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Municipal Guide To Clean Water: Conducting Sanitary Surveys to Improve Coastal Water Quality

Background on Microorganisms and Fecal Indicator Bacteria

Microorganisms (microbes) are ubiquitous and live almost everywhere on earth. They are almost always microscopic (invisible to the naked eye). Of the many different types

of microorganisms, some can cause human illness or even death (Table 1). Microbe populations can change quickly, growing or dying rapidly depending on environmental conditions.6

What are the indicators that harmful pathogens could be present?

Microbes are found in the digestive tracts of warm- blooded animals, and bacteria associated with human and animal waste—such as Enterococci, total coliform, and E.coli or fecal coliform—indicate the possible pres- ence of other, disease-causing pathogens that can cause illness, disease, or even death in humans. Because most pathogens are difficult to detect and expensive to monitor, these “indicator bacteria” are used to measure water qual- ity. While reliance on indicator bacteria comes with some limitations,7 this strategy is currently the best available for comprehensive public health monitoring programs.

Bacterial pathogens are the leading cause of impair- ment to rivers, streams, and coastal waters.1 Pathogens or disease-causing organisms commonly associated with water-related illnesses include bacteria, viruses, and pro- tozoans that live and travel in water. Of greatest concern are pathogens that are released into the environment in large numbers, are highly infectious to humans in small doses, can multiply outside of their host (under favorable conditions), can survive in the environment for long peri- ods of time, and are highly resistant to water treatment.7 Pathways of exposure to pathogens in recreational waters include ingestion, inhalation, and dermal contact leading to ear, eye, skin, and respiratory illness. Studies have found a strong correlation between human sources of contamina- tion and gastrointestinal (GI) illness.8, 9 Humans also are ex- posed to dangerous pathogens when they eat contaminated shellfish (clams, mussels). Shellfish are filter feeders: they take in large quantities of seawater, and as a result they can easily become contaminated by polluted water.

Studies conducted over the past two decades have shown that Enterococci survive longer (0-45 days)10 in salt water compared to other fecal indicator bacteria, and Enterococci densities in recreational marine waters are most strongly correlated with GI illness. In other words, as the level of


Description/Common Sympto


Source of pathogen


Acute diarrhea

Dogs, cats, birds, wild animal feces


Vomiting, diarrhea

Cattle feces


Acute respiratory illness

Aquatic environments

Leptospirosis (Weil’s disease)

Fever, jaundice

Urine of livestock, dogs, rodents, wild animals

Salmonella typhi (Typhoid fever)

High fever, diarrhea, ulceration of small intestine

Domestic and wild animal feces



Domestic and wild animal feces, human feces


Bacillary dysentery

Infected humans


Acute diarrhea

Sediments, shellfish, asymptomatic human carriers



Animal feces, pork, unpasteurized milk

Table 1. Water-related (waterborne) diseases, associated symptoms and sources.

Human and non-human animals can transmit diseases to humans.7, 14, 15

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