High-Throughput Microfluidic Quantitative PCR Platform for the Simultaneous Quantification of Pathogens, Fecal Indicator Bacteria, and Microbial Source Tracking Markers

Elizabeth R Hill; Chan Lan Chun; Kerry Hamilton; Satoshi Ishii

doi:10.1021/acsestwater.3c00169

High-Throughput Microfluidic Quantitative PCR Platform for the Simultaneous Quantification of Pathogens, Fecal Indicator Bacteria, and Microbial Source Tracking Markers

ACS ES T Water. 2023 Jul 24;3(8):2647-2658. doi: 10.1021/acsestwater.3c00169. eCollection 2023 Aug 11.

Authors

Elizabeth R Hill¹, Chan Lan Chun^{1

2

3}, Kerry Hamilton^{4

5}, Satoshi Ishii^{1

6

7}

Affiliations

¹ Water Resource Science Graduate Program, University of Minnesota, 173 McNeal Hall, 1985 Buford Avenue, St. Paul, Minnesota 55108, United States.
² Natural Resources Research Institute, University of Minnesota, 5013 Miller Trunk Highway, Duluth, Minnesota 55811, United States.
³ Department of Civil Engineering, University of Minnesota, 221 Swenson Civil Engineering, 1405 University Drive, Duluth, Minnesota 55812, United States.
⁴ School of Sustainable Engineering and the Built Environment, Arizona State University, 660 S. College Avenue, Tempe, Arizona 85281, United States.
⁵ Biodesign Center for Environmental Health Engineering, Arizona State University, 727 E. Tyler Street, Tempe, Arizona 85281, United States.
⁶ BioTechnology Institute, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States.
⁷ Department of Soil, Water, and Climate, University of Minnesota, 439 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, Minnesota 55108, United States.

PMID: 37593240
PMCID: PMC10428101 (available on 2024-07-24)
DOI: 10.1021/acsestwater.3c00169

Abstract

Contamination of water with bacterial, viral, and protozoan pathogens can cause human diseases. Both humans and nonhumans can release these pathogens through their feces. To identify the sources of fecal contamination in the water environment, microbial source tracking (MST) approaches have been developed; however, the relationship between MST markers and pathogens is still not well understood most likely due to the lack of comprehensive datasets of pathogens and MST marker concentrations. In this study, we developed a novel microfluidic quantitative PCR (MFQPCR) platform for the simultaneous quantification of 37 previously validated MST markers, two fecal indicator bacteria (FIB), 22 bacterial, 11 viral, and five protozoan pathogens, and three internal amplification/process controls in many samples. The MFQPCR chip was applied to analyze pathogen removal rates during the wastewater treatment processes. In addition, multiple host-specific MST markers, FIB, and pathogens were successfully quantified in human and avian-impacted surface waters. While the genes for pathogens were relatively infrequently detected, positive correlations were observed between some potential pathogens such as Clostridium perfringens and Mycobacterium spp., and human MST markers. The MFQPCR chips developed in this study, therefore, can provide useful information to monitor and improve water quality.