Culture

Specimen collection is important. For diagnosis of infectious disease, the rule of thumb is sample where the infection is. For skin 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 Nucleic Acid–Based Identification Methods for Infectious Disease Nucleic acid–based methods detect organism-specific DNA or RNA sequences extracted from the microorganism. Sequences may or may not be amplified in vitro. Nucleic acid–based (molecular) identification... read more 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 to 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 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 species), 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 Overview of Anaerobic Bacteria Bacteria can be classified by their need and tolerance for oxygen: Facultative: Grow aerobically or anaerobically in the presence or absence of oxygen Microaerophilic: Require a low oxygen concentration... read more should not be cultured from sites where they are part of the 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 Tuberculosis (TB) Tuberculosis is a chronic, progressive mycobacterial infection, often with an asymptomatic latent period following initial infection. Tuberculosis most commonly affects the lungs. Symptoms include... read more 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 weeks vs ≥ 4 weeks 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 weeks before being discarded. M. ulcerans, which causes Buruli ulcer Cutaneous disease , requires up to 12 weeks at 32° C on Lowenstein-Jensen agar. If an atypical mycobacterium is suspected, the laboratory should be notified.

Viruses Diagnosis Viruses are among the smallest microbes, typically ranging from 0.02 to 0.3 micrometer, although several very large viruses up to 1 micrometer in length (megavirus, pandoravirus) have recently... read more are generally cultured from swabs and tissue specimens; they are 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 hour of collection. Standard tissue cultures are most sensitive. The shell vial culture technique, in which the specimen is centrifuged onto a cell monolayer within a vial, provides more rapid results (2 days vs 7 to 14 days). Some common viruses cannot be detected using routine culture methods and require alternative methods for diagnosis (see table ), 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 weeks before being deemed negative and discarded.