Public Health Microbiology

The Vermont Department of Health Laboratory's Microbiology Program provides a broad range of testing services to diagnose diseases of public health importance -- including sexually transmitted diseases, HIV, tuberculosis, influenza, rabies, hepatitis B & C, foodborne illnesses.

The Microbiology Program includes the following laboratories:

The Program also provides training and consultation, and support of epidemiological investigations, public health surveillance, and other public health responses (including bioterrorism, pandemic influenza, and naturally occurring emergencies such as floods).

For more information contact Vermont Public Health Laboratory.

Enteric Bacteriology

The Enteric Bacteriology Laboratory isolates and identifies those bacteria most commonly associated with food-borne illnesses through a combination of culture, biochemicals, and enzyme immunoassay tests.  Stool specimens are accepted if submitted in a VDHL Kit #1, and all steps have been taken to follow the collection, packaging, and shipping instructions.

Specimens submitted for an Enteric Screen are tested for the following organisms:

Once pathogenic organisms have been isolated and identified, they are further discriminated by serotype using traditional typing methods such as slide and tube agglutination.  Since the organisms listed above are found on the State of Vermont Reportable Laboratory Findings list, a positive result for an enteric screen is followed-up with an interview by a VDH Public Health Nurse and/or Epidemiologist.  Salmonella, Shigella, and shiga-toxin producing E. coli isolates are further characterized by pulsed field gel electrophoresis in the molecular lab, Refer to the PulseNet section for more information.

See the Clinical Lab Services Manual for specimen submission requirements and tests available.

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Reference Bacteriology

The Reference Bacteriology laboratory serves as a referral lab for the culture and identification of bacterial isolates that are unusual or difficult to identify. Certain clinical samples are acceptable for primary isolation, but otherwise pure isolates are required for identification and serotyping.  Anaerobic testing is not performed at Health Department Laboratory.

The isolation and/or identification of the following organisms are available from the VDHL Reference Bacteriology Lab:

See the Clinical Lab Services Manual for specimen submission requirements and tests available.

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Food Bacteriology

The Food Microbiology test area analyzes food samples from outbreak situations, biothreat events and from the Department of Agriculture. Food samples are collected by sanitarians from the Department of Health Protection, Meat inspectors from the Department of Agriculture, or the state HazMat Team.

The Health Department Laboratory is a FDA Food Emergency Response Laboratory (FERN) and has the capability of analyzing food samples for the select agents of bioterrorism.

Testing services available from the Food Microbiology Lab:

For outbreak situations and biothreat events all requests must receive prior approval from Epidemiology.

For information on food safety visit our Food Safety Facts web page.

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About Influenza Routine Surveillance Testing

The Influenza Surveillance program is a year-round program that monitors the presence of influenza viruses circulating among Vermont's human population. The collection of clinical specimens for viral culture is vital, because only culture isolates can provide specific information concerning circulating strains and subtypes of influenza viruses. The information about what strains are identified in Vermont are sent to the Centers for Disease Control and Prevention(CDC). The CDC uses this information to compare current circulating influenza strains with vaccine strains, to carry out decisions regarding influenza treatment and chemoprophylaxis, and to prepare vaccine for the coming year. Virus isolates also are needed to monitor the emergence of antiviral resistance and of novel influenza A subtypes that might pose a pandemic threat.

The Laboratory's Influenza Routine Surveillance test area analyzes clinical specimens from participating sentinel influenza providers, hospital emergency departments enrolled in the Early Aberration Reporting System (EARS), long-term care facilities or other institutions, and providers with special circumstances (e.g., hospitalized patient with influenza-like-illness or a suspect H5N1 case).

The Influenza Routine Surveillance testing lab is available for Influenza A and B detection by:

About Pandemic/Avian Influenza Testing

Important: If a patient meets the criteria for a suspect Influenza A (H5) case, or if you have any questions or concerns relating to H5N1, please contact the Epidemiology Division.

Specimens for H5N1 analysis will only be accepted at the Health Department Laboratory with prior approval from the Epidemiology Division.

The following services are available from the Pandemic/Avian Influenza testing lab:

Additional Information

For more information about Influenza visit the Health Department's Influenza (Flu) Information web page.

For specimen submission requirements and tests available go to the Clinical Lab Services Manual.

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Molecular analysis is a new generation of test method carried out at the Health Department Laboratory.  Molecular testing is used as a stand alone test or in conjunction with traditional testing methods.  This new generation of testing has an increased sensitivity and specificity while decreasing the turn-around time for results.

Molecular testing is performed in the following areas:

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The Mycobacteriology Laboratory identifies Mycobacterium tuberculosis, the causative agent of tuberculosis (TB) and other clinically significant Mycobacterium species with a combination of culture, DNA probes and biochemical testing. Both pulmonary and non-pulmonary specimens are accepted for testing. The mycobacteriology lab also performs mycology testing. Yeast are identified with the Vitek system and filamentous fungi are referred to FAHC or Focus Diagnostics for identification.

TB Testing services:

Primary Drug Susceptibility Testing:

The Laboratory provides primary drug testing (isoniazid, rifampin, ethambol and pyrazinamide) for all initial M. tuberculosis complex isolates.

All M. tuberculosis complex respiratory isolates are forwarded to the designated CDC laboratory for genotyping.

For more information on TB visit the Health Department Tuberculosis web page.

See the Clinical Lab Services Manual for specimen submission requirements and tests available.

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The Parasitology laboratory identifies pathogenic and commensal intestinal parasites from stool specimens. A total of three stool specimens should be submitted in the VDHL Kit # 2 (contains SAF preservative) and collected on alternating days.  Test options include:

See the Clinical Lab Services Manual for specimen submission requirements and tests available.

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The Serology/STD Laboratory tests for a variety of infectious disease and STD agents. Our services include a nucleic acid amplified test (NAAT) for the dual detection of chlamydia and gonorrhea in urogential specimens. Serological assays for the detection of vaccine preventable viral infections, new and chronic syphilis cases, hepatitis B and C infections, and HIV screening and confirmation testing are also provided. We work with the VDH Epidemiology Program when suspect cases or outbreaks occur.

See the Clinical Lab Services Manual for specimen submission requirements and tests available.

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About PulseNet

PulseNet is a program that was developed by, and is run under the guidance of the Centers for Disease Control and Prevention (CDC).  PulseNet is a function of all fifty state public health laboratories, as well as USDA, FDA, and international public health labs.

The goals of PulseNet are to:

How PulseNet works in Vermont

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West Nile Virus

The West Nile Virus (WNV) unit serves as a referral laboratory for the post-mortem detection of West Nile Virus in birds state wide.

The Laboratory works in conjunction with the department's epidemiologists who interface with the general public to coordinate WNV testing on various birds .

Testing in Vermont is done on a seasonal basis and for surveillance purposes only. Any dead bird found by the general public in the months of June through October, should be reported to the Central Dead Bird Reporting Line at 1-800-913-1139. Currently, WNV testing services are limited to pre-determined target species. These birds include all corvids, raptors, and robins.

WNV testing encompasses brain removal form the specimen, isolation/extraction of the WNV-specific RNA from the brain tissue, and amplification/detection of the WNV-specific RNA by reverse transciption-polymerase chain reaction (RT-PCR).

For additional information, please visit our West Nile virus Surveillance website.

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The laboratory's Rabies Unit serves as a referral laboratory for the post-mortem detection of rabies virus in animals state wide.

The laboratory works in conjunction with the department's epidemiologists who interface with state veterinary services, animal control officers, game wardens, USDA wildlife services and the general public to coordinate rabies virus testing on various mammals throughout the state.  All specimens submitted for rabies testing must have prior approval by the Epidemiology Program.

Rabies testing can be requested for a variety of reasons, including surveillance, veterinary diagnosis, domestic animal exposure or human exposure.  The laboratory works intermittently with various organizations on special projects involving rabies, including the annual bait drop surveillance program performed in partnership with the USDA for over a decade. This program helps contain raccoon strain rabies virus from moving across our northern border with Canada and westward into New York state.

Rabies virus testing is performed by completing a brain dissection of the suspect animal; making direct impression smears of brain material, including the hippocampus, cerebellum, and brain stem; performing a direct fluorescent antibody (DFA) test on the impression smears, and observing the stained slides microscopically for the presence of rabies virus-specific fluorescence.

On occasion, the laboratory will collaborate with the Wadsworth Center of the New York Department of Health for more advanced molecular based strain typing of rabies virus. More information is available from the the New York Department of Health: NYS Wadsworth Center Homepage.

For additional information about rabies in Vermont, please visit our Rabies Homepage.

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Water Bacteriology

The Water Bacteriology Laboratory performs Total Coliform/E.coli bacterial testing for public water supplies, homeowners with private wells, and recreational areas.

Coliform bacteria test are commonly used to evaluate drinking water quality. The term coliform refers to a group of bacteria found in the soil and in the intestines of warm blooded animals, including humans. Although these bacteria may not be harmful themselves, their presence indicates that disease-causing agents may be present in the water.

The total coliform /E.coli test is used to simultaneously detect if any coliform bacteria and E.coli are present in your drinking sample. The presence of E.coli in drinking water is serious because these bacteria are usually associated with sewage or animal waste.

The Health Department Laboratory has the following test types available:

For more information on water safety visit our Safe Water Resource Guide.

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The Bioterrorism Test Area serves as a referral laboratory for the confirmatory identification of suspect bioterrorism agents.  Certain clinical samples are acceptable for primary isolation, but otherwise pure isolates are required for identification. 

The following agents will only be accepted if the provider has consulted with the Vermont Department of Health Laboratory Bioterrorism Testing Area and has received approval for testing:

The Vermont Department of Health Laboratory must be notified prior to submission of specimens.  Transport supplies will be provided if requested.

The Health Department Lab is a Reference Laboratory of the Laboratory Response network (LRN) and assists Sentinel Labs (hospital labs) by providing training and support in specimen collection, storage, shipment, evidence control measures, and recognition of BT agents. 

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