Microbiology Specimen Collection

Bacterial Cultures

The proper selection of specimens is extremely important for the laboratory. While not always feasible, specimens should be collected before the administration of antimicrobial agents. Specimens should be collected in a manner that minimizes contamination with indigenous flora. When multiple tests are ordered, sufficient samples or volume should be submitted in order to provide for the ideal recovery of organisms. Specimens should be collected using appropriate collection devices and should be tightly sealed to prevent leaks. Specimen containers should be bagged and delivered to the laboratory in a timely manner under the appropriate transport temperatures for optimal recovery of microbial organisms.

Tissues

Transport piece of tissue in an empty sterile container. Do not add fluid to the container. Larger pieces of tissue are ideal and maintain anaerobic conditions within the interior of the tissue.

Fluid Aspirates

Aspirate the fluid using a syringe. Remove the needle and replace it with a stopper. Alternately, collect the fluid in an empty sterile container. Do not add fluid to an ESwab as this will dilute the specimen and may compromise culture results.

Swabs

See the specimen collection swabs chart.

ESwabs are recommended for the transport and processing of specimens. Do not remove the liquid transport media in the ESwab as this is needed for processing the sample. Alternatively, samples may be collected using Amies gel transport swabs for culture, however, they may not be suitable for all tests. Dry swabs are not acceptable for bacterial culture testing.

After swabbing the site to be tested, return the swab to a plastic sleeve or insert the swab deep into the transport medium and break off the applicator just below the point where it was held or the scored mark on the shaft of the swab. On the request form, clearly indicate the site of the body the sample was collected from. Note: See below for more information on the Virology swab collection.

Non-Wound Specimens (bacterial cultures)

May include throat, nasal, endocervical, urethral, rectal, or vaginal sites.

Wound (bacterial cultures)

Remove debris around the wound by gently wiping the area with cotton soaked in sterile saline or water (do not moisten the swab with fluid containing bacteriostatic substances or antibiotics). Obtain specimen from the most active site of the wound. Take care not to swab the normal skin area.

Blood Culture

Recommended 2 sets per 24-hour period. Each set contains one aerobic and one anaerobic bottle. Ideally, add 10 mL of blood to each bottle. Note the original volume of media in the bottle before inoculating and add to a 10 mL mark above. Do not overfill bottles. The minimum volume of blood for an adult is 5 mL in each bottle. For infants, the minimum volume is 0.5 mL in one aerobic bottle. Indicate the draw site for each set on the requisition. For UW Medicine only: If unable to draw directly into a blood culture bottle, draw into a SPS tube (not ACD) and the specimen will be transferred to bottles in the UW Microbiology laboratory.

For quantitative blood cultures, blood must be drawn from the same site into a SPS tube in addition to both the aerobic and anaerobic bottles. Quantitative cultures will be rejected if the SPS tube is not collected.

For AFB blood cultures, draw the blood into an SPS tube and the HMC microbiology lab will transfer the specimen to a bottle.

For organisms that grow best on plated media (Histoplasma sp. or Bartonella sp.), the blood must be drawn into a 10 mL Wampole Isolator tube. The Isolator tube must be filled to the line on the side. If the tube is not filled completely it must, at a minimum, be half full otherwise the blood to anticoagulant ratio is not correct and the specimen will be rejected. In cases of short draws or pediatric patients, it is recommended to use a pediatric 1.5 mL Isolator tube.

Miscellaneous Devices, Hardware or Catheter Tips

Transport in sterile containers as quickly as possible. Catheter tips specimens should be the segment near the skin and tip end and must not exceed 2 inches for a quantitative culture. Longer tip segments can be cultured but will not be given a colony count. Note: Foley catheter tips are not useful for diagnosis of urinary tract infections.

Sputum

First morning specimen is best. Reduce irrelevant flora by rinsing mouth and/or cleansing tracheostomy site. Instruct patient on the need for sputum rather than saliva. Collect specimens in a sterile container. A good specimen will show purulent material. If the specimen is watery and almost clear, it is probably saliva and is therefore inadequate for culturing.

Stool

Special specimen containers are available for all testing on stool specimens. Transport in Cary-Blair for bacterial culture and Enteric Pathogen PCR testing. For parasite exams transport in EcoFix vials. For fecal leukocytes or C. difficile testing transport fresh stool in a clean container. Formed stools will be rejected for C. difficile testing. Container lids should be tightly sealed to prevent leaking into the specimen bag.

Urine

Bacterial Cultures

It is of utmost importance to follow proper cleansing procedures for obtaining a clean catch or catheterized specimen. Submit in an approved transport device (BD urine transport which contains boric acid as a preservative) or refrigerate until transport. For Viral culture, clean catch urine without preservatives is required. Morning voids have the highest titers.

Random Urine Collection

For random urines, the patient should void into a clean container. The specimen should be labeled and refrigerated until pick up. A clean catch or midstream specimen is preferred. The patient should void a small amount of urine before collecting in a clean container.