Pathogens and Microbiomes in the Built Environment

Investigating tiny things for a big impact.

Our lab combines molecular biology, metagenomics, and bioinformatic tools to investigate how built environment microbial communities impact human health. Combining fieldwork and lab-based experiments, our work not only enhances understanding of microbial threats but also helps inform strategies to protect and improve public health in diverse, real-world settings.

Active Projects

Expanding Wastewater Surveillance Targets

Methodologies for wastewater-based surveillance—monitoring wastewater for health-relevant targets to make inferences about the health of the contributing community—have rapidly improved through the surveillance of SARS-CoV-2. Wastewater is an inherently pooled sample that can provide community-scale data on disease trends at a much lower cost than widespread individual testing and while overcoming some of the biases of clinical testing. Using sequencing-based approaches, we aim to expand wastewater surveillance to several bacterial and fungal targets, including antibiotic resistance, vector-borne diseases, and causative agents of pneumonia. The utility of wastewater surveillance for these targets is challenged by issues such as potential propagation in the environment, widespread colonization without disease that obscures health implications, questionable fecal shedding upon infection, and an absence of targeted approaches that improve detection limits.

  • Characterize sewer biofilms and potential contributions to wastewater signal

  • Optimize methods for bacterial serotyping through wastewater

  • Determine the utility of hospital-scale wastewater surveillance for early detection of HAIs and as sentinels of the broader community

Widening the global reach of environmental surveillance

Methods for wastewater surveillance in the absence of centralized sanitation systems are lacking. Therefore, as wastewater surveillance has been increasingly implemented globally, many communities are deprived of this low-cost resource for health data.

  • Highlight additional challenges posed by tropical climates to wastewater surveillance

  • Locally-informed selection of surveillance targets

  • Lower limits of detection for surveillance of sewage-impacted environmental waters

Battling Healthcare-Acquired Infections (HAIs)

Annually, approximately 2 million patients suffer from healthcare-acquired infections (HAIs) in the United States, with nearly 90,000 deaths and direct costs to hospitals ranging from $28 billion to $45 billion, with a higher burden among minoritized patients. Hospital sink drain biofilms can be sources of nosocomial antibiotic-resistant infections. Under favorable conditions, bacteria can mobilize from the drain pipe to sink surfaces where transmission to patients can occur via droplet dispersion during sink use. Because of the close interactions of diverse microorganisms, biofilms can be reservoirs for antibiotic resistance bacteria and hotspots for acquisition of antibiotic resistance genes through horizontal gene transfer. In addition to antibiotic exposure, subminimum inhibitory concentrations of disinfectants can promote emergence of ARB.

  • Characterize microbial communities of hospital water systems

  • Quantify the contributions of plumbing exposures to HAIs for better resource allocation

  • Engineer resilient biofilm microbial communities to prevent colonization of drain biofilms with pathogenic taxa

Investigating climate-driven changes to microbial exposures in the urban environment

The higher temperatures and higher frequency of extreme weather events induced by climate change could have significant impacts on microbial water quality. Higher temperatures are correlated with higher bacterial growth and selection of some opportunistic pathogen biofilm organisms, including Legionella pneumophila. L. pneumophila is the leading cause of waterborne deaths in the United States, with most cases in warm, summer months. Moreover, epidemiological connections have been made between heavy precipitation events and outbreaks of Legionnaire’s disease. We still lack a mechanistic understanding for the associations of these outbreaks with weather. Elevated disease incidence may be caused by increased exposure due to elevated pathogen growth, increased virulence modulated by environmental conditions, increased transmission due to improved viability in aerosols, or increased host susceptibility. Furthermore, it is unknown whether the same weather-driven mechanisms apply to other opportunistic pathogens beyond Legionella. Characterizing the responses of drinking water microbial communities to environmental pressures will enable guidance to communities about water safety following weather events and allow the optimization of infrastructure construction, treatment design, and management that consider changing conditions due to climate change.

  • Characterize microbiomes of puddles and urban floodwaters

  • Investigate how weather patterns impact microbial communities in drinking water distribution systems

Publications

  1. Healy, H. G.,  Manchanda, S., Nelson, K. (Accepted). Implementing Universal Design for Learning Principles in a Graduate-level Environmental Engineering Course. Advances in Engineering Education.

  2. Healy, H. G.,  Ehde, A., Bartholow, A., Kantor, R., Nelson, K. (2024) Responses of Drinking Water Bulk and Biofilm Microbiota to Elevated Water Age in Bench-Scale Simulated Distribution Systems. NPJ Biofilms and Microbiomes.

  3. Dowdell, K. S.*, Healy, H. G.*, Joshi, S., Grimard-Conea, M., Pitell, S., Song, Y., ... & Rhoads, W. J. (2023). Legionella pneumophila occurrence in reduced-occupancy buildings in 11 cities during the COVID-19 pandemic. Environmental Science: Water Research & Technology.

  4. Kennedy, L. C., Miller, S. E., Kantor, R. S., Greenwald, H., Adelman, M. J., Seshan, H., ... & Nelson, K. L. (2023). Stay in the loop: lessons learned about the microbial water quality in pipe loops transitioned from conventional to direct potable reuse water. Environmental Science: Water Research & Technology, 9(5), 1436-1454.

  5. Greenwald, H., Nelson, K. L., Kantor, R., Kennedy, L. C., Ehde, A., Duan, Y., & Olivares, C. I. (2022) Is flushing necessary during building closures? A study of water quality and bacterial communities during extended reductions in building occupancy. Frontiers in Water, 135.   

  6. Miller, S., Greenwald, H., Kennedy, L.C., Kantor, R.S., …& Nelson, K. L. (2022). Microbial Water Quality through a Full-Scale Advanced Wastewater Treatment Demonstration Facility. ES&T Engineering

  7. Kantor, R. S., Greenwald, H. D., Kennedy, L. C., Hinkle, A., Harris-Lovett, S., Metzger, M., ... & Nelson, K. L. (2022). Operationalizing a routine wastewater monitoring laboratory for SARS-CoV-2. PLOS Water, 1(2), e0000007.

  8. Greenwald, H. D.*, Kennedy, L. C.*, Hinkle, A., Whitney, O. N., Fan, V. B., Crits-Christoph, A., ... & Nelson, K. L. (2021). Tools for interpretation of wastewater SARS-CoV-2 temporal and spatial trends demonstrated with data collected in the San Francisco Bay Area. Water Research X.

  9. Kantor, R. S., Nelson, K. L., Greenwald, H. D., & Kennedy, L. C. (2021). Challenges in Measuring the Recovery of SARS-CoV-2 from Wastewater. Environmental Science & Technology, 55(6), 3514-3519.

  10. Crits-Christoph, A., Kantor, R. S., Olm, M. R., Whitney, O. N., Al-Shayeb, B., Lou, Y. C., Flamholz, A., Kennedy, L.C., Greenwald, H. ... & Nelson, K. L. (2021). Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants. MBio, 12(1), e02703-20.

  11. Whitney, O. N., Kennedy, L. C., Fan, V. B., Hinkle, A., Kantor, R., Greenwald, H., ... & Nelson, K. L. (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(8), 4880-4888.