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Real-time genomic pathogen, resistance, and host range characterization from passive water sampling of wetland ecosystems.

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Title: Real-time genomic pathogen, resistance, and host range characterization from passive water sampling of wetland ecosystems.
Authors: Perlas, Albert1,2 perlasalbert@gmail.com, Reska, Tim1,2,3 timreska@gmail.com, Sánchez-Cano, Alberto4, Mejías-Molina, Cristina5,6, Gygax, Daniel1,2,3,7, Martínez-Puchol, Sandra5,6, Rusiñol, Marta5,6, Eger, Elias8, Schaufler, Katharina8,9, Höfle, Ursula4, Croville, Guillaume10, Le Loc'h, Guillaume10, Guérin, Jean-Luc10, Urban, Lara1,2,3,11 lara.h.urban@gmail.com
Source: Applied & Environmental Microbiology. May2026, Vol. 92 Issue 5, p1-23. 23p.
Subjects: Water sampling, DNA sequencing, Metagenomics, Microbial genomics, Avian influenza A virus, Drug resistance in microorganisms, Wetland ecology
Abstract: Wetland ecosystems provide interfaces for the transmission of microbial pathogens and antimicrobial resistances (AMR) between migratory birds, wild and domestic animals, and human populations. The efficient surveillance of wetlands is, however, challenging, since the typically low concentration of pathogens requires the sampling of large volumes of water and subsequent targeted detection, which is inherently limited to a few pathogens or AMR genes of interest. Here, we present a holistic, accessible, and cost-efficient framework to characterize the pathogen and resistance load of water sources together with their potential associated hosts by combining passive water sampling through torpedo-shaped devices with nanopore sequencing technology. We used this framework to characterize anthropogenically influenced and natural wetland ecosystems along the East Atlantic Flyway, where we obtained robust assessments of the microbial communities from long-read metagenomic and RNA virome data and showed that anthropogenically impacted wetland ecosystems consistently exhibited higher relative abundances of pathogens and AMR genes. By focusing on avian influenza viruses (AIV), we finally highlight the additional need for targeted screening and whole-genome sequencing of pathogens of interest; we detected and characterized AIV at a third of the monitored sites and used environmental DNA to explore potential animal hosts to better understand the role of wetland ecosystems as One Health interfaces, where the health of animals, humans, and the environment are interconnected and pathogen transmission can occur across these domains. [ABSTRACT FROM AUTHOR]
Copyright of Applied & Environmental Microbiology is the property of American Society for Microbiology and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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Header DbId: egs
DbLabel: Engineering Source
An: 194351812
AccessLevel: 6
PubType: Academic Journal
PubTypeId: academicJournal
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  Data: Real-time genomic pathogen, resistance, and host range characterization from passive water sampling of wetland ecosystems.
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  Data: <searchLink fieldCode="AR" term="%22Perlas%2C+Albert%22">Perlas, Albert</searchLink><relatesTo>1,2</relatesTo><i> perlasalbert@gmail.com</i><br /><searchLink fieldCode="AR" term="%22Reska%2C+Tim%22">Reska, Tim</searchLink><relatesTo>1,2,3</relatesTo><i> timreska@gmail.com</i><br /><searchLink fieldCode="AR" term="%22Sánchez-Cano%2C+Alberto%22">Sánchez-Cano, Alberto</searchLink><relatesTo>4</relatesTo><br /><searchLink fieldCode="AR" term="%22Mejías-Molina%2C+Cristina%22">Mejías-Molina, Cristina</searchLink><relatesTo>5,6</relatesTo><br /><searchLink fieldCode="AR" term="%22Gygax%2C+Daniel%22">Gygax, Daniel</searchLink><relatesTo>1,2,3,7</relatesTo><br /><searchLink fieldCode="AR" term="%22Martínez-Puchol%2C+Sandra%22">Martínez-Puchol, Sandra</searchLink><relatesTo>5,6</relatesTo><br /><searchLink fieldCode="AR" term="%22Rusiñol%2C+Marta%22">Rusiñol, Marta</searchLink><relatesTo>5,6</relatesTo><br /><searchLink fieldCode="AR" term="%22Eger%2C+Elias%22">Eger, Elias</searchLink><relatesTo>8</relatesTo><br /><searchLink fieldCode="AR" term="%22Schaufler%2C+Katharina%22">Schaufler, Katharina</searchLink><relatesTo>8,9</relatesTo><br /><searchLink fieldCode="AR" term="%22Höfle%2C+Ursula%22">Höfle, Ursula</searchLink><relatesTo>4</relatesTo><br /><searchLink fieldCode="AR" term="%22Croville%2C+Guillaume%22">Croville, Guillaume</searchLink><relatesTo>10</relatesTo><br /><searchLink fieldCode="AR" term="%22Le+Loc'h%2C+Guillaume%22">Le Loc'h, Guillaume</searchLink><relatesTo>10</relatesTo><br /><searchLink fieldCode="AR" term="%22Guérin%2C+Jean-Luc%22">Guérin, Jean-Luc</searchLink><relatesTo>10</relatesTo><br /><searchLink fieldCode="AR" term="%22Urban%2C+Lara%22">Urban, Lara</searchLink><relatesTo>1,2,3,11</relatesTo><i> lara.h.urban@gmail.com</i>
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  Data: <searchLink fieldCode="JN" term="%22Applied+%26+Environmental+Microbiology%22">Applied & Environmental Microbiology</searchLink>. May2026, Vol. 92 Issue 5, p1-23. 23p.
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  Data: <searchLink fieldCode="DE" term="%22Water+sampling%22">Water sampling</searchLink><br /><searchLink fieldCode="DE" term="%22DNA+sequencing%22">DNA sequencing</searchLink><br /><searchLink fieldCode="DE" term="%22Metagenomics%22">Metagenomics</searchLink><br /><searchLink fieldCode="DE" term="%22Microbial+genomics%22">Microbial genomics</searchLink><br /><searchLink fieldCode="DE" term="%22Avian+influenza+A+virus%22">Avian influenza A virus</searchLink><br /><searchLink fieldCode="DE" term="%22Drug+resistance+in+microorganisms%22">Drug resistance in microorganisms</searchLink><br /><searchLink fieldCode="DE" term="%22Wetland+ecology%22">Wetland ecology</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: Wetland ecosystems provide interfaces for the transmission of microbial pathogens and antimicrobial resistances (AMR) between migratory birds, wild and domestic animals, and human populations. The efficient surveillance of wetlands is, however, challenging, since the typically low concentration of pathogens requires the sampling of large volumes of water and subsequent targeted detection, which is inherently limited to a few pathogens or AMR genes of interest. Here, we present a holistic, accessible, and cost-efficient framework to characterize the pathogen and resistance load of water sources together with their potential associated hosts by combining passive water sampling through torpedo-shaped devices with nanopore sequencing technology. We used this framework to characterize anthropogenically influenced and natural wetland ecosystems along the East Atlantic Flyway, where we obtained robust assessments of the microbial communities from long-read metagenomic and RNA virome data and showed that anthropogenically impacted wetland ecosystems consistently exhibited higher relative abundances of pathogens and AMR genes. By focusing on avian influenza viruses (AIV), we finally highlight the additional need for targeted screening and whole-genome sequencing of pathogens of interest; we detected and characterized AIV at a third of the monitored sites and used environmental DNA to explore potential animal hosts to better understand the role of wetland ecosystems as One Health interfaces, where the health of animals, humans, and the environment are interconnected and pathogen transmission can occur across these domains. [ABSTRACT FROM AUTHOR]
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  Data: <i>Copyright of Applied & Environmental Microbiology is the property of American Society for Microbiology and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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      – Type: doi
        Value: 10.1128/aem.02543-25
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      – Code: eng
        Text: English
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        PageCount: 23
        StartPage: 1
    Subjects:
      – SubjectFull: Water sampling
        Type: general
      – SubjectFull: DNA sequencing
        Type: general
      – SubjectFull: Metagenomics
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      – SubjectFull: Microbial genomics
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      – SubjectFull: Avian influenza A virus
        Type: general
      – SubjectFull: Drug resistance in microorganisms
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      – SubjectFull: Wetland ecology
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              Text: May2026
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