mSphere

The use of wastewater-based epidemiology (WBE) for early detection of virus circulation and response during the SARS-CoV-2 pandemic increased interest in and use of virus concentration protocols that are quick, scalable, and efficient. One such protocol involves sample clarification by size fractionation using either low-speed centrifugation to produce a clarified supernatant or membrane filtration to produce an initial filtrate depleted of solids, eukaryotes and bacterial present in wastewater ...

The COVID-19 pandemic has exacerbated the disparities in healthcare delivery in the US. Many communities had, and continue to have, limited access to COVID-19 testing, making it difficult to track the spread and impact of COVID-19 in early days of the outbreak. To address this issue we monitored severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA at the population-level using municipal wastewater influent from 19 cities across the state of Minnesota during the COVID-19 outbreak in S...

Candida auris is an emerging, multidrug-resistant fungal pathogen that poses a significant public health threat in healthcare settings. Despite yearly clinical cases rapidly increasing from 77 to 8,131 in the last decade, surveillance data on its distribution and prevalence remains limited. We implemented a novel assay for C. auris detection on a nationwide scale prospectively from September 2023 to March 2024, analyzing a total of 13,842 samples from 190 wastewater treatment plants across 41 U....

Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer-related deaths in the United States. Individual screening is typically done with either a clinical stool-based test or direct clinical examination such as a colonoscopy. Given the low compliance with current screening recommendations and the high morbidity and mortality observed in areas with health disparities, we consider whether population-based testing using human RNA biomarkers in wastewater might...

The COVID-19 pandemic has given rise to diverse approaches to track infections. The causative agent, SARS-CoV-2, is a fecally-shed RNA virus, and many groups have assayed wastewater for viral RNA fragments by quantitative reverse transcription polymerase chain reaction (qRT-PCR) as a proxy for COVID-19 prevalence in the community. Most groups report low levels of viral RNA that often skirt the methods theoretical limits of detection and quantitation. Here, we demonstrate the presence of SARS-CoV...

BackgroundEnteric infections are important causes of morbidity and mortality, yet clinical surveillance is limited. Wastewater-based epidemiology (WBE) has been used to study community circulation of individual enteric viruses and panels of respiratory diseases, but there is limited work studying concurrent circulation of a suite of important enteric viruses. MethodsA retrospective WBE study was carried out at two wastewater treatment plants located in California, United States. Using droplet d...

We assessed concentrations of parvovirus B19 DNA from two wastewater treatment plants in a county with a known outbreak in 2024. Wastewater viral concentrations correlated significantly with clinical cases, demonstrating wastewaters potential for tracking parvovirus B19 infections. Peaks in wastewater concentrations were aligned with the peak in hydrops fetalis diagnoses.

Wastewater sampling could be a low-cost strategy for assessing patterns of antibacterial resistance across urban populations. We aimed to quantify fluoroquinolone-resistant (FQ-R) Enterobacterales, third-generation cephalosporin-resistant (3GC-R) Enterobacterales, carbapenem-resistant Enterobacterales, and the blaCTX-M-15 and blaKPC genes in influent wastewater from 12 diverse sewersheds across metro Atlanta over 2 seasons; examine associations between culture- and digital PCR-based outcomes; an...

Enterovirus D68 (EV-D68) is a respiratory virus that can cause severe illness and is associated with acute flaccid myelitis (AFM), yet testing is uncommon and no vaccine exists. Here, we analyzed 43,876 wastewater samples collected from 147 U.S. treatment plants across 40 states between July 2023 and July 2025. We quantified EV-D68 RNA in wastewater solids to identify the center of season and the season duration of EV-D68, assessed climatic and sociodemographic factors of variation, and compared...

The rapid emergence of wastewater based surveillance has led to a wide array of SARS-CoV-2 RNA quantification methodologies being employed. Here we compare methods to store samples, inactivate viruses, capture/concentrate viruses, and extract/measure viral RNA from primary influent into wastewater facilities. We found that heat inactivation of the viruses led to a 1-3 log10 decrease compared to chemical inactivation. Freezing influent prior to concentration caused a 1-4 log10 decrease compared t...

Robust early warning of emerging viruses requires sampling populations that drive spread coupled with assays capable of detecting new viral variants or species. Untargeted viral metagenomic sequencing can, in principle, detect any virus, including completely novel ones. Composite airplane wastewater enables monitoring long-distance travelers from central collection points; however, the performance of untargeted viral metagenomic sequencing in this sample type remains unknown. In municipal wastew...

Wastewater surveillance is a powerful tool for monitoring the prevalence of infectious disease. Systems for wastewater monitoring were put in place throughout the world during the COVID-19 pandemic. These systems use viral RNA copies as the basis of estimates of COVID-19 cases in the sewershed area, thereby providing data critical for public health responses. However, the potential to measure other biomarkers in wastewater during outbreaks has not been fully explored. Here we report a novel appr...

The ability of wastewater-based surveillance (WBS) to infer viral loads in communities was showcased during the COVID-19 pandemic. Whether WBS could be used to track other microorganisms is less studies. We tested for Salmonella enterica, a common foodborne pathogen, in community wastewater and investigated whether such isolates could be linked to past or ongoing outbreaks. During June 2022, composite wastewater samples were collected from treatment facilities in two communities in central Penns...

BackgroundRespiratory disease is a major cause of morbidity and mortality; however, current surveillance for circulating respiratory viruses is passive and biased. Seasonal circulation of respiratory viruses changed dramatically during the COVID-19 pandemic. More active methods for understanding respiratory disease dynamics are needed to better inform public health response and to guide clinical decision making. Wastewater-based epidemiology has been used to understand COVID-19, influenza A, and...

Wastewater-based epidemiology is an important tool for monitoring SARS-CoV-2 and other molecular targets in populations, using wastewater as a pooled sample. We compared the sensitivity, susceptibility to inhibition, and quantification of reverse transcription quantitative PCR (RT-qPCR), microfluidic well digital RT-PCR (RT-dPCR), and droplet digital RT-PCR (RT-ddPCR) measurements of SARS-CoV-2 (N1 gene target) and Pepper Mild Mottle Virus (PMMoV) RNA in 40 wastewater RNA extracts. All three met...

Wastewater surveillance may represent a complementary approach to measure the presence and even prevalence of infectious diseases when the capacity for clinical testing is limited. Moreover, aggregate, population-wide data can help inform modeling efforts. We tested wastewater collected at a major urban treatment facility in Massachusetts and found the presence of SARS-CoV-2 at high titers in the period from March 18 - 25 using RT-qPCR. We then confirmed the identity of the PCR product by direct...

Wastewater monitoring can provide insights into respiratory disease occurrence in communities that contribute to the wastewater system. Using daily measurements of RNA of influenza A (IAV), respiratory syncytial virus (RSV), and human metapneumovirus (HMPV), as well as SARS-CoV-2 in wastewater solids from eight publicly owned treatment works in the Greater San Francisco Bay Area of California between July 2022 until early May 2023, we identify a "tripledemic" when concentrations of IAV, RSV, and...

Wastewater surveillance is an effective approach for monitoring populations of antibiotic-resistant bacteria and tracking the spread of antimicrobial resistance (AMR) across clinical and environmental settings. In this study, hospital and municipal wastewater were collected monthly for 12 months from hospital and municipal locations in the greater Pittsburgh area to quantify the presence of antibiotic-resistant bacteria and investigate their genomic diversity. After quantitative culturing on six...

Wastewater represents a composite biological sample from the entire contributing population. People infected with monkeypox excrete monkeypox virus DNA via skin lesions, saliva, feces and urine and these can enter the wastewater via toilets, sinks, and shower drains. To test whether monkeypox can be detected and monitored in wastewater during a period when publicly reported monkey cases in the region were increasing, we deployed digital PCR assays that target genomic DNA from the monkeypox virus...

ObjectiveThis study analyzed the metatranscriptome of wastewater samples from different sites with a focus of identifying antibiotic resistance genes and the bacterial community. MethodsTwenty-four wastewater samples were collected from a hospital, university sewer, and the influent and effluent of a wastewater treatment plant (WWTP). The metatranscriptome was sequenced to identify antimicrobial resistance genes (ARGs), mobile genetic elements, and bacterial community composition. ResultsMetat...