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      Measuring Environmental Exposure to Enteric Pathogens in Low-Income Settings: Review and Recommendations of an Interdisciplinary Working Group

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          Abstract

          Infections with enteric pathogens impose a heavy disease burden, especially among young children in low-income countries. Recent findings from randomized controlled trials of water, sanitation, and hygiene interventions have raised questions about current methods for assessing environmental exposure to enteric pathogens. Approaches for estimating sources and doses of exposure suffer from a number of shortcomings, including reliance on imperfect indicators of fecal contamination instead of actual pathogens and estimating exposure indirectly from imprecise measurements of pathogens in the environment and human interaction therewith. These shortcomings limit the potential for effective surveillance of exposures, identification of important sources and modes of transmission, and evaluation of the effectiveness of interventions. In this review, we summarize current and emerging approaches used to characterize enteric pathogen hazards in different environmental media as well as human interaction with those media (external measures of exposure), and review methods that measure human infection with enteric pathogens as a proxy for past exposure (internal measures of exposure). We draw from lessons learned in other areas of environmental health to highlight how external and internal measures of exposure can be used to more comprehensively assess exposure. We conclude by recommending strategies for advancing enteric pathogen exposure assessments.

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          Most cited references173

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          First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community

          Infection with SARS-CoV-2, the etiologic agent of the ongoing COVID-19 pandemic, is accompanied by the shedding of the virus in stool. Therefore, the quantification of SARS-CoV-2 in wastewater affords the ability to monitor the prevalence of infections among the population via wastewater-based epidemiology (WBE). In the current work, SARS-CoV-2 RNA was concentrated from wastewater in a catchment in Australia and viral RNA copies were enumerated using reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) resulting in two positive detections within a six day period from the same wastewater treatment plant (WWTP). The estimated RNA copy numbers observed in the wastewater were then used to estimate the number of infected individuals in the catchment via Monte Carlo simulation. Given the uncertainty and variation in the input parameters, the model estimated a median range of 171 to 1090 infected persons in the catchment, which is in reasonable agreement with clinical observations. This work highlights the viability of WBE for monitoring infectious diseases, such as COVID-19, in communities. The work also draws attention to the need for further methodological and molecular assay validation for enveloped viruses in wastewater.
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            Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

            Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.
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              The shared antibiotic resistome of soil bacteria and human pathogens.

              Soil microbiota represent one of the ancient evolutionary origins of antibiotic resistance and have been proposed as a reservoir of resistance genes available for exchange with clinical pathogens. Using a high-throughput functional metagenomic approach in conjunction with a pipeline for the de novo assembly of short-read sequence data from functional selections (termed PARFuMS), we provide evidence for recent exchange of antibiotic resistance genes between environmental bacteria and clinical pathogens. We describe multidrug-resistant soil bacteria containing resistance cassettes against five classes of antibiotics (β-lactams, aminoglycosides, amphenicols, sulfonamides, and tetracyclines) that have perfect nucleotide identity to genes from diverse human pathogens. This identity encompasses noncoding regions as well as multiple mobilization sequences, offering not only evidence of lateral exchange but also a mechanism by which antibiotic resistance disseminates.
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                Author and article information

                Journal
                Environ Sci Technol
                Environ Sci Technol
                es
                esthag
                Environmental Science & Technology
                American Chemical Society
                0013-936X
                1520-5851
                19 August 2020
                06 October 2020
                : 54
                : 19
                : 11673-11691
                Affiliations
                [a ]Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University , Atlanta, Georgia 30322, United States
                [b ]Bill and Melinda Gates Foundation , Seattle, Washington 98109, United States
                [c ]School of Civil and Environmental Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
                [d ]Centers for Disease Control and Prevention Foundation , Atlanta, Georgia 30308, United States
                [e ]Division of Epidemiology and Biostatistics, School of Public Health, University of California−Berkeley , Berkeley, California 94720, United States
                [f ]Department of Epidemiology, University of Michigan School of Public Health , Ann Arbor, Michigan 48109, United States
                [g ]Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695, United States
                [h ]U.S. Agency for International Development , Washington, DC 20004, United States
                [i ]Department of Environmental and Occupational Health Sciences, University of Washington , Seattle, Washington 98105, United States
                [j ]Division of Infectious Diseases and Geographic Medicine, Stanford University , California 94305, United States
                [k ]Center for Global Safe Water, Sanitation and Hygiene, Rollins School of Public Health, Emory University , Atlanta, Georgia 30322, United States
                [l ]Department of Civil and Environmental Engineering, School of Engineering, Tufts University , Medford, Massachusetts 02155, United States
                [m ]Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina , Chapel Hill, North Carolina 27599, United States
                [n ]Mortenson Center in Global Engineering, University of Colorado Boulder , Boulder, Colorado 80303, United States
                [o ]Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia , Charlottesville, Virginia 22903, United States
                Author notes
                Article
                10.1021/acs.est.0c02421
                7547864
                32813503
                045aeaca-39c8-4b6c-8e24-77cdea647711

                This is an open access article published under a Creative Commons Attribution (CC-BY) License, which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited.

                History
                : 17 April 2020
                : 19 August 2020
                : 18 August 2020
                Categories
                Critical Review
                Custom metadata
                es0c02421
                es0c02421

                General environmental science
                General environmental science

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