New methods enable tracking of beach contamination sources

By guest authors: Alan Steinman, Ph.D.1 and Charlyn Partridge, Ph.D.2
1Allen and Helen Hunting Research Professor and 2Associate Professor Annis Water Resources Institute, Grand Valley State University

In an email issued earlier this summer, FLOW quite appropriately noted the beauty and allure of our Great Lakes beaches, and also the potential dangers of entering these coastal waters due to possible contamination by pathogens. FLOW’s reference to the extremely high counts of E. coli on an Old Mission Peninsula beach was disconcerting, if not downright alarming. It is absolutely critical to identify, and remediate, the sources of this bacterium, so we can feel safe recreating in these highly valued waters.

It is natural to assume, as FLOW suggested, that the likely sources of E. coli were leaking septic systems, stormwater runoff, and/or confined animal feeding operations (CAFOs).  After all, these places have been identified time and time again as sources of pathogens. However, it is also possible that non-human sources can be responsible for high E. coli and fecal coliform counts. So, let’s explore the science behind this problem.

First, it is important to recognize that the E. coli being measured at our beaches is not necessarily pathogenic. Rather, its presence serves as an indicator that other, more pathogenic, groups are likely present, such as those that can cause diarrhea, including Cryptosporidium, norovirus, and Shigella. But because E. coli is a more understood target to measure, regulatory agencies and health departments in Michigan have traditionally resorted to its use[DD1] .

Second, we need to avoid assumptions about sources. The E. coli measured at Haserot Beach on Old Mission Peninsula could have come from waterfowl that defecated on the beach rather than unmaintained septic systems. Indeed, Canada geese, ring-billed gulls, and mallard ducks have all been implicated as sources of E. coli on Great Lakes beaches (Hansen et al. 2011). With the advent of microbial (also known by molecular) source tracking (MST), it is possible to differentiate between human and non-human sources of fecal contamination. In addition, some methods allow scientists to assign fecal contamination to individual animal species (Griffith et al. 2003)1.

Current MST approaches use molecular tools to determine whether host-specific fecal bacteria are present within a water sample. Some fecal bacterial groups have adapted so well to their host’s gut environment, that they are not found in guts of other species or taxa. One example of this is fecal members of the group Bacteroidales (Mieszkin et al., 2009). By targeting these bacterial groups, we can use this host-specificity to help identify the source of fecal pollution. Specific gene targets for host-specific bacteria are amplified through either quantitative polymerase chain reaction (qPCR) or droplet digital PCR (ddPCR), and then quantified to determine the amount of bacteria present within a water sample.  Based on current MST methods used throughout Michigan, markers for humans, general avian (bird), gull, pig, dog, general ruminant, and cow are commonly used for assessing the source of fecal contamination when E. coli levels are high.

The benefit of MST is that it has the ability to identify “who” is contributing to the pollution, whereas traditional culture-based methods only tell you “if” and “when” fecal contamination is present.  Given the human health implications of fecal contamination along our Great Lakes beaches, it is important to limit assumptions as to where these sources of contamination are coming from without proper testing. As we grow our knowledge base, data generation, and technical know-how of environmental science, the challenge of sharing this information with the public, resource managers, and elected officials grows as well.   Hopefully, the next time there is an E. coli outbreak on Haserot Beach (or any Great Lakes basin beach), state-of-the-art scientific methods will be employed not only to identify the “who” but also target the appropriate remedial actions to prevent or limit its occurrence in the future.

1FLOW address some of these matters in a May 2023 blog post

Literature Cited:

Griffith, J.F., Weisberg, S.B. and McGee, C.D. 2003. Evaluation of microbial source tracking methods using mixed fecal sources in aqueous test samples. Journal of Water and Health. 1(4): 141-151.

Hansen, D.L., Ishii, S., Sadowsky, M.J. and Hicks, R.E. 2011. Waterfowl abundance does not predict the dominant avian source of beach Escherichia coli. Journal of Environmental Quality. 40(6): 1924-1931.

Mieszkin, S., Yala, J. F., Joubrel, R., and Gourmelon, M. 2010. Phylogenetic analysis of Bacteroidales 16S rRNA gene sequences from human and animal effluents and assessment of ruminant faecal pollution by real‐time PCR. Journal of Applied Microbiology. 108(3): 974-984.

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