This page has only limited features, please log in for full access.
Wastewater-based testing for SARS-CoV-2 is a novel tool for public health monitoring, but additional laboratory capacity is needed to provide routine monitoring at all locations where it has the potential to be useful. Few standardization practices for SARS-CoV-2 wastewater analysis currently exist, and quality assurance/quality control procedures may vary across laboratories. Alongside counterparts at many academic institutions, we built out a laboratory for routine monitoring of wastewater at the University of California, Berkeley. Here, we detail our group's establishment of a wastewater testing laboratory including standard operating procedures, laboratory buildout and workflow, and a quality assurance plan. We present a complete data analysis pipeline and quality scoring framework and discuss the data reporting process. We hope that this information will aid others at research institutions, public health departments, and wastewater agencies in developing programs to support wastewater monitoring for public health decision-making.
Rose S. Kantor; Hannah D. Greenwald; Lauren C. Kennedy; Adrian Hinkle; Sasha Harris-Lovett; Matthew Metzger; Melissa M. Thornton; Justin M. Paluba; Kara L. Nelson. Operationalizing a routine wastewater monitoring laboratory for SARS-CoV-2. 2021, 1 .
AMA StyleRose S. Kantor, Hannah D. Greenwald, Lauren C. Kennedy, Adrian Hinkle, Sasha Harris-Lovett, Matthew Metzger, Melissa M. Thornton, Justin M. Paluba, Kara L. Nelson. Operationalizing a routine wastewater monitoring laboratory for SARS-CoV-2. . 2021; ():1.
Chicago/Turabian StyleRose S. Kantor; Hannah D. Greenwald; Lauren C. Kennedy; Adrian Hinkle; Sasha Harris-Lovett; Matthew Metzger; Melissa M. Thornton; Justin M. Paluba; Kara L. Nelson. 2021. "Operationalizing a routine wastewater monitoring laboratory for SARS-CoV-2." , no. : 1.
Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA can be integrated with COVID-19 case data to inform timely pandemic response. However, more research is needed to apply and develop systematic methods to interpret the true SARS-CoV-2 signal from noise introduced in wastewater samples (e.g., from sewer conditions, sampling and extraction methods, etc.). In this study, raw wastewater was collected weekly from five sewersheds and one residential facility, and wastewater SARS-CoV-2 concentrations were compared to geocoded COVID-19 clinical testing data. SARS-CoV-2 was reliably detected (95% positivity) in frozen wastewater samples when reported daily new COVID-19 cases were 2.4 or more per 100,000 people. To adjust for variation in sample fecal content, crAssphage, pepper mild mottle virus, Bacteroides ribosomal RNA (rRNA), and human 18S rRNA were evaluated as normalization biomarkers, and crAssphage displayed the least spatial and temporal variability. Both unnormalized SARS-CoV-2 RNA signal and signal normalized to crAssphage had positive and significant correlation with clinical testing data (Kendall’s Tau-b (τ)=0.43 and 0.38, respectively). Locational dependencies and the date associated with testing data impacted the lead time of wastewater for clinical trends, and no lead time was observed when the sample collection date (versus the result date) was used for both wastewater and clinical testing data. This study supports that trends in wastewater surveillance data reflect trends in COVID-19 disease occurrence and presents approaches that could be applied to make wastewater signal more interpretable and comparable across studies.
Hannah D. Greenwald; Lauren C. Kennedy; Adrian Hinkle; Oscar N. Whitney; Vinson B. Fan; Alexander Crits-Christoph; Sasha Harris-Lovett; Avi I. Flamholz; Basem Al-Shayeb; Lauren D. Liao; Matt Beyers; Daniel Brown; Alicia R. Chakrabarti; Jason Dow; Dan Frost; Mark Koekemoer; Chris Lynch; Payal Sarkar; Eileen White; Rose Kantor; Kara L. Nelson. Interpretation of temporal and spatial trends of SARS-CoV-2 RNA in San Francisco Bay Area wastewater. 2021, 1 .
AMA StyleHannah D. Greenwald, Lauren C. Kennedy, Adrian Hinkle, Oscar N. Whitney, Vinson B. Fan, Alexander Crits-Christoph, Sasha Harris-Lovett, Avi I. Flamholz, Basem Al-Shayeb, Lauren D. Liao, Matt Beyers, Daniel Brown, Alicia R. Chakrabarti, Jason Dow, Dan Frost, Mark Koekemoer, Chris Lynch, Payal Sarkar, Eileen White, Rose Kantor, Kara L. Nelson. Interpretation of temporal and spatial trends of SARS-CoV-2 RNA in San Francisco Bay Area wastewater. . 2021; ():1.
Chicago/Turabian StyleHannah D. Greenwald; Lauren C. Kennedy; Adrian Hinkle; Oscar N. Whitney; Vinson B. Fan; Alexander Crits-Christoph; Sasha Harris-Lovett; Avi I. Flamholz; Basem Al-Shayeb; Lauren D. Liao; Matt Beyers; Daniel Brown; Alicia R. Chakrabarti; Jason Dow; Dan Frost; Mark Koekemoer; Chris Lynch; Payal Sarkar; Eileen White; Rose Kantor; Kara L. Nelson. 2021. "Interpretation of temporal and spatial trends of SARS-CoV-2 RNA in San Francisco Bay Area wastewater." , no. : 1.
Wastewater surveillance for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging approach to help identify the risk of a coronavirus disease (COVID-19) outbreak. This tool can contribute to public health surveillance at both community (wastewater treatment system) and institutional (e.g., colleges, prisons, and nursing homes) scales. This paper explores the successes, challenges, and lessons learned from initial wastewater surveillance efforts at colleges and university systems to inform future research, development and implementation. We present the experiences of 25 college and university systems in the United States that monitored campus wastewater for SARS-CoV-2 during the fall 2020 academic period. We describe the broad range of approaches, findings, resources, and impacts from these initial efforts. These institutions range in size, social and political geographies, and include both public and private institutions. Our analysis suggests that wastewater monitoring at colleges requires consideration of local information needs, sewage infrastructure, resources for sampling and analysis, college and community dynamics, approaches to interpretation and communication of results, and follow-up actions. Most colleges reported that a learning process of experimentation, evaluation, and adaptation was key to progress. This process requires ongoing collaboration among diverse stakeholders including decision-makers, researchers, faculty, facilities staff, students, and community members.
Sasha Harris-Lovett; Kara Nelson; Paloma Beamer; Heather Bischel; Aaron Bivins; Andrea Bruder; Caitlyn Butler; Todd Camenisch; Susan De Long; Smruthi Karthikeyan; David Larsen; Katherine Meierdiercks; Paula Mouser; Sheree Pagsuyoin; Sarah Prasek; Tyler Radniecki; Jeffrey Ram; D. Roper; Hannah Safford; Samendra Sherchan; William Shuster; Thibault Stalder; Robert Wheeler; Katrina Korfmacher. Wastewater Surveillance for SARS-CoV-2 on College Campuses: Initial Efforts, Lessons Learned, and Research Needs. International Journal of Environmental Research and Public Health 2021, 18, 4455 .
AMA StyleSasha Harris-Lovett, Kara Nelson, Paloma Beamer, Heather Bischel, Aaron Bivins, Andrea Bruder, Caitlyn Butler, Todd Camenisch, Susan De Long, Smruthi Karthikeyan, David Larsen, Katherine Meierdiercks, Paula Mouser, Sheree Pagsuyoin, Sarah Prasek, Tyler Radniecki, Jeffrey Ram, D. Roper, Hannah Safford, Samendra Sherchan, William Shuster, Thibault Stalder, Robert Wheeler, Katrina Korfmacher. Wastewater Surveillance for SARS-CoV-2 on College Campuses: Initial Efforts, Lessons Learned, and Research Needs. International Journal of Environmental Research and Public Health. 2021; 18 (9):4455.
Chicago/Turabian StyleSasha Harris-Lovett; Kara Nelson; Paloma Beamer; Heather Bischel; Aaron Bivins; Andrea Bruder; Caitlyn Butler; Todd Camenisch; Susan De Long; Smruthi Karthikeyan; David Larsen; Katherine Meierdiercks; Paula Mouser; Sheree Pagsuyoin; Sarah Prasek; Tyler Radniecki; Jeffrey Ram; D. Roper; Hannah Safford; Samendra Sherchan; William Shuster; Thibault Stalder; Robert Wheeler; Katrina Korfmacher. 2021. "Wastewater Surveillance for SARS-CoV-2 on College Campuses: Initial Efforts, Lessons Learned, and Research Needs." International Journal of Environmental Research and Public Health 18, no. 9: 4455.
Wastewater-based epidemiology is an emerging tool to monitor COVID-19 infection levels by measuring the concentration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. There remains a need to improve wastewater RNA extraction methods’ sensitivity, speed, and reduce reliance on often expensive commercial reagents to make wastewater-based epidemiology more accessible. We present a kit-free wastewater RNA extraction method, titled “Sewage, Salt, Silica and SARS-CoV-2” (4S), that employs the abundant and affordable reagents sodium chloride (NaCl), ethanol, and silica RNA capture matrices to recover sixfold more SARS-CoV-2 RNA from wastewater than an existing ultrafiltration-based method. The 4S method concurrently recovered pepper mild mottle virus (PMMoV) and human 18S ribosomal subunit rRNA, which have been proposed as fecal concentration controls. The SARS-CoV-2 RNA concentrations measured in three sewersheds corresponded to the relative prevalence of COVID-19 infection determined via clinical testing. Lastly, controlled experiments indicate that the 4S method prevented RNA degradation during storage of wastewater samples, was compatible with heat pasteurization, and in our experience, 20 samples can be processed by one lab technician in approximately 2 h. Overall, the 4S method is promising for effective, economical, and accessible wastewater-based epidemiology for SARS-CoV-2, providing another tool to fight the global pandemic.
Oscar N. Whitney; Lauren C. Kennedy; Vinson B. Fan; Adrian Hinkle; Rose Kantor; Hannah Greenwald; Alexander Crits-Christoph; Basem Al-Shayeb; Mira Chaplin; Anna C. Maurer; Robert Tjian; Kara L. Nelson. Sewage, Salt, Silica, and SARS-CoV-2 (4S): An Economical Kit-Free Method for Direct Capture of SARS-CoV-2 RNA from Wastewater. Environmental Science & Technology 2021, 55, 4880 -4888.
AMA StyleOscar N. Whitney, Lauren C. Kennedy, Vinson B. Fan, Adrian Hinkle, Rose Kantor, Hannah Greenwald, Alexander Crits-Christoph, Basem Al-Shayeb, Mira Chaplin, Anna C. Maurer, Robert Tjian, Kara L. Nelson. Sewage, Salt, Silica, and SARS-CoV-2 (4S): An Economical Kit-Free Method for Direct Capture of SARS-CoV-2 RNA from Wastewater. Environmental Science & Technology. 2021; 55 (8):4880-4888.
Chicago/Turabian StyleOscar N. Whitney; Lauren C. Kennedy; Vinson B. Fan; Adrian Hinkle; Rose Kantor; Hannah Greenwald; Alexander Crits-Christoph; Basem Al-Shayeb; Mira Chaplin; Anna C. Maurer; Robert Tjian; Kara L. Nelson. 2021. "Sewage, Salt, Silica, and SARS-CoV-2 (4S): An Economical Kit-Free Method for Direct Capture of SARS-CoV-2 RNA from Wastewater." Environmental Science & Technology 55, no. 8: 4880-4888.
Wastewater-based epidemiology is an emerging tool for tracking the spread of SARS-CoV-2 through populations. However, many factors influence recovery and quantification of SARS-CoV-2 from wastewater, complicating data interpretation. Specifically, these factors may differentially affect the measured virus concentration, depending on the laboratory methods used to perform the test. Many laboratories add a proxy virus to wastewater samples to determine losses associated with concentration and extraction of viral RNA. While measuring recovery of a proxy virus is an important process control, in this piece, we describe the caveats and limitations to the interpretation of this control, including that it typically does not account for losses during RNA extraction. We recommend reporting the directly measured concentration data alongside the measured recovery efficiency, rather than attempting to correct the concentration for recovery efficiency. Even though the ability to directly compare SARS-CoV-2 concentrations from different sampling locations determined using different methods is limited, concentration data (uncorrected for recovery) can be useful for public health response.
Rose S. Kantor; Kara L. Nelson; Hannah D. Greenwald; Lauren C. Kennedy. Challenges in Measuring the Recovery of SARS-CoV-2 from Wastewater. Environmental Science & Technology 2021, 55, 3514 -3519.
AMA StyleRose S. Kantor, Kara L. Nelson, Hannah D. Greenwald, Lauren C. Kennedy. Challenges in Measuring the Recovery of SARS-CoV-2 from Wastewater. Environmental Science & Technology. 2021; 55 (6):3514-3519.
Chicago/Turabian StyleRose S. Kantor; Kara L. Nelson; Hannah D. Greenwald; Lauren C. Kennedy. 2021. "Challenges in Measuring the Recovery of SARS-CoV-2 from Wastewater." Environmental Science & Technology 55, no. 6: 3514-3519.
Hannah Greenwald; Lauren C Kennedy; Vinson Fan; Rose Kantor; Kara L Nelson. One-Step RT-qPCR for SARS-CoV-2 Wastewater Surveillance: N1, PMMoV, BCoV, SOC, CrAssphage, Bacteroides rRNA, 18S rRNA v2. protocols.io 2021, 1 .
AMA StyleHannah Greenwald, Lauren C Kennedy, Vinson Fan, Rose Kantor, Kara L Nelson. One-Step RT-qPCR for SARS-CoV-2 Wastewater Surveillance: N1, PMMoV, BCoV, SOC, CrAssphage, Bacteroides rRNA, 18S rRNA v2. protocols.io. 2021; ():1.
Chicago/Turabian StyleHannah Greenwald; Lauren C Kennedy; Vinson Fan; Rose Kantor; Kara L Nelson. 2021. "One-Step RT-qPCR for SARS-CoV-2 Wastewater Surveillance: N1, PMMoV, BCoV, SOC, CrAssphage, Bacteroides rRNA, 18S rRNA v2." protocols.io , no. : 1.
Background Wastewater surveillance for SARS-CoV-2 is an emerging approach to help identify the risk of a COVID-19 outbreak. This tool can contribute to public health surveillance at both community (wastewater treatment system) and institutional (e.g., colleges, prisons, nursing homes) scales. Objectives This research aims to understand the successes, challenges, and lessons learned from initial wastewater surveillance efforts at colleges and university systems to inform future research, development and implementation. Methods This paper presents the experiences of 25 college and university systems in the United States that monitored campus wastewater for SARS-CoV-2 during the fall 2020 academic period. We describe the broad range of approaches, findings, resource needs, and lessons learned from these initial efforts. These institutions range in size, social and political geographies, and include both public and private institutions. Discussion Our analysis suggests that wastewater monitoring at colleges requires consideration of information needs, local sewage infrastructure, resources for sampling and analysis, college and community dynamics, approaches to interpretation and communication of results, and follow-up actions. Most colleges reported that a learning process of experimentation, evaluation, and adaptation was key to progress. This process requires ongoing collaboration among diverse stakeholders including decision-makers, researchers, faculty, facilities staff, students, and community members.
Sasha Harris-Lovett; Kara Nelson; Paloma Beamer; Heather N. Bischel; Aaron Bivins; Andrea Bruder; Caitlyn Butler; Todd D. Camenisch; Susan K. De Long; Smruthi Karthikeyan; David A. Larsen; Katherine Meierdiercks; Paula Mouser; Sheree Pagsuyoin; Sarah Prasek; Tyler S. Radniecki; Jeffrey L. Ram; D. Keith Roper; Hannah Safford; Samendra P. Sherchan; William Shuster; Thibault Stalder; Robert T. Wheeler; Katrina Smith Korfmacher. Wastewater surveillance for SARS-CoV-2 on college campuses: Initial efforts, lessons learned and research needs. 2021, 1 .
AMA StyleSasha Harris-Lovett, Kara Nelson, Paloma Beamer, Heather N. Bischel, Aaron Bivins, Andrea Bruder, Caitlyn Butler, Todd D. Camenisch, Susan K. De Long, Smruthi Karthikeyan, David A. Larsen, Katherine Meierdiercks, Paula Mouser, Sheree Pagsuyoin, Sarah Prasek, Tyler S. Radniecki, Jeffrey L. Ram, D. Keith Roper, Hannah Safford, Samendra P. Sherchan, William Shuster, Thibault Stalder, Robert T. Wheeler, Katrina Smith Korfmacher. Wastewater surveillance for SARS-CoV-2 on college campuses: Initial efforts, lessons learned and research needs. . 2021; ():1.
Chicago/Turabian StyleSasha Harris-Lovett; Kara Nelson; Paloma Beamer; Heather N. Bischel; Aaron Bivins; Andrea Bruder; Caitlyn Butler; Todd D. Camenisch; Susan K. De Long; Smruthi Karthikeyan; David A. Larsen; Katherine Meierdiercks; Paula Mouser; Sheree Pagsuyoin; Sarah Prasek; Tyler S. Radniecki; Jeffrey L. Ram; D. Keith Roper; Hannah Safford; Samendra P. Sherchan; William Shuster; Thibault Stalder; Robert T. Wheeler; Katrina Smith Korfmacher. 2021. "Wastewater surveillance for SARS-CoV-2 on college campuses: Initial efforts, lessons learned and research needs." , no. : 1.
Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread. Recently, RT-qPCR of municipal wastewater has been used to quantify the abundance of SARS-CoV-2 in several regions globally. However, metatranscriptomic sequencing of wastewater can be used to profile the viral genetic diversity across infected communities. Here, we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate complete and nearly complete SARS-CoV-2 genomes. The major consensus SARS-CoV-2 genotypes detected in the sewage were identical to clinical genomes from the region. Using a pipeline for single nucleotide variant calling in a metagenomic context, we characterized minor SARS-CoV-2 alleles in the wastewater and detected viral genotypes which were also found within clinical genomes throughout California. Observed wastewater variants were more similar to local California patient-derived genotypes than they were to those from other regions within the United States or globally. Additional variants detected in wastewater have only been identified in genomes from patients sampled outside California, indicating that wastewater sequencing can provide evidence for recent introductions of viral lineages before they are detected by local clinical sequencing. These results demonstrate that epidemiological surveillance through wastewater sequencing can aid in tracking exact viral strains in an epidemic context.
Alexander Crits-Christoph; Rose S. Kantor; Matthew R. Olm; Oscar N. Whitney; Basem Al-Shayeb; Yue Clare Lou; Avi Flamholz; Lauren C. Kennedy; Hannah Greenwald; Adrian Hinkle; Jonathan Hetzel; Sara Spitzer; Jeffery Koble; Asako Tan; Fred Hyde; Gary Schroth; Scott Kuersten; Jillian F. Banfield; Kara L. Nelson. Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants. mBio 2021, 12, 1 .
AMA StyleAlexander Crits-Christoph, Rose S. Kantor, Matthew R. Olm, Oscar N. Whitney, Basem Al-Shayeb, Yue Clare Lou, Avi Flamholz, Lauren C. Kennedy, Hannah Greenwald, Adrian Hinkle, Jonathan Hetzel, Sara Spitzer, Jeffery Koble, Asako Tan, Fred Hyde, Gary Schroth, Scott Kuersten, Jillian F. Banfield, Kara L. Nelson. Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants. mBio. 2021; 12 (1):1.
Chicago/Turabian StyleAlexander Crits-Christoph; Rose S. Kantor; Matthew R. Olm; Oscar N. Whitney; Basem Al-Shayeb; Yue Clare Lou; Avi Flamholz; Lauren C. Kennedy; Hannah Greenwald; Adrian Hinkle; Jonathan Hetzel; Sara Spitzer; Jeffery Koble; Asako Tan; Fred Hyde; Gary Schroth; Scott Kuersten; Jillian F. Banfield; Kara L. Nelson. 2021. "Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants." mBio 12, no. 1: 1.
Wastewater-based epidemiology is an emerging tool to monitor COVID-19 infection levels by measuring the concentration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. There remains a need to improve wastewater RNA extraction methods' sensitivity, speed, and reduce reliance on often expensive commercial reagents to make wastewater-based epidemiology more accessible. We present a kit-free wastewater RNA extraction method, titled "Sewage, Salt, Silica and SARS-CoV-2" (4S), that employs the abundant and affordable reagents sodium chloride (NaCl), ethanol and silica RNA capture matrices to recover 6-fold more SARS-CoV-2 RNA from wastewater than an existing ultrafiltration-based method. The 4S method concurrently recovered pepper mild mottle virus (PMMoV) and human 18S ribosomal subunit rRNA, both suitable as fecal concentration controls. The SARS-CoV-2 RNA concentrations measured in three sewersheds corresponded to the relative prevalence of COVID-19 infection determined via clinical testing. Lastly, controlled experiments indicate that the 4S method prevented RNA degradation during storage of wastewater samples, was compatible with heat pasteurization, and could be performed in approximately 3 hours. Overall, the 4S method is promising for effective, economical, and accessible wastewater-based epidemiology for SARS-CoV-2, providing another tool to fight the global pandemic.
Oscar N. Whitney; Lauren C. Kennedy; Vinson Fan; Adrian Hinkle; Rose Kantor; Hannah Greenwald; Alexander Crits-Christoph; Basem Al-Shayeb; Mira Chaplin; Anna C. Maurer; Robert Tjian; Kara L. Nelson. Sewage, Salt, Silica and SARS-CoV-2 (4S): An economical kit-free method for direct capture of SARS-CoV-2 RNA from wastewater. 2020, 1 .
AMA StyleOscar N. Whitney, Lauren C. Kennedy, Vinson Fan, Adrian Hinkle, Rose Kantor, Hannah Greenwald, Alexander Crits-Christoph, Basem Al-Shayeb, Mira Chaplin, Anna C. Maurer, Robert Tjian, Kara L. Nelson. Sewage, Salt, Silica and SARS-CoV-2 (4S): An economical kit-free method for direct capture of SARS-CoV-2 RNA from wastewater. . 2020; ():1.
Chicago/Turabian StyleOscar N. Whitney; Lauren C. Kennedy; Vinson Fan; Adrian Hinkle; Rose Kantor; Hannah Greenwald; Alexander Crits-Christoph; Basem Al-Shayeb; Mira Chaplin; Anna C. Maurer; Robert Tjian; Kara L. Nelson. 2020. "Sewage, Salt, Silica and SARS-CoV-2 (4S): An economical kit-free method for direct capture of SARS-CoV-2 RNA from wastewater." , no. : 1.
Hannah Greenwald; Lauren C Kennedy; Vinson Fan; Rose Kantor; Kara L Nelson. One-Step RT-qPCR for SARS-CoV-2 Wastewater Surveillance: N1, PMMoV, BCoV, SOC v1. protocols.io 2020, 1 .
AMA StyleHannah Greenwald, Lauren C Kennedy, Vinson Fan, Rose Kantor, Kara L Nelson. One-Step RT-qPCR for SARS-CoV-2 Wastewater Surveillance: N1, PMMoV, BCoV, SOC v1. protocols.io. 2020; ():1.
Chicago/Turabian StyleHannah Greenwald; Lauren C Kennedy; Vinson Fan; Rose Kantor; Kara L Nelson. 2020. "One-Step RT-qPCR for SARS-CoV-2 Wastewater Surveillance: N1, PMMoV, BCoV, SOC v1." protocols.io , no. : 1.
This work demonstrates insights gained from monitoring absolute microbial abundance in full-scale disinfected drinking water distribution systems and lays a foundation for statistical approaches that could provide a basis for applying these tools.
Lauren C. Kennedy; Scott E. Miller; Rose S. Kantor; Kara L. Nelson. Effect of disinfectant residual, pH, and temperature on microbial abundance in disinfected drinking water distribution systems. Environmental Science: Water Research & Technology 2020, 7, 78 -92.
AMA StyleLauren C. Kennedy, Scott E. Miller, Rose S. Kantor, Kara L. Nelson. Effect of disinfectant residual, pH, and temperature on microbial abundance in disinfected drinking water distribution systems. Environmental Science: Water Research & Technology. 2020; 7 (1):78-92.
Chicago/Turabian StyleLauren C. Kennedy; Scott E. Miller; Rose S. Kantor; Kara L. Nelson. 2020. "Effect of disinfectant residual, pH, and temperature on microbial abundance in disinfected drinking water distribution systems." Environmental Science: Water Research & Technology 7, no. 1: 78-92.
Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread. Recently, RT-qPCR of municipal wastewater has been used to quantify the abundance of SARS-CoV-2 in several regions globally. However, metatranscriptomic sequencing of wastewater can be used to profile the viral genetic diversity across infected communities. Here, we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate complete and near-complete SARS-CoV-2 genomes. The major consensus SARS-CoV-2 genotypes detected in the sewage were identical to clinical genomes from the region. Using a pipeline for single nucleotide variant (SNV) calling in a metagenomic context, we characterized minor SARS-CoV-2 alleles in the wastewater and detected viral genotypes which were also found within clinical genomes throughout California. Observed wastewater variants were more similar to local California patient-derived genotypes than they were to those from other regions within the US or globally. Additional variants detected in wastewater have only been identified in genomes from patients sampled outside of CA, indicating that wastewater sequencing can provide evidence for recent introductions of viral lineages before they are detected by local clinical sequencing. These results demonstrate that epidemiological surveillance through wastewater sequencing can aid in tracking exact viral strains in an epidemic context.
Alexander Crits-Christoph; Rose S. Kantor; Matthew R. Olm; Oscar N. Whitney; Basem Al-Shayeb; Yue C. Lou; Avi Flamholz; Lauren C. Kennedy; Hannah Greenwald; Adrian Hinkle; Jonathan Hetzel; Sara Spitzer; Jeffery Koble; Asako Tan; Fred Hyde; Gary Schroth; Scott Kuersten; Jillian F. Banfield; Kara L. Nelson. Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants. 2020, 1 .
AMA StyleAlexander Crits-Christoph, Rose S. Kantor, Matthew R. Olm, Oscar N. Whitney, Basem Al-Shayeb, Yue C. Lou, Avi Flamholz, Lauren C. Kennedy, Hannah Greenwald, Adrian Hinkle, Jonathan Hetzel, Sara Spitzer, Jeffery Koble, Asako Tan, Fred Hyde, Gary Schroth, Scott Kuersten, Jillian F. Banfield, Kara L. Nelson. Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants. . 2020; ():1.
Chicago/Turabian StyleAlexander Crits-Christoph; Rose S. Kantor; Matthew R. Olm; Oscar N. Whitney; Basem Al-Shayeb; Yue C. Lou; Avi Flamholz; Lauren C. Kennedy; Hannah Greenwald; Adrian Hinkle; Jonathan Hetzel; Sara Spitzer; Jeffery Koble; Asako Tan; Fred Hyde; Gary Schroth; Scott Kuersten; Jillian F. Banfield; Kara L. Nelson. 2020. "Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants." , no. : 1.
Intermittent piped water supply is common in low- and middle-income countries and is inconvenient for users, particularly when supply schedules are unreliable. In this study, supply schedules and operational challenges were characterized in intermittent areas of the Arraiján, Panama distribution network based on one year of pressure and flow monitoring in four study zones, analysis of three years of pipe break data, and observations of system operation. Service quality was found to vary among users and supply schedules were often irregular and unpredictable. Direct causes of unanticipated supply outages included pump failures, chronic pipe breaks in specific parts of the system, transmission main breaks, irregular valve operations, and treatment plant outages. The extent and duration of these outages were often increased by high rates of water loss, insufficient storage capacity, and difficulty detecting and resolving infrastructure failures. Factors associated with intermittent supply, such as intermittent pumping, appeared to be associated with a higher frequency of pipe breaks. However, the analysis did not indicate a strong general correlation between intermittent supply and pipe breaks. Pressure and flow monitoring in intermittent supply areas, similar to that undertaken in this study, could be a valuable tool to improve regular operations as well as longer-term planning and prioritization of system improvements. Water loss reduction and adequate distribution storage capacity could also mitigate the effects of operational failures. Investments in monitoring and data analysis have the potential to improve the reliability of intermittent supply in cases where continuous supply is not immediately feasible.
John J. Erickson; Yamileth C. Quintero; Kara L. Nelson. Characterizing Supply Variability and Operational Challenges in an Intermittent Water Distribution Network. Water 2020, 12, 2143 .
AMA StyleJohn J. Erickson, Yamileth C. Quintero, Kara L. Nelson. Characterizing Supply Variability and Operational Challenges in an Intermittent Water Distribution Network. Water. 2020; 12 (8):2143.
Chicago/Turabian StyleJohn J. Erickson; Yamileth C. Quintero; Kara L. Nelson. 2020. "Characterizing Supply Variability and Operational Challenges in an Intermittent Water Distribution Network." Water 12, no. 8: 2143.
Brian Pecson and Daniel Gerrity present an Editorial Perspective which focuses on the impact of SARS-CoV-2 on the water industry.
Brian Pecson; Daniel Gerrity; Kyle Bibby; Jörg E. Drewes; Charles Gerba; Richard Gersberg; Raul Gonzalez; Charles N. Haas; Kerry A. Hamilton; Kara L. Nelson; Adam Olivieri; Channah Rock; Joan Rose; Mark Sobsey. Editorial Perspectives: will SARS-CoV-2 reset public health requirements in the water industry? Integrating lessons of the past and emerging research. Environmental Science: Water Research & Technology 2020, 6, 1761 -1764.
AMA StyleBrian Pecson, Daniel Gerrity, Kyle Bibby, Jörg E. Drewes, Charles Gerba, Richard Gersberg, Raul Gonzalez, Charles N. Haas, Kerry A. Hamilton, Kara L. Nelson, Adam Olivieri, Channah Rock, Joan Rose, Mark Sobsey. Editorial Perspectives: will SARS-CoV-2 reset public health requirements in the water industry? Integrating lessons of the past and emerging research. Environmental Science: Water Research & Technology. 2020; 6 (7):1761-1764.
Chicago/Turabian StyleBrian Pecson; Daniel Gerrity; Kyle Bibby; Jörg E. Drewes; Charles Gerba; Richard Gersberg; Raul Gonzalez; Charles N. Haas; Kerry A. Hamilton; Kara L. Nelson; Adam Olivieri; Channah Rock; Joan Rose; Mark Sobsey. 2020. "Editorial Perspectives: will SARS-CoV-2 reset public health requirements in the water industry? Integrating lessons of the past and emerging research." Environmental Science: Water Research & Technology 6, no. 7: 1761-1764.
Understanding household-level transmission pathways of fecal pathogens can provide insight for developing effective strategies to reduce diarrheal illness in low- and middle-income countries. We applied whole bacterial community analysis to investigate pathways of bacterial transmission in 50 rural Bangladeshi households. SourceTracker was used to quantify the shared microbial community in household reservoirs (stored water, soil, and hands) and estimate the percentage of fecal-associated bacteria from child and mothers' feces in these reservoirs. Among the reservoirs studied, most bacterial transfer occurred between mothers' and child hands and between mothers' hands and stored water. The relative percentage of human fecal-associated bacteria in all household reservoirs was low. We also quantified the number of identical amplicon sequence variants within and between individual households to assess bacterial community exchange in the domestic environment. Intra-household sharing of bacteria between mothers' and children's hands and between hands and soil was significantly greater than inter-household sharing.
Erica R. Fuhrmeister; Ayse Ercumen; Jessica A. Grembi; Mahfuza Islam; Amy J. Pickering; Kara L. Nelson. Shared bacterial communities between soil, stored drinking water, and hands in rural Bangladeshi households. Water Research X 2020, 9, 100056 .
AMA StyleErica R. Fuhrmeister, Ayse Ercumen, Jessica A. Grembi, Mahfuza Islam, Amy J. Pickering, Kara L. Nelson. Shared bacterial communities between soil, stored drinking water, and hands in rural Bangladeshi households. Water Research X. 2020; 9 ():100056.
Chicago/Turabian StyleErica R. Fuhrmeister; Ayse Ercumen; Jessica A. Grembi; Mahfuza Islam; Amy J. Pickering; Kara L. Nelson. 2020. "Shared bacterial communities between soil, stored drinking water, and hands in rural Bangladeshi households." Water Research X 9, no. : 100056.
Diarrheal illnesses from enteric pathogens are a leading cause of death in children under five in low-and-middle income countries (LMICs). Sanitation is one way to reduce the spread of enteric pathogens in the environment; however, few studies have investigated the effectiveness of sanitation in rural LMICs in reducing pathogens in the environment. In this study, we measured the impact of a sanitation intervention (dual pit latrines, sani-scoop, child potties delivered as part of a randomized control trial, WASH Benefits) in rural Bangladeshi household compounds by assessing prevalence ratios, differences, and changes in concentration of pathogen genes and host-specific fecal markers. We found no difference in prevalence of pathogenic E. coli, norovirus, or Giardia genes in the domestic environment in the sanitation and control arms. The prevalence of the human fecal marker was lower on child hands and the concentration of animal fecal marker was lower on mother hands in the sanitation arm in adjusted models, but these associations were not significant after correcting for multiple comparisons. In the subset of households with ≥ 10 individuals per compound, the prevalence of enterotoxigenic E. coli genes on child hands was lower in the sanitation arm. Incomplete removal of child and animal feces or the compound (versus community-wide) scale of intervention could explain the limited impacts of improved sanitation.
Erica R. Fuhrmeister; Ayse Ercumen; Amy J. Pickering; Kaitlyn M. Jeanis; Yoshika Crider; Mahaa Ahmed; Sara Brown; Mahfuja Alam; Debashis Sen; Sharmin Islam; Mir Himayet Kabir; Mahfuza Islam; Mahbubur Rahman; Laura H. Kwong; Benjamin F. Arnold; Stephen P. Luby; John M. Colford; Kara L. Nelson. Effect of Sanitation Improvements on Pathogens and Microbial Source Tracking Markers in the Rural Bangladeshi Household Environment. Environmental Science & Technology 2020, 54, 4316 -4326.
AMA StyleErica R. Fuhrmeister, Ayse Ercumen, Amy J. Pickering, Kaitlyn M. Jeanis, Yoshika Crider, Mahaa Ahmed, Sara Brown, Mahfuja Alam, Debashis Sen, Sharmin Islam, Mir Himayet Kabir, Mahfuza Islam, Mahbubur Rahman, Laura H. Kwong, Benjamin F. Arnold, Stephen P. Luby, John M. Colford, Kara L. Nelson. Effect of Sanitation Improvements on Pathogens and Microbial Source Tracking Markers in the Rural Bangladeshi Household Environment. Environmental Science & Technology. 2020; 54 (7):4316-4326.
Chicago/Turabian StyleErica R. Fuhrmeister; Ayse Ercumen; Amy J. Pickering; Kaitlyn M. Jeanis; Yoshika Crider; Mahaa Ahmed; Sara Brown; Mahfuja Alam; Debashis Sen; Sharmin Islam; Mir Himayet Kabir; Mahfuza Islam; Mahbubur Rahman; Laura H. Kwong; Benjamin F. Arnold; Stephen P. Luby; John M. Colford; Kara L. Nelson. 2020. "Effect of Sanitation Improvements on Pathogens and Microbial Source Tracking Markers in the Rural Bangladeshi Household Environment." Environmental Science & Technology 54, no. 7: 4316-4326.
Multi-barrier advanced treatment trains are able to purify wastewater to drinking water standards, but improved methods are needed to better understand microbial concentrations, viability, and growth potential throughout treatment and distribution.
Scott E. Miller; Roberto A. Rodriguez; Kara L. Nelson. Removal and growth of microorganisms across treatment and simulated distribution at a pilot-scale direct potable reuse facility. Environmental Science: Water Research & Technology 2020, 6, 1370 -1387.
AMA StyleScott E. Miller, Roberto A. Rodriguez, Kara L. Nelson. Removal and growth of microorganisms across treatment and simulated distribution at a pilot-scale direct potable reuse facility. Environmental Science: Water Research & Technology. 2020; 6 (5):1370-1387.
Chicago/Turabian StyleScott E. Miller; Roberto A. Rodriguez; Kara L. Nelson. 2020. "Removal and growth of microorganisms across treatment and simulated distribution at a pilot-scale direct potable reuse facility." Environmental Science: Water Research & Technology 6, no. 5: 1370-1387.
Fecal indicator organisms are measured to indicate the presence of fecal pollution, yet the association between indicators and pathogens varies by context. The goal of this study was to empirically evaluate the relationships between indicator Escherichia coli, microbial source tracking markers, select enteric pathogen genes, and potential sources of enteric pathogens in 600 rural Bangladeshi households. We measured indicators and pathogen genes in stored drinking water, soil, and on mother and child hands. Additionally, survey and observational data on sanitation and domestic hygiene practices were collected. Log10 concentrations of indicator E. coli were positively associated with the prevalence of pathogenic E. coli genes in all sample types. Given the current need to rely on indicators to assess fecal contamination in the field, it is significant that in this study context indicator E. coli concentrations, measured by IDEXX Colilert-18, provided quantitative information on the presence of pathogenic E. coli in different sample types. There were no significant associations between the human fecal marker (HumM2) and human-specific pathogens in any environmental sample type. There was an increase in the prevalence of Giardia lamblia genes, any E. coli virulence gene, and the specific E. coli virulence genes stx1/2 with every log10 increase in the concentration of the animal fecal marker (BacCow) on mothers' hands. Thus, domestic animals were important contributors to enteric pathogens in these households.
Erica R. Fuhrmeister; Ayse Ercumen; Amy J. Pickering; Kaitlyn M. Jeanis; Mahaa Ahmed; Sara Brown; Benjamin F. Arnold; Alan E. Hubbard; Mahfuja Alam; Debashis Sen; Sharmin Islam; Mir Himayet Kabir; Laura H. Kwong; Mahfuza Islam; Leanne Unicomb; Mahbubur Rahman; Alexandria B. Boehm; Stephen P. Luby; John M. Colford; Kara L. Nelson. Predictors of Enteric Pathogens in the Domestic Environment from Human and Animal Sources in Rural Bangladesh. Environmental Science & Technology 2019, 53, 10023 -10033.
AMA StyleErica R. Fuhrmeister, Ayse Ercumen, Amy J. Pickering, Kaitlyn M. Jeanis, Mahaa Ahmed, Sara Brown, Benjamin F. Arnold, Alan E. Hubbard, Mahfuja Alam, Debashis Sen, Sharmin Islam, Mir Himayet Kabir, Laura H. Kwong, Mahfuza Islam, Leanne Unicomb, Mahbubur Rahman, Alexandria B. Boehm, Stephen P. Luby, John M. Colford, Kara L. Nelson. Predictors of Enteric Pathogens in the Domestic Environment from Human and Animal Sources in Rural Bangladesh. Environmental Science & Technology. 2019; 53 (17):10023-10033.
Chicago/Turabian StyleErica R. Fuhrmeister; Ayse Ercumen; Amy J. Pickering; Kaitlyn M. Jeanis; Mahaa Ahmed; Sara Brown; Benjamin F. Arnold; Alan E. Hubbard; Mahfuja Alam; Debashis Sen; Sharmin Islam; Mir Himayet Kabir; Laura H. Kwong; Mahfuza Islam; Leanne Unicomb; Mahbubur Rahman; Alexandria B. Boehm; Stephen P. Luby; John M. Colford; Kara L. Nelson. 2019. "Predictors of Enteric Pathogens in the Domestic Environment from Human and Animal Sources in Rural Bangladesh." Environmental Science & Technology 53, no. 17: 10023-10033.
Increasing access to piped water in low-income and middle-income countries combined with the many factors that threaten our drinking water supply infrastructure mean that intermittent water supply (IWS) will remain a common practice around the world. Common features of IWS include water stagnation, pipe drainage, intrusion, backflow, first flush events, and household storage. IWS has been shown to cause degradation as measured by traditional microbial water quality indicators. In this review, we build on new insights into the microbial ecology of continuous water supply systems revealed by sequencing methods to speculate about how intermittent supply conditions may further influence the drinking water microbiome, and identify priorities for future research.
Quyen M Bautista-De Los Santos; Karina A Chavarria; Kara L Nelson. Understanding the impacts of intermittent supply on the drinking water microbiome. Current Opinion in Biotechnology 2019, 57, 167 -174.
AMA StyleQuyen M Bautista-De Los Santos, Karina A Chavarria, Kara L Nelson. Understanding the impacts of intermittent supply on the drinking water microbiome. Current Opinion in Biotechnology. 2019; 57 ():167-174.
Chicago/Turabian StyleQuyen M Bautista-De Los Santos; Karina A Chavarria; Kara L Nelson. 2019. "Understanding the impacts of intermittent supply on the drinking water microbiome." Current Opinion in Biotechnology 57, no. : 167-174.
Advanced treatment facilities for potable water reuse of wastewater are designed to achieve high removal levels of specific pathogens, as well as many other constituents. However, changes to the microbial community throughout treatment, storage, and distribution of this water have not been well characterized. We applied high-throughput amplicon sequencing, read-based, assembly-based, and genome-resolved metagenomics, and flow cytometry to investigate the microbial communities present in a pilot-scale advanced water treatment facility. Advanced treatment of secondary-treated wastewater consisted of ozonation, chloramination, microfiltration, reverse osmosis (RO), advanced oxidation (UV/H2O2), granular activated carbon (GAC) filtration, and chlorination. Treated water was fed into bench-scale simulated distribution systems (SDS). Cell counts and microbial diversity in bulk water decreased until GAC filtration, and the bacterial communities were significantly different following each treatment step. Bacteria grew within GAC media and contributed to a consistent microbial community in the filtrate, which included members of the Rhizobiales and Mycobacteriaceae. After chlorination, some of the GAC filtrate community was maintained within the SDS, and community shifts were associated with stagnation. Putative antibiotic resistance genes and potential opportunistic pathogens were identified before RO and after advanced oxidation, although few if any members of the wastewater microbial community passed through these treatment steps. These findings can contribute to improved design of advanced treatment trains and management of microbial communities in post-treatment steps.
Rose S. Kantor; Scott E. Miller; Kara L. Nelson. The Water Microbiome Through a Pilot Scale Advanced Treatment Facility for Direct Potable Reuse. Frontiers in Microbiology 2019, 10, 993 .
AMA StyleRose S. Kantor, Scott E. Miller, Kara L. Nelson. The Water Microbiome Through a Pilot Scale Advanced Treatment Facility for Direct Potable Reuse. Frontiers in Microbiology. 2019; 10 ():993.
Chicago/Turabian StyleRose S. Kantor; Scott E. Miller; Kara L. Nelson. 2019. "The Water Microbiome Through a Pilot Scale Advanced Treatment Facility for Direct Potable Reuse." Frontiers in Microbiology 10, no. : 993.