Raw wastewater irrigation for urban agriculture in Africa increases the diversity of transferable antibiotic resistances genes in soil, including those encoding ESBLs

Abstract

A metagenomic study was conducted to investigate the impact of raw wastewater use for irrigation in urban agriculture on the development of bacterial resistance in soil. Soil samples were collected in two African countries, from three different cities (each with irrigated and non-irrigated plots). Basic physical and chemical analysis were conducted, and the presence of selected antibiotic residues was assessed. Microbial DNA was extracted, quantified and sequenced. Microbial population structure and function, presence of horizontally transferable antibiotic resistance genes and Enterobacteriaceae plasmids replicons were analysed using bioinformatics. The relative prevalence of Proteobacteria and Bacteroidetes and sequence reads coding for microbial adaptation and growth were higher in irrigated fields; 33 and 26 transferable ARGs were found in irrigated and non-irrigated fields sequence reads, respectively. Extended spectrum β-lactam genes identified in irrigated fields included bla CARB-3, bla OXA-347, bla OXA-5 and bla Rm3. Concentration of sulfamethoxazole, ciprofloxacin and enrofloxacin in soils influenced the selection of antibiotic resistance genes encoding resistance against amphenicol, β-lactams, and tetracyclines. Ten Enterobacteriaceae plasmid amplicon groups were identified in the fields, five were common to both, two (IncW and IncP1) and three (IncY, IncFIB and IncFIA) were found in irrigated and non-irrigated fields, respectively.In conclusion, wastewater irrigation affected both soil microbial diversity and functions. Irrigated fields have more diverse transferable antibiotic resistance genes, including ESBL genes that encode resistance to βlactams antibiotics, except cephamycins and carbapenems. Even more, critical concentrations of antibiotic residues select for multiple and cross resistance. The findings from African cities show that wastewater irrigation in urban agriculture presents a serious public health risk for farmworkers and consumers by spread of bacterial resistance.