Bureau of Aquaculture & Laboratory Services

The Department of Agriculture/Bureau of Aquaculture (DoAG) maintains an on-site laboratory that processes all of the samples necessary to ensure that Connecticut shellfish are safe for consumption. To maintain compliance with the sampling requirements outlined in the National Shellfish Sanitation Program Model Ordinance (NSSP-MO), the DoAG laboratory annually processes over 5,000 water samples, 150 shellfish meat samples, 10 viral samples, 200 harmful algal bloom samples, 12 biotoxin samples, and Vibrio parahaemolyticus samples as necessary. Since shellfish are filter feeders, they can concentrate potentially pathogenic bacteria and viruses, biotoxins, and other harmful substances in their tissues; therefore, the DoAG lab uses microbiological techniques and indicator organisms to ensure shellfish are safe for human consumption. 

Fecal Coliform Testing in Seawater and Shellfish Tissue | Viral Testing | Harmful Algal Bloom and Biotoxin Testing | Vibrio parahaemolyticus Testing

Fecal Coliform Testing in Seawater and Shellfish Tissue

In the microbiology laboratory, seawater samples are analyzed for fecal coliform bacteria. Fecal coliforms have a high association with fecal matter from warm-blooded animals. Human sewage contains potentially pathogenic bacteria, viruses, and parasites, which can accumulate in the gut of filter-feeding shellfish and cause illness in people who eat them. Fecal coliforms are a sub-set of the larger coliform group of bacteria. Although coliforms are easily detected, their association with fecal contamination is questionable because some coliforms are found naturally in environmental samples (Caplenas and Kanarek 1984). Fecal coliforms are readily and inexpensively analyzed in the lab, and have been selected by the U.S. Food and Drug Administration (FDA) as an indicator organism suitable for the evaluation of the sanitary condition of seawater.

Shellfish tissue samples provide valuable information about fecal coliform levels inside the shellfish tissue to supplement water samples. Shellfish tissue samples are critical for Connecticut’s advanced relay system and for establishing the criteria for re-opening growing areas faster without compromising public safety. 


Viral Testing

Bacteriophages are viruses that infect and replicate in bacteria. Coliphages are a sub-group of bacteriophages that target Escherichia coli (E. coli), and are consequently present in sewage. Male specific coliphage (MSC) is a viral indicator used by the DoAG laboratory to monitor for the presence of viruses in shellfish. While MSC is not harmful to humans, its presence indicates the possibility for potentially pathogenic viruses, like Norovirus and Hepatitis, to also be present. MSC has been shown to be more reflective of infectious virus levels than fecal coliform bacteria (Borrego et al. 1987; Havelaar et al. 1993; Mandilara et al. 2006; McMinn et al. 2017) and have a similar or greater resistance to degradation relative to infectious viruses (Havelaar 1987; reviewed in Grabow 2001). MSC testing is particularly useful following sewage treatment bypasses or failures when large quantities of viruses may have been released and transported to shellfish growing waters. Virus survival increases with cooler temperatures; therefore, MSC testing is used more heavily in the late fall, winter, and early spring (Dancer et al. 2010; Lipp et al. 2001; reviewed in Rzezutka and Cook 2004). MSC can be used in conjunction with fecal coliform testing to reopen shellfish beds that have potentially been impacted by sewage spills/bypasses.


Harmful Algal Bloom and Biotoxin Testing

Phytoplankton are microscopic organisms that are invisible to the naked eye, except during favorable conditions when they can bloom and potentially discolor the water. A subset of phytoplankton is called harmful algal bloom (HAB) species because they are in some way “harmful” to humans (e.g. through toxin production), the environment and/or the economy. Biotoxin and harmful algal bloom testing was initiated in Connecticut in 1985 and 1997, respectively. See the “Harmful Algal Bloom” section of this website for more information about the monitoring program and types of shellfish poisoning syndromes.


Vibrio Testing

Vibrio are bacteria that are naturally-occurring and are more abundant during the summer as the water warms. Vibrio parahaemolyticus is the leading cause of seafood-associated gastroenteritis in the U.S and world (FDA 2005), and caused shellfish closures in 2012 and closures and recalls in 2013 in Darien, Norwalk, and Westport, CT. Since 2013, DoAG developed extremely effective rapid-cooling procedures, which have significantly reduced Vibrio parahaemolyticus illnesses associated with Connecticut shellfish. 

Connecticut invested in a real-time polymerized chain reaction (qPCR) testing method, which can directly detect the genetic material of Vibrio parahaemolyticus to determine if it is present in shellfish meat samples. The DoAG lab uses the FDA-developed qPCR method that analyzes the genes thermolabile hemolysin (tlh), thermostable direct hemolysin (tdh), and TDH-related hemolysin (trh). tlh is considered a universal marker for Vibrio parahaemolyticus (pathogenic and non-pathogenic) (McCarthy et al. 1999; Taniguchi et al. 1986), while tdh and trh are accepted as pathogenic markers (Honda and Iida 1993; Miyamoto et al. 1969; Shirai et al. 1990). Therefore, the DoAG lab can determine if Vibrio parahaemolyticus is present in shellfish and if it is potentially pathogenic when detected. More information about Vibrio parahaemolyticus and other Vibrio species can be found on the Center for Disease Control (CDC) website.

The DoAG added Vibrio vulnificus testing to the lab's platform in 2022. There was an increase in the number of Vibrio vulnificus wound infections in 2020, which were not related to shellfish consumption infections. The DoAG has never detected Vibrio vulnificus in CT shellfish, and no CT shellfish have ever been associated with Vibrio vulnificus infections. Additional information about Vibrio vulnificus can be found on the DoAG website.



Borrego, J.J., Morinigo, M.A., de Vicente, A., Cornax, R., Romero, P. 1987. Coliphages as an indicator of fecal pollution in water. Its relationship with indicator and pathogenic microorganisms. Water Research. 12: 1473-1480.

Caplenas, N.R. and Kanarek, M.S. 1984. Thermotolerant non-fecal source Klebsiella pneumonia: validity of the fecal coliform test in recreational waters. American Journal of Public Health. 74: 1273-1275.

Dancer, D., Rangdale, R.E., Lowther, J.A., Lees, D.N. 2010. Human Norovirus RNA Persists in Seawater under Simulated Winter Conditions but Does Not Bioaccumulate Efficiently in Pacific Oysters (Crassostrea gigas). Journal of Food Protection. 73: 2123-2127.

Food and Drug Administration (FDA). 2005. Vibrio parahaemolyticus risk assessment: quantitative risk assessment on the public health impact of pathogenic Vibrio parahaemolyticus in raw oysters. FDA, Washington, DC. http://www.fda.gov.pallas2.tcl.sc.edu/Food/ScienceResearch/ResearchAreas/RiskAssessmentSafetyAssessment /ucm050421.htm.

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Lipp, E.K, Kurz, R., Vincent, R., Rodriguez-Palacios, C., Farrah, S.R., Rose, J.B. 2001. The Effects of Seasonal Variability and Weather on Microbial Fecal Pollution and Enteric Pathogens in a Subtropical Estuary. Estuaries. 24: 266-276.

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McCarthy, S.A., DePaola, A., Cook, D.W., Kaysner, A., Hill, W.E. 1999. Evaluation of alkaline phosphatase and digoxigenin-labelled probes for detection of the thermolabile hemolysin (tlh) gene of Vibrio parahaemolyticus. Letters in Applied Microbiology. 28: 66-70. 

McMinn, B.R., Ashbolt, N.J., Korajkic, A. 2017. Bacteriophages as indicators of fecal pollution and enteric virus removal. Letters in Applied Microbiology. 65: 11-26.

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Shirai, H. Ito, H., Hirayama, T., Nakabayashi, Y., Humagai, K., Takeda, Y., Nishibuchi, M. 1990. Molecular epidemiological evidence for association of thermostable direct hemolysin (TDH) and TDH-related hemolysin of Vibrio parahaemolyticus with gastroenteritis. Infection and Immunity. 58: 3568-3573

Taniguchi, H., Hirano, H., Kubomura, S., Higashi, K., Mizuguchi, Y. 1986. Comparison of the nucleotide sequences of the genes for the thermostable direct hemolysin and the thermolabile hemolysin from Vibrio parahaemolyticus. Microbial Pathogenesis. 5: 425-432.