State of art metagenomics were used to investigate the microbial population, antibiotic resistance genes and plasmids of medical interest in wastewater used for urban agriculture in Ouagadougou (Burkina Faso). Wastewater samples were collected from three canals near agricultural fields in three neighbourhoods. Assessment of microbial population diversity revealed different microbial patterns among the different samples. Sequencing reads from the wastewaters revealed different functional specializations of microbial communities, with the predominance of carbohydrates and proteins metabolism functions. Eleven pathogen-specific and 56 orthologous virulence factor genes were detected in the wastewater samples. These virulence factors are usually found in human pathogens that cause gastroenteritis and/or diarrhoea. A wide range of antibiotic resistance genes was identified; 81 are transmissible by mobile genetic elements. These included seven different extended spectrum β-lactamase genes encoding synthesis of four enzyme families, including two metallo-β-lactamases (bla_AIM-1 and bla_GES-21). Ten different incompatibility groups of Enterobacteriaceae plasmid replicons (ColE, FIB, FIC, FII, P, Q, R, U, Y, and A/C), and 30 plasmid replicon types from Gram-positive bacteria. All are implicated in the wide distribution of antibiotic resistance genes. We conclude that wastewater used for urban agriculture in the city represents a high risk for spreading bacteria and antimicrobial resistance among humans and animals.

最先进的宏基因组学用于调查瓦加杜古（布基纳法索）城市农业废水中的微生物种群，抗生素抗性基因和医学感兴趣的质粒。从三个地区的农田附近的三个运河中收集了废水样品。对微生物种群多样性的评估揭示了不同样品之间的不同微生物模式。废水中的测序数据显示，微生物群落具有不同的功能专长，主要是碳水化合物和蛋白质的代谢功能。在废水样品中检测到11种病原体特异性和56种直系同源毒力因子基因。这些致病因子通常在引起肠胃炎和/或腹泻的人类病原体中发现。鉴定了广泛的抗生素抗性基因。81个是可以通过遗传基因传播的。其中包括七个不同的广谱β-内酰胺酶基因，它们编码四个酶家族的合成，其中包括两个金属-β-内酰胺酶（bla _AIM-1和bla _GES-21）。肠杆菌科细菌复制子有十种不同的不相容性组（ColE，FIB，FIC，FII，P，Q，R，U，Y和A / C），还有来自革兰氏阳性细菌的30种质粒复制子。所有这些都与抗生素抗性基因的广泛分布有关。我们得出的结论是，城市中用于城市农业的废水代表着在人类和动物之间传播细菌和产生耐药性的高风险。