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Routine Health Monitoring and Quarantine

Sample Collection & Shipping Guidelines

Fecal Pellet Collection

Feces: Fecal pellets for PCR evaluation should be collected with clean gloves and sterile forceps and placed in individually labeled sterile tubes.

• If testing individual mice/rats, submit fecal pellets from each animal. Two or three pellets per animal are adequate.
• If multiple animals of the same microbiologic status are being evaluated, up to 10 fecal pellets can be pooled and tested as one sample. If collecting fecal pellets from multiple animals, gloves should be changed and forceps replaced between animals to prevent cross-contamination. Alternatively, forceps can be wiped clean and immersed in diluted bleach (10%) solution for 10 minutes prior to reuse.
• Fecal samples are stable and can be held at room temperature if packaged the same day for shipping or stored in the refrigerator until ready to send. For long-term storage, samples can be frozen.
• Place labeled sample tubes in a rigid box and ship overnight to our laboratory. Samples can be shipped at ambient temperature or on ice packs.

Pelt Swab Sample Collection

Pelt Swab: Using a sterile, dry flocked swab, thoroughly swab the fur against the direction of the hair coat of the animal. It is important to swab around the face, back, tail base, and belly for the best results.

• Insert the swab halfway into a labeled sterile tube, close the tube lid against the swab shaft, and pull down on the swab shaft to break the shaft. The tip end will fall into the tube, and the tube can be capped.
• Place labeled sample tubes in a rigid box and ship overnight to our laboratory. Samples can be shipped at ambient temperature or on ice packs. 

Oral Swab Collection (for PCR Testing)

Oral Swab: Using a sterile, dry flocked swab, restrain the mouse/rat with one hand so that the head is not able to move from side to side.

• Insert the oral swab starting at the corner of the mouth to encourage the animal to open its mouth.
• Slowly twirl the swab to collect the sample.
• Insert the swab halfway into a labeled sterile tube, close the tube lid against the swab shaft, and pull down on the swab shaft to break the shaft. The tip end will fall into the tube, and the tube can be capped.
• Place labeled sample tubes in a rigid box and ship overnight to our laboratory. Samples can be shipped at ambient temperature or on ice packs.
  
  

Opti-Spot® Sample Collection

1. Materials required 
   • Opti-Spot^® card (available from IDEXX BioAnalytics at no charge)
   • Lancet or needle
2.  Sample labeling
   • Label one Opti-Spot^®
   • card with a unique identification number for each sample strip.
3. Opti-Spot^® cards and strips
   • The Opti-Spot^® cards are constructed with 5 individual strips separated by perforations. The strips are easily separated along the perforation lines for individual use.
   • On each strip, a 1.0 cm circle is printed on the face of the Opti-Spot^® membrane as a guide. It is not necessary that the blood spot be centered within the circle.
4. Opti-Spot^® sample collection
   • Ante-mortem blood samples may be obtained by lancing the lateral saphenous, facial or the temporal vein. Touch the Opti-Spot^® membrane to blood drop as it forms on the surface of the skin.
   • If the blood sample is taken by cardiocentesis, quickly dispense one drop of whole blood onto the Opti-Spot^® strip.
   • The blood spot should be of sufficient size (approximately 1 cm²) to nearly fill the printed circle and be of sufficient volume to saturate the membrane. The blood spot will appear similar on both sides of the membrane.
   • Allow the blood spot to dry for a minimum of one hour.
   • Once dried, fold the protective upper tab over the blood spot and tuck under the lower tab.
5. Sample Shipment
   • It is important that the Opti-Spot^® strip is protected from moisture. Once dry, place Opti-Spot^® samples in a water-tight plastic bag containing the provided silica gel desiccant pack, and ship samples overnight by medical express.

Environmental Monitoring Sample Collection 

Exhaust Air Dust Collection Devices: In an effort to decrease the use of sentinel animals and increase the diagnostic sensitivity of monitoring rodent colonies for infectious agents, centralized whole rack level monitoring is being used as an adjunct to or a replacement for the use of soiled bedding sentinels. IDEXX BioAnalytics has a full suite of diagnostic real-time PCR assays based on the proprietary IDEXX BioAnalytics platform to provide testing for all of your environmental samples.

1. Exhaust air debris collection filters, membranes, or matrices measuring up to 6 cm x 9.5 cm can be placed lengthwise in a 30 ml conical tube. 
   1. For matrices suspended in the exhaust air stream, the upward facing side of the matrix should face the center of the collection tube.
   2. For thin filters placed perpendicular to the air stream, the side of the filter facing the airflow should face the center of the collection tube. 
2. A sample of exhaust air dust may be collected and placed directly in a 2.0 ml microcentrifuge tube for testing. 
3. Swabs of plenums, prefilters, dust, or other surfaces can be placed in a 2.0 ml microcentrifuge tube and the swab head either snapped or cut so that only the swab head is in the tube. Collect as much debris/dust as the swab will hold from the dirtiest portion of the surfaces being swabbed.
4. Cage Swab: Using a sterile, dry flocked swab, thoroughly swab the inside perimeter at the level of the bedding of the empty, soiled cage. Up to 10 cages can be swabbed using the same swab.
   • Insert the swab halfway into a labeled sterile tube, close the tube lid against the swab shaft, and pull down on the swab shaft to break the shaft. The tip end will fall into the tube and the tube can be capped.
   • Place labeled sample tubes in a rigid box and ship overnight to our laboratory. Samples can be shipped at ambient temperature or on ice packs.

Aquatics Testing

Sample Collection & Shipping Guidelines

Zebrafish and other laboratory fishes

• For submission of fish for PCR only: Please submit frozen fish with sufficient ice packs to ensure that fish remain frozen during transit. Dry ice is not required.
• For submission of fish embryos or larvae for PCR: Please euthanize embryos and submit frozen on ice or cold packs. Dry ice is not required.
• For submission of fish for histopathology only: Please either submit fish fixed in 10% buffered formalin or another formalin-based fixative such as Dietrich’s, Davidson’s, or Bouin’s fixative (please indicate). To ensure proper fixation, open up the coelom (abdomen). This can be accomplished by making a lengthwise incision through the body wall or by removing a small piece of the body wall.  Fish cannot be pooled for histopathology. Samples may be shipped at ambient temperatures by overnight courier.
• For submission of fish for both histopathology and PCR from an individual fish: Please submit fish that have been frozen flat in liquid nitrogen or at -80°C. Please package and label each fish individually (e.g., by wrapping each fish flat in aluminum foil), and then place the individually packaged and labeled fish into a larger, rigid plastic container such as a large conical tube. Samples should be shipped on dry ice by overnight courier.

Environmental samples and feeds

• For submission of detritus (biofilm or sediment) for PCR: Please collect 1 mL of detritus into a tube and submit frozen with cold packs. Dry ice is not required. Collection of detritus is recommended over environmental swabs.
• For submission of fish feces for PCR: Please collect a pool of fish feces into a microcentrifuge tube and submit frozen with cold packs. Dry ice is not required.
• For submission of live feed cultures for PCR: Please submit at least 1 mL of live feed cultures (e.g., Artemia, rotifer, or Paramecium) frozen with cold packs. Dry ice is not required.

Samples for bacterial or fungal culture

• For submission of culture swabs: Please submit culture swabs collected from skin, gills, or lesioned organs in a culturette containing a suitable transport medium, such as Amies Medium without charcoal. Swabs should be shipped with cold packs in an insulated container by express courier.
• For identification of bacterial and fungal cultures by MALDI-TOF mass spectrometry: Please submit cultures on agar plates wrapped in Parafilm^®, or submit cultures on culture swabs with a suitable transport medium, such as Amies Medium without charcoal. Swabs and plates should be shipped with cold packs in an insulated container by express courier.
• For culture of water samples: Please submit 50 mL of water in a plastic container with a tight-fitting lid that will not leak in transit. Water samples should be shipped with cold packs in an insulated container by express courier.

Microbiology Testing

Sample Collection & Shipping Guidelines

Oral Swab Collection SOP for Microbiology

Obtain a small wire shaft culture swab with Amies gel transport medium without charcoal (e.g. Becton Dickenson BBL CultureSwab Plus with Amies Gel medium without charcoal for aerobic organisms. BBL cat. # 220118; Fisher Scientific cat. # L4320118). Manually restrain the mouse or rat and swab the oral cavity. Securely place the swab in the transport medium. Send the culture swabs in transport medium by overnight courier in an insulated container on ice packs, making sure that there is insulation (e.g. bubble pack) between the ice packs and the culture swabs so the swabs do not freeze.

Anaerobic and Fastidious Bacterial Swab Collection SOP for Microbiology

Obtain a culture swab designed for the collection and transport of anaerobic and fastidious organisms (e.g Becton Dickenson BBL ESwab Collection Kit. BBL cat.# 220245; Fisher Scientific cat.#22-349-700). Collect the specimen with the swab. Aseptically unscrew and remove the cap from the transport tube. Insert the swab into the transport tube and break the swab shaft at the indicated breakpoint. Replace the cap and screw the cap on tightly. Send the culture swabs by overnight courier in an insulated container on ice packs, making sure that there is insulation (e.g. bubble pack) between the ice packs and the culture swabs so the swabs do not freeze.

Microbiome Analysis 

Sample Collection & Shipping Guidelines

Mouse/Rat Fecal Sample Collection 

Following is the procedure for collection of murine fecal samples to be used for characterization of the fecal microbiota via 16S rRNA sequencing. 

Materials: 

• Sterile toothpicks.
• Autoclaved microisolator cages (completely empty).
• Sterile 1.5 mL Eppendorf tubes.

Procedure: 

1. Pre-label Eppendorf tubes (one per mouse/rat). 
   1. Sample ID (minimum).
   2. Treatment group, if applicable.
   3. Any other metadata you would like associated with the sample.
2. Place individual animal in empty autoclaved cage (no bedding). 
3. Allow mouse/rat to defecate normally and collect the first two fecal pellets per animal into an empty 1.5 mL Eppendorf tube using a sterile toothpick. Close tube securely. Discard toothpick after each animal. 
4. Place Eppendorf tube containing fecal pellets in -80°C freezer IMMEDIATELY. 
5. Maintain samples at -80°C until ready to ship. Samples may remain at -80°C for extended periods. 
6. Ship samples overnight with sufficient dry ice (2-3 day transport time) to ensure the samples stay frozen. 

Note: We recommend collection of all samples at the same time of day, preferably in the morning, as the microbiome content varies over the course of the day. 

CellCheck

Sample Collection & Shipping Guidelines

To submit cells: 

• Send one cryovial (or other screw-top tube) of each sample with a minimum of 1x10⁶ cells/vial. 
• Cells may be in the form of a pellet or in growth media, freeze media or phosphate-buffered saline. 
• NOTE: cells are preferred, but high-quality DNA may also be submitted.

To submit tissue/solid tumor samples: 

• Send a 1.5 mL snap top or screw top tube of each sample with a minimum of 30 mg of tissue (2-3 mm size fragment or larger). 

To submit DNA: 

• DNA must be submitted as high quality extracted DNA (crude lysate extractions are not suitable for STR analysis) 
• DNA needs to be submitted with a minimum of 150 ng of DNA in a minimum volume of 15 μl. 
• Optimal concentrations submitted are preferred at >20 ng/μl. DNA concentration must be at least 10 ng/μl. 
• NOTE: Frozen cell cultures or tissue are preferred. Submission of cells allows extraction of the DNA in our facility for optimal DNA quality and test results. 
• Send DNA in a tube with screw top cap if available. If a snap top tube is used, secure the top with Parafilm™ before shipping. DNA samples can be shipped at room temperature by regular ground shipment. During hot weather, ship samples overnight with an ice pack to prevent exposure to excessive heat. 

Mycoplasma

Sample Collection and Shipping Guidelines

Collection of material should be performed aseptically to prevent contamination of samples.

If submitting cells, cell culture or liquid sample:

• Submit one cryovial containing a minimum of 1x10⁶ cells/vial of each biological or cultured cell sample. If limited amounts are available or require evaluation, call for more information. Cells may be in the form of a pellet or in growth media, freeze media or phosphate buffered saline (PBS). For liquid samples, one cryovial of each sample with 0.5 mL of sample/vial.  

If submitting antibody sample:

• Submit 0.5 mL antibody for testing. If optimal sample volume is not available, we recommend submission of at least the amount of antibody that will be injected into a single animal. While this amount is not considered optimal, our Mycoplasma assay is very sensitive, and allows detection of 1-100 genome copies.

IMPACT or h-IMPACT

Sample Collection & Shipping Guidelines

Collection of material should be performed aseptically to prevent contamination of samples. 

To submit cells, cell culture or liquid sample:

• Submit one cryovial containing a minimum of 1x10⁶ cells/vial of each biological or cultured cell sample. If limited amounts or samples are available or require evaluation, call for more information. Cells may be in the form of a pellet or in growth media, freeze media or phosphate buffered saline (PBS). For liquid samples, submit one cryovial of each sample with 0.5 mL of sample/vial. 

To submit tissue/solid tumor samples: 

• Submit a 1.5 mL snap top or screw top tube of each sample with a minimum of 30 mg of tissue (2-3 mm size fragment or larger).  

To submit antibody samples: 

• Submit 0.5 mL antibody for testing. If optimal sample volume is not available, we recommend submission of at least the amount of antibody that will be injected into a single animal. While this amount is not considered optimal, our IMPACT assays are very sensitive and allow detection of 1-100 virions. 

• Ship samples to our Kornwestheim, Germany lab (clients from outside EU: Please call for details) by express courier with sufficient ice packs or dry ice so that samples remain frozen during shipment.

Sterility Testing

Sample Collection and Shipping Guidelines

All samples should be shipped via overnight courier, packed with adequate ice packs to maintain cool temperature and adequate insulation to prevent freezing.

Direct Inoculation Method 

The optimal sample will include both tissue culture media and cellular material (if present) because some micro-organisms are intracellular or highly cell-associated. Any remaining material is held at 4°C during the course of incubation as a backup or possible confirmatory testing. 

The inoculum size per medium is 100 μL; submitters should submit a sample volume of 1000-1500 μL (1-1.5 mL) so that repeat testing can be performed if deemed advisable (no additional charge). 100 μL is provided to the IDEXX BioAnalytics PCR laboratory if Mycoplasma is requested.  

All manipulations are performed in a laminar flow hood for Sterility profiles.

Identification of Microbial Contaminants 

Identification of microbial contaminants is available. Please contact Client Support  IDEXXBioAnalytics-Europe@idexx.com  for details and pricing.