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.

Fluoroquinolone-resistant Escherichia coli (E. coli) from faecal matter of non-human primates (NHP) and their carriage of plasmid-mediated quinolone resistance genes were investigated in this study. Faecal samples were collected from six accredited zoological and tourism gardens in South-western and Northern Nigeria. Five fluoroquinolone-resistant E. coli were obtained from the 43 NHP sampled. Three of the isolates were from Agodi gardens, Ibadan, and one each from Osun Osogbo grove and University of Ibadan Zoological garden. The isolates were from Green monkeys (3), Mona Monkey (1) and Anubis baboon (1). They showed varying antibiotic resistance levels, with 100% resistance observed only towards sulfamethoxazole-trimethoprim. None of the isolates was positive for ESBL production. All the isolates carried qnrD, with three each carrying qnrA and qnrS. Only one isolate carried qnrB. The carriage of qnr genes by captive animals could portend serious public health risks.

Background: Pet birds are housed and reared exclusively for ornamental use. These include psittaciformes (parrots, parakeets, budgerigars, love birds) and passeriformes (e.g. canaries, finches, sparrows, also called songbirds). E. coli is a Gram negative bacterium. In birds, it is called Avian Pathogenic E. coli and is a causative agent of avian colibacillosis. Antimicrobial resistance is the process through which bacteria evade the activity of antibiotics. According to WHO (World Health Organization), antibiotic resistance is the result of indiscriminate use of these drugs which are used both in Veterinary and human medicine. Case presentation: A one and half year old yellow female budgerigar pet bird (Melopsittacus undulatus) with patches of black and white on wings and back, kept as companion (one out of four) was presented dead at the avian clinic section of the Veterinary Teaching Hospital, University of Ibadan, Nigeria. It was reported to have presented signs of anorexia and diarrhea for two days before death. Provisional diagnosis was colibacillosis. Intestinal samples were sent for microbial culture and sensitivity. The samples yielded growth of E. coli. Antimicrobial susceptibility revealed that the organism showed resistance to all tested antibiotics. Conclusions: Multidrug-resistant Escherichia coli constitutes a major public health concern. The constant interaction between household companion birds and humans gives room for disease transmission. Wild birds kept as pets or companions harbor pathogenic and zoonotic pathogens, hence a threat to public health.