Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems

• Published in: Scientific reports Vol. 8; no. 1; pp. 11907 - 13
• Main Authors: Hu, Yue O. O., Ndegwa, Nelson, Alneberg, Johannes, Johansson, Sebastian, Logue, Jürg Brendan, Huss, Mikael, Käller, Max, Lundeberg, Joakim, Fagerberg, Jens, Andersson, Anders F.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 09.08.2018; Nature Publishing Group
• Subjects: 45; 45/22; 45/41; 45/77; 631/61/168; 704/172; Cattle; Contamination; DNA sequencing; E coli; Environmental Science; Escherichia coli; Fecal coliforms; Feces; Food processing industry; Humanities and Social Sciences; Intestinal microflora; Microbiomes; Miljövetenskap; multidisciplinary; rRNA 16S; Science; Science (multidisciplinary); Sewer systems; Sewers; Stormwater; Wastewater; Wastewater pollution
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-018-29920-7

Urban sewer systems consist of wastewater and stormwater sewers, of which only wastewater is processed before being discharged. Occasionally, misconnections or damages in the network occur, resulting in untreated wastewater entering natural water bodies via the stormwater system. Cultivation of faecal indicator bacteria (e.g. Escherichia coli ; E . coli ) is the current standard for tracing wastewater contamination. This method is cheap but has limited specificity and mobility. Here, we compared the E . coli culturing approach with two sequencing-based methodologies (Illumina MiSeq 16S rRNA gene amplicon sequencing and Oxford Nanopore MinION shotgun metagenomic sequencing), analysing 73 stormwater samples collected in Stockholm. High correlations were obtained between E . coli culturing counts and frequencies of human gut microbiome amplicon sequences, indicating E . coli is indeed a good indicator of faecal contamination. However, the amplicon data further holds information on contamination source or alternatively how much time has elapsed since the faecal matter has entered the system. Shotgun metagenomic sequencing on a subset of the samples using a portable real-time sequencer, MinION, correlated well with the amplicon sequencing data. This study demonstrates the use of DNA sequencing to detect human faecal contamination in stormwater systems and the potential of tracing faecal contamination directly in the field.