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ARS Home » Midwest Area » Columbia, Missouri » Cropping Systems and Water Quality Research » Research » Publications at this Location » Publication #389455
Research Project: Long-term Management of Water Resources in the Central Mississippi River Basin

Location: Cropping Systems and Water Quality Research

Title: A novel genetic marker and a PCR method for the detection of Clade II through Clade VIII cryptic Escherichia coli

Author
item ZHENG, GUOLU - Lincoln University Of Missouri
item MIRE, MARGO - Lincoln University Of Missouri
item KIM, CHYER - Virginia State University
item Baffaut, Claire

Submitted to: The 1890 Association of Research Directors Biennial Research Symposium
Publication Type: Abstract Only
Publication Acceptance Date: 10/29/2021
Publication Date: 4/2/2022
Citation: Zheng, G., Mire, M., Kim, C., Baffaut, C. 2022. A novel genetic marker and a PCR method for the detection of Clade II through Clade VIII cryptic Escherichia coli [abstract]. Association of 1890 Research Directors Biennial Research Symposium, April 2-5, 2022, Atlanta, Georgia. p. 212-213.

Interpretive Summary:

Technical Abstract: Escherichia coli (E. coli) bacteria are a common fecal indicator used to manage water quality. Recent studies suggest that “cryptic E. coli” may be living in water environments. Because current standard methods of enumerating E. coli are unable to differentiate between E. coli and cryptic E. coli, the existence of cryptic E. coli may cause false alarms of fecal pollution. In the past decade, eight clades of cryptic E. coli, namely clade I through clade VIII (C-I through C-VIII), have been reported. Much investigation has been done on the prevalence of C-I through C-V, but not of C-VI through C-VIII because they are newly identified and a rapid method for their detection is missing. The objective of this study is to investigate the prevalence of cryptic E. coli. By using the BLAST program and the publicly available draft genomes of 76 strains of cryptic E. coli, our study found that one gene, cec (cryptic E. coli), was shared by all strains of C-II through C-VIII, while cec was not found in any genome of C-I or any other bacteria. Based on the DNA sequence of cec, a classic PCR method (cec-PCR) has been developed for the rapid and accurate detection of C-II through C-VIII. With 22 strains of known cryptic E. coli, cec-PCR demonstrated 100% specificity and 100% sensitivity. Therefore, the PCR assay can be used for investigations on the prevalence of cryptic E. coli. The research is supported by USDA NIFA's 1890 CBG, award # 2020-38821-31085.