Cloacal swab samples were collected from 350 apparently healthy commercial layers in Oyo and Osun states, Nigeria. Nine fluoroquinolone-resistant Salmonella species belonging to serovar Infantis (n=4), Heidelberg (n=3), and Saintpaul (n=2) were isolated from the sampled birds. The isolates were multidrug resistant with Multiple Antibiotic Resistance Index (MAR) ranging from 0.15 to 0.54. There was high resistance to fluoroquinolones, with 88.9% resistance to pefloxacin and ofloxacin, 77.8% to nalidixic acid and ciprofloxacin. None of the isolates were ESBL positive. All the nine isolates did not carry qnrA gene; 11.1%, 22.2% and 88.9% possessed qnrB, qnrD and qnrS, respectively. This study isolated plasmid mediated fluoroquinolone resistant rare Salmonella serovars from commercial layers in Nigeria.

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.

Sheep farming plays a significant role in global livestock production, contributing to the output of meat, wool, and milk, and providing income for millions of livestock farmers, especially in developing countries. In this review, the role of bacteria in the aetiology and pathology of neonatal lamb mortality, including management and prevention strategies, is discussed. Several bacteria are known to cause neonatal mortality in sheep, with Escherichia coli consistently identified as the most common pathogen, responsible for 15–20% of neonatal deaths worldwide. Other important bacterial pathogens include Salmonella spp., Pasteurella multocida , and Mannheimia haemolytica . Additionally, Brucella melitensis and Campylobacter fetus subsp. fetus , among others, have also been recognised as bacterial causes of neonatal mortality in lambs. This review demonstrates that bacterial infections cause lamb losses in sheep during the first two weeks of life. Effective management and preventative strategies— such as prompt vaccination, adequate colostrum intake, good sanitation, responsible antibiotic use, and supportive care—can significantly reduce bacterial infections in newborn lambs. This reduction will lower neonatal mortality rates, support sustainable sheep production, and contribute to global food security.