Digital PCR (dPCR) analysis was performed using a the QuantStudio® 3D Digital PCR System (Thermo Scientific, UK). The dPCR reaction was made up according to manufacturer instructions of QuantStudio® 3D Digital PCR Master Mix, appropriate TaqMan™ primers with MGB probes, sterile water, and DNA sample. Due to similarities in gene abundance in wastewater samples, intI1 and sul1 were duplexed allowing quantification of both genes on one chip with intI1 having this in FAM™ dye and sul1 with VIC® dye. The mixture was then portioned onto dPCR chip wells and sealed.