Exclusive 2024 Microbes in Wastewater Symposium Video Highlights
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Prediciting pandemics: What cholera has taught us about Covid-19
Microbes in Wastewater: Molecular Approaches in Pathogen & AMR Surveillance, Laguna Beach, California. January 18, 2024
Rita R. Colwell, Ph.D, D.Sc. Distinguished University Professor, University of Maryland College Park
Video Summary:
The talk focuses on the relationship between Vibrio cholerae and environmental factors, particularly how these contribute to cholera outbreaks. Key speaker, Dr. Rita Colwell discusses her work on cholera, emphasizing the role of zooplankton in the bacterium's lifecycle. Cholera is a global disease, with outbreaks often triggered by environmental changes. Dr. Colwell's research includes using satellite data to predict cholera outbreaks based on factors like sea surface temperature, chlorophyll levels, and population movements.
She mentions a notable application of her work in Yemen during 2017-2018, where predictive modeling helped locate areas of high cholera risk, allowing for preemptive medical interventions. This approach, involving satellite sensors and metagenomic data, has significantly improved cholera outbreak predictions and has been applied to other countries like Ethiopia and Malawi. Dr. Colwell's work highlights the integration of environmental data, technology, and public health to mitigate the impact of pandemics like cholera.
Tao Yan from the University of Hawaii discusses the complexities and implications of wastewater antimicrobial resistance (AMR) during a presentation focused on using wastewater analysis to inform public health policies. The presentation emphasizes that wastewater is rich in human microbiomes, which can be a double-edged sword; it provides vital health information but also poses challenges in extracting relevant data amidst a mix of diverse microbial sources, including human, animal, and environmental inputs. Yan advocates for wastewater as a valuable platform for monitoring AMR, particularly in pathogens like Salmonella, and highlights the importance of distinguishing between clinically significant antibiotic resistance and that which poses no direct threat to human health. The presentation outlines methodologies used to correlate Salmonella concentrations in wastewater with clinical case numbers, noting fluctuations in concentrations related to seasonal changes. It discusses isolating Salmonella strains from wastewater samples and comparing them to clinical isolates, demonstrating that certain serotypes in wastewater can correlate with disease outbreaks in the community. Yan details efforts in whole-genome sequencing to detect antibiotic resistance genes, providing insights into the relationship between wastewater data and public health. The talk concludes with acknowledgment of ongoing research to understand AMR dynamics in wastewater and the potential impacts on human health.
Dr. Tao Yan, Professor, University of Hawaii
Helena Solo-Gabriele from the University of Miami presented insights on wastewater-based epidemiology beyond the COVID-19 pandemic, focusing on the South Florida RAD project. The initiative, supported by the NIH RADx RAD program and additional funding from RADx UP, aims to standardize data and integrate wastewater measurements with human health surveillance to inform public health decision-making. Collaborating with experts in various fields, including environmental engineering and bioinformatics, the project developed innovative methodologies for analyzing wastewater samples, allowing for rapid detection of SARS-CoV-2 and other pathogens. Key findings highlighted correlations between wastewater data and clinical cases, with wastewater surveillance providing early warnings for emerging variants like Delta and Omicron. The team is now looking to expand their focus beyond SARS-CoV-2 to include other pathogens and to enhance methodologies for broader environmental monitoring, including air and surfaces. They emphasize the need for standardized data interpretation and collaboration with health authorities for effective public health responses.
Dr. Helena Solo-Gabriele, Professor, University of Miami
Ivan Liachko from Phase Genomics discussed the significant challenges in studying antibiotic resistance, particularly the difficulty of associating genetic material with its bacterial origin. He emphasized that during DNA purification from microbial communities, critical data is lost, especially regarding plasmids and phages. To address this, his team has adapted a sequencing technique called proximity ligation, which preserves the spatial relationships between DNA sequences within intact cells. This method allows for the identification of connections between plasmids, antibiotic resistance genes, and their host bacteria. Liachko presented findings from various projects, including a large-scale study funded by the Gates Foundation that highlighted how plasmids are key players in the transfer of antibiotic resistance genes across different bacterial hosts. He also showcased research using fecal transplant data to reveal hidden reservoirs of resistance genes. By utilizing this innovative technology, Phase Genomics aims to provide detailed genomic insights from diverse samples, enhancing the understanding of antibiotic resistance and the dynamics of microbial communities.
Dr. Ivan Liachko, Co-founder and CEO, Phase Genomics
The talk focuses on the relationship between Vibrio cholerae and environmental factors, particularly how these contribute to cholera outbreaks. Key speaker, Dr. Rita Colwell discusses her work on cholera, emphasizing the role of zooplankton in the bacterium's lifecycle. Cholera is a global disease, with outbreaks often triggered by environmental changes. Dr. Colwell's research includes using satellite data to predict cholera outbreaks based on factors like sea surface temperature, chlorophyll levels, and population movements. She mentions a notable application of her work in Yemen during 2017-2018, where predictive modeling helped locate areas of high cholera risk, allowing for preemptive medical interventions. This approach, involving satellite sensors and metagenomic data, has significantly improved cholera outbreak predictions and has been applied to other countries like Ethiopia and Malawi. Dr. Colwell's work highlights the integration of environmental data, technology, and public health to mitigate the impact of pandemics like cholera.
Dr. Rita Colwell, Distinguished Professor, University of Maryland; Founder, CosmosID, Inc.
The talk discusses a presentation by Dr. Amy Pruden on antimicrobial resistance (AMR) and its connection to wastewater treatment. Dr. Pruden, an environmental scientist, focuses on the role of water systems in managing pathogens and antibiotic resistance. She highlights the urgency of AMR, comparing its global death toll to the COVID-19 pandemic, and emphasizes the need for effective surveillance, particularly through wastewater-based monitoring. Dr. Pruden details a study funded by the Water Research Foundation to monitor AMR in wastewater, highlighting the challenges of selecting appropriate monitoring targets. She explains different methods, including culture, qPCR, and metagenomic sequencing, with a focus on metagenomics for its comprehensive data on antibiotic resistance genes (ARGs) and mobile genetic elements like plasmids. The study found differences in AMR levels across countries, influenced by factors like prescription practices. She also discusses how wastewater treatment plants can both reduce and disseminate AMR, and introduces tools like MetaCompare, which assesses metagenomic data to evaluate the risk of resistance spreading through treated water. Dr. Pruden concludes by stressing the importance of continuous monitoring and the development of better databases for tracking AMR in the environment.
Dr. Amy Pruden, Distinguished Professor, Virginia Tech
Dr. Katrine Whiteson from UC Irvine presented her team's research on wastewater sequencing, particularly during the COVID-19 pandemic. She credited Jason Rothman and his team for their efforts in this shift from their usual focus on the human microbiome to wastewater. The team used sewage samples to hunt for phages, which are viruses that infect bacteria, with the aim of finding alternatives to antibiotics. They had success in identifying phages that target specific pathogens, even from older sewage samples. During the pandemic, they expanded their research to include RNA sequencing of wastewater to track the presence of viruses, including SARS-CoV-2. They collected samples from eight wastewater treatment plants in Southern California, representing 16 million people. Despite the challenges, such as pasteurizing samples at 70°C, they successfully sequenced RNA and detected various viruses, including tomato viruses which were unexpectedly the most abundant. The team employed both direct RNA sequencing and enrichment methods, including the Illumina respiratory virus panel and Arctic primers, to enhance their analysis. They discovered a high diversity of viral variants, some of which were detected in wastewater before being identified in clinical samples. Whiteson emphasized the importance of considering data that doesn't match existing databases, as there is still much "dark matter" in genomic sequencing, with many unknowns in both human and environmental samples. Whiteson concluded by encouraging researchers to explore larger databases and use K-mer analysis to better classify unknown sequences. She also highlighted ongoing efforts to improve standards in microbiome research, mentioning collaborations between various organizations to advance the field.
Dr. Katrine Whiteson, Professor, University of California Irvine
Raul Gonzalez discussed the use of molecular forensics to detect sewage contamination in urban surface waters. Drawing on his experience with the Hampton Roads Sanitation District (HRSD) in Virginia, he explained how microbial source tracking (MST), particularly the use of the HF183 molecular marker, has been instrumental in identifying human fecal contamination from compromised sewer infrastructure. This method, targeting bacteria from the human gut, allows precise detection of recent sewage events in stormwater systems. Over the last decade, HRSD has developed an in-house molecular lab, leading to more actionable MST data by focusing on single markers across multiple samples. This targeted approach enables the tracing of sewer pipe failures, identifying contamination sources through stormwater outfall sampling. Gonzalez shared success stories of detecting and fixing leaks, reducing health risks at recreational water sites. He also highlighted the program's adoption across Virginia, its influence on regulations, and the importance of ongoing infrastructure monitoring and repair to maintain public health.
Dr. Raul A. Gonzalez, Co-Founder, H2O Molecular
Alexandria Boehm, a Stanford professor and pioneer in wastewater-based surveillance, discussed her team's work on monitoring infectious diseases through wastewater solids. Boehm explained why her team focuses on solids rather than liquids, as viruses tend to adhere more to solids. She introduced the Wastewater SCAN project, which monitors various pathogens in wastewater across the U.S., including influenza, RSV, and dengue. Her team found strong correlations between viral RNA in wastewater solids and clinical data, such as hospitalization and positivity rates for diseases like influenza and RSV. Boehm highlighted knowledge gaps in understanding viral shedding and challenges in validating wastewater data due to limited clinical data. She emphasized the value of wastewater as a tool for tracking infectious diseases and its rapid adoption during the COVID-19 pandemic.
Dr. Alexandria Boehm, Professor, Stanford University; Principal Investigator, WastewaterSCAN
Dr. John Griffiths, head of the biology department at Southern California Coastal Water Research Project, presented findings on antibiotic resistance in wastewater. His study was prompted by concerns over superbugs in wastewater treatment plants. The research aimed to determine if treatment processes reduce antibiotic-resistant bacteria and genes, particularly focusing on multi-resistant strains like MRSA and carbapenem-resistant Klebsiella. Results showed that while treatment significantly reduced resistant bacteria, traces of antibiotic-resistant genes persisted, especially in plants with less stringent treatment protocols. The study also highlighted the potential for lateral gene transfer of these resistance genes into the environment. Further research is needed to assess the long-term impact on human health and the environment, particularly in marine ecosystems. The study underscores the variability in treatment efficacy across plants and the need for more stringent treatment in facilities discharging water into sensitive areas.
Dr. John Griffith, Department Head of Microbiology, SCCWRP
The presentation discussed the critical role of wastewater treatment plants in controlling the spread of antibiotic-resistant microorganisms (AMR). In LA County, 11 treatment plants, 10 of which produce reclaimed water, play a key role in reusing wastewater for various purposes, such as irrigation and groundwater recharge. These plants are crucial control points for limiting the spread of AMR into the environment. However, knowledge gaps exist in understanding the transmission of antibiotic-resistant bacteria through the treatment process. The research focused on two main goals: identifying the types of antibiotic-resistant bacteria in wastewater and assessing how effectively treatment processes remove antibiotic-resistant genes. Data showed a significant decline in antibiotic-resistant bacteria through tertiary wastewater treatment processes, reducing concentrations by five orders of magnitude. A shift in bacterial populations was observed during treatment, with a decline in Klebsiella pneumoniae and E. coli and an increase in species like Enterobacter in final effluents. The study also examined antibiotic-resistant genes through qPCR analysis, showing significant reductions in beta-lactamase and sulfonamide resistance genes during treatment, with the most substantial decreases in tertiary effluent. The use of tertiary filtration combined with chlorine disinfection was shown to produce synergistic reductions in resistant plasmids. These findings highlight the complexity of AMR, driven by both inherent and acquired resistance mechanisms, and the importance of wastewater plants as control points to curb AMR's environmental impact.
Dr. Ryan Reinke, Research Scientist, Los Angeles County Sanitation Districts
Dr. Prabhu Gounder, currently with LA County Health and previously at the CDC, discusses the integration of wastewater surveillance in public health, particularly for respiratory diseases like influenza and COVID-19. He outlines the traditional methods of respiratory disease surveillance before the pandemic, which primarily focused on influenza due to its significant morbidity and mortality rates. Challenges included underreporting due to asymptomatic cases and difficulties in data management from multiple testing methods. With the onset of COVID-19, public health surveillance evolved to include systematic reporting of positive and negative COVID tests, enhancing case tracking and resource allocation. The pandemic led to infrastructure improvements that allowed linking COVID cases to vaccination data and disease outcomes. Additionally, wastewater surveillance emerged as a valuable tool, showing correlations with community transmission, particularly during the omicron surge when reported cases lagged behind actual transmission levels. Dr. Gounder emphasizes the need for effective communication of wastewater data to the public, ensuring that it aligns with public health messaging to avoid confusion during varying transmission rates. Overall, he highlights the evolution of surveillance practices and the importance of adapting methods to effectively respond to public health challenges.
Dr. Prabhu Gounder, Medical Epidemiologist, Los Angeles County Dept. of Public Health
In this presentation, Daniel Gerrity discusses the significance of C. auris in Southern Nevada, highlighting the urgency of addressing this antifungal-resistant infection, particularly in immunocompromised populations. He notes that the mortality rate for invasive C. auris infections can be as high as 33%. With C. auris emerging as a significant public health threat since 2013, its resistance to common antifungals poses a critical challenge. In Nevada, C. auris cases have been classified into different clades, with clade 1 and clade 3 showing high resistance to fluconazole. Gerrity outlines the timeline of C. auris cases in Southern Nevada, noting the first confirmed case in August 2021 and subsequent investigations that revealed additional colonizations, particularly in NICUs. Collaborative efforts led to successful wastewater surveillance, which identified C. auris in Las Vegas’s wastewater, establishing it as a viable method for tracking the infection. This method was later applied to the St. George area in Utah, where C. auris was detected following the introduction of patients with confirmed infections. The presentation emphasizes the need for continuous surveillance and intervention strategies to combat the spread of C. auris.,
Dr. Daniel Gerrity, Principal Research Microbiologist, Southern Nevada Water Authority
The core of Dr. Kyle Bibby's talk centered on the rich diversity of pathogenic viruses found in sewage, emphasizing the implications for public health. His early research on sewage sludge unveiled numerous pathogens, prompting a shift in focus toward wastewater-based epidemiology. Bibby highlighted the straightforward concept of WBE—detecting pathogens shed by infected individuals in wastewater to gain community health insights. He presented a typical workflow for WBE programs and discussed challenges related to sampling methods, pathogen detection limits, and the dilution effects of water usage on signal strength. His approach included modeling pathogen genome shedding and utilizing Monte Carlo simulations to predict detection probabilities based on varying infection rates and PCR replicates. Bibby provided two case studies: the assessment of monkeypox (mpox) and Zika virus. His findings indicated that while WBE for mpox is feasible under certain conditions, Zika detection presents more challenges due to lower shedding rates. He underscored the importance of local water use and infection rates, advocating for a more nuanced understanding of target development in wastewater surveillance. In conclusion, Bibby called for the scientific community to be thoughtful about target selection for WBE, stressing that while modeling is a valuable tool, it should complement rather than replace empirical methods. He welcomed questions and offered his contact information for further inquiries.
Dr. Kyle Bibby, Professor, University of Notre Dame
Dr. Kyle McClary from the Aladdin Bioinformatics Foundation presents an innovative platform designed to simplify wastewater bioinformatics, allowing users to analyze sequencing data without needing advanced coding skills. He highlights the growing importance of wastewater sequencing for pathogen detection and environmental health, emphasizing the challenges in managing and processing data. The Aladdin platform enables users to run analyses in a user-friendly browser interface, facilitating data visualization and report generation. With features like customizable pipelines and collaborative workspaces, the platform aims to democratize bioinformatics. Dr. McClary invites collaboration and feedback from the audience to enhance the platform's capabilities.
Dr. Kyle McClary, Director of Data, Aladdin Bioinformatics Foundation
Angela Rabe from the California Department of Public Health presents on the state's wastewater surveillance program for monitoring pathogens, including COVID-19 and MPOX. She emphasizes the importance of wastewater surveillance, explaining how a single sample can provide insights into community trends, potentially covering thousands to millions of residents. The presentation discusses the initial challenges of convincing stakeholders about the value of wastewater surveillance during the COVID-19 pandemic and highlights the successful establishment of the Cal Sewers network. This network has expanded its capabilities, allowing for monitoring of multiple pathogens, including RSV, influenza, norovirus, and Candida auris. Rabe shares the correlation between wastewater data and clinical case data throughout different COVID-19 variants, noting divergence in data trends due to the rise of at-home testing. The team has also applied wastewater surveillance to monitor MPOX, demonstrating strong correlations between wastewater detections and clinical cases. The presentation highlights the program's adaptability to various pathogens and the collaborative efforts with partners across California, including local health departments and academic institutions. Rabe concludes by discussing the remaining questions and challenges in wastewater surveillance, such as understanding shedding dynamics, risk communication, and the need for standard laboratory methods. The presentation ends with acknowledgments of the collaborative efforts essential for the program's success.
Angela Rabe, M.S., Wastewater Epidemiologist, California Dept. of Public Health
Tao Yan from the University of Hawaii discusses the complexities and implications of wastewater antimicrobial resistance (AMR) during a presentation focused on using wastewater analysis to inform public health policies. The presentation emphasizes that wastewater is rich in human microbiomes, which can be a double-edged sword; it provides vital health information but also poses challenges in extracting relevant data amidst a mix of diverse microbial sources, including human, animal, and environmental inputs. Yan advocates for wastewater as a valuable platform for monitoring AMR, particularly in pathogens like Salmonella, and highlights the importance of distinguishing between clinically significant antibiotic resistance and that which poses no direct threat to human health. The presentation outlines methodologies used to correlate Salmonella concentrations in wastewater with clinical case numbers, noting fluctuations in concentrations related to seasonal changes. It discusses isolating Salmonella strains from wastewater samples and comparing them to clinical isolates, demonstrating that certain serotypes in wastewater can correlate with disease outbreaks in the community. Yan details efforts in whole-genome sequencing to detect antibiotic resistance genes, providing insights into the relationship between wastewater data and public health. The talk concludes with acknowledgment of ongoing research to understand AMR dynamics in wastewater and the potential impacts on human health.
Dr. Tao Yan, Professor, University of Hawaii
Helena Solo-Gabriele from the University of Miami presented insights on wastewater-based epidemiology beyond the COVID-19 pandemic, focusing on the South Florida RAD project. The initiative, supported by the NIH RADx RAD program and additional funding from RADx UP, aims to standardize data and integrate wastewater measurements with human health surveillance to inform public health decision-making. Collaborating with experts in various fields, including environmental engineering and bioinformatics, the project developed innovative methodologies for analyzing wastewater samples, allowing for rapid detection of SARS-CoV-2 and other pathogens. Key findings highlighted correlations between wastewater data and clinical cases, with wastewater surveillance providing early warnings for emerging variants like Delta and Omicron. The team is now looking to expand their focus beyond SARS-CoV-2 to include other pathogens and to enhance methodologies for broader environmental monitoring, including air and surfaces. They emphasize the need for standardized data interpretation and collaboration with health authorities for effective public health responses.
Dr. Helena Solo-Gabriele, Professor, University of Miami
Ivan Liachko from Phase Genomics discussed the significant challenges in studying antibiotic resistance, particularly the difficulty of associating genetic material with its bacterial origin. He emphasized that during DNA purification from microbial communities, critical data is lost, especially regarding plasmids and phages. To address this, his team has adapted a sequencing technique called proximity ligation, which preserves the spatial relationships between DNA sequences within intact cells. This method allows for the identification of connections between plasmids, antibiotic resistance genes, and their host bacteria. Liachko presented findings from various projects, including a large-scale study funded by the Gates Foundation that highlighted how plasmids are key players in the transfer of antibiotic resistance genes across different bacterial hosts. He also showcased research using fecal transplant data to reveal hidden reservoirs of resistance genes. By utilizing this innovative technology, Phase Genomics aims to provide detailed genomic insights from diverse samples, enhancing the understanding of antibiotic resistance and the dynamics of microbial communities.
Dr. Ivan Liachko, Co-founder and CEO, Phase Genomics
The talk focuses on the relationship between Vibrio cholerae and environmental factors, particularly how these contribute to cholera outbreaks. Key speaker, Dr. Rita Colwell discusses her work on cholera, emphasizing the role of zooplankton in the bacterium's lifecycle. Cholera is a global disease, with outbreaks often triggered by environmental changes. Dr. Colwell's research includes using satellite data to predict cholera outbreaks based on factors like sea surface temperature, chlorophyll levels, and population movements. She mentions a notable application of her work in Yemen during 2017-2018, where predictive modeling helped locate areas of high cholera risk, allowing for preemptive medical interventions. This approach, involving satellite sensors and metagenomic data, has significantly improved cholera outbreak predictions and has been applied to other countries like Ethiopia and Malawi. Dr. Colwell's work highlights the integration of environmental data, technology, and public health to mitigate the impact of pandemics like cholera.
Dr. Rita Colwell, Distinguished Professor, University of Maryland; Founder, CosmosID, Inc.
The talk discusses a presentation by Dr. Amy Pruden on antimicrobial resistance (AMR) and its connection to wastewater treatment. Dr. Pruden, an environmental scientist, focuses on the role of water systems in managing pathogens and antibiotic resistance. She highlights the urgency of AMR, comparing its global death toll to the COVID-19 pandemic, and emphasizes the need for effective surveillance, particularly through wastewater-based monitoring. Dr. Pruden details a study funded by the Water Research Foundation to monitor AMR in wastewater, highlighting the challenges of selecting appropriate monitoring targets. She explains different methods, including culture, qPCR, and metagenomic sequencing, with a focus on metagenomics for its comprehensive data on antibiotic resistance genes (ARGs) and mobile genetic elements like plasmids. The study found differences in AMR levels across countries, influenced by factors like prescription practices. She also discusses how wastewater treatment plants can both reduce and disseminate AMR, and introduces tools like MetaCompare, which assesses metagenomic data to evaluate the risk of resistance spreading through treated water. Dr. Pruden concludes by stressing the importance of continuous monitoring and the development of better databases for tracking AMR in the environment.
Dr. Amy Pruden, Distinguished Professor, Virginia Tech
Dr. Katrine Whiteson from UC Irvine presented her team's research on wastewater sequencing, particularly during the COVID-19 pandemic. She credited Jason Rothman and his team for their efforts in this shift from their usual focus on the human microbiome to wastewater. The team used sewage samples to hunt for phages, which are viruses that infect bacteria, with the aim of finding alternatives to antibiotics. They had success in identifying phages that target specific pathogens, even from older sewage samples. During the pandemic, they expanded their research to include RNA sequencing of wastewater to track the presence of viruses, including SARS-CoV-2. They collected samples from eight wastewater treatment plants in Southern California, representing 16 million people. Despite the challenges, such as pasteurizing samples at 70°C, they successfully sequenced RNA and detected various viruses, including tomato viruses which were unexpectedly the most abundant. The team employed both direct RNA sequencing and enrichment methods, including the Illumina respiratory virus panel and Arctic primers, to enhance their analysis. They discovered a high diversity of viral variants, some of which were detected in wastewater before being identified in clinical samples. Whiteson emphasized the importance of considering data that doesn't match existing databases, as there is still much "dark matter" in genomic sequencing, with many unknowns in both human and environmental samples. Whiteson concluded by encouraging researchers to explore larger databases and use K-mer analysis to better classify unknown sequences. She also highlighted ongoing efforts to improve standards in microbiome research, mentioning collaborations between various organizations to advance the field.
Dr. Katrine Whiteson, Professor, University of California Irvine
Raul Gonzalez discussed the use of molecular forensics to detect sewage contamination in urban surface waters. Drawing on his experience with the Hampton Roads Sanitation District (HRSD) in Virginia, he explained how microbial source tracking (MST), particularly the use of the HF183 molecular marker, has been instrumental in identifying human fecal contamination from compromised sewer infrastructure. This method, targeting bacteria from the human gut, allows precise detection of recent sewage events in stormwater systems. Over the last decade, HRSD has developed an in-house molecular lab, leading to more actionable MST data by focusing on single markers across multiple samples. This targeted approach enables the tracing of sewer pipe failures, identifying contamination sources through stormwater outfall sampling. Gonzalez shared success stories of detecting and fixing leaks, reducing health risks at recreational water sites. He also highlighted the program's adoption across Virginia, its influence on regulations, and the importance of ongoing infrastructure monitoring and repair to maintain public health.
Dr. Raul A. Gonzalez, Co-Founder, H2O Molecular
Alexandria Boehm, a Stanford professor and pioneer in wastewater-based surveillance, discussed her team's work on monitoring infectious diseases through wastewater solids. Boehm explained why her team focuses on solids rather than liquids, as viruses tend to adhere more to solids. She introduced the Wastewater SCAN project, which monitors various pathogens in wastewater across the U.S., including influenza, RSV, and dengue. Her team found strong correlations between viral RNA in wastewater solids and clinical data, such as hospitalization and positivity rates for diseases like influenza and RSV. Boehm highlighted knowledge gaps in understanding viral shedding and challenges in validating wastewater data due to limited clinical data. She emphasized the value of wastewater as a tool for tracking infectious diseases and its rapid adoption during the COVID-19 pandemic.
Dr. Alexandria Boehm, Professor, Stanford University; Principal Investigator, WastewaterSCAN
Dr. John Griffiths, head of the biology department at Southern California Coastal Water Research Project, presented findings on antibiotic resistance in wastewater. His study was prompted by concerns over superbugs in wastewater treatment plants. The research aimed to determine if treatment processes reduce antibiotic-resistant bacteria and genes, particularly focusing on multi-resistant strains like MRSA and carbapenem-resistant Klebsiella. Results showed that while treatment significantly reduced resistant bacteria, traces of antibiotic-resistant genes persisted, especially in plants with less stringent treatment protocols. The study also highlighted the potential for lateral gene transfer of these resistance genes into the environment. Further research is needed to assess the long-term impact on human health and the environment, particularly in marine ecosystems. The study underscores the variability in treatment efficacy across plants and the need for more stringent treatment in facilities discharging water into sensitive areas.
Dr. John Griffith, Department Head of Microbiology, SCCWRP
The presentation discussed the critical role of wastewater treatment plants in controlling the spread of antibiotic-resistant microorganisms (AMR). In LA County, 11 treatment plants, 10 of which produce reclaimed water, play a key role in reusing wastewater for various purposes, such as irrigation and groundwater recharge. These plants are crucial control points for limiting the spread of AMR into the environment. However, knowledge gaps exist in understanding the transmission of antibiotic-resistant bacteria through the treatment process. The research focused on two main goals: identifying the types of antibiotic-resistant bacteria in wastewater and assessing how effectively treatment processes remove antibiotic-resistant genes. Data showed a significant decline in antibiotic-resistant bacteria through tertiary wastewater treatment processes, reducing concentrations by five orders of magnitude. A shift in bacterial populations was observed during treatment, with a decline in Klebsiella pneumoniae and E. coli and an increase in species like Enterobacter in final effluents. The study also examined antibiotic-resistant genes through qPCR analysis, showing significant reductions in beta-lactamase and sulfonamide resistance genes during treatment, with the most substantial decreases in tertiary effluent. The use of tertiary filtration combined with chlorine disinfection was shown to produce synergistic reductions in resistant plasmids. These findings highlight the complexity of AMR, driven by both inherent and acquired resistance mechanisms, and the importance of wastewater plants as control points to curb AMR's environmental impact.
Dr. Ryan Reinke, Research Scientist, Los Angeles County Sanitation Districts
Dr. Prabhu Gounder, currently with LA County Health and previously at the CDC, discusses the integration of wastewater surveillance in public health, particularly for respiratory diseases like influenza and COVID-19. He outlines the traditional methods of respiratory disease surveillance before the pandemic, which primarily focused on influenza due to its significant morbidity and mortality rates. Challenges included underreporting due to asymptomatic cases and difficulties in data management from multiple testing methods. With the onset of COVID-19, public health surveillance evolved to include systematic reporting of positive and negative COVID tests, enhancing case tracking and resource allocation. The pandemic led to infrastructure improvements that allowed linking COVID cases to vaccination data and disease outcomes. Additionally, wastewater surveillance emerged as a valuable tool, showing correlations with community transmission, particularly during the omicron surge when reported cases lagged behind actual transmission levels. Dr. Gounder emphasizes the need for effective communication of wastewater data to the public, ensuring that it aligns with public health messaging to avoid confusion during varying transmission rates. Overall, he highlights the evolution of surveillance practices and the importance of adapting methods to effectively respond to public health challenges.
Dr. Prabhu Gounder, Medical Epidemiologist, Los Angeles County Dept. of Public Health
In this presentation, Daniel Gerrity discusses the significance of C. auris in Southern Nevada, highlighting the urgency of addressing this antifungal-resistant infection, particularly in immunocompromised populations. He notes that the mortality rate for invasive C. auris infections can be as high as 33%. With C. auris emerging as a significant public health threat since 2013, its resistance to common antifungals poses a critical challenge. In Nevada, C. auris cases have been classified into different clades, with clade 1 and clade 3 showing high resistance to fluconazole. Gerrity outlines the timeline of C. auris cases in Southern Nevada, noting the first confirmed case in August 2021 and subsequent investigations that revealed additional colonizations, particularly in NICUs. Collaborative efforts led to successful wastewater surveillance, which identified C. auris in Las Vegas’s wastewater, establishing it as a viable method for tracking the infection. This method was later applied to the St. George area in Utah, where C. auris was detected following the introduction of patients with confirmed infections. The presentation emphasizes the need for continuous surveillance and intervention strategies to combat the spread of C. auris.,
Dr. Daniel Gerrity, Principal Research Microbiologist, Southern Nevada Water Authority
The core of Dr. Kyle Bibby's talk centered on the rich diversity of pathogenic viruses found in sewage, emphasizing the implications for public health. His early research on sewage sludge unveiled numerous pathogens, prompting a shift in focus toward wastewater-based epidemiology. Bibby highlighted the straightforward concept of WBE—detecting pathogens shed by infected individuals in wastewater to gain community health insights. He presented a typical workflow for WBE programs and discussed challenges related to sampling methods, pathogen detection limits, and the dilution effects of water usage on signal strength. His approach included modeling pathogen genome shedding and utilizing Monte Carlo simulations to predict detection probabilities based on varying infection rates and PCR replicates. Bibby provided two case studies: the assessment of monkeypox (mpox) and Zika virus. His findings indicated that while WBE for mpox is feasible under certain conditions, Zika detection presents more challenges due to lower shedding rates. He underscored the importance of local water use and infection rates, advocating for a more nuanced understanding of target development in wastewater surveillance. In conclusion, Bibby called for the scientific community to be thoughtful about target selection for WBE, stressing that while modeling is a valuable tool, it should complement rather than replace empirical methods. He welcomed questions and offered his contact information for further inquiries.
Dr. Kyle Bibby, Professor, University of Notre Dame
Dr. Kyle McClary from the Aladdin Bioinformatics Foundation presents an innovative platform designed to simplify wastewater bioinformatics, allowing users to analyze sequencing data without needing advanced coding skills. He highlights the growing importance of wastewater sequencing for pathogen detection and environmental health, emphasizing the challenges in managing and processing data. The Aladdin platform enables users to run analyses in a user-friendly browser interface, facilitating data visualization and report generation. With features like customizable pipelines and collaborative workspaces, the platform aims to democratize bioinformatics. Dr. McClary invites collaboration and feedback from the audience to enhance the platform's capabilities.
Dr. Kyle McClary, Director of Data, Aladdin Bioinformatics Foundation
Angela Rabe from the California Department of Public Health presents on the state's wastewater surveillance program for monitoring pathogens, including COVID-19 and MPOX. She emphasizes the importance of wastewater surveillance, explaining how a single sample can provide insights into community trends, potentially covering thousands to millions of residents. The presentation discusses the initial challenges of convincing stakeholders about the value of wastewater surveillance during the COVID-19 pandemic and highlights the successful establishment of the Cal Sewers network. This network has expanded its capabilities, allowing for monitoring of multiple pathogens, including RSV, influenza, norovirus, and Candida auris. Rabe shares the correlation between wastewater data and clinical case data throughout different COVID-19 variants, noting divergence in data trends due to the rise of at-home testing. The team has also applied wastewater surveillance to monitor MPOX, demonstrating strong correlations between wastewater detections and clinical cases. The presentation highlights the program's adaptability to various pathogens and the collaborative efforts with partners across California, including local health departments and academic institutions. Rabe concludes by discussing the remaining questions and challenges in wastewater surveillance, such as understanding shedding dynamics, risk communication, and the need for standard laboratory methods. The presentation ends with acknowledgments of the collaborative efforts essential for the program's success.
Angela Rabe, M.S., Wastewater Epidemiologist, California Dept. of Public Health
Tao Yan from the University of Hawaii discusses the complexities and implications of wastewater antimicrobial resistance (AMR) during a presentation focused on using wastewater analysis to inform public health policies. The presentation emphasizes that wastewater is rich in human microbiomes, which can be a double-edged sword; it provides vital health information but also poses challenges in extracting relevant data amidst a mix of diverse microbial sources, including human, animal, and environmental inputs. Yan advocates for wastewater as a valuable platform for monitoring AMR, particularly in pathogens like Salmonella, and highlights the importance of distinguishing between clinically significant antibiotic resistance and that which poses no direct threat to human health. The presentation outlines methodologies used to correlate Salmonella concentrations in wastewater with clinical case numbers, noting fluctuations in concentrations related to seasonal changes. It discusses isolating Salmonella strains from wastewater samples and comparing them to clinical isolates, demonstrating that certain serotypes in wastewater can correlate with disease outbreaks in the community. Yan details efforts in whole-genome sequencing to detect antibiotic resistance genes, providing insights into the relationship between wastewater data and public health. The talk concludes with acknowledgment of ongoing research to understand AMR dynamics in wastewater and the potential impacts on human health.
Dr. Tao Yan, Professor, University of Hawaii
Helena Solo-Gabriele from the University of Miami presented insights on wastewater-based epidemiology beyond the COVID-19 pandemic, focusing on the South Florida RAD project. The initiative, supported by the NIH RADx RAD program and additional funding from RADx UP, aims to standardize data and integrate wastewater measurements with human health surveillance to inform public health decision-making. Collaborating with experts in various fields, including environmental engineering and bioinformatics, the project developed innovative methodologies for analyzing wastewater samples, allowing for rapid detection of SARS-CoV-2 and other pathogens. Key findings highlighted correlations between wastewater data and clinical cases, with wastewater surveillance providing early warnings for emerging variants like Delta and Omicron. The team is now looking to expand their focus beyond SARS-CoV-2 to include other pathogens and to enhance methodologies for broader environmental monitoring, including air and surfaces. They emphasize the need for standardized data interpretation and collaboration with health authorities for effective public health responses.
Dr. Helena Solo-Gabriele, Professor, University of Miami
Ivan Liachko from Phase Genomics discussed the significant challenges in studying antibiotic resistance, particularly the difficulty of associating genetic material with its bacterial origin. He emphasized that during DNA purification from microbial communities, critical data is lost, especially regarding plasmids and phages. To address this, his team has adapted a sequencing technique called proximity ligation, which preserves the spatial relationships between DNA sequences within intact cells. This method allows for the identification of connections between plasmids, antibiotic resistance genes, and their host bacteria. Liachko presented findings from various projects, including a large-scale study funded by the Gates Foundation that highlighted how plasmids are key players in the transfer of antibiotic resistance genes across different bacterial hosts. He also showcased research using fecal transplant data to reveal hidden reservoirs of resistance genes. By utilizing this innovative technology, Phase Genomics aims to provide detailed genomic insights from diverse samples, enhancing the understanding of antibiotic resistance and the dynamics of microbial communities.
Dr. Ivan Liachko, Co-founder and CEO, Phase Genomics