Specimen Collection and Handling for Diagnosis of Infectious Diseases

Appropriate specimen collection, transport, and processing are crucial preanalytical steps in the accurate diagnosis of infectious diseases.

Key Points

Appropriate specimen collection, transport, and processing are crucial preanalytical steps in the accurate diagnosis of infectious diseases. Guidelines for specimen handling are discussed in this chapter. General principles are reviewed first, followed by discussion of the most common types of specimens submitted to the clinical microbiology laboratory for testing.

General Principles

Timing of Specimen Collection

For optimal detection of the pathogens responsible for an infectious disease, specimens should be collected at a time when the likelihood of recovering the suspected agent is greatest. For example, the likelihood of recovering most viruses is greatest in the acute phase of the illness. Specimens for recovery of bacteria should ideally be collected before antimicrobial therapy is started.

Specimen Volume

The volume of specimen collected must be adequate for performance of the microbiological studies requested. If insufficient volume is received, the health care worker caring for the patient should be notified; either additional sample can be obtained or the physician must prioritize the requests. If a swab is used to collect the specimen, a polyester-tipped swab on a plastic shaft is acceptable for most organisms. Calcium alginate should be avoided for collection of samples for viral culture, because it could inactivate herpes simplex virus (HSV); cotton may be toxic to Neisseria gonorrhoeae; and wooden shafts should be avoided, because the wood may be toxic to Chlamydia trachomatis. Swabs are not optimal for detection of anaerobes, mycobacteria, or fungi, and they should not be used when these organisms are suspected. An actual tissue sample or fluid aspirate is always superior to a swab specimen for the recovery of pathogenic organisms.

Specimen Collection

Specimens should be obtained from the site of infection with minimal contamination from adjacent tissues and organ secretions and, with the exception of stool, should be collected in a sterile container. All specimens should be labeled with the name and identification number of the person from whom the specimen was collected, the source of the specimen, and the date and time it was collected.

Specimen Transport

After collection, specimens should be placed in a biohazard bag and transported to the laboratory as soon as possible. If a delay is unavoidable, urine, sputum and other respiratory specimens, stool, and specimens for detection of C. trachomatis or viruses should be refrigerated to prevent overgrowth of normal flora. Cerebrospinal fluid (CSF) and other body fluids, blood, and specimens collected for recovery of N. gonorrhoeae should be held at room temperature, because refrigeration adversely affects recovery of potential pathogens from these sources.

Unacceptable Specimens

Each laboratory director must establish criteria for rejecting specimens unsuitable for culture. Most clinical microbiologists agree that the following specimens should be rejected:

The following specimens should be rejected for anaerobic culture:

Universal Precautions

Universal precautions must be followed when handling all specimens. Appropriate barriers are used to prevent exposure of skin and mucous membranes to the specimen. Gloves and a lab coat must be worn at all times, and masks, goggles (or working behind a plastic shield), and impermeable gowns or aprons must be worn when there is risk of splashes or droplet formation. Optimally, all specimen containers but, at a minimum, those containing respiratory secretions and those submitted specifically for detection of mycobacteria or fungi should be opened in a biological safety cabinet. Specimens collected for virus isolation should be handled in a biological safety cabinet to prevent contamination of the cell cultures.

Referral Testing

When specimens or cultures must be shipped to a reference laboratory, they must be packaged according to dangerous goods shipping guidelines (see International Air Transport Association website). Specimens must be limited to no more than 40 mL. Cultures of bacteria and fungi should be grown on solid media in tubes. The cap of the primary container (tube or vial) should be sealed with waterproof tape and inserted into a second container, surrounded by sufficient packing material to absorb the entire volume of the culture or specimen if the primary container were to leak or break. If several primary tubes are placed in a second container, they must be either individually wrapped or separated so as to prevent contact between them and there must be secondary packaging, which must be leakproof. The second container should be capped and placed in a shipping container made of corrugated fiberboard or hard plastic. An itemized list of contents must be enclosed between the secondary and outer packaging. The secondary and outer containers should be of sufficient strength to maintain their integrity at temperature and air pressures to which they will be subjected. If a specimen must be shipped on dry ice (which is considered to be a hazardous material), it must be marked “Dry ice, frozen medical specimen.” The dry ice should be placed outside the second container with the packing material in such a way that the container does not become loose inside the outer container as the dry ice evaporates. All infectious shipping packages must be labeled with an official label containing the address and contents as well as the name and telephone number of the person responsible for the shipment.