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  1. AU="Steele, Joshua A."
  2. AU="Behnampour, Naser"
  3. AU="Stucki, Brenton"
  4. AU="J. Lohse"
  5. AU="Lopez-Plaza, Ileana"
  6. AU="Degorce, Sebastien L"
  7. AU="Wodchis, Walter"
  8. AU="Charles DeCarli"
  9. AU=Glied Sherry
  10. AU="Kesarwani, Manoj"
  11. AU="Cubas-Atienza, Ana I"
  12. AU="Thickens, Anna S"
  13. AU="Anderson, Emilie"
  14. AU=Starace Fabrizio
  15. AU="Ochin, Evelina"
  16. AU="Gijzen, Linda"
  17. AU="van Groeningen, Kees Jan"
  18. AU="Pakserian, Diana"
  19. AU="Joly-Chevrier, Maxine"
  20. AU="Genovesi, Piero"
  21. AU="Ersöz, Gülden"
  22. AU="Jeffrey J Babon"
  23. AU="Rehana Masood"
  24. AU="Sandra Heskamp"
  25. AU="Omid Sadeghi"
  26. AU="Antaya, Richard"
  27. AU="Papadopoulos, G"
  28. AU="Boughen, Santiago"
  29. AU="Brink, P. L."

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  1. Artikel: The challenges of microbial source tracking at urban beaches for Quantitative Microbial Risk Assessment (QMRA)

    Zimmer-Faust, Amity G / Steele, Joshua A / Griffith, John F / Schiff, Ken

    Marine pollution bulletin. 2020 Nov., v. 160

    2020  

    Abstract: Urban beaches are frequently impacted from multiple sources of fecal contamination. This along with high beach usage underscores the importance of appropriate management that protects swimmer health. The USEPA has enabled the use of QMRA as a tool for ... ...

    Abstract Urban beaches are frequently impacted from multiple sources of fecal contamination. This along with high beach usage underscores the importance of appropriate management that protects swimmer health. The USEPA has enabled the use of QMRA as a tool for quantifying swimmer health risk and setting site-specific water quality objectives. This study illustrates the challenges associated with human and non-human source identification and how these challenges influence the decision of whether QMRA at typical urban beaches for water quality management is appropriate. In this study, a similar and correlated spatial relationship with elevated Enterococcus and avian-specific markers was observed, suggesting shorebirds as a primary source of FIB. However, human-associated markers were also detected frequently but at low concentrations. Ultimately, a QMRA was not conducted because pathogen loading from potential human sources could not be confidently quantified, having consequences for health risk in receiving waters where recreational contact occurs.
    Schlagwörter Enterococcus ; United States Environmental Protection Agency ; humans ; marine pollution ; microbiological risk assessment ; pathogens ; risk ; water quality
    Sprache Englisch
    Erscheinungsverlauf 2020-11
    Erscheinungsort Elsevier Ltd
    Dokumenttyp Artikel
    Anmerkung NAL-AP-2-clean
    ZDB-ID 2001296-2
    ISSN 1879-3363 ; 0025-326X
    ISSN (online) 1879-3363
    ISSN 0025-326X
    DOI 10.1016/j.marpolbul.2020.111546
    Datenquelle NAL Katalog (AGRICOLA)

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  2. Artikel ; Online: Longitudinal sequencing and variant detection of SARS-CoV-2 across Southern California wastewater from April 2020 – August 2021

    Rothman, Jason A. / Saghir, Andrew / Zimmer-Faust, Amity G. / Langlois, Kylie / Steele, Joshua A. / Griffith, John F. / Whiteson, Katrine L.

    medRxiv

    Abstract: Wastewater based epidemiology (WBE) is a useful method to detect pathogen prevalence and may serve to effectively monitor diseases at a broad scale. WBE has been used throughout the COVID-19 pandemic to track localized and population-level disease burden ...

    Abstract Wastewater based epidemiology (WBE) is a useful method to detect pathogen prevalence and may serve to effectively monitor diseases at a broad scale. WBE has been used throughout the COVID-19 pandemic to track localized and population-level disease burden through the quantification of SARS-CoV-2 RNA present in wastewater. Aside from case load estimation, WBE is being used to assay viral genomic diversity and the emergence of potential SARS-CoV-2 variants. Here, we present a study in which we sequenced RNA extracted from sewage influent samples obtained from eight wastewater treatment plants representing 16 million people in Southern California over April 2020 - August 2021. We sequenced SARS-CoV-2 with two methods: Illumina Respiratory Virus Enrichment and metatranscriptomic sequencing (N = 269), and QIAseq SARS-CoV-2 tiled amplicon sequencing (N = 95). We were able to classify SARS-CoV-2 reads into lineages and sublineages that approximated several named variants across a full year, and we identified a diversity of single nucleotide variants (SNVs) of which many are putatively novel SNVs, and SNVs of unknown potential function and prevalence. Through our retrospective study, we also show that several sublineages of SARS-CoV-2 were detected in wastewater up to several months before clinical detection, which may assist in the prediction of future Variants of Concern. Lastly, we show that sublineage diversity was similar between wastewater treatment plants across Southern California, and that diversity changed by sampling month indicating that WBE is effective across megaregions. As the COVID-19 pandemic moves to new phases, and additional SARS-CoV-2 variants emerge, the ongoing monitoring of wastewater is important to understand local and population-level dynamics of the virus. Our study shows the potential of WBE to detect SARS-CoV-2 variants throughout Southern California9s wastewater and track the diversity of viral SNVs and strains in urban and suburban locations. These results will aid in our ability to monitor the evolutionary potential of SARS-CoV-2 and help understand circulating SNVs to further combat COVID-19.
    Schlagwörter covid19
    Sprache Englisch
    Erscheinungsdatum 2023-04-15
    Verlag Cold Spring Harbor Laboratory Press
    Dokumenttyp Artikel ; Online
    DOI 10.1101/2023.04.14.23288559
    Datenquelle COVID19

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  3. Artikel: Correlation between wastewater and COVID-19 case incidence rates in major California sewersheds across three variant periods.

    Rabe, Angela / Ravuri, Sindhu / Burnor, Elisabeth / Steele, Joshua A / Kantor, Rose S / Choi, Samuel / Forman, Stanislav / Batjiaka, Ryan / Jain, Seema / León, Tomás M / Vugia, Duc J / Yu, Alexander T

    Journal of water and health

    2023  Band 21, Heft 9, Seite(n) 1303–1317

    Abstract: Monitoring for COVID-19 through wastewater has been used for adjunctive public health surveillance, with SARS-CoV-2 viral concentrations in wastewater correlating with incident cases in the same sewershed. However, the generalizability of these findings ... ...

    Abstract Monitoring for COVID-19 through wastewater has been used for adjunctive public health surveillance, with SARS-CoV-2 viral concentrations in wastewater correlating with incident cases in the same sewershed. However, the generalizability of these findings across sewersheds, laboratory methods, and time periods with changing variants and underlying population immunity has not been well described. The California Department of Public Health partnered with six wastewater treatment plants starting in January 2021 to monitor wastewater for SARS-CoV-2, with analyses performed at four laboratories. Using reported PCR-confirmed COVID-19 cases within each sewershed, the relationship between case incidence rates and wastewater concentrations collected over 14 months was evaluated using Spearman's correlation and linear regression. Strong correlations were observed when wastewater concentrations and incidence rates were averaged (10- and 7-day moving window for wastewater and cases, respectively, ρ = 0.73-0.98 for N1 gene target). Correlations remained strong across three time periods with distinct circulating variants and vaccination rates (winter 2020-2021/Alpha, summer 2021/Delta, and winter 2021-2022/Omicron). Linear regression revealed that slopes of associations varied by the dominant variant of concern, sewershed, and laboratory (β = 0.45-1.94). These findings support wastewater surveillance as an adjunctive public health tool to monitor SARS-CoV-2 community trends.
    Mesh-Begriff(e) Humans ; COVID-19/epidemiology ; SARS-CoV-2 ; Wastewater ; Incidence ; Wastewater-Based Epidemiological Monitoring ; California/epidemiology
    Chemische Substanzen Wastewater
    Sprache Englisch
    Erscheinungsdatum 2023-09-27
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2123845-5
    ISSN 1996-7829 ; 1477-8920
    ISSN (online) 1996-7829
    ISSN 1477-8920
    DOI 10.2166/wh.2023.173
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: The challenges of microbial source tracking at urban beaches for Quantitative Microbial Risk Assessment (QMRA).

    Zimmer-Faust, Amity G / Steele, Joshua A / Griffith, John F / Schiff, Ken

    Marine pollution bulletin

    2020  Band 160, Seite(n) 111546

    Abstract: Urban beaches are frequently impacted from multiple sources of fecal contamination. This along with high beach usage underscores the importance of appropriate management that protects swimmer health. The USEPA has enabled the use of QMRA as a tool for ... ...

    Abstract Urban beaches are frequently impacted from multiple sources of fecal contamination. This along with high beach usage underscores the importance of appropriate management that protects swimmer health. The USEPA has enabled the use of QMRA as a tool for quantifying swimmer health risk and setting site-specific water quality objectives. This study illustrates the challenges associated with human and non-human source identification and how these challenges influence the decision of whether QMRA at typical urban beaches for water quality management is appropriate. In this study, a similar and correlated spatial relationship with elevated Enterococcus and avian-specific markers was observed, suggesting shorebirds as a primary source of FIB. However, human-associated markers were also detected frequently but at low concentrations. Ultimately, a QMRA was not conducted because pathogen loading from potential human sources could not be confidently quantified, having consequences for health risk in receiving waters where recreational contact occurs.
    Mesh-Begriff(e) Bathing Beaches ; Environmental Monitoring ; Feces ; Humans ; Risk Assessment ; Water Microbiology ; Water Pollution/analysis ; Water Quality
    Sprache Englisch
    Erscheinungsdatum 2020-09-05
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2001296-2
    ISSN 1879-3363 ; 0025-326X
    ISSN (online) 1879-3363
    ISSN 0025-326X
    DOI 10.1016/j.marpolbul.2020.111546
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel: Pathogenic

    Diner, Rachel E / Kaul, Drishti / Rabines, Ariel / Zheng, Hong / Steele, Joshua A / Griffith, John F / Allen, Andrew E

    mSystems

    2021  Band 6, Heft 4, Seite(n) e0057121

    Abstract: Interactions between vibrio bacteria and the planktonic community impact marine ecology and human health. Many ... ...

    Abstract Interactions between vibrio bacteria and the planktonic community impact marine ecology and human health. Many coastal
    Sprache Englisch
    Erscheinungsdatum 2021-07-06
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 2379-5077
    ISSN 2379-5077
    DOI 10.1128/mSystems.00571-21
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  6. Artikel: A Combined Digital PCR and Next Generation DNA-Sequencing Based Approach for Tracking Nearshore Pollutant Dynamics Along the Southwest United States/Mexico Border.

    Zimmer-Faust, Amity G / Steele, Joshua A / Xiong, Xianyi / Staley, Christopher / Griffith, Madison / Sadowsky, Michael J / Diaz, Margarita / Griffith, John F

    Frontiers in microbiology

    2021  Band 12, Seite(n) 674214

    Abstract: Ocean currents, multiple fecal bacteria input sources, and jurisdictional boundaries can complicate pollution source tracking and associated mitigation and management efforts within the nearshore coastal environment. In this study, multiple microbial ... ...

    Abstract Ocean currents, multiple fecal bacteria input sources, and jurisdictional boundaries can complicate pollution source tracking and associated mitigation and management efforts within the nearshore coastal environment. In this study, multiple microbial source tracking tools were employed to characterize the impact and reach of an ocean wastewater treatment facility discharge in Mexico northward along the coast and across the Southwest United States- Mexico Border. Water samples were evaluated for fecal indicator bacteria (FIB),
    Sprache Englisch
    Erscheinungsdatum 2021-08-06
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2021.674214
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel ; Online: Sources of variability in methods for processing, storing, and concentrating SARS-CoV-2 in influent from urban wastewater treatment plants

    Steele, Joshua A / Zimmer-Faust, Amity G / Griffith, John F / Weisberg, Stephen B

    medRxiv

    Abstract: The rapid emergence of wastewater based surveillance has led to a wide array of SARS-CoV-2 RNA quantification methodologies being employed. Here we compare methods to store samples, inactivate viruses, capture/concentrate viruses, and extract/measure ... ...

    Abstract The rapid emergence of wastewater based surveillance has led to a wide array of SARS-CoV-2 RNA quantification methodologies being employed. Here we compare methods to store samples, inactivate viruses, capture/concentrate viruses, and extract/measure viral RNA from primary influent into wastewater facilities. We found that heat inactivation of the viruses led to a 1-3 log<sub>10</sub> decrease compared to chemical inactivation. Freezing influent prior to concentration caused a 1-4 log<sub>10</sub> decrease compared to processing fresh samples, but viral capture by membrane adsorption prior to freezing was robust to freeze-thaw variability. Concentration vs. direct extraction, and PCR platform also affected outcome, but by a smaller amount. The choice of nucleocapsid gene target had nearly no effect. Pepper mild-mottle virus was much less sensitive to these methodological differences than was SARS-CoV-2, which challenges its use as a population-level control among studies using different methods. Better characterizing the variability associated with different methodologies, in particular the impact of methods on sensitivity, will aid decision makers in following the effects of vaccination campaigns, early detection of future outbreaks, and potentially monitoring the appearance of SARS-CoV-2 variants in the population.
    Schlagwörter covid19
    Sprache Englisch
    Erscheinungsdatum 2021-06-21
    Verlag Cold Spring Harbor Laboratory Press
    Dokumenttyp Artikel ; Online
    DOI 10.1101/2021.06.16.21259063
    Datenquelle COVID19

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  8. Artikel: Assessing cross‐laboratory performance for quantifying coliphage using EPA Method 1642

    Zimmer‐Faust, Amity G. / Griffith, John F. / Steele, Joshua A. / Asato, Laralyn / Chiem, Tania / Choi, Samuel / Diaz, Arturo / Guzman, Joe / Padilla, Michele / Quach‐Cu, Jennipher / Ruiz, Victor / Santos, Bryan / Woo, Mary / Weisberg, Stephen B.

    Journal of applied microbiology. 2022 Aug., v. 133, no. 2

    2022  

    Abstract: AIMS: Widespread adoption of the new U.S. Environmental Protection Agency (USEPA) Method 1642 for enumeration of coliphage in recreational water requires demonstration that laboratories consistently meet internal method performance goals and yield ... ...

    Abstract AIMS: Widespread adoption of the new U.S. Environmental Protection Agency (USEPA) Method 1642 for enumeration of coliphage in recreational water requires demonstration that laboratories consistently meet internal method performance goals and yield results that are consistent across laboratories. METHODS AND RESULTS: Here we assess the performance of six laboratories processing a series of blind wastewater‐ and coliphage‐spiked samples along with laboratory blanks. All laboratories met the method‐defined recovery requirements when performance was averaged across samples, with the few failures on individual samples mostly occurring for less‐experienced laboratories on the initial samples processed. Failures that occurred on later samples were generally attributed to easily correctable activities. Failure rates were higher for somatic vs. F+ coliphage, attributable to the more stringent performance criteria associated with somatic coliphage. There was no difference in failure rate between samples prepared in a marine water matrix compared to that in phosphate‐buffered saline. CONCLUSIONS: Variation among laboratories was similar to that previously reported for enterococci, the current bacterial indicator used for evaluating beach water quality for public health protection. SIGNIFICANCE AND IMPACT OF THE STUDY: These findings suggest that laboratory performance is not an inhibitor to the adoption of coliphage as a new indicator for assessing recreational health risk.
    Schlagwörter Enterococcus ; United States Environmental Protection Agency ; coliphages ; health promotion ; risk ; water quality
    Sprache Englisch
    Erscheinungsverlauf 2022-08
    Umfang p. 340-348.
    Erscheinungsort John Wiley & Sons, Ltd
    Dokumenttyp Artikel
    Anmerkung JOURNAL ARTICLE
    ZDB-ID 1358023-1
    ISSN 1365-2672 ; 1364-5072
    ISSN (online) 1365-2672
    ISSN 1364-5072
    DOI 10.1111/jam.15523
    Datenquelle NAL Katalog (AGRICOLA)

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    Verfügbar in ZB MED Köln/Königswinter

    Zs.A 259: Hefte anzeigen Standort:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  9. Artikel: Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes.

    Rothman, Jason A / Saghir, Andrew / Chung, Seung-Ah / Boyajian, Nicholas / Dinh, Thao / Kim, Jinwoo / Oval, Jordan / Sharavanan, Vivek / York, Courtney / Zimmer-Faust, Amity G / Langlois, Kylie / Steele, Joshua A / Griffith, John F / Whiteson, Katrine L

    bioRxiv : the preprint server for biology

    2022  

    Abstract: Municipal wastewater provides a representative sample of human fecal waste across a catchment area and contains a wide diversity of microbes. Sequencing wastewater samples provides information about human-associated and medically-important microbial ... ...

    Abstract Municipal wastewater provides a representative sample of human fecal waste across a catchment area and contains a wide diversity of microbes. Sequencing wastewater samples provides information about human-associated and medically-important microbial populations, and may be useful to assay disease prevalence and antimicrobial resistance (AMR). Here, we present a study in which we used untargeted metatranscriptomic sequencing on RNA extracted from 275 sewage influent samples obtained from eight wastewater treatment plants (WTPs) representing approximately 16 million people in Southern California between August 2020 - August 2021. We characterized bacterial and viral transcripts, assessed metabolic pathway activity, and identified over 2,000 AMR genes/variants across all samples. Because we did not deplete ribosomal RNA, we have a unique window into AMR carried as ribosomal mutants. We show that AMR diversity varied between WTPs and that the relative abundance of many individual AMR genes/variants increased over time and may be connected to antibiotic use during the COVID-19 pandemic. Similarly, we detected transcripts mapping to human pathogenic bacteria and viruses suggesting RNA sequencing is a powerful tool for wastewater-based epidemiology and that there are geographical signatures to microbial transcription. We captured the transcription of gene pathways common to bacterial cell processes, including central carbon metabolism, nucleotide synthesis/salvage, and amino acid biosynthesis. We also posit that due to the ubiquity of many viruses and bacteria in wastewater, new biological targets for microbial water quality assessment can be developed. To the best of our knowledge, our study provides the most complete longitudinal metatranscriptomic analysis of a large population's wastewater to date and demonstrates our ability to monitor the presence and activity of microbes in complex samples. By sequencing RNA, we can track the relative abundance of expressed AMR genes/variants and metabolic pathways, increasing our understanding of AMR activity across large human populations and sewer sheds.
    Sprache Englisch
    Erscheinungsdatum 2022-08-02
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2022.08.02.502560
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  10. Artikel ; Online: Assessing cross-laboratory performance for quantifying coliphage using EPA Method 1642.

    Zimmer-Faust, Amity G / Griffith, John F / Steele, Joshua A / Asato, Laralyn / Chiem, Tania / Choi, Samuel / Diaz, Arturo / Guzman, Joe / Padilla, Michele / Quach-Cu, Jennipher / Ruiz, Victor / Santos, Bryan / Woo, Mary / Weisberg, Stephen B

    Journal of applied microbiology

    2022  Band 133, Heft 2, Seite(n) 340–348

    Abstract: Aims: Widespread adoption of the new U.S. Environmental Protection Agency (USEPA) Method 1642 for enumeration of coliphage in recreational water requires demonstration that laboratories consistently meet internal method performance goals and yield ... ...

    Abstract Aims: Widespread adoption of the new U.S. Environmental Protection Agency (USEPA) Method 1642 for enumeration of coliphage in recreational water requires demonstration that laboratories consistently meet internal method performance goals and yield results that are consistent across laboratories.
    Methods and results: Here we assess the performance of six laboratories processing a series of blind wastewater- and coliphage-spiked samples along with laboratory blanks. All laboratories met the method-defined recovery requirements when performance was averaged across samples, with the few failures on individual samples mostly occurring for less-experienced laboratories on the initial samples processed. Failures that occurred on later samples were generally attributed to easily correctable activities. Failure rates were higher for somatic vs. F+ coliphage, attributable to the more stringent performance criteria associated with somatic coliphage. There was no difference in failure rate between samples prepared in a marine water matrix compared to that in phosphate-buffered saline.
    Conclusions: Variation among laboratories was similar to that previously reported for enterococci, the current bacterial indicator used for evaluating beach water quality for public health protection.
    Significance and impact of the study: These findings suggest that laboratory performance is not an inhibitor to the adoption of coliphage as a new indicator for assessing recreational health risk.
    Mesh-Begriff(e) Coliphages ; Enterococcus ; Feces/microbiology ; Laboratories ; Water Microbiology ; Water Quality
    Sprache Englisch
    Erscheinungsdatum 2022-04-13
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 1358023-1
    ISSN 1365-2672 ; 1364-5072
    ISSN (online) 1365-2672
    ISSN 1364-5072
    DOI 10.1111/jam.15523
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

    Volltext online

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    Kategorien

    Verfügbar in ZB MED Köln/Königswinter

    Zs.A 259: Hefte anzeigen Standort:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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    Dieser Service ist kostenpflichtig (siehe Lieferbedingungen von subito). Bestellungen, die einen Artikel nebst Supplementary Material umfassen, werden grundsätzlich wie mehrfache Bestellungen bearbeitet. Gebühren fallen in diesen Fällen für jede einzelne Bestellung an.

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