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Genomic analysis of pandemic lineages of Avian Pathogenic Escherichia coli (APEC) focusing surveillance of Avian Colibacillosis in Brazil

Grant number: 22/11917-1
Support Opportunities:Regular Research Grants
Duration: March 01, 2023 - February 28, 2025
Field of knowledge:Agronomical Sciences - Veterinary Medicine - Animal Pathology
Principal Investigator:Terezinha Knöbl
Grantee:Terezinha Knöbl
Host Institution: Faculdade de Medicina Veterinária e Zootecnia (FMVZ). Universidade de São Paulo (USP). São Paulo , SP, Brazil
Associated researchers:André Becker Simões Saidenberg


Avian Pathogenic Escherichia coli (APEC) is responsible for colibacillosis, an extra intestinal disease associated with significant economic losses in the poultry industry. Some pandemic clonal groups have been linked to outbreaks of avian colibacillosis, as well as the occurrence of human diseases, because some avian strains share virulence factors with the pathotypes associated with urinary tract infections (UPEC), neonatal meningoencephalitis (NMEC), and sepsis (SEPEC). The zoonotic potential has been investigated in experimental models and showed no specificity by hosts, reinforcing the hypothesis of food acquired APEC. The withdrawal of grow promoters represented a challenge to the sector, particularly for the control of Enterobacteriaceae infections. In 2019, many poultry producers reported an increase in initial mortality and carcass condemnation at the slaughterhouse, with lesions of avian colibacillosis. Research based on the sequencing of the APEC genome has been important in several countries for establish the epidemiology of APEC and establish the disease control, using vaccines. In Brazil, these data are very scarce. The aim of this project is to develop an epidemiological survey of pandemic strains that are circulating in Brazil, through whole genome sequencing (WGS). 250 APEC strains will be evaluated, coming from the five states with the highest poultry production (RS, PR, SC, SP and MG), isolated from 2018 to 2022. The isolates will be screened by PCR to determine the virulence factors and phylo groups, and the clonal clustering will be performed by the AFLP technique. After screening, 50 strains, representative of different clades and virulence profiles, will be selected for whole genome sequencing. In silico analysis of these isolates will determine serogroups and sequence types (STs), genotypic and phylogenetic characteristics, including the most recent patterns of acquisition of emerging determinants of antimicrobial resistance and virulence, between groups. The analysis will also allow a global comparison with available APEC sequences deposited in databases. The results will bring a better understanding of epidemiology of these APEC and will contribute for the control of high risks clones. (AU)

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