Food animals like cattle and poultry are often regarded as reservoirs for Campylobacter infections in human. This study investigated the occurrence of Campylobacter coli in cattle and local chickens and their antibiotic susceptibility to commonly used antibiotics in Ibadan, Oyo State, Nigeria. A total of 250 samples comprising 100 rectal swabs, 100 gall bladder contents from cattle and 50 cloacal swabs from local chickens that were apparently healthy, were subjected to standard microbiological identification and antibiotic susceptibility tests. Overall, 51 (20.4%) C. coli were isolated including 34/100 (34%) from rectal swabs, 12/100 (12%) from gall bladders and 5/50 (10%) from the cloaca. All the isolated C. coli displayed multiple antibiotic resistances to between 4 and 10 of the antibiotics tested showing up to 40 different resistance patterns. The cattle C. coli displayed a high frequency of resistance to erythromycin and ciprofloxacin, while all the chicken isolates were resistant to erythromycin, the drug of choice for the treatment of the Campylobacter infections in Nigeria. This investigation carried out in apparently healthy animals identified cattle and local chickens as potential reservoir hosts for C. coli infection in the study area. Key words: Campylobacter coli, local chickens, multiple antibiotic resistance, Ibadan.

The aim of this study was to isolate Salmonella species and other enteric bacteria in rats cohabiting with poultry; in order to consider the potential role of rats in their transmissions to poultry and humans. Four hundred samples comprising 200 oral swabs and 200 anal swabs were collected from rats cohabiting with poultry from 5 local government areas in Ibadan. The samples were subjected to standard bacteriological analysis. A total of 228 Gram negative bacteria including 21 different species of both Lactose fermenters and non-Lactose fermenters were isolated. The identified organisms include: Salmonella subspecies 1, Salmonella Arizonae, Escherichia coli, Escherichia coli inactive, Pseudomonas aeruginosa, Pseudomonas fluorescens, Enterobacter cloacae, Enterobacter hormaechei, Enterobacter agglomerans, Enterobacter dissolvens, Enterobacter gergoviae, and Aeromonas hydrophila, Proteus mirabilis, Proteus vulgaris, Hafnia alvei, Morganella morganii biogp 1,Morganella morganii subspecies Siboni 1, Citrobacter diversus, Serratia liquefaciens, Pragia fontium and Providencia alcalifaciens. The organisms were identified using Oxoid Microbact GNB 24E® (MB24E) and accompanying computer software package (Oxoid Microbact®) 2000 version 2.03. Some of the isolated bacteria from rats’ cohabitating with poultry have been associated with diseases in poultry and humans. The findings therefore serves to create fresh awareness among poultry farmers and other stakeholders in the industry from the studied area, that rats do not only constitute physical threat in terms of destruction of infrastructures and feeding on poultry feeds, they also pose a great risk in terms of transmission of bacterial infection to poultry and men associated with poultry production. Possible measures to control rats’ infestations within poultry houses are highlighted. Key words: Rats, poultry, co-habitating, Gram negative Bacteria.

Background: Despite the huge burden of deaths associated with or attributable to antimicrobial resistance, studies on sequencing based antimicrobial resistance (AMR) monitoring in Africa are scarce, specifically in the animal sector. Objective and Methods: With a view to deploy rapid AMR monitoring through leveraging advanced technologies, in the current study, nanopore sequencing was performed with 10 E. coli strains isolated from rectal swabs of pigs and poultry layers in Nigeria. Two sequence analysis methods including command line, where bacterial genomes were assembled, and subsequently antimicrobial resistance genes (ARGs) were detected through online databases, and EPI2ME, an integrated cloud-based data analysis platform with MinION, was used to detect ARGs. Results: A total of 95 ARGs were identified and most of the genes are known to be expressed in the chromosome. Interestingly, few genes including qnrS1, qnrS15, qnrS10, kdpE, cmlA1, MIR-14, sul3 and dfrA12 were identified which were previously reported as transferred through Mobile Genetic Elements (MGEs). The antibiotic susceptibility assay determined that the E. coli isolates were resistant to Penicillin (100%), Ciprofloxacin (70%), tetracycline (50%) and Ampicillin (40%). The accuracies of the command line and EPI2ME methods have been found to be 57.14% and 32.14%, respectively, in predicting AMR. Moreover, the analysis methods showed 62.5% agreement in predicting AMR for the E. coli isolates. Conclusions: Considering the multiple advantages of nanopore sequencing, the application of this rapid and field-feasible sequencing technique holds promise for rapid AMR monitoring in low- and middle-income countries (LMICs), including Nigeria. However, the development of a robust sequence analysis pipeline and the optimization of the existing analysis tools are crucial to streamline the deployment of nanopore sequencing in LMICs for AMR monitoring both in animal and human sectors.

Shiga toxin-producing Escherichia coli (STEC) are significant zoonotic pathogens worldwide, causing diseases ranging from diarrhea to hemolytic uremic syndrome (HUS). Ruminants, mainly cattle, are considered the primary reservoirs; however, the role of horses in the epidemiology of STEC remains poorly understood in Nigeria. A total of 231 rectal swabs were collected from horses across selected equine facilities in five Nigerian states. Samples were processed following standard procedures, and isolates were confirmed using the Analytical Profile Index (API 20E) kit. Antibiotic susceptibility testing (AST) was performed using the Kirby-Bauer disk diffusion method with a panel of nine antibiotics, and the isolated Escherichia (E.) coli were classified as sensitive or resistant according to CLSI guidelines. The Multiple Antibiotic Resistance (MAR) index was calculated to assess the risk of contamination. The E. coli isolates were screened for selected Shiga toxin genes (stx1, stx2 and eae) using polymerase chain reaction (PCR). Fourteen isolates (6%) were identified as Shiga toxin-producing E. coli; of these, 78.6% (11/14) expressed at least one virulence gene: 42.9% (6/14) carried stx2, 35.7% (5/14) carried eae, and no isolate carried stx1. All confirmed STEC isolates exhibited multidrug resistance (MDR). The isolates showed complete resistance (100%) to cefuroxime and ciprofloxacin, while all were susceptible to ofloxacin. MAR indices ranged from 0.2 to 0.8, with 77.8% of isolates exhibiting MAR indices ≥0.5. This study reports the detection of MDR STEC in horses in Nigeria, revealing high-level resistance to clinically important antibiotics and significant carriage of virulence genes. The high MAR indices indicate high-risk contamination sources. The detection of MDR STEC in this study underscores a significant health risk to horses, with potential for zoonotic transmission to humans and the environment.