EccBR: Genomic surveillance of Enterobacter cloacae complex in One Health for the control, diagnostic and management of antimicrobial resistance in Brazil

• Grant number: 24/07885-2
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: May 01, 2025
• End date: August 31, 2026
• Field of knowledge: Biological Sciences - Microbiology - Applied Microbiology
• Principal Investigator: Nilton Erbet Lincopan Huenuman
• Grantee: Karine Sousa Dantas
• Host Institution: Instituto de Ciências Biomédicas (ICB). Universidade de São Paulo (USP). São Paulo , SP, Brazil

Abstract

The investigation of emerging pathogens, correct taxonomic identification and determination of the antibiotic resistance profile are essential for the control and management of infectious diseases that may have an endemic or pandemic evolution, with consequences for human, animal, and environmental health, and should be addressed within One Health concept. The high prevalence and endemicity of Enterobacter cloacae complex (ECC) species in healthcare-associated infections has been supported by the combination of virulence and antimicrobial resistance genes acquisition. Although Enterobacter spp. resistant to broad-spectrum cephalosporins and carbapenems has been classified as critical priority pathogens by the WHO, laboratory diagnostic systems still fail to differentiate ECC species. The present project aims to carry out genomic surveillance of the E. cloacae complex in One Health in Brazil, to identify the real prevalence of ECC species in human and animal infections; generate and make data available to assist in the diagnosis, control, and management of antimicrobial resistance. Isolates of Enterobacter spp. will be sent by clinical laboratories and researchers to identify the species (MALDI-TOF) and the antibacterial sensitivity profile (disk-diffusion; minimum inhibitory concentration, MIC). Isolates with different resistance profiles will be selected for Illumina sequencing (NextSeq), and the genomes will be analyzed using bioinformatics tools for assembly; annotation; prediction of the resistome, mobilome, virulome, CRISPR, MLST and pMLST; and phylogenomic analysis through the construction of phylogenetic trees based on SNPs (single nucleotide polymorphism). Furthermore, the EccBR database will be created in the OneBR domain (http://www.onehealthbr.com/), to provide microbiological and genomic data of clinical and epidemiological importance.