ANTIBIOTIC RESISTANCE AND WHOLE GENOME SEQUENCING OF E. COLI ISOLATED FROM READY-TO-EAT (RTE) MEATS IN ONE HEALTH CONTEXT, IN ACCRAMETROPOLIS OF GHANA

Abstract

Meat is an essential part of human daily diet due to its nutrient composition and the vital roles it plays in human growth, development and proper functioning. It has equal favorable environment for the growth and multiplication of microorganisms including pathogenic ones. This study seeks to determine the prevalence rate of Escherichia coli (E. coli) in ready-to-eat (RTE) meats using one health approach. The study also determined the antibiotic resistance and presence of antimicrobial resistance genes, plasmid replicons, virulence genes and multilocus sequence typing (MLST) types of the E. coli. In all, 360 ready-to-eat meat and associated samples were randomly collected. The protocol in the USA-FDA Bacteriological Analytical Manual was used for identification of E. coli. The disk diffusion method was used for antibiotic resistance tests. Antimicrobial resistance genes, plasmid replicons, virulence genes and MLST types were determined using whole genome sequencing. The findings revealed that 25 samples were contaminated with E. coli, representing 7% with RTE beef (15%) being the most contaminated, followed by RTE chicken (10%) and the least was spices (2%) used for preparing RTE meats. The prevalence of E. coli in animal (RTE beef, chicken and mutton), human (hands of RTE meat sellers) and environmental (knives for cutting RTE meats and spices for preparing RTE meats) sources was 10%, 3% and 4.2%, respectively. E. coli isolates showed resistant mostly toAmoxicillin (100.0%), followed by Suphamethoxazole/trimethoprim (36.0%) and Tetracycline (32.0%), with the lowest resistant being Ceftriaxone (0.0%). The multiple antibiotic resistant (MAR) index ranged from 0.1-0.6. Three of the E. coli isolates from Maamobi, Agbogboloshie and Malata beef were resistant to five different antibiotics namely AZM-AML-C-TE-SXT, AML-TE-SXT-AUG-CIP and AML-TE-SXT-AUG-CIP, respectively with MAR index of 0.6. Whole genome sequencing revealed that 52.4% of the E. coli isolates harboured antimicrobial resistance genes, and a total of 54 antimicrobial resistance genes made up of 19 different genes were detected. Plasmid replicons were detected in 81.0% of the E. coli isolates with a total of 28 plasmid replicons made up of 13 different types. Virulence genes were detected in all the E. coli isolates (100%) and in all 156 virulence genes were present made up of 45 different types for multilocus sequence typing, 81.0% were typed, the remaining 19% possessed an unknown MLST types and in all 17 MLST types made up of 12 different types were present. This study reveals the presence of E. coli in some of the RTE meats and it associated samples. This E. coli exhibited varying resistance to antibiotics and AMR genes, plasmid replicons, virulence genes and known and unknown MLST types were detected