Microbiome Analysis for Wastewater Surveillance during COVID-19
ABSTRACT Wastewater surveillance (WS), when coupled with advanced molecular techniques, offers near real-time monitoring of community-wide transmission of SARS-CoV-2 and allows assessing and mitigating COVID-19 outbreaks, by evaluating the total microbial assemblage in a community. Composite wastewa...
| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
American Society for Microbiology
2022-08-01
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| Series: | mBio |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/mbio.00591-22 |
| _version_ | 1818473301872214016 |
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| author | Kyle D. Brumfield Menu Leddy Moiz Usmani Joseph A. Cotruvo Ching-Tzone Tien Suzanne Dorsey Karlis Graubics Brian Fanelli Isaac Zhou Nathaniel Registe Manoj Dadlani Malinda Wimalarante Dilini Jinasena Rushan Abayagunawardena Chiran Withanachchi Anwar Huq Antarpreet Jutla Rita R. Colwell |
| author_facet | Kyle D. Brumfield Menu Leddy Moiz Usmani Joseph A. Cotruvo Ching-Tzone Tien Suzanne Dorsey Karlis Graubics Brian Fanelli Isaac Zhou Nathaniel Registe Manoj Dadlani Malinda Wimalarante Dilini Jinasena Rushan Abayagunawardena Chiran Withanachchi Anwar Huq Antarpreet Jutla Rita R. Colwell |
| author_sort | Kyle D. Brumfield |
| collection | DOAJ |
| description | ABSTRACT Wastewater surveillance (WS), when coupled with advanced molecular techniques, offers near real-time monitoring of community-wide transmission of SARS-CoV-2 and allows assessing and mitigating COVID-19 outbreaks, by evaluating the total microbial assemblage in a community. Composite wastewater samples (24 h) were collected weekly from a manhole between December 2020 and November 2021 in Maryland, USA. RT-qPCR results showed concentrations of SARS-CoV-2 RNA recovered from wastewater samples reflected incidence of COVID-19 cases. When a drastic increase in COVID-19 was detected in February 2021, samples were selected for microbiome analysis (DNA metagenomics, RNA metatranscriptomics, and targeted SARS-CoV-2 sequencing). Targeted SARS-CoV-2 sequencing allowed for detection of important genetic mutations, such as spike: K417N, D614G, P681H, T716I, S982A, and D1118H, commonly associated with increased cell entry and reinfection. Microbiome analysis (DNA and RNA) provided important insight with respect to human health-related factors, including detection of pathogens and their virulence/antibiotic resistance genes. Specific microbial species comprising the wastewater microbiome correlated with incidence of SARS-CoV-2 RNA, suggesting potential association with SARS-CoV-2 infection. Climatic conditions, namely, temperature, were related to incidence of COVID-19 and detection of SARS-CoV-2 in wastewater, having been monitored as part of an environmental risk score assessment carried out in this study. In summary, the wastewater microbiome provides useful public health information, and hence, a valuable tool to proactively detect and characterize pathogenic agents circulating in a community. In effect, metagenomics of wastewater can serve as an early warning system for communicable diseases, by providing a larger source of information for health departments and public officials. IMPORTANCE Traditionally, testing for COVID-19 is done by detecting SARS-CoV-2 in samples collected from nasal swabs and/or saliva. However, SARS-CoV-2 can also be detected in feces of infected individuals. Therefore, wastewater samples can be used to test all individuals of a community contributing to the sewage collection system, i.e., the infrastructure, such as gravity pipes, manholes, tanks, lift stations, control structures, and force mains, that collects used water from residential and commercial sources and conveys the flow to a wastewater treatment plant. Here, we profile community wastewater collected from a manhole, detect presence of SARS-CoV-2, identify genetic mutations of SARS-CoV-2, and perform COVID-19 risk score assessment of the study area. Using metagenomics analysis, we also detect other microorganisms (bacteria, fungi, protists, and viruses) present in the samples. Results show that by analyzing all microorganisms present in wastewater, pathogens circulating in a community can provide an early warning for contagious diseases. |
| first_indexed | 2024-04-14T04:22:30Z |
| format | Article |
| id | doaj.art-fe2143e83f744cc79ad32340c886bc3c |
| institution | Directory Open Access Journal |
| issn | 2150-7511 |
| language | English |
| last_indexed | 2024-04-14T04:22:30Z |
| publishDate | 2022-08-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mBio |
| spelling | doaj.art-fe2143e83f744cc79ad32340c886bc3c2022-12-22T02:12:28ZengAmerican Society for MicrobiologymBio2150-75112022-08-0113410.1128/mbio.00591-22Microbiome Analysis for Wastewater Surveillance during COVID-19Kyle D. Brumfield0Menu Leddy1Moiz Usmani2Joseph A. Cotruvo3Ching-Tzone Tien4Suzanne Dorsey5Karlis Graubics6Brian Fanelli7Isaac Zhou8Nathaniel Registe9Manoj Dadlani10Malinda Wimalarante11Dilini Jinasena12Rushan Abayagunawardena13Chiran Withanachchi14Anwar Huq15Antarpreet Jutla16Rita R. Colwell17Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USAEssential Environmental and Engineering Systems, Huntington Beach, California, USAGeohealth and Hydrology Laboratory, Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida, USAJoseph Cotruvo and Associates LLC, Washington, DC, USAMaryland Department of Environment, Baltimore, Maryland, USAMaryland Department of Environment, Baltimore, Maryland, USACosmosID Inc., Germantown, Maryland, USACosmosID Inc., Germantown, Maryland, USACosmosID Inc., Germantown, Maryland, USACosmosID Inc., Germantown, Maryland, USACosmosID Inc., Germantown, Maryland, USAInspection Experts Inc., Columbia, Maryland, USAInspection Experts Inc., Columbia, Maryland, USAInspection Experts Inc., Columbia, Maryland, USAInspection Experts Inc., Columbia, Maryland, USAMaryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USAGeohealth and Hydrology Laboratory, Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida, USAMaryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USAABSTRACT Wastewater surveillance (WS), when coupled with advanced molecular techniques, offers near real-time monitoring of community-wide transmission of SARS-CoV-2 and allows assessing and mitigating COVID-19 outbreaks, by evaluating the total microbial assemblage in a community. Composite wastewater samples (24 h) were collected weekly from a manhole between December 2020 and November 2021 in Maryland, USA. RT-qPCR results showed concentrations of SARS-CoV-2 RNA recovered from wastewater samples reflected incidence of COVID-19 cases. When a drastic increase in COVID-19 was detected in February 2021, samples were selected for microbiome analysis (DNA metagenomics, RNA metatranscriptomics, and targeted SARS-CoV-2 sequencing). Targeted SARS-CoV-2 sequencing allowed for detection of important genetic mutations, such as spike: K417N, D614G, P681H, T716I, S982A, and D1118H, commonly associated with increased cell entry and reinfection. Microbiome analysis (DNA and RNA) provided important insight with respect to human health-related factors, including detection of pathogens and their virulence/antibiotic resistance genes. Specific microbial species comprising the wastewater microbiome correlated with incidence of SARS-CoV-2 RNA, suggesting potential association with SARS-CoV-2 infection. Climatic conditions, namely, temperature, were related to incidence of COVID-19 and detection of SARS-CoV-2 in wastewater, having been monitored as part of an environmental risk score assessment carried out in this study. In summary, the wastewater microbiome provides useful public health information, and hence, a valuable tool to proactively detect and characterize pathogenic agents circulating in a community. In effect, metagenomics of wastewater can serve as an early warning system for communicable diseases, by providing a larger source of information for health departments and public officials. IMPORTANCE Traditionally, testing for COVID-19 is done by detecting SARS-CoV-2 in samples collected from nasal swabs and/or saliva. However, SARS-CoV-2 can also be detected in feces of infected individuals. Therefore, wastewater samples can be used to test all individuals of a community contributing to the sewage collection system, i.e., the infrastructure, such as gravity pipes, manholes, tanks, lift stations, control structures, and force mains, that collects used water from residential and commercial sources and conveys the flow to a wastewater treatment plant. Here, we profile community wastewater collected from a manhole, detect presence of SARS-CoV-2, identify genetic mutations of SARS-CoV-2, and perform COVID-19 risk score assessment of the study area. Using metagenomics analysis, we also detect other microorganisms (bacteria, fungi, protists, and viruses) present in the samples. Results show that by analyzing all microorganisms present in wastewater, pathogens circulating in a community can provide an early warning for contagious diseases.https://journals.asm.org/doi/10.1128/mbio.00591-22COVID-19SARS-CoV-2wastewatermicrobiomewastewater-based epidemiologywastewater monitoring |
| spellingShingle | Kyle D. Brumfield Menu Leddy Moiz Usmani Joseph A. Cotruvo Ching-Tzone Tien Suzanne Dorsey Karlis Graubics Brian Fanelli Isaac Zhou Nathaniel Registe Manoj Dadlani Malinda Wimalarante Dilini Jinasena Rushan Abayagunawardena Chiran Withanachchi Anwar Huq Antarpreet Jutla Rita R. Colwell Microbiome Analysis for Wastewater Surveillance during COVID-19 mBio COVID-19 SARS-CoV-2 wastewater microbiome wastewater-based epidemiology wastewater monitoring |
| title | Microbiome Analysis for Wastewater Surveillance during COVID-19 |
| title_full | Microbiome Analysis for Wastewater Surveillance during COVID-19 |
| title_fullStr | Microbiome Analysis for Wastewater Surveillance during COVID-19 |
| title_full_unstemmed | Microbiome Analysis for Wastewater Surveillance during COVID-19 |
| title_short | Microbiome Analysis for Wastewater Surveillance during COVID-19 |
| title_sort | microbiome analysis for wastewater surveillance during covid 19 |
| topic | COVID-19 SARS-CoV-2 wastewater microbiome wastewater-based epidemiology wastewater monitoring |
| url | https://journals.asm.org/doi/10.1128/mbio.00591-22 |
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