Culture is microbial growth on or in a nutritional solid or liquid medium; increased numbers of organisms simplify identification. Culture also facilitates testing of antimicrobial susceptibility.
Communication with the laboratory is essential. Although most specimens are placed on general purpose media (eg, blood or chocolate agar), some pathogens require inclusion of specific nutrients and inhibitors (see table Selective Media for Isolation of Common Bacteria Selective Media for Isolation of Common Bacteria Culture is microbial growth on or in a nutritional solid or liquid medium; increased numbers of organisms simplify identification. Culture also facilitates testing of antimicrobial susceptibility... read more ) or other special conditions for incubation (eg, a specific temperature, oxygen or carbon dioxide concentration, or duration). If one of these more fastidious pathogens is suspected or if the patient has been taking antimicrobials, the laboratory should be advised. The specimen’s source is reported so that the laboratory can differentiate pathogens from site-specific normal flora.
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 Nucleic Acid–Based Identification Methods for Infectious Disease Nucleic acid–based (molecular) identification has become commonplace in clinical settings; the resulting rapid identification allows the patient to be placed on specific antimicrobial therapy... 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 (TB) is a chronic, progressive mycobacterial infection, often with a period of latency following initial infection. TB most commonly affects the lungs. Symptoms include productive... 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 Mycobacteria other than the tubercle bacillus sometimes infect humans. These organisms (called nontuberculous mycobacteria) are commonly present in soil and water and are much less virulent... read more , 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 the smallest parasites, typically ranging from 0.02 to 0.3 micrometer, although several very large viruses up to 1 micrometer long (megavirus, pandoravirus) have recently been discovered... read more 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 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 Diagnostic Tests for Common Pathogens Diagnostic Tests for Common Pathogens Laboratory tests may identify organisms directly (eg, visually, using a microscope, growing the organism in culture) or indirectly (eg, identifying antibodies to the organism). General types... read more ), as for the following:
Enzyme immunoassay Enzyme immunoassays Immunologic tests use one of the following: Antigen to detect antibodies to a pathogen in the patient's specimen Antibody to detect an antigen of the pathogen in the patient’s specimen Specimen... read more for Epstein-Barr virus Diagnosis Infectious mononucleosis is caused by Epstein-Barr virus (EBV, human herpesvirus type 4) and is characterized by fatigue, fever, pharyngitis, and lymphadenopathy. Fatigue may persist weeks or... read more , hepatitis B virus Diagnosis Hepatitis B is caused by a DNA virus that is often parenterally transmitted. It causes typical symptoms of viral hepatitis, including anorexia, malaise, and jaundice. Fulminant hepatitis and... read more , hepatitis E virus Diagnosis Hepatitis E is caused by an enterically transmitted RNA virus and causes typical symptoms of viral hepatitis, including anorexia, malaise, and jaundice. Fulminant hepatitis and death are rare... read more , HIV Diagnosis Human immunodeficiency virus (HIV) infection results from 1 of 2 similar retroviruses (HIV-1 and HIV-2) that destroy CD4+ lymphocytes and impair cell-mediated immunity, increasing risk of certain... read more , and human T-lymphotropic virus
Serologic tests for hepatitis A virus Diagnosis Hepatitis A is caused by an enterically transmitted RNA virus that, in older children and adults, causes typical symptoms of viral hepatitis, including anorexia, malaise, and jaundice. Young... read more and hepatitis D virus Diagnosis Hepatitis D is caused by a defective RNA virus (delta agent) that can replicate only in the presence of hepatitis B virus. It occurs uncommonly as a coinfection with acute hepatitis B or as... read more
Nucleic acid–based methods Nucleic acid–based methods Susceptibility tests determine a microbe’s vulnerability to antimicrobial drugs by exposing a standardized concentration of organism to specific concentrations of antimicrobial drugs. Susceptibility... read more for HIV Diagnosis Human immunodeficiency virus (HIV) infection results from 1 of 2 similar retroviruses (HIV-1 and HIV-2) that destroy CD4+ lymphocytes and impair cell-mediated immunity, increasing risk of certain... read more , influenza Influenza Influenza is a viral respiratory infection causing fever, coryza, cough, headache, and malaise. Mortality is possible during seasonal epidemics, particularly among high-risk patients (eg, those... read more , respiratory syncytial virus (RSV) Respiratory Syncytial Virus (RSV) and Human Metapneumovirus Infections Respiratory syncytial virus and human metapneumovirus infections cause seasonal lower respiratory tract disease, particularly in infants and young children. Disease may be asymptomatic, mild... read more , SARS-CoV2 COVID-19 Coronaviruses are enveloped RNA viruses that cause respiratory illnesses of varying severity from the common cold to fatal pneumonia. Numerous coronaviruses, first discovered in domestic poultry... read more
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 discarded.