Specimen collection is important. For diagnosis of infectious disease, the rule of thumb is sample where the infection is. For lesions, the leading edge, not the center, should be sampled.

Use of swabs is discouraged. However, if a swab is used, a flocked swab is preferred because it can recover more specimen. Swabs used for molecular assays (see Nucleic Acid–Based Identification Methods for Infectious Disease) must be compatible for the specific molecular assay for which they are intended. The wrong type of swab can produce false-negative results. Wooden-shafted swabs are toxic to some viruses. Cotton-tipped swabs are toxic for some bacteria, including chlamydiae.

Blood cultures require decontamination and disinfection of the skin (eg, povidone iodine swab, allowed to dry, removed with 70% alcohol). Multiple samples, each from a different site are generally used; they are taken nearly simultaneously with fever spikes if possible. Normal flora of skin and mucous membranes that grows in only a single blood sample is usually interpreted as contamination. If a blood specimen is obtained from a central line, a peripheral blood specimen should also be obtained to help differentiate systemic bacteremia from catheter infection. Cultures from infected catheters generally turn positive more quickly and contain more organisms than simultaneously drawn peripheral blood cultures. Some fungi, particularly molds (eg, Aspergillus spp), usually cannot be cultured from blood.

The specimen must be transported rapidly, in the correct medium, and in conditions that limit growth of any potentially contaminating normal flora. For accurate quantification of the pathogen, additional pathogen growth must be prevented; specimens should be transported to the laboratory immediately or, if transport is delayed, refrigerated (in most cases).

Certain cultures have special considerations.

Anaerobic bacteria should not be cultured from sites where they are normal flora because differentiation of pathogens from normal flora may be impossible. Specimens must be shielded from air, which can be difficult. For swab specimens, anaerobic transport media are available. However, fluid specimens (eg, abscess contents) are superior to swab specimens for recovery of anaerobic bacteria. Fluid specimens should be collected with a syringe from which all air was expressed (to minimize contact of the specimen with oxygen) and sent to a laboratory in the syringe (capped without the needle) or transferred to an anaerobic transport vial.

Mycobacteria are difficult to culture. Specimens containing normal flora (eg, sputum) must first be decontaminated and concentrated. Mycobacterium tuberculosis and some other mycobacteria grow slowly. Growth of M. tuberculosis is typically faster in liquid than in solid media; routine use of automated systems with liquid media can result in growth within 2 wk vs ≥ 4 wk on solid media such as Lowenstein-Jensen agar. In addition, few organisms may be present in a specimen. Multiple specimens from the same site may help maximize yield. Specimens should be allowed to grow for 8 wk before being discarded. If an atypical mycobacterium is suspected, the laboratory should be notified.

Viruses are generally cultured from swabs and tissue specimens usually transported in media that contain antibacterial and antifungal agents. Specimens are inoculated onto tissue cultures that support the suspected virus and inhibit all other microbes. Viruses that are highly labile (eg, varicella zoster) should be inoculated onto tissue cultures within 1 h of collection. Standard tissue cultures are most sensitive. Rapid tissue cultures (shell vials) may provide more rapid results. Some common viruses cannot be detected using routine culture methods and require alternative methods for diagnosis (see Table: Diagnostic Tests for Common Viruses That Do Not Grow in Routine Viral Cultures), as for the following:

Fungi specimens obtained from nonsterile sites must be inoculated onto media containing antibacterial agents. Specimens should be allowed to grow for 3 to 4 wk before being discarded.