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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 considered.

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 and mortality.


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.

Source Control:

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 exceptions.

Antimicrobial Resistance:

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.

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