Chromosome Mediated Fluoroquinolone and Extended Spectrum Beta-lactamase Resistant Genes in E. coli of Poultry Origin in Ekiti State

Background: One health approach aimed at solving global health crisis links human, animal, and environmental health. This inclusive strategy has contributed to antibiotic classification in both human and animal medicine.

Aims: The aims of this research work are to determine the phylogenetic relationship of E. coli isolated from poultry and waste sources. The presence of chromosome mediated fluoroquinolone and extended spectrum beta-lactamase resistant genes will also be detected in the isolates.

Study Design: Experimental design.

Methodology: Data on farming attitudes of poultry farmers were collected using a questionnaire. E. coli was isolated from fresh poultry droppings and waste disposal sites using eosine methylene blue agar. The antibiotic sensitivity profile of the isolates was determined using the modified Kirby Bauer disc diffusion method. Phenotypic expression of fluoroquinolone (qnrS) and beta-lactamase (blaCMY) resistant traits were further detected using Polymerase Chain Reaction. The 16S rRNA gene sequencing was carried out followed by sequence alignment of E. coli genes with those from GenBank sources to determine the molecular identity of the isolates. Spearman’s correlation coefficient (rs) was run to determine the relationship between antibiotic treatment and resistant profile of the isolates. The phylogenetic relationship of the isolates was determined using Bio edit and Mega 6 software.

Results: Organic poultry farming was practiced by small-scaled, peasant farmers who raised free range birds while antibiotics were widely used on farms that adopted intensive mode of farming. The percentage occurrence of E. coli from waste disposal sources was lesser than that from fresh poultry droppings. Highest percentage of antibiotic resistance to the fluoroquinolones was found while the carbapenemase recorded the lowest. Statistical analysis shows that antibiotic treatment in poultry and resistant profile of isolates to antibiotics are directly related. The percentage similarity of gene sequence with those from Gene Data Bank (≥99.29%) validates the identity of the isolates as E. coli. About, 60% of the sampled population had the qnrS gene with a band size of approximately 322 base pair. Besides, 40% of the sampled isolates possessed the blaCMY gene with a band size of approximately 460 base pair. Both genes co-existed in the chromosome of 15% of the sampled isolates sourced from poultry droppings and waste sources. Phylogenetic classification links the origin of isolates from waste disposal sources to poultry production sites. Besides, variant strains of multiple antibiotic resistant E. coli from poultry with antibiotic treatment were more diverse compared to those obtained from birds raised without antibiotics.

Conclusion: The qnrS and blaCMY genes found in multiple antibiotic resistant E. coli mediated resistance to critically important antibiotics. The co-existence of these genes in variants strains of E. coli occupying different phylogenetic clusters suggests that antibiotics were widely used on the birds. Antibiotic treatment regimen in poultry may be responsible for the expression of antibiotic resistant genes found in the chromosome of the variant strains of E. coli.