Whole genome sequencing as a tool for determining the role of conventional and alternative broiler industries regarding the promotion of bacterial resistance of Salmonella spp., Escherichia coli and Enterococcus spp

• Grant number: 21/12215-8
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• Start date: December 01, 2022
• End date: September 30, 2024
• Field of knowledge: Agronomical Sciences - Veterinary Medicine - Preventive Veterinary Medicine
• Principal Investigator: Juliano Gonçalves Pereira
• Grantee: Camila Koutsodontis Cerqueira Cézar
• Host Institution: Faculdade de Medicina Veterinária e Zootecnia (FMVZ). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil

Abstract

Antimicrobial resistance is one of the most discussed subjects related to public health nowadays. It is estimated that in 30 years the bacterial resistance to antibiotics used in human medicine will be responsible for more deaths than cancer. Pathogens such as Salmonella spp., Enteropathogenic Escherichia coli, and Enterococcus spp. are commonly found in products of animal origin and are responsible for outbreaks and deaths, especially in immunocompromised humans. Chicken meat is one of the main sources of human contamination, being widely consumed worldwide and easily accessible. However, fecal-originated bacteria naturally found in poultry poses a great risk of environmental contamination and interaction with other microorganisms transferring resistance genes, alongside frequent contact with humans. The wide and careless use of antibiotics in conventional animal husbandry is an important factor in increasing bacterial resistance and new resources must be explored to reduce it. Organic animal husbandry is increasing worldwide and one of its guidelines is the non-recurring use of antibiotics, which is a possible alternative to reduce the issue of antimicrobial resistance. Thus, the present study aims to evaluate the genetic and phenotypic profile of resistance to antibiotics of Salmonella spp., Escherichia coli, and Enterococcus spp. isolated from chicken meat from alternative and conventional production systems. Therefore, samples of certified chicken meat from both systems will be collected from grocery stores in the county of Botucatu- SP, to obtain 46 isolates from each system and each pathogen to be analyzed. The samples will be subjected to microbiology research followed by molecular and MALDI-TOF confirmation. The isolates of microorganisms from chicken meat of both systems will be subjected to the determination of antibiotic resistance profile according to CLSI. From the analysis on resistance, isolates will be then subjected to whole genome sequencing. After performing the phenotypic and genetic analyzes, all data will be statistically treated to verify possible interferences of production systems in the induction of antibiotic resistance, allowing a discussion of the real participation of each system in the appearance of new resistance genes. If results show a tendency towards less antimicrobial resistance in alternative chicken meat, already practiced procedures in this system may be suggested to conventional ones to minimize consequences from the abuse of antimicrobials in animals, humans, and environment. (AU)