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Microorganisms
Special Issues
Surveillance of Health-Relevant Pathogens Employing Wastewater
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Surveillance of Health-Relevant Pathogens Employing Wastewater

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: 28 February 2026 | Viewed by 1822

Special Issue Editors

Dr. Bernd Manfred Gawlik

E-Mail Website
Guest Editor
European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy
Interests: wastewater and environmental surveillance (WES); SARS-CoV-2; public health; COVID-19 pandemic; pathogen monitoring
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Gernot Marx

E-Mail Website
Guest Editor
Department of Intensive Care Medicine, University Hospital RWTH Aachen, 52074 Aachen, Germany
Interests: critical care medicine; infectious diseases; telemedicine; digital transformation

Special Issue Information

Dear Colleagues,

We are pleased to introduce the second edition of our Special Issue “Surveillance of SARS-CoV-2 Employing Wastewater” (https://www.mdpi.com/journal/microorganisms/special_issues/EZWTO53D8J), now entitled "Surveillance of Health-Relevant Pathogens Employing Wastewater". Building on the success of the initial edition focused on SARS-CoV-2, this edition broadens the scope to capture the evolving landscape of Wastewater and Environmental Surveillance (WES), particularly its application in monitoring emerging pathogens and antimicrobial resistance (AMR) as we move into 2025 and beyond.

Wastewater has become a potent source of information, not just for public health, but also for significant economic sectors such as hospitals, aviation, tourism, and agriculture. The encoded data in wastewater offers early insights into pathogen prevalence, for instance, empowering healthcare facilities with timely intervention strategies and aiding in the design of effective infection control protocols. In the aviation and tourism industries, understanding regional pathogen dynamics enables the establishment of informed policies to safeguard the health of travellers. Similarly, in agriculture, insights gleaned from surveillance can inform practices related to livestock management and food safety, as well as addressing concerns associated with AMR.

This Special Issue delves into the advancements in WES that have enabled such comprehensive applications. It emphasizes the progression of health sector leadership, ethical practices, and the integration of wastewater data into broader public health and economic frameworks. By covering key aspects such as sampling, storage, laboratory analysis, data normalization, and communication, this edition underscores the vital role WES plays in enhancing global health security.

By synthesizing the various applications and opportunities offered by wastewater surveillance, this edition aims to illustrate its expanding influence on health preparedness and its potential to safeguard economically relevant sectors against emerging health threats. We look forward to exploring these dimensions with you.

Dr. Bernd Manfred Gawlik
Prof. Dr. Gernot Marx
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • wastewater and environmental surveillance (WES)
  • emerging pathogens
  • antimicrobial resistance
  • public health
  • pathogen monitoring
  • global health security

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Published Papers (3 papers)

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Research

16 pages, 2167 KB  
Article
Continuous Circulation of Hepatitis E and A Viruses During COVID-19 Pandemic Lockdowns in Munich, Germany—Experience from Three Years of Wastewater Surveillance
by Jasmin Javanmardi, Mathias Schemmerer, Karina Wallrafen-Sam, Jessica Neusser, Raquel Rubio-Acero, Michael Hoelscher, Thomas Kletke, Bernhard Boehm, Michael Schneider, Elisabeth Waldeck, Martin Hoch, Merle M. Böhmer, Christof Geldmacher, Jan Hasenauer, Jürgen J. Wenzel and Andreas Wieser
Microorganisms 2025, 13(10), 2379; https://doi.org/10.3390/microorganisms13102379 - 15 Oct 2025
Viewed by 463
Abstract
The COVID-19 pandemic has increased interest in wastewater-based epidemiology (WBE) as a reliable and cost-effective framework for monitoring the spread of microbes. However, WBE frameworks have rarely been applied to the study of fecal–oral transmissible diseases, except for poliomyelitis. Here, we investigated the [...] Read more.
The COVID-19 pandemic has increased interest in wastewater-based epidemiology (WBE) as a reliable and cost-effective framework for monitoring the spread of microbes. However, WBE frameworks have rarely been applied to the study of fecal–oral transmissible diseases, except for poliomyelitis. Here, we investigated the presence of hepatitis A virus (HAV) and hepatitis E virus (HEV) in wastewater in Munich. We collected wastewater samples between July 2020 and November 2023. A total of 186 samples were processed using centrifugation and analyzed for HAV- and HEV-RNA using RT-qPCR. As a reference, we used notification data from clinically or laboratory-diagnosed hepatitis A and E cases. Lockdown stringency levels were derived from official documentation. Our results show that 87.6% of wastewater samples were positive for HEV at concentrations of 9.0 × 101 to 2.5 × 105 copies/L, while HAV was only detectable in 7.5% of the samples at viral loads of 4.6 × 101 to 2.4 × 103 copies/L. We also detected differences in HEV concentrations but not in case numbers when comparing lockdown and no-lockdown periods. This study covers all but the first lockdowns in Bavaria. We present a unique real-world dataset evaluating the impact of lockdown interventions on hepatitis A and E case numbers, as well as on the concentrations of HAV and HEV in wastewater. Person-to-person spread and eating out appear to have contributed to the transmission of HEV. In addition, the consistently high HEV concentrations in sewage support the findings of serological studies, indicating a substantial burden of undetected subclinical infections. Full article
(This article belongs to the Special Issue Surveillance of Health-Relevant Pathogens Employing Wastewater)
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16 pages, 1146 KB  
Article
Rotavirus Quantification and Genotyping in Wastewater: A Molecular Surveillance Study in Italy (2024–2025)
by Giusy Bonanno Ferraro, Carolina Veneri, Agata Franco, David Brandtner, Daniele Congiu, Pamela Mancini, Marcello Iaconelli, Elisabetta Suffredini and Giuseppina La Rosa
Microorganisms 2025, 13(10), 2319; https://doi.org/10.3390/microorganisms13102319 - 7 Oct 2025
Viewed by 544
Abstract
Rotavirus remains a leading cause of acute gastroenteritis worldwide, particularly in young children, despite widespread vaccination efforts. This study aims to evaluate rotavirus circulation at the population level through wastewater-based epidemiology (WBE), offering a non-invasive, complementary approach to clinical surveillance. Between 2024 and [...] Read more.
Rotavirus remains a leading cause of acute gastroenteritis worldwide, particularly in young children, despite widespread vaccination efforts. This study aims to evaluate rotavirus circulation at the population level through wastewater-based epidemiology (WBE), offering a non-invasive, complementary approach to clinical surveillance. Between 2024 and 2025, a total of 172 composite 24 h samples were collected from eight urban wastewater treatment plants across Northern, Central, and Southern Italy. Viral RNA was concentrated by PEG precipitation and quantified using digital RT-PCR, while genotypes were determined via nested PCR targeting VP7 and VP4 genes. Rotavirus RNA was detected in 143 out of 172 samples (83.1%), with viral loads ranging between 4.2 × 102 to 7.3 × 105 genome copies per liter (g.c./L). Genotyping revealed G3 as the predominant VP7 type, followed by G1, G2, G6, and G9. All VP4-positive samples were classified as P8. This investigation expands current knowledge of rotavirus epidemiology in Italy using molecular surveillance of urban wastewater. By combining digital RT-PCR and genotyping, it offers a robust framework for integrating WBE into rotavirus monitoring programs, especially in settings where clinical surveillance is limited. Full article
(This article belongs to the Special Issue Surveillance of Health-Relevant Pathogens Employing Wastewater)
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13 pages, 557 KB  
Article
Uncovering DENV, CHIKV, and ZIKV in Urban Wastewater in Brazil Through Genomic and Molecular Screening
by Juliana Calabria de Araujo, Ana Paula A. Carvalho, Talita Adelino, Felipe Campos M. Iani, Natalia Rocha Guimaraes, Sara Candida F. Santos, Cintia D. Leal, Manuelle Natividade, Mauricio Lima, Mariana Almada, Ana Carolina Bertuce, Augusto Guerra, Maria Cristina M. Costa, Flavia Saia, Vagner Fonseca, Marta Giovanetti, Livia V. Frutuoso and Luiz Carlos Junior Alcantara
Microorganisms 2025, 13(9), 2164; https://doi.org/10.3390/microorganisms13092164 - 17 Sep 2025
Viewed by 653
Abstract
This study evaluated and compared molecular methods (Whole Genome Sequencing-WGS, MinION, and RT-qPCR) for the detection of arboviruses Dengue (DENV), Chikungunya (CHIKV), and Zika (ZIKV) in 63 hospital and municipal wastewater samples collected from July 2022 to May 2023 in the region of [...] Read more.
This study evaluated and compared molecular methods (Whole Genome Sequencing-WGS, MinION, and RT-qPCR) for the detection of arboviruses Dengue (DENV), Chikungunya (CHIKV), and Zika (ZIKV) in 63 hospital and municipal wastewater samples collected from July 2022 to May 2023 in the region of Belo Horizonte, Brazil. Detection rates varied substantially across the methods (WGS, MinION, and RT-qPCR). DENV was identified in 24% (15/63) of samples using a hybrid capture method of WGS and MinION sequencing and in 66.6% (20/30) using only WGS but was not detected using the CDC Trioplex RT-PCR Assay Kit or ZDC (IBMP). CHIKV was detected in 19.0% (12/63) of the samples by WGS and MinION and in 85.7% (12/14) using only MinION sequencing. Using the RT-qPCR kit to detect CHIKV yielded a rate of 4.7% (3/63) in false positives. ZIKV was found in only one sample (1/63) by WGS, while RT-qPCR yielded a high false positive rate (65.1%, 41/63). These findings highlight the operational advantage of these methods (WGS and MinION) for enhancing early-warning surveillance where standard RT-qPCR might underperform in low-prevalence settings. This is the first study that has compared these methods to detect and genetically characterize DENV, CHICK, and ZIKV in wastewater in Brazil and has indicated that hospital wastewater can be used as a sentinel system for arbovirus surveillance. The relative effectiveness of genomic wastewater surveillance for arboviruses was demonstrated, and it was found that diagnostic RT-qPCR kits used for clinical samples were not directly suitable for environmental surveillance. The feasibility of arbovirus wastewater surveillance as an epidemiological tool was demonstrated, although absolute quantifications were not performed. Full article
(This article belongs to the Special Issue Surveillance of Health-Relevant Pathogens Employing Wastewater)
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