Caeca from free-range Ghanaian chickens in rural, urban and industrial production settings were collected as well as faecal samples from rural and urban Ghanaian pigs. Using shotgun metagenomics, both the resistomes and microbiomes were quantified and characterised. The Ghanaian samples were further compared with pig and poultry samples from 9 European countries (ENA accession number: PRJEB22062).
The escalating prevalence of antimicrobial resistance in farm animals continues to challenge public health and necessitates global attention, particularly in less studied parts of the globe such as Africa. We quantified and characterized the antimicrobial resistance gene (ARG) pools (resistomes) of 30 pigs and 60 free-range (rural and urban) and industrialized poultry across Ghana. We quantified acquired ARGs using the ResFinder database and the bacterial composition using the Silva database. The data were compared to similar data from pigs and poultry obtained from nine European countries. The pig and poultry were very different in ARG and bacterial abundance and composition. The bacteriome of the Ghanaian samples also differed substantially from the European samples and was especially driven by a much higher abundance in both poultry and pigs of Subdoligranulum. We found lower AMR loads in Ghanaian pigs, compared to European. For poultry the urban free-range had lower ARG abundances than the lowest European, the rural free-range comparable to the European average and the industrialized higher than European samples. Despite the major differences in abundance the resistome composition of Ghanaian urban, rural and industrialized poultry samples were similar and differences from European samples were mainly driven by increased abundances of different tetracycline resistance genes among the samples from Ghana and increased abundances of ARGs encoding resistance to macrolides, beta-lactams and trimethoprim among samples from Europe. Among pig samples the main differences were caused by ARGs encoding resistance to nitroimidazoles, beta-lactams and macrolides in European samples.  In conclusion, this study is to the best of our knowledge the first report on the resistome measured using metagenomics in livestock from Sub-saharan Africa. We find a very different microbiome among both pigs and poultry compared to similar samples from Europe. For pigs and urban free-range poultry we find a very low abundance of ARGs, whereas rural free-range poultry is similar to the European average and industrialized poultry higher.