Molecular Profiling of Antibiotic-resistant Bacteria Isolated from Cloacal Swab Samples of Slaughtered Chickens in Bauchi Metropolis

Abstract

Background: Poultry, particularly chickens, are a major source of protein worldwide. However, the overuse of antibiotics in poultry farming has led to the emergence of multidrug-resistant (MDR) bacteria, which can pose serious public health risks. The cloacal region of chickens can harbor these resistant bacteria, which may enter the food chain during slaughter and processing. Molecular characterization of these pathogens helps in identifying resistance genes and tracking their spread. Aim: The study aims to isolate and molecularly characterize multidrug-resistant bacteria from cloacal swab samples of slaughtered chickens in Bauchi Metropolis. Place and Duration of Study: This study was carried out in the Abubakar Tafawa Balewa University (ATBU), Bauchi, Nigeria, in a period extended from August 2024 to March 2025. Results:  In the study, the multidrug resistance (MDR) profiles of bacterial isolates were analyzed across various antibiotic groups. Escherichia coli exhibited the highest resistance, with 51.4% of isolates resistant to beta-lactams, followed by 22.8% to fluoroquinolones. Enterobacter aerogenes showed significant resistance as well, with 35.7% to beta-lactams and 28.5% to aminoglycosides. Among all tested species, Shigella showed notable resistance, particularly to aminoglycosides (50%) and fluoroquinolones (50%). The study also revealed that 10% of bacterial isolates (including Escherichia coli, Salmonella typhi, and Klebsiella pneumoniae) were resistant to both beta-lactams and aminoglycosides, with E. coli making up 40% of this dual resistance group. Molecular analysis of MDR isolates showed that 60% of E. coli strains carried targeted MDR genes, blaSHV, blaCTX-M, while 20% of Klebsiella pneumoniae and Streptococcus pyogenes isolates carried   aac(6')-Ia gene. Methodology: A total of 111 bacterial isolates were collected from a previous study for molecular analysis. The antimicrobial resistance patterns of these isolates were determined using the disc diffusion method on Mueller-Hinton Agar, testing against beta-lactam and aminoglycoside classes of antibiotics. DNA extraction was performed using the Accu Prep Genomic DNA Extraction Kit, followed by Polymerase Chain Reaction (PCR) to amplify specific resistance genes related to beta-lactam and aminoglycoside resistance. The PCR products were visualized through agarose gel electrophoresis to confirm the presence of the target resistance genes. The study aimed to identify genetic factors contributing to resistance and determine the prevalence of multidrug-resistant strains in poultry, with a focus on beta-lactam and aminoglycoside resistance. Conclusion:  This study confirms the high prevalence of multidrug-resistant (MDR) bacteria, particularly Escherichia coli, with significant resistance to beta-lactam and aminoglycoside antibiotics. Molecular analysis revealed that only half of the phenotypically resistant isolates carried known MDR genes, highlighting the complexity of resistance mechanisms. The findings underscore the urgent need for targeted surveillance, prudent antibiotic use, and further molecular studies to better understand and combat the spread of MDR bacteria, especially in environments with heavy antibiotic exposure like poultry farms.