Coffee cartridge filtration: a rapid, inexpensive, and easy method to concentrate nucleic acids from pathogens and fecal biomarkers in wastewater

AIMS: We propose coffee cartridge filtration as an alternative method for the concentration of nucleic acids from microorganisms in wastewater. METHODS AND RESULTS: In this study, coffee cartridge filtration was directly compared with PEG precipitation through mass balance analysis. The utility of coffee cartridge filtration was further demonstrated through a 10-month longitudinal analysis of Giardia, human norovirus genogroup I and II, and hepatitis A virus in 45 wastewater samples from Guelph, Ontario, Canada. Fourteen of these wastewater samples were enriched with the Illumina Viral Surveillance Panel v2 and sequenced with the Illumina NextSeq 1000. PEG precipitation was more efficient at concentrating nucleic acids from all microorganisms and viruses, but all endogenous targets were detected following coffee cartridge filtration. Hepatitis A was detected in four wastewater samples and best correlated with four clinical cases when a 1-week wastewater lead time was applied. HuNoV-GI and HuNoV-GII were detected within the RT-qPCR linear dynamic range in 44/45 samples. Nucleic acids from the Polyomaviridae, Astroviridae, and Caliciviridae families were most identified in coffee cartridge-filtered wastewater samples. CONCLUSIONS: Coffee cartridge filtration is an effective method to concentrate nucleic acids from microorganisms in wastewater in resource-limited settings.