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Pathogens are viruses, bacteria, algae, and protozoans that cause diseases in humans, plants, and other animals. Pathogens that may be found in marine waters in the United States include those causing gastroenteritis, salmonellosis, and hepatitis A. Pathogens can enter marine waters in untreated or partially treated human sewage and in wild and domestic animal waste. Humans may encounter the pathogens through direct contact with or ingestion of contaminated water or by eating raw  or partially cooked bivalve shellfish harvested from contaminated waters.

Pathogen loadings to the Peconic Estuary System are of concern because of the potential health risks associated with consumption of contaminated shellfish, health risks associated with direct water contact and/or ingestion, and the economic losses associated with the closure of shellfish beds and beaches.

 In order to protect shellfish consumers and beach goers from the human health risks associated with  pathogens, the State of New York regularly monitors water quality in the marine waters of New York State and the Suffolk County Department of Health Services (SCDHS) monitors for pathogen indicators at public beaches. When water quality parameters fail to meet the established human health criteria, beaches and shellfish beds are closed.