Clinical Laboratory - Microbiology

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Microbiologic Testing

Common Schemes for Identifying Infectious Agents

Many human infections are due to a relatively small number of pathogenic organisms that can infect different areas of the body. In general, bacterial infections produce acute infection with signs and symptoms of acute inflammation. They can produce elevations in the white blood cell count, particularly neutrophils. Infected areas are typically erythematous, swollen, warm, and tender. Exudates (pus) may be present. The most common bacterial organisms by site are listed below.

Infections by Body Region

Acute Meningitis

The most common bacterial organisms include:

Age of Patient Most Common Oganisms
Newborn Streptococcus group B, Escherichia coli, Listeria monocytogenes
Infants and Children Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae
Adolescents, Young Adults Neisseria meningiditis, Streptococcus pneumoniae

Acute Bacterial Pneumonias

The bacterial pathogens causing pneumonia have traditionally been rank-ordered by causation of either "community acquired" or "nosocomial" infections. However, the list and workup is essentially the same for both. Organisms can include:

  • Streptococcus pneumoniae
  • Pseudomonas aeruginosa
  • Staphylococcus aureus
  • Enterobacteriaciase, such as Klebsiella pneumonia
  • Legionella pneumophila
  • Haemophilus influenzae

Viral Pneumonias

Viral pneumonias are more difficult to diagnose because culture of viruses is complex and prolonged. The most common respiratory viral pathogens, which can be detected with direct fluorescent antigen (DFA) testing or PCR, include:

  • Influenza A and B
  • Parainfluenza 1, 2, and 3
  • Respiratory syncytial virus
  • Adenovirus
  • Human metapneumovirus

Stool Pathogens

Diarrheal illnesses may be caused by many different agents, including bacteria, viruses, and parasites. If parasites are suspected, such as those producing amebiasis, then a "stool for ova and parasites" is ordered. The most common viral pathogen is rotavirus, and this can be detected by a serologic test. If a bacterial infectious cause is suspected, particularly if there is dysentery (blood in the stool), then the panel of agents typically tested include:

  • Salmonella
  • Shigella
  • Campylobacter
  • Shiga toxin producing E. coli

Urinary Tract Infection

The vast majority of them are caused by bacterial organisms, and the most common bacteria implicated are the Enterobacteriaciae, streptococcal (enterococci), and staphylococcal (S. saprophyticus) organisms. The majority of UTIs are caused by E. coli.

Urine dipsticks can detect leukocyte esterase, which indicates the presence of neutrophils indicative of acute inflammation with UTI. The dipstick nitrite test may be positive in the presence of bacteria, particularly gram negative organisms, has a low sensitivity, but high specificity. Urine microscopic examination can be performed with unspun (uncentrifuged) urine, and >20 WBC/mL correlates with UTI.

Diagnosis in more complex cases is aided by urine culture. However, the method of urine collection has a bearing on results. A standard random voided urine sample is often contaminated by lower urethral and skin flora. The urine sample is put on a culture plate and the colonies (colony forming units, or CFUs) is counted. Thus, one criterion for UTI in women is the presence of more than 100,000 colonies/mL of a single species of bacterium, and for men 1,000/mL. Few organisms or multiple species suggest contamination. A 'clean catch' specimen is better, but not easy to obtain. Catheterization can introduce organisms into the bladder. A 'suprapubic tap" with urine removed via needle aspiration avoids contamination, but is not popular with patients.

Common bacterial organisms:

  • Proteus vulgaris or P. mirabilis
  • Providencia stuartii
  • E. coli
  • Other Enterobacteriaciae (Citrobacter, Serratia)
  • Streptococci

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