Building a Foundation of Next-Generation Environmental Infectious Disease Surveillance: Cross-disciplinary and Fit-for-Purpose Tool Development for Wastewater-Based Epidemiology and Indoor Pathogen Monitoring

Abstract

Environmental surveillance for pathogens has seen considerable growth in popularity and in breadth of application since the COVID-19 pandemic. The measurement and/or quantification of pathogens in air, water, and on surfaces provides data complementary to conventional public health surveillance which serves to improve the quality and timeliness of data available about infectious disease outbreaks. This dissertation seeks to advance several areas of need of environmental surveillance broadly, including characterizing pathogen shedding rates and contextualizing their importance as well as developing analysis tools to aid in measurement interpretation. The lack of high-resolution fecal shedding data for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) limits our ability to link wastewater-based epidemiology (WBE) measurements to disease burden. In chapter 2 of this dissertation, we present longitudinal, quantitative fecal shedding data for SARS-CoV-2 RNA, as well as for the commonly used fecal indicators pepper mild mottle virus (PMMoV) RNA and crAss-like phage (crAssphage) DNA. These results provide us with a missing link needed to connect laboratory WBE results with mechanistic models, and this will aid in more accurate estimates of COVID-19 burden in sewersheds. Additionally, the PMMoV and crAssphage data are critical for evaluating their utility as fecal strength normalizing measures and for source-tracking applications.

In chapter 3 we apply the aforementioned fecal shedding data to develop a mechanistic model of WBE systems and investigate their representativeness under different conditions. In this study, we use high-quality, longitudinal data of SARS-CoV-2, PMMoV, and crAssphage fecal shedding to simulate the viral wastewater concentrations at different sewershed population sizes. The fecal indicator signals stabilize with increasing population size, and results suggest that neither PMMoV nor crAssphage normalization effectively normalizes pathogen signals when working with small population sizes. Ultimately, these simulations improve our understanding of how wastewater signals arise from populations with SARS-CoV-2 infections. Our proof-of-concept approach can be applied to other pathogens of interest with longitudinal fecal shedding data. In chapter 4, we turn our focus to indoor pathogen detection. The utility of respiratory biomarkers in WBE makes clear the need for their development in indoor systems. To address this, we evaluate the prevalence and abundance of three human commensal bacterial targets, Streptococcus salivarius, Streptococcus sanguinis, and Neisseria subflava in human respiratory samples. Overall, the three targets were highly prevalent in the samples with the least prevalent being N. subflava, which was present in 83.5% of all saliva samples tested. These results paired with associated collection data gathered from used N95 masks support their further investigation as respiratory biomarkers and provide data which can be used for the interpretation of environmental measurements. In chapter 5, we measure the three bacterial candidates in environmental samples collected from several childcare centers. Overall, the targets were relatively prevalent on surfaces with a minimum overall detection rate of 76.6% (S. sanguinis). While less prevalent in air samples (Min: 49%, S. sanguinis), they were observed periodically at reasonably high concentrations, reaching up to 1.16 x 104 copies/m3-air. These results provide useful information about sampling methodology and serve to provide context for future measurements of pathogens and statistical associations with epidemiological data. This dissertation provides needed information and theoretical context for next-generation application of WBE and indoor pathogen monitoring. The results presented here serve as a foundation for the continued advancement of environmental pathogen surveillance.