Abstract

Contamination of poultry products with pathogenic bacteria and fungi poses significant public health risks and economic losses. This study aimed to molecularly identify and detect resistance genes in bacteria (Escherichia coli, Staphylococcus aureus, Campylobacter spp.) and fungi (Fusarium spp., Aspergillus flavus, Penicillium spp.) isolated from samples of chicken parts (breast, gizzard, and cloacae) obtained from three (3) poultry farms.  Total heterotrophic bacteria count was 3.36 × 10⁶ CFU/g. Total occurrence of the isolates in all the chicken parts were; Escherichia coli 32 × 10⁶CFU/g, Staphylococcus aureus 30 × 10⁶CFU/g, Campylobacter 25 × 10⁶CFU/g. Total fungi was 26 × 10⁴CFU/g, Fusarium sp 23 × 10³CFU/g, Penicillium sp 19 × 10³CFU/g, Aspergillus flavus 16 × 10³CFU/g. DNA was extracted from the isolates and analyzed using polymerase chain reaction (PCR) with species-specific primers targeting the 16S rRNA gene for bacteria and ITS regions for fungi. Molecular characterization identified the isolates as; Escherichia coli AM944637.2, Staphylococcus aureus AP017923.1, Campylobacter upsaliensis AB980278.1, Fusarium solani EU329657.1, Aspergillus flavus MT594359.1 and Penicillium oxalicum MK389646.1. The detection of antibiotic resistance gene and Agarose Gel Electrophoresis image showing amplification of ESBL (OXA-48) gene at 450bp revealed that, Staphylococcus aureus and Campylobacter upsaliensis showed positive amplification meaning that the gene is present in the isolates. While the amplification of antibiotic resistance gene and Quinolones gene (qnrB) at 250bp were positive to Escherichia coli and Campylobacter upsaliensis. This study highlights the potential risks associated with poultry contamination and emphasizes the need for stringent monitoring and control measures in the indiscriminate use of antibiotics in poultry production and processing