A comprehensive database for biological data derived from sewage in five European cities

Ágnes Becsei; Patrick Munk; Alessandro Fuschi; Saria Otani; József Stéger; Dávid Visontai; Krisztián Papp; Christian Brinch; Ravi Kant; Ilya Weinstein; Olli Vapalahti; Miranda de Graaf; Claudia M. E. Schapendonk; Jeroen Roelfsema; Maaike van den Beld; Roan Pijnacker; Eelco Franz; Patricia Alba; Antonio Battisti; Alessandra De Cesare; Valentina Indio; Fulvia Troja; Tarja Sironen; Chiara Oliveri; Frédérique Pasquali; Ivan Liachko; Benjamin Auch; Colman O'Cathail; Krisztián Bányai; Magdolna Makó; Péter Pollner; Marion Koopmans; Istvan Csabai; Daniel Remondini; Frank M. Aarestrup

doi:10.1093/database/baaf089

A comprehensive database for biological data derived from sewage in five European cities

Ágnes Becsei^*
, Patrick Munk
, Alessandro Fuschi
, Saria Otani
, József Stéger
, Dávid Visontai
, Krisztián Papp
, Christian Brinch
, Ravi Kant
, Ilya Weinstein
, Olli Vapalahti
, Miranda de Graaf
, Claudia M. E. Schapendonk
, Jeroen Roelfsema
, Maaike van den Beld
, Roan Pijnacker
, Eelco Franz
, Patricia Alba
, Antonio Battisti
, Alessandra De Cesare

Valentina Indio, Fulvia Troja, Tarja Sironen, Chiara Oliveri, Frédérique Pasquali, Ivan Liachko, Benjamin Auch, Colman O'Cathail, Krisztián Bányai, Magdolna Makó, Péter Pollner, Marion Koopmans, Istvan Csabai, Daniel Remondini, Frank M. Aarestrup

^*Corresponding author for this work

Eötvös Loránd University
University of Bologna
Medical University of Gdańsk
University of Helsinki
Erasmus University Medical Center
National Institute of Public Health and the Environment
Experimental Zooprophylactic Institute of Lazio and Toscana
Phase Genomics, Inc.
European Bioinformatics Institute
University of Veterinary Medicine Budapest
Budapest Sewage Works Pte. Ltd
Health Services Management Training Centre

Research output: Contribution to journal › Journal article › Research › peer-review

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Abstract

Sewage metagenomics is a powerful tool for proactive pathogen surveillance and understanding microbial community dynamics. To support such efforts, we present a highly curated and accessible longitudinal dataset of 239 sewage samples collected from five European cities. The dataset, processed through metagenomic sequencing, includes rich analytical outputs such as taxonomic profiles, identified antimicrobial resistance genes, assembled contigs with annotated origins, metagenome-assembled genomes with functional gene annotations, and metadata. Given the computational intensity and time required to reproduce such analyses, we share this dataset to promote reuse and advance research. In addition to the metagenomic data, qPCR was used to identify specific pathogens, and Hi-C sequencing was performed on a subset of the samples to strengthen genomic linkage analysis. Central to this resource is a publicly available PostgreSQL database, designed to facilitate efficient exploration and reuse of the data. This comprehensive database allows users to perform targeted queries, subset data, and streamline access to this extensive resource.

Original language	English
Article number	baaf089
Journal	Database: The Journal of Biological Databases and Curation
Volume	2026
Number of pages	7
ISSN	1758-0463
DOIs	https://doi.org/10.1093/database/baaf089
Publication status	Published - 2026

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Becsei, Á., Munk, P., Fuschi, A., Otani, S., Stéger, J., Visontai, D., Papp, K., Brinch, C., Kant, R., Weinstein, I., Vapalahti, O., de Graaf, M., Schapendonk, C. M. E., Roelfsema, J., van den Beld, M., Pijnacker, R., Franz, E., Alba, P., Battisti, A., ... Aarestrup, F. M. (2026). A comprehensive database for biological data derived from sewage in five European cities. Database: The Journal of Biological Databases and Curation, 2026, Article baaf089. https://doi.org/10.1093/database/baaf089

@article{385182796bb748c89122c47d5190d6ba,

title = "A comprehensive database for biological data derived from sewage in five European cities",

abstract = "Sewage metagenomics is a powerful tool for proactive pathogen surveillance and understanding microbial community dynamics. To support such efforts, we present a highly curated and accessible longitudinal dataset of 239 sewage samples collected from five European cities. The dataset, processed through metagenomic sequencing, includes rich analytical outputs such as taxonomic profiles, identified antimicrobial resistance genes, assembled contigs with annotated origins, metagenome-assembled genomes with functional gene annotations, and metadata. Given the computational intensity and time required to reproduce such analyses, we share this dataset to promote reuse and advance research. In addition to the metagenomic data, qPCR was used to identify specific pathogens, and Hi-C sequencing was performed on a subset of the samples to strengthen genomic linkage analysis. Central to this resource is a publicly available PostgreSQL database, designed to facilitate efficient exploration and reuse of the data. This comprehensive database allows users to perform targeted queries, subset data, and streamline access to this extensive resource.",

author = "{\'A}gnes Becsei and Patrick Munk and Alessandro Fuschi and Saria Otani and J{\'o}zsef St{\'e}ger and D{\'a}vid Visontai and Kriszti{\'a}n Papp and Christian Brinch and Ravi Kant and Ilya Weinstein and Olli Vapalahti and \{de Graaf\}, Miranda and Schapendonk, \{Claudia M. E.\} and Jeroen Roelfsema and \{van den Beld\}, Maaike and Roan Pijnacker and Eelco Franz and Patricia Alba and Antonio Battisti and \{De Cesare\}, Alessandra and Valentina Indio and Fulvia Troja and Tarja Sironen and Chiara Oliveri and Fr{\'e}d{\'e}rique Pasquali and Ivan Liachko and Benjamin Auch and Colman O'Cathail and Kriszti{\'a}n B{\'a}nyai and Magdolna Mak{\'o} and P{\'e}ter Pollner and Marion Koopmans and Istvan Csabai and Daniel Remondini and Aarestrup, \{Frank M.\}",

year = "2026",

doi = "10.1093/database/baaf089",

language = "English",

volume = "2026",

journal = "Database: The Journal of Biological Databases and Curation",

issn = "1758-0463",

publisher = "Oxford University Press",

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Becsei, Á, Munk, P, Fuschi, A, Otani, S, Stéger, J, Visontai, D, Papp, K, Brinch, C, Kant, R, Weinstein, I, Vapalahti, O, de Graaf, M, Schapendonk, CME, Roelfsema, J, van den Beld, M, Pijnacker, R, Franz, E, Alba, P, Battisti, A, De Cesare, A, Indio, V, Troja, F, Sironen, T, Oliveri, C, Pasquali, F, Liachko, I, Auch, B, O'Cathail, C, Bányai, K, Makó, M, Pollner, P, Koopmans, M, Csabai, I, Remondini, D & Aarestrup, FM 2026, 'A comprehensive database for biological data derived from sewage in five European cities', Database: The Journal of Biological Databases and Curation, vol. 2026, baaf089. https://doi.org/10.1093/database/baaf089

TY - JOUR

T1 - A comprehensive database for biological data derived from sewage in five European cities

AU - Becsei, Ágnes

AU - Munk, Patrick

AU - Fuschi, Alessandro

AU - Otani, Saria

AU - Stéger, József

AU - Visontai, Dávid

AU - Papp, Krisztián

AU - Brinch, Christian

AU - Kant, Ravi

AU - Weinstein, Ilya

AU - Vapalahti, Olli

AU - de Graaf, Miranda

AU - Schapendonk, Claudia M. E.

AU - Roelfsema, Jeroen

AU - van den Beld, Maaike

AU - Pijnacker, Roan

AU - Franz, Eelco

AU - Alba, Patricia

AU - Battisti, Antonio

AU - De Cesare, Alessandra

AU - Indio, Valentina

AU - Troja, Fulvia

AU - Sironen, Tarja

AU - Oliveri, Chiara

AU - Pasquali, Frédérique

AU - Liachko, Ivan

AU - Auch, Benjamin

AU - O'Cathail, Colman

AU - Bányai, Krisztián

AU - Makó, Magdolna

AU - Pollner, Péter

AU - Koopmans, Marion

AU - Csabai, Istvan

AU - Remondini, Daniel

AU - Aarestrup, Frank M.

PY - 2026

Y1 - 2026

N2 - Sewage metagenomics is a powerful tool for proactive pathogen surveillance and understanding microbial community dynamics. To support such efforts, we present a highly curated and accessible longitudinal dataset of 239 sewage samples collected from five European cities. The dataset, processed through metagenomic sequencing, includes rich analytical outputs such as taxonomic profiles, identified antimicrobial resistance genes, assembled contigs with annotated origins, metagenome-assembled genomes with functional gene annotations, and metadata. Given the computational intensity and time required to reproduce such analyses, we share this dataset to promote reuse and advance research. In addition to the metagenomic data, qPCR was used to identify specific pathogens, and Hi-C sequencing was performed on a subset of the samples to strengthen genomic linkage analysis. Central to this resource is a publicly available PostgreSQL database, designed to facilitate efficient exploration and reuse of the data. This comprehensive database allows users to perform targeted queries, subset data, and streamline access to this extensive resource.

AB - Sewage metagenomics is a powerful tool for proactive pathogen surveillance and understanding microbial community dynamics. To support such efforts, we present a highly curated and accessible longitudinal dataset of 239 sewage samples collected from five European cities. The dataset, processed through metagenomic sequencing, includes rich analytical outputs such as taxonomic profiles, identified antimicrobial resistance genes, assembled contigs with annotated origins, metagenome-assembled genomes with functional gene annotations, and metadata. Given the computational intensity and time required to reproduce such analyses, we share this dataset to promote reuse and advance research. In addition to the metagenomic data, qPCR was used to identify specific pathogens, and Hi-C sequencing was performed on a subset of the samples to strengthen genomic linkage analysis. Central to this resource is a publicly available PostgreSQL database, designed to facilitate efficient exploration and reuse of the data. This comprehensive database allows users to perform targeted queries, subset data, and streamline access to this extensive resource.

U2 - 10.1093/database/baaf089

DO - 10.1093/database/baaf089

M3 - Journal article

C2 - 41556498

SN - 1758-0463

VL - 2026

JO - Database: The Journal of Biological Databases and Curation

JF - Database: The Journal of Biological Databases and Curation

M1 - baaf089

ER -

A comprehensive database for biological data derived from sewage in five European cities

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