Summer 2020 Maine DMR Public Health Newsletter


Investigating Pollution Sources with Microbial Source Tracking

By Meryl Grady, DMR Water Quality Scientist

DMR closes areas of the coast to the harvest of shellfish when there are elevated fecal coliform scores present. Fecal coliform bacteria are associated with the digestive tracts of warm-blooded animals and thus can indicate contamination in the water column by feces of said warm-blooded animals. Many towns, and now more recently aquaculturists, have become interested in determining the source of pollution in order to possibly open their harvest area sooner, as opposed to waiting for the elevated fecal scores to "flush" out of the data set. The golden question has been, "Where is this poop coming from"?

One method that can assist in pollution identification, or where the poop is coming from, is microbial source tracking, also known as MST. MST compares the bacteria from the collected water sample to a "library" of bacteria from known pollution sources to identify which type(s) of bacteria is/are present in the water sample. The sample can be run for either regular PCR (presence/absence) or quantitative PCR (if present, at what level) for source-specific target DNA. Some examples of target DNA are mammal, bird, human, canine, ruminant, gull, and horse. MST can be completed at laboratories that are independent of the DMR water quality lab, such as the University of New Hampshire. The DMR water quality lab does not offer MST testing. Below are some pros and cons of microbial source tracking.


  • Can identify pollution source(s) and therefore help direct remediation efforts
  • Can eliminate possible sources that were thought to be causing the pollution
  • Can give direction as to where to expend resources (money, time, etc)
  • Can help mitigate the effects of the pollution source by providing insight


  • May not result in the identification of the "smoking gun" pollution source
  • May require multiple rounds of samples
  • Can be expensive
  • Can be time consuming, including sample collection and transportation
  • Can produce more questions

MST is only one of many options for pollution source investigation. If a shellfish commission or municipality is interested in pursuing pollution source investigation, get in touch with your area water quality scientist. Though pollution source investigation and remediation falls under the responsibility of the municipality (if there is interest), DMR is happy to assist in providing input and data where necessary.

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Klebsiella pneumoniae

By Kelsey Woodhead, Marine Resource Specialist

Last year, elevated fecal coliform scores in one shellfish growing area brought up the discussion of potential false positive results on the m-TEC agar that the DMR water quality lab uses with the membrane filtration method. Klebsiella pneumoniae is a bacterium similar to Escherichia coli in that it is a gram negative, lactose fermenting, and gas producing thermotolerant coliform (Feng et al., 1998). K. pneumoniae has been discussed as a potential false positive with the membrane filtration method since it produces yellow, countable bacterial colonies on m-TEC agar just as E. coli does.

However, as mentioned in the last newsletter, the DMR water quality lab is required to test for all fecal coliforms, not just E. coli specifically, in accordance with the National Shellfish Sanitation Program Guide for the control of Molluscan Shellfish. Since K. pneumoniae can be found in the gastrointestinal tract of 30-40% of mammals, including humans, and some strains pass fecal coliform tests, it can be considered fecal coliform positive in many cases (Bagley and Seidler, 1977). Some strains of K. pneumoniae do originate from the environment, which could cause potential false positives as DMR is monitoring for sources of recent human fecal contamination. This would mainly be an issue around coastal paper and pulp mills since K. pneumoniae can be found commonly in bark (Caplenas and Kanarek, 1984), but the lack of operating paper and pulp mills along the coast of Maine makes this source of false positives less of a concern.

Environmental strains of K. pneumoniae, while not good indicators of recent human fecal contamination, still have the potential to cause infections such as pneumonia and meningitis, as well as kidney, soft tissue, and urinary tract infections (Holt et al., 2015). There have not been any documented cases of waterborne Klebsiella causing any of these illnesses, although there have been multiple studies that suggest clinical and environmental strains of K. pneumoniae are similarly virulent (Holt et al, 2015; Struve and Krogfelt, 2004). The presence of K. pneumoniae in a water sample may result in a small number of falsely-counted colonies on m-TEC agar, but since it's potentially virulent and there are strains found in the gastrointestinal tract, colony counts including Klebsiella help to reduce the public health risk associated with bacterial contamination of shellfish.


  1. Bagley, S., & Seidler, R. (1977). Significance of Fecal Coliform-Positive Klebsiella. Applied and Environmental Microbiology, 33(5), 1141-1148. Retrieved from
  2. Caplenas, N. R., & Kanarek, M. S. (1984). Thermotolerant non-fecal source Klebsiella pneumoniae: validity of the fecal coliform test in recreational waters. American Journal of Public Health, 74(11), 1273-1275. doi: 10.2105/ajph.74.11.1273
  3. Ciebin, B. W., Brodsky, M. H., Eddington, R., Horsnell, G., Choney, A., Palmateer, G., - Shears, G. (1995). Comparative Evaluation of Modified m-FC and m-TEC Media for Membrane Filter Enumeration of Escherichia coli in Water. Applied and Environmental Microbiology, 61(11), 3940-3942. Retrieved from
  4. Dufour, A. P., Strickland, E. R., & Cabelli, V. J. (1975). Enumeration Method for Thermotolerant E. Coli. Proceedings, Ninth National Shellfish Sanitation Workshop, 79-81.
  5. Duncan, I. B. R. (1988). Waterborne Klebsiella and Human Disease. Environmental Toxicology, 3(5), 581-598. doi:
  6. Feng, P., Weagant, S. D., Grant, M. A., & Burkhardt, W. (1998). BAM 4: Enumeration of Escherichia coli and the Coliform Bacteria. In Bacteriological Analytical Manual (8th ed.). doi:
  7. 7. Holt, K., Wertheim, H., Zadoks, R., Baker, S., Whitehouse, C., & Dance, D. et al. (2015). Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proceedings Of The National Academy Of Sciences, 112(27), E3574-E3581. doi: 10.1073/pnas.1501049112
  8. Struve, C., & Krogfelt, K. A. (2004). Pathogenic potential of environmental Klebsiella pneumoniae isolates. Environmental Microbiology, 6(6), 584-590. doi: 10.1111/j.1462-2920.2004.00590.x

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Challenges Faced by Public Health Bureau During COVID 19

By Erick Schaefer, Public Health Bureau Scientist

Maine operates under the National Shellfish Sanitation Program Model Ordinance or NSSP (PDF). This program is developed by the Interstate Shellfish Sanitation Program and audited by the U.S. Food and Drug Administration. Maine must comply with the standards set forth by this program to not only protect public health but to also sell our product across state lines and internationally.

Maine's coast is divided into 47 shellfish growing areas and every 12 years each one of these growing areas goes through an evaluation process that consists of a sanitary survey. This sanitary survey looks at and evaluates all actual and potential sources of pollution that may impact the waters and, ultimately, the shellfish resource of the growing area. Waste water treatment plants, private septic systems, animal farms, streams, and licensed discharges are just a few of the potential sources evaluated along the entire coast. This is accomplished by door to door visits of all properties located within 250' of the shore.

Next, bacterial water quality is monitored through the testing of over 1200 samples sites scattered from Kittery to Calais. These sample sites are located to monitor known or potential pollution sources as well as high resource areas. Samples are taken throughout the year under all conditions following a random schedule. The data from these sites is evaluated yearly and includes analysis of how weather conditions, tides, currents, and other factors may affect the distribution of pollutants in the area. Each station also has a P90 score (weighted average) calculated using the most recent 30 samples from that station. This score is used to determine the classification of the area and how or if shellfish may be harvested or grown in that growing area. Most of these stations are located on private property and are sampled with the permission of the landowner. A minimum of six samples a year are required to stay in compliance.

During normal times DMR's Bureau of Public Health (BPH) accomplishes this efficiently and effectively. During the COVID 19 emergency declaration things have become harder and more complicated. DMR has taken the following steps to assure the safety of both its employees and the public we serve.

  1. Employees who can work from home are doing so.
  2. Employees still in DMR offices are in areas where the 6' social distancing rule can be applied.
  3. Offices have been closed to public access.
  4. Only one DMR employee is allowed per vehicle
  5. Employees wear masks in all common areas
  6. Trucks and boats are sanitized after every use.
  7. Hand sanitizer and masks have been provided to all employees.
  8. All Shoreline Survey work has been suspended.
  9. DMR is reviewing sample station locations and will try to minimize intrusion on private property.
  10. Meetings are conducted remotely.
  11. Samplers maintain the 6' social distancing rule while in the field and try to minimize any interactions with the public.

Water Quality Sampling Concerns
BPH staff are encountering more people at sampling locations due to the stay at home order issued by the Governor as well as many people leaving COVID 19 hot spot areas to shelter at seasonal homes along the coast of Maine. Most of these interactions are positive; however, some people have expressed that they do not want anyone on their property due to COVID 19 concerns. In these instances, BPH personnel record this information and report it to their supervisor. The water quality scientist who manages the area will review the information to determine if an alternate location can be found. If another sample location cannot be found the station is added to a list of all stations where access has been lost to COVID 19. When things return to normal, BPH staff will reach out to these owners to see if permission can again be given for sampling. In cases where the station is necessary for maintaining compliance every effort will be made to find a nearby location.

Shoreline Survey Concerns
As stated above each growing area must undergo a shoreline survey every twelve years to remain in compliance with the NSSP Model Ordinance. This involves a door to door survey of all properties located within 250' of the shore. To comply with the social distancing directive and to minimize contact between BPH employees and the general public all shoreline survey activities have been suspended. We are hoping that this restriction can be lifted before the year's end so that required shoreline survey work can be completed within the twelve-year time period. A pilot project conducting shoreline survey by boat will be implemented and evaluated in certain areas.

The BPH commitment during these trying times is to maintain compliance with all aspects of the NSSP Model Ordinance so Maine's shellfish industry can continue to work and harvest a safe product. No wide spread closures or shut downs are expected due to COVID 19. Rest assured BPH staff will continue to perform their essential work so that shellfish can continue to be harvested and sold.

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Rockweed: Biology 101

By Ari Leach, Area Biologist

The Bureau of Public Health not only has responsibility for the state's shellfish sanitation program, but also for several intertidal and nearshore marine resources including seaweeds, periwinkles, whelks and marine worms. Rockweed has long been an important resource in Maine and if you have ever stepped foot on a beach in Maine, chances are you have seen rockweed, whether realizing or not.


Rockweed is perhaps the most prevalent seaweed species along the Maine coast, ranging from the North-western coast of England and East coast of Greenland to the cold waters of the Northern Atlantic. Also known as Ascophyllum nodosum, rockweed is a common commercial species and is harvested for use in fertilizers, soil conditioners, animal feed and other products. Rockweed is very closely related to another important seaweed species found in Maine, wormweed (Ascophyllum nodosum, f. scorpioides). Wormweed has yellow fronds when mature and its holdfast is easily dislodged in storms and is most commonly found growing near the high tide mark where there is ample protection from breakage.

Rockweed grows from a holdfast attached to rocks and boulders and can reach lengths of up to 2 meters. The fronds of rockweed are tough and leathery with large, egg-shaped air bladders that keep the plant afloat when the tide is up. Fronds are olive-green and regenerate new fronds from the base when one of the larger fronds is damaged, either from harvest or wave action.

Rockweed fronds are either male or female, releasing either eggs or sperm into the water column for reproduction during the spring. Rockweed can very quickly become the dominant species in an area, except in zones where there is little shelter from wave action. The average lifespan of individual plants is between 10-15 years and it may take up to 5 years before a plant reaches fertile maturity.

Maine has a rich history of rockweed harvest dating back to the 1960s. Rockweed has been used as packaging material to ship lobsters and marine baitworms to other parts of the world and is used to monitor concentrations of heavy metals in seawater through aging different parts of the shoots. Rockweed can be found in everyday products in most households including lotions, soaps, toothpaste, and even ice cream. A wonderfully versatile plant with strong ties to Maine's commercial harvest industry, rockweed continues to play an important role in the lives of Maine people in more ways that we realize.

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From Herring Boats to Shellfish Sanitation and Face Masks

By James Becker - Seafood Technology Supervisor

From marine biology to shellfish sanitation, March 2020 was full of big personal changes. For over fifteen years I have been chasing Atlantic herring boats from Jonesport, Maine to the Delaware Bay as the field coordinator for the Atlantic Herring Sampling Program. On March 9, that changed, and I started my new job as the Seafood Technology Supervisor managing the Dealer Inspection Program for the Bureau of Public Health at the DMR.

James BeckerI stepped away from the world of marine biology and into a new position with an entirely different set of state and federal laws, regulations and standards, with big shoes to fill and big responsibilities to uphold. The primary objective is the supervision of the Certified Shellfish Dealer Program. Duties span from shellfish illness investigations, to seafood handling procedures, ensuring compliance with federal and state regulations, and advising on seafood safety and public health. Moreover, I supervise three veteran shellfish inspectors, who combined, inspect over 160 Maine shellfish dealers, from the Canadian border to Kittery.

My third day on the job, the first case of COVID-19 reached Maine and changed not only my job, but the entire state forever. Obviously, myself and my shellfish inspectors were concerned like all Mainers about our health and our families' wellbeing. Things were chaotic to say the least. However, not only did my program and inspectors adapt and continue forward, but so did the whole DMR and the entire state. Within no time, the bulk of DMR staff were working remotely from home and in the field to maintain "social distancing". Field personnel were required to wear masks and gloves and soldiered on conducting sampling and shellfish sanitation inspections in order to support the industry.

One question that arose among the DMR team and the industry is, were all the shellfish dealers in Maine going to be inspected on time, properly, and most importantly, safely? Now, at the end of May, most shellfish inspections that were due by the end of this month have been completed with only a few remaining. I couldn't be prouder of the DMR's three shellfish inspectors and all the certified shellfish dealers that have worked with them.

I have settled into my new job and acclimated to the unexpected curveball of the COVID-19 component. New challenges and unexpected situations continue to come my way but leave me nothing but excited and prepared for the future of the shellfish sanitation program and Maine's valuable shellfish dealers.

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