoding genes will be screened: extended-spectrum betalactamases (ESBL) (blaCTX-M group 1, blaCTX-M group 2, blaCTX-M group 8, blaCTX-M group 9, blaTEM and blaSHV), carbapenemases (blaKPC, blaOXA-48-like, blaNDM), mobilized colistin resistance (MCR) (mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, mcr-6, mcr-7, mcr-8, mcr-9) and plasmid-mediated quinolone resistance (PMQR) (qnrA, qnrB, qnrS, oqxB, oqxA, qepA and aac(6¿)-Ib). The isolates will be typed in phylogroups (A, B1, B2, C, D, E, F and G) and by single enzyme amplified fragment length polymorphism (SE-AFLP), followed by whole genome sequencing to analyze the resistome, virulome, mobilome and plasmidome. Descriptive statistical analyses will be carried out on the phenotypic and genotypic profile of AMR, phylogroups, genotypes of the bacterial isolates and statistical tests of association to correlate phenotypic and genotypic profiles of AMR and the rescue regions of the animals.