Main antibiotic routes into the soil and waterways. 1 Uptake of resistant bacteria in the food chain. 2 Excreted antibiotics and their metabolites enter the sewage system. 3 Water treatment facilities are not completely effective at removing bacteria which then enter waterways. 4 Animal waste, containing resistant bacteria and unmetabolised antibiotics, contaminates soil and water directly and is also used to fertilise crops. 5 Antibiotics in crop sprays contaminate soil and waterways directly. 6 Pharmaceutical waste containing antibiotics may be released directly into the environment.