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Wastewater surveillance gained prominence during the pandemic. Where is it now?

Panelists present on wastewater surveillance at APHL ID Lab Con.

By: Erin Morin, specialist, Environmental Health, APHL

While wastewater testing is typically used in environmental health applications, wastewater testing for infectious diseases was a prominent discussion topic at the inaugural APHL ID Lab Con. This surveillance approach is relatively new in the United States and rose to prominence during the COVID-19 pandemic in large part due to CDC’s National Wastewater Surveillance System. Wastewater surveillance was a reoccurring theme throughout the conference, and two major ideas emerged: it’s useful and it should be here to stay.

What is Wastewater Surveillance?

Wastewater surveillance is a strategy for early detection of disease trends in a community and serves as a complement to clinical data. Since most of the US population is connected to municipal sewage treatment systems, wastewater surveillance creates a snapshot of how diseases and pathogens move through a community. Wastewater surveillance can gather data regardless of whether community members are symptomatic or if they seek medical attention when they are feeling sick. This can be because of their own choices, opportunities or access to healthcare, or are using COVID at home testing kits. It also provides relatively quick, reliable data that can help inform public health action. Wastewater surveillance has been used for decades for polio surveillance in other countries and gained popularity in the US during the COVID-19 pandemic. But it isn’t limited to just SARS-CoV-2, the virus that causes COVID. Many laboratories are expanding to other pathogens of concern and implementing wastewater surveillance as a staple tool in public health.

There were three different sessions at ID Lab Con that focused on wastewater surveillance and I learned new information from all of them. Below are summaries of the presentations made during each session. There is a lot here, but I found each presentation to be so interesting that I couldn’t hold back.

Wastewater Surveillance: Building Systems that Lead to Actionable Data

During this plenary session, panelists discussed their experiences collaborating with the US Food and Drug Administration (FDA), technical challenges faced when translating data to epidemiological practice, using wastewater surveillance for novel targets, and using it to inform public health actions.

Lauren Turner, PhD, of the Virginia Department of Consolidated Laboratory Services (DCLS) presented on their collaborative project with FDA that piloted wastewater surveillance efforts for SARS-CoV-2 variants in Virginia from 2021-2022. They implemented wastewater surveillance in targeted food production areas within the state such as tree nut, fruit and animal meat processing facilities due to the impact of the COVID-19 pandemic on worker illness rates and food manufacturing productivity. They were able to leverage national sequencing protocols established by the FDA Center for Food Safety and Applied Nutrition (CFSAN) to efficiently complete this project. Virginia developed the wastewater surveillance assay for SARS-CoV-2 quantification, then collaborated with FDA to determine a sequencing protocol and created a bioinformatics pipeline to collaborate with bioinformaticians to better understand the data. Overall, the data provided insight into SARS-CoV-2 viral load proportions in the sample in general as well as the representation of different variants. After the successful completion of the pilot project, DCLS will continue performing wastewater surveillance for SARS-COV-2 and will expand to other pathogens of concern. They have created their own two-step pipeline, affectionately named SPLINTER after the Teenage Mutant Ninja Turtles character, which analyzes their sequencing results using FDA’s sequencing protocols. While DCLS noted the challenges posed by a new technology, such as complex mixed sample analysis, they are thankful for the FDA pilot project and excited to see where wastewater surveillance takes them next.

Dagmara Antkiewicz, PhD, began her presentation, “Technical Challenges to Enhanced Integration of Wastewater-based Pathogen Data in Epidemiological Practice” by providing a brief background on wastewater surveillance work at the Wisconsin State Laboratory of Hygiene (WSLH). As early adopters of wastewater surveillance, WSLH began using this innovative technology in the fall of 2020, less than one year into the COVID-19 pandemic. Their program covers 50% of the state’s population with geographical coverage ranging from large cities to small municipalities. WSLH has also been performing weekly whole genome sequencing on a subset of the wastewater surveillance samples for over a year and has successfully on-boarded wastewater influenza and respiratory syncytial virus (RSV) assays. Genomic surveillance of wastewater is a relatively new approach as wastewater surveillance was typically used to quantify SARS-CoV-2 during the pandemic. Although uncommon right now, sequencing may be the new frontier for wastewater surveillance. However impressive WSLH’s wastewater program may be, Antkiewicz focused this presentation on the challenges of this testing. Noting that wastewater surveillance is here to stay, she posed the question, “How do we move forward with it?”

The biggest challenge Antkiewicz mentioned was the lack of a standard method. While APHL and the US Centers for Disease Control and Prevention (CDC) have come out with some guidance, every laboratory is running different tests based on what works best for them. Another noted challenge stemmed from the relative infancy of this testing in the US. As an epidemiological tool, there is still much to be uncovered—laboratory testing sensitivity, normalization and turnaround time all appear to be sufficient, but long-term data will tell if current approaches are adequate. Going forward, WSLH plans to continue using wastewater surveillance for SARS-CoV-2, influenza and RSV, while evolving the system to provide new sources of data to help understand how diseases move through a community.

With all the hype around the new show The Last of Us, it’s no surprise a fungus made it to the stage at ID Lab Con.Alessandro Rossi, PhD, Utah Public Health Laboratory, shared their work using wastewater surveillance to detect Candida auris.C. auris is a fungus that causes severe infections that are often resistant to medication and difficult to identify. This fungus is becoming more common and can spread in hospitals and nursing homes. Although at the start of this project, there was no documented evidence of person-to-person transmission of C. auris in Utah, Rossi and his colleagues thought it would be useful to determine whether wastewater surveillance could detect it in the environment. Leveraging infrastructure implemented during the COVID-19 pandemic, they transitioned to looking for C. auris. With just a few tweaks to a clinical culture method they were able to recover the fungus from wastewater sent from neighboring Nevada in May 2022. This result allowed them to establish an epidemiological link between wastewater isolates and healthcare facilities within the sampled sewershed. In collaboration with the Southern Nevada Water Authority, they also used community-level wastewater surveillance via PCR to follow the transfer of a C. auris– infected patient from Nevada to a city in Utah where the pathogen was not previously detected. The patient was admitted in early November and in only a few weeks, the laboratory was detecting the fungus in the wastewater. No other cases were identified, but C. auris was detected until mid-February. Efforts that began from curiosity of whether C. auris could be recovered from wastewater turned into an organism-specific proof-of-concept study on the feasibility of wastewater based epidemiology.

With SARS-CoV-2 detection under their belt, many laboratories have begun to branch out to see if wastewater surveillance technologies can be applied to other pathogens. One major component of wastewater surveillance is the use of sequencing to determine the presence of specific pathogens in the community that are not commonly looked for in other surveillance measures. In his presentation, Eric Vaughn and the DC Public Health Laboratory detailed their sequencing journey. To use laboratory bench time most efficiently, they determined the best kit for their workflow: a rapid sequencing kit. Thanks to this choice, they were able to find genes representative of sexually transmitted infections, and a host of E. coli, tuberculosis and Salmonella that wouldn’t have known otherwise. As they continued sequencing, they would move on to emerging infections just as mpox cases began to pop up around the country. By using a simple kit, they were able to make a significant discovery—identifying how much of a wastewater sample’s viral load was made up of the mpox virus. The very same library prep kit would also allow them to see seasonal viruses such as influenza A and B. Next, the DC laboratory set their sights on Salmonella. In DC, there is no mandatory reporting, meaning the laboratory is not guaranteed to catch every Salmonella case that goes to a DC hospital. However, using wastewater surveillance, they can determine a baseline of Salmonella within the city over time. By determining the prevalence of different Salmonella serotypes in the area, they can create a baseline that allows the laboratory to notice if something new or unusual shows up in the wastewater. This will enable the laboratory to communicate a potential Salmonella outbreak in the city to epidemiologists without the need for clinical data. Looking to the future, the DC Public Health Laboratory will continue to identify increased prevalence of pathogens, especially around long-term care facilities and schools.

Pushing Back the Frontiers if Science: A Review of This Year’s Literature

During this plenary session, panelists discussed the current literature on various aspects of public health. Topics ranged from respiratory viruses, mycology, next generation sequencing and, of course, wastewater surveillance, presented by Michael Pentella, PhD, D(ABMM), director of the State Hygienic Laboratory at the University of Iowa.

While wastewater surveillance is a relatively new technology in the US, there is no shortage of scientific literature on the topic—in fact, Pentella found over 1,200 papers when preparing his presentation. The first paper he covered was a systematic review that proves wastewater surveillance is a useful tool in the public health toolbox. The next articles were split into pre-analytical, analytical and post-analytical, with pre-analytical focusing on sampling approaches and the analytical part focusing on methods. But the post-analytical paper focused on ethics—an emerging conversation in wastewater surveillance that discusses the need for wastewater results to be considered as human health data. If wastewater data are treated similarly to clinical data, it will protect privacy and advance this science more efficiently as ethical concerns would likely hinder progress. While still a new technology to the US, available literature shows that wastewater surveillance has established itself as a powerful tool to identify, locate and manage outbreaks, but ethical considerations will need to underlie scientific decisions moving forward.

Responding to Emerging Infectious Disease

During this session, panelists shared their expertise on responding to various infectious diseases that have plagued the country these past few years. Kirsten St. George, PhD, Wadsworth Center, discussed how they leveraged their wastewater surveillance infrastructure developed during the pandemic to respond to a polio outbreak.

St. George began her presentation with a brief background on polio and its vaccinations. As polio had been declared eradicated in the US decades ago, vaccination efforts ceased nearly 20 years ago. Most notably, only 30% of infected individuals show symptoms, allowing this dangerous virus to silently travel though communities. In June 2022, when an immunocompetent adult presented at the hospital with fever, fatigue and stiff joints, nothing seemed to be exceptionally out of the ordinary. Samples were collected from the patient and sent to the Wadsworth Center where they were confirmed to be positive for enterovirus, which again, was nothing out of the ordinary. Everything was business as usual until the laboratory manager came to St. George with shocking news: they had received the routine VP1 sequencing results and the sample was positive for poliovirus. Her immediate response was “run them again.” Unfortunately, the sample had been evaluated three separate times with the same results. After confirmation from CDC, it was official: polio had been resurrected in New York. After some investigation, it was determined the patient had been exposed in the US. Wadsworth Center needed to track the virus to find out how long it had been present, so they turned to a newer addition in their public health arsenal: wastewater surveillance. To do this, they used legacy samples from fourteen counties near the initial case and found poliovirus had already been circulating before the initial case was identified. The laboratory continued to use wastewater data to guide epidemiologists and inform public health interventions such as vaccination efforts in low vaccination-rate regions. New York will continue to monitor the wastewater for poliovirus in the fourteen counties and areas with high travel rates since poliovirus is still endemic in other parts of the world. The laboratory has also developed a plan to scale up surveillance should another case arise. Due to the significant percentage of asymptomatic polio, wastewater surveillance and clinical data provided public health officials with the information they needed to keep this outbreak under control. It also provided the rationale to comprehensively plan for future responses.

While wastewater surveillance certainly has its challenges as a new technology in the US, attendees at APHL ID Lab Con learned it can play a key role in public health practice. With its ability to detect disease trends within a community in an unbiased way, identify the presence of diseases without clinical case data, and distinguish additional pathogens of concern, laboratories have been able to transition their pandemic-developed wastewater surveillance infrastructure into a versatile tool for a variety of post-pandemic public health needs.

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