Some of the most common tests performed on patients are the procurement
of tissue or body fluids for direct detection of pathogenic organisms
to prove or disprove the presence of infection. The results of these
tests are critical in guiding the selection of antibiotics for targeted
therapy. The following clinical microbiology principles must be
Severity or Degree of Risk:
There is a difference between an otherwise healthy patient with
a complaint of dysuria consistent with a UTI versus a patient with
neutropenia and a high fever. The first needs a simple urinalysis with
a routine bacterial culture. The second needs a “pan” culture
(as in the prefix “pan-,” meaning “all” or “every”),
which includes a pair of blood cultures, urinalysis with culture
and sensitivity, sputum sample if a productive cough is present),
and a chest x-ray to rule out pneumonia. The second patient also
needs prompt treatment with empiric broad-spectrum antibiotics because
she is at high risk of septicemia and death.
Broad Coverage with Empiric Antibiotics:
Initiation of antibiotics that broadly cover a
newly recognized infection in a timely and appropriate manner often
is lifesaving. Selecting the wrong antibiotic, the wrong dose, an
improper route, or delaying treatment, however, can increase morbidity
Whenever feasible, specimens should be obtained and cultures
performed before antibiotics are started. However, antibiotics should
never be delayed in the face of a possible life-threatening infection,
such as meningitis. After the culture data become available, antibiotic
therapy can be narrowed or “de-escalated” to the
antibiogram of the recovered organism.
Collections of pus and infected fluids such as abscesses and
empyema must be drained if at all possible. Failure
to drain pockets of infection can compromise the outcome. The classic
example is necrotizing fasciitis, which is a surgical
emergency. Without surgery, mortality approaches 100%.
True Infection versus Contamination and Colonization:
True infection is almost always accompanied by inflammation,
usually marked by the presence of neutrophils in clinical specimens
(absent in neutropenia) and clinical signs and symptoms. The presence
of a large number of epithelial cells in a sample or the growth
of normal skin flora often signifies contamination and colonization
secondary to improper collection of specimens, although there are
Drug resistance is a serious problem in modern medicine. In
the past medicine stayed ahead of antimicrobial resistance with
the development of new antibiotics to overcome new resistance patterns.
Now, as vancomycin-resistant enterococci spread throughout the health
care system and new clones of methicillin-resistant Staphylococcus aureus become more prevalent,
antibiotic resistance is minimized only through proper antibiotic
stewardship. To this end the CDC has launched a 12-step program
for preventing antimicrobial resistance in hospitals.
|CDC Campaign to Prevent Antimicrobial Resistance in Healthcare
Settings: 12 Steps to Prevent Antimicrobial Resistance Among Hospitalized Adults|
|Step 1. Vaccinate: Give influenza/pneumococcal
vaccine to at-risk patients before discharge; get influenza vaccine annually.
|Step 2. Get the Catheters Out: Use catheters
only when essential; use the correct catheter; use proper insertion
and catheter-care protocols; remove catheters when they are no longer essential.
|Diagnose and Treat Infection Effectively|
|Step 3. Target the Pathogen: Obtain cultures;
target empiric therapy to likely pathogens and local antibiogram;
target definitive therapy to known pathogens and antimicrobial susceptibility
|Step 4. Access the Experts: Consult infectious
diseases experts about patients with serious infections.
|Use Antimicrobials Wisely|
|Step 5. Practice Antimicrobial Control: Engage
in local antimicrobial control efforts.
|Step 6. Use Local Data: Know your antibiogram;
know your patient population.
|Step 7. Treat Infection, Not Contamination: Use
proper antisepsis for blood and other cultures; culture the blood,
not the skin or catheter hub; use proper methods to obtain and process
|Step 8. Treat Infection, Not Colonization: Treat
pneumonia, not the tracheal aspirate. Treat bacteremia, not the
catheter tip or hub. Treat UTI, not the indwelling catheter.|
|Step 9. Know When to Say “No” to
Vanco: Treat infection, not contaminants or colonization. Fever
in a patient with an IV catheter is not a routine indication for
|Step 10. Stop Antimicrobial Treatment: When
infection is cured; when cultures are negative and infection is
unlikely; when infection is not diagnosed. |
|Step 11. Isolate the Pathogen: Use standard
infection control precautions. Contain infectious body fluids (follow
airborne, droplet, and contact precautions). When in doubt, consult
infection control experts.
|Step 12. Break the Chain of Contagion: Stay
home when you are sick. Keep your hands clean. Set an example.
Acid-Fast Stain (AFB Smear, Kinyoun Stain)
Clinical microbiology labs can perform a “modified” acid-fast
stain for organisms that are weakly acid-fast staining (eg, Nocardia spp.). Acid-fast bacilli (AFB)
stain red to bright pink against the light blue background (Mycobacterium tuberculosis [TB], Mycobacterium scrofulaceum, M. avium-intracellulare, and
others). These organisms have a beaded rod appearance under oil
immersion and must be cultured on specialized media. Rapid-growing
AFB include Mycobacterium abscessus, Mycobacterium
chelonae, and Mycobacterium fortuitum and
can usually be cultured in fewer than 7 d. Most other AFB (M. tuberculosis, M. avium complex, Mycobacterium kansasii, Mycobacterium marinum)
take at least 7–10 d to grow. Mycobacterium
gordonae is thought to be nonpathogenic.
Peripheral cultures are always preferred over cultures drawn
through a catheter. All bloodstream catheters become colonized over
time, which causes a high rate of false-positive cultures. To help distinguish
contamination from true bacteremia, always draw culture specimens
in pairs with at least one and preferably both specimens drawn from
- 1. Review the technique
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