Cultures and Associated Labs Notes
Cultures and Associated Labs
Routine Blood Culture
Used for detection of bloodstream infections (BSIs) due to common aerobic and anaerobic bacterial and yeast pathogens.
Indications:
Sepsis syndrome: fever, chills, malaise, hypotension, poor perfusion, toxicity, tachycardia, and hyperventilation.
Evaluation of serious localized infections such as pneumonia, urinary tract infections (UTIs), and meningitis.
Methods:
Most commercially available blood culture systems recommend inoculation of blood into two broth media: one aerobic and one anaerobic.
Turnaround time:
Generally, incubation for 5–7 days.
Most true-positive blood cultures become positive within 24–48 hours after inoculation.
Special instructions:
Decontamination of the collection site is the most important factor in preventing contaminated blood cultures.
Contamination may result in a falsely positive culture.
Often two blood cultures are drawn from different locations on the patient.
If concerned for infective endocarditis, three blood cultures are sometimes drawn due to the difficulty in detecting this disease.
Expected results:
No growth.
Positive results: Bacteremia or fungemia present.
Treat the patient, not the culture result.
In true positive patients, the pathogen is typically isolated from a majority of cultures/bottles.
In false positive patients, a common contaminant is typically isolated in a single culture or bottle, whereas other cultures that are drawn during evaluation remain negative.
Negative results: Bacteremia and fungemia at the time of specimen collection are unlikely.
False-negative results may be seen in patients with prior antimicrobial therapy.
Cultures should be drawn before antibiotics given if feasible based on clinical presentation.
False-negative results may be caused by inoculation of blood culture bottles with less than the recommended volume of blood.
Aerobic Culture
Specimens may be inoculated on several types of aerobic culture plates and broth media and may include selective and enriched media.
Selective media to suppress the growth of specific types of bacteria in specimens likely to be contaminated with normal flora, like feces.
Enriched media to isolate organisms with special nutritional requirements, like chocolate agar.
Solid versus broth media:
Solid media (culture plates) are inoculated with a small amount of specimen.
Mixed cultures are recognized by differences in colony morphology.
The amount of each type of organism (and relative proportions in mixed cultures) can be estimated (e.g., rare, light, moderate, or heavy).
Broth media can be inoculated with a larger volume of specimen than agar plates.
May improve detection of infections with low concentrations of pathogens, like bacteremia.
Amount of bacteria in the specimen cannot be estimated from broth cultures.
Bacterial Cultures in Broth Media
Turbidity: cloudiness of the broth, indicating bacterial growth
Sterile (uninoculated broth) - clear media
Broth showing slight turbidity (some bacterial growth)
Broth showing significant turbidity (a lot of bacterial growth)
Broth that hasn't been agitated (shaken)
Sediment
Anaerobic Culture
Strict anaerobes only grow in 0% .
Aerotolerant organisms may tolerate 5% .
Infections associated with anaerobic pathogens include:
Surgical and traumatic wounds
Sinusitis and pararespiratory infections
Pelvic and intra-abdominal infections
Osteomyelitis
Myositis
Gangrene
Necrotic wounds
Abscesses
Special Instructions:
Successful anaerobic culture depends on maintaining strict anaerobic conditions.
Because of the anaerobic endogenous flora, specimens from the following sites should not be submitted for anaerobic culture:
Sputum or other lower respiratory specimens
Swabs from skin or mucosal surfaces
Specimens from the GI tract (including fistulae, stoma surfaces, and so on)
Superficial ulcers or eschars, including decubitus ulcers
Vaginal or cervical swabs
Urine (except suprapubic aspirate urine)
Turnaround time: Incubation for 5–7 days
Anaerobic infections are frequently polymicrobial.
Final results may require several weeks.
Expected results: No anaerobic pathogen isolated.
Limitations:
Initial isolation and aerotolerance testing may require repeated subculture.
Many anaerobic pathogens are slow growing; testing of isolates slower than most aerobics.
Patient care decisions must often be made before results of testing are available.
Sexually Transmitted Infections
NA amplification tests (NAATs) are the most sensitive for C. trachomatis, N. gonorrhoeae, and T. vaginalis.
Endocervical, vaginal, and male urethral swab specimens.
Female and male urine specimens.
Culture techniques require specialized conditions that are often not realized in clinical practice.
Sensitivity and specificity (>95%).
Turnaround time: 24–72 hours.
Expected results: Negative.
Positive results: A positive result establishes a diagnosis in patients with compatible symptoms and risk for STD.
Positive results must be interpreted with caution in patients with low risk for STD.
Repeat testing on a new specimen using a different test platform is recommended if false-positive suspected.
Negative results: Infection is unlikely.
Poor collection technique, low target levels, or other factors may cause false-negative results.
Limitations:
Accuracy depends on proper specimen collection.
Failure may result in false-negative results, cancelation of test by lab.
NAAT should not be used for test of cure (within 4 weeks of treatment), because DNA may be detectable after viable organisms are eliminated.
NAAT not intended for the evaluation of suspected sexual abuse or for other medicolegal indications.
For those patients for whom a false-positive result may have adverse psychosocial impact, the CDC recommends retesting to confirm infection.
Stool Culture
Definition: Routine stool culture should be considered for patients with acute diarrheal illness.
Fever may be present; not a prominent feature in uncomplicated enteric infection.
Special Collection and Transport Instructions:
Liquid stool is ideal; rectal swab also OK.
Sterile collection containers are not required.
The container should be free of detergent or preservative.
“O & P x 3” – Three specimens on consecutive days are recommended.
Specimens collected on toilet paper or diapers are not acceptable.
Specimens contaminated by urine are not acceptable.
Use:
All should be capable of detecting Salmonella, Shigella, and Campylobacter species by routine or special fecal cultures.
Other pathogens may be included, like Shiga toxin–producing E. coli, depending on local prevalence.
FDA-approved multiplexed NAATs are commercially available and may include relevant bacterial pathogens.
Turnaround time: Cultures are examined for growth at 24 and 48 hours.
Limitations:
Effective detection of enteric infection due to enterohemorrhagic E. coli (e.g., E. coli O157:H7), Yersinia enterocolitica, Vibrio species, Aeromonas species, C. difficile, or other bacterial pathogens requires special cultures for sensitive detection.
Diarrheal illness caused by parasitic or viral pathogens requires special test methods.
Limitations
C. difficile testing should be considered as an alternative to routine enteric pathogen testing for inpatients.
Stool culture may be negative in invasive enteric infections, like typhoid fever.
Blood cultures are recommended for primary gastrointestinal infections that progress to significant fever associated with signs of systemic infection.
Rectal swabs can collect only a small amount of feces; their use should be restricted to infants.
Streptococcus Antigen Testing
Direct detection tests for group A β-hemolytic streptococci (GABHS) / Streptococcus pyogenes are used for direct diagnosis of streptococcal pharyngitis.
Method:
Extracted antigen is detected by specific antibodies using immunologic techniques.
Sensitivity of antigen tests varies by technique and specific kit used, ranging from 60% to 95%.
Specificity of most tests exceeds 95%.
Throat culture or molecular tests have been recommended to confirm negative antigen results.
DNA / PCR Strep Testing
DNA probe test for specific S. pyogenes rRNA sequences.
Sensitivity of the assay is 88–95% with specificity of 98–99.7%.
These allow test results to stand without the need for confirmation of positive or negative tests.
PCR assay for S. pyogenes
PCR has the highest sensitivity and specificity for detection of S. pyogenes
Turnaround time: <4 hours for antigen tests, rapid molecular PCR tests; <24 hours DNA probe assay.
Throat Culture
Primarily used to detect group A β-hemolytic Streptococcus (GABHS) / Streptococcus pyogenes.
This test is used, usually in children, who present with symptoms of streptococcal pharyngitis
Throat culture often recommended to confirm negative GABHS antigen screening tests in children.
Confirmatory cultures not needed for teens/adults if the sensitivity of RAT used is >80%.
The importance of diagnosis of GABHS pharyngitis is for the prevention of nonsuppurative sequelae.
A throat culture is not recommended for test of cure; cultures may demonstrate carriage.
Special collection and transport instructions:
Affected tonsillar and posterior pharyngeal mucosa is rubbed vigorously with a swab.
Avoid contamination by the tongue, buccal, or other mucosal surface.
Cultures are incubated for 24–48 hours.
S. pyogenes isolates are predictably susceptible to penicillin
Turnaround time: Cultures are examined for 24–48 hours. Additional time may be required for heavily contaminated specimens.
Interpretation
Expected results: No growth of group A β-hemolytic Streptococcus.
Positive results: In the absence of symptoms, positive cultures may indicate carriage.
Negative results: Throat cultures may be negative if there is poor specimen collection.
Limitations
Anti-streptolysin-O titer may be required if patient has nonsuppurative GABHS complications
Urine Culture
Urine culture is used for the detection of UTI caused by common bacteria and yeast.
The risk of UTI, including complicated UTI, is increased in:
Patients with urinary tract prosthetic materials, like stents
GU tract malformations
History of GU surgery
Pregnancy
Neurologic disorders (due to urinary retention)
Diabetes mellitus
Acceptable specimens:
Low contamination rates are associated with:
Clean-catch midstream urine (complicated due to body habitus in some patients)
Straight catheterization
Suprapubic aspirates
Urine from indwelling catheters or pediatric collection bag is frequently contaminated
Urine for culture should never be taken from a catheter collection bag
For patients at risk for clinically significant UTI at lower concentrations of uropathogens, a larger amount of urine than usual may be inoculated
Resulting in a lower detection level of organisms per milliliter
Turnaround time:
Urine cultures from patients at low risk for complicated UTI should be incubated for a minimum of 16 hours
Cultures from patients at risk for complicated UTI should be incubated for a minimum of 48 hours before signing out as negative
Several additional days may be required for final identification and susceptibility testing in positive cultures
Common pitfalls:
Contamination limits the value of a significant proportion of specimens submitted.
Due to poorly collected or transported urine samples
Wound Culture
Used to identify pathogenic bacteria causing wound infections
Infections may be caused by organisms:
Introduced from the external environment
Bite and surgical and traumatic wounds
Derived from the patient’s endogenous flora
Peritonitis associated with a ruptured appendix
Wound culture should be considered when a wound shows S/Sx typical of infection
Special Collection and Transport Instructions
Specimens should be collected from the site of active infection
Collection of infected tissue or aspirate, at least 1 g, is recommended
Collection using swabs is not recommended
Collection and transport under anaerobic conditions are recommended, especially for closed wounds
Use
Specimens for bacterial wound cultures should be examined by Gram staining
Specimens from superficial wounds showing a significant numbers of epithelial cells are likely to be contaminated by endogenous flora unrelated to the infection
Turnaround time:
Cultures are incubated for 48–72 hours. Additional time is required for isolation, identification, susceptibility testing, and further characterization, as needed.
Other Considerations
Pyogenic infections are usually associated with heavy growth ( CFU/mL) of the responsible pathogen.
Certain pathogens are associated with specific types of wound infections
P. aeruginosa with penetrating foot wounds through footwear
Pasteurella multocida with dog, cat bites
These infections may require special laboratory techniques for optimal detection; alert the laboratory when suspected.