Purpose
Use this page as a reference for how to collect bacterial, parasitic, viral, or chemical specimens during outbreak investigations.
Instructions for collecting specimens
Label each specimen in a waterproof manner, and put the samples in sealed, waterproof containers (i.e., plastic bags). Batch the collection and send in overnight mail to arrive at the testing laboratory on a weekday during business hours unless other arrangements have been made in advance with the testing laboratory. Contact the testing laboratory before shipping, and give the testing laboratory as much advance notice as possible so that testing can begin as soon as samples arrive. When an etiology is unclear and syndrome is nonspecific, all 4 types of specimens may be appropriate to collect (stool, urine, blood, vomitus).
Bacterial
When to collect
During period of active diarrhea (preferably as soon as possible after onset of illness).
How much to collect
A fresh stool sample from 10 ill persons; samples from 10 controls also can be submitted. Two rectal swabs or swabs of fresh stool from 10 ill persons can be substituted if necessary.
Method for collection
For rectal swabs, moisten 2 swabs in an appropriate transport medium (e.g., Cary-Blair, Stuart, Amies; buffered glycerol-saline is suitable for E. coli, Salmonella, Shigella, and Y. enterocolitica but not for Campylobacter and Vibrio). Insert swab 1-1.5 inches into rectum and gently rotate. Place both swabs into the same tube deep enough that medium covers the cotton tips. Break off top portion of sticks and discard. Alternatively, swab whole stools and put them into Cary-Blair medium.
Specimen storage
Refrigerate swabs in transport media at 4°C. When possible, test within 48 hours after collection; otherwise, freeze samples at -70°C. Refrigerate whole stool, process it within 2 hours after collection. Store portion of each stool specimen frozen at less than-15°C for antigen or PCR testing.
Transportation
For refrigeration: Follow instructions for viral samples. For frozen samples: Place bagged and sealed samples on dry ice. Mail in insulated box by overnight mail.
Parasitic
When to collect
Any time after onset of illness (preferably as soon as possible).
How much to collect
A fresh stool sample from 10 ill persons; samples from 10 controls also can be submitted. To enhance detection, 3 stool specimens per patient can be collected >48 hours apart.
Method for collection
Collect bulk stool specimen, unmixed with urine, in a clean container. Place a portion of each stool sample into 10% formalin and polyvinyl alcohol preservative (PVA) at a ratio of one part stool to three parts preservative. Mix well. Important: Also save a portion of the unpreserved stool in a leakproof container without fixative for antigen or PCR testing.
Specimen storage
Store specimen in fixative at room temperature, or refrigerate unpreserved specimen at 4°C. The unpreserved stool specimen may be frozen at less than -15°C for antigen or PCR testing.
Transportation
For refrigeration: Follow instructions for viral samples. For room-temperature samples: Mail in waterproof container.
Viral
When to collect
Within 48-72 hours after onset of illness.
How much to collect
As much stool sample as possible from 10 ill persons (a minimum of 10 mL of stool from each); samples also can be obtained from 10 controls.
Method for collection
Place fresh stool specimens (liquid preferable), unmixed with urine, in clean, dry containers (e.g., urine specimen cups).
Specimen storage
Immediately refrigerate at 4°C. Store portion of each stool specimen frozen at less than -15°C for antigen or PCR testing.
Transportation
Keep refrigerated. Place bagged and sealed specimens on ice or with frozen refrigerant packs in an insulated box. Send by overnight mail. Send frozen specimens on dry ice for antigen or PCR testing.
Chemical
When to collect
Soon after onset of illness (preferably within 48 hours of exposure to contaminant).
How much to collect
A fresh urine sample (50 mL) from 10 ill persons; samples from 10 controls also can be submitted. Collect vomitus, if vomiting occurs within 12 hours of exposure. Collect 5-10 mL whole blood if a toxin/poison is suspected that is not excreted in urine.
Method for collection
Collect urine, blood, or vomitus in prescreened containers.
- Prescreened containers: the containers have been tested for the presence of the chemical of interest prior to use.
If prescreened containers are not available, submit field blanks with samples.
- Field Blanks: Unused specimen collection containers that have been brought in to the field and subjected to the same field conditions as the used containers. These containers are then tested for trace amounts of the chemical of interest.
Most analyses from blood require separation of serum from red cells. Cyanide, lead, and mercury analyses require whole blood collected in prescreened EDTA tubes. Volatile organic compounds require whole blood collected in a specially prepared gray-top tube.
Specimen storage
Immediately refrigerate at 4°C and if possible freeze urine, serum, and vomitus specimens at less than -15°C. Refrigerate whole blood for volatile organic compounds and metals at 4°C.
Transportation
Immediately refrigerate at 4°C and if possible freeze urine, serum, and vomitus specimens at less than -15°C. Refrigerate whole blood for volatile organic compounds and metals at 4°C.Place double bagged and sealed urine, serum, and vomitus specimens on dry ice. Mail in an insulated box by overnight mail. Ship whole blood in an insulated container with pre-frozen ice packs. Avoid placing specimens directly on ice packs.