Medical Microbiology

Preschool-aged children with CAP (community acquired pneumonia) frequently do not require antibiotics, as most disease is caused by viral infections.  Children with suspected CAP of bacterial origin should usually receive amoxicillin for outpatient treatment, or ampicillin or penicillin G for inpatient treatment. These agents have sufficient activity against the common bacterial pathogens causing CAP without being unnecessarily broad. Third-generation cephalosporins should be reserved for children who are unimmunized or with severe infection, or where there are high rates of penicillin-resistance among invasive pneumococcal isolates. Additional agents may be indicated in cases of suspected staphylococcal pneumonia, atypical pathogens, or influenza.

Bacterial growth in cultures of bag urine specimens are more likely to be falsely positive in young children with suspected urinary tract infection (UTI) due to contamination with perineal flora. A bag urine culture cannot therefore be used to establish the diagnosis of UTI and may lead to overtreatment. Although a negative bag culture would rule out a UTI, a positive culture requires confirmation by a more specific method, incurring substantial delay. Cultures of urine specimens obtained by catheterization or suprapubic aspiration are more specific and as such are preferred as the routine method of urine collection in non-toilet trained children. Clean-catch, the standard technique of urine collection for toilet-trained children, is a non-invasive method sometimes attempted in infants but is also associated with relatively high rates of contamination.

Infants are commonly asymptomatic carriers of C. difficile (14-63%), but clinical illness is rarely reported before 12-24 months of age. It has been hypothesized that infants lack the cellular machinery for Clostridium toxin internalization. When investigating an infant with diarrhea, alternative diagnoses should be considered even with a positive test for C. difficile. Testing should be limited to immunosuppressed infants or those with underlying intestinal conditions (e.g. Hirschsprung disease, inflammatory bowel disease) when other etiologies have been ruled out. Therefore, it is prudent to avoid routine testing in children less than 12 months, and for children 1-3 years of age, test for other causes of diarrhea first, particularly viral.

Large retrospective cohort studies have shown no difference in treatment failure rate between children with uncomplicated acute hematogenous osteomyelitis treated with prolonged IV therapy when compared with shorter IV therapy and early transition to oral, to complete the course of therapy. “Prolonged” IV therapy definitions varied and ranged from 7 days or more in one cohort to the entire treatment course of 3 to 6 weeks in another. Of note, complications with PICC lines in the prolonged treatment arms were seen at a rate between 3-15%. Consideration for use of prolonged IV therapy is in complicated disease (significant bone destruction; resistant or unusual pathogen; immunocompromised patient; sepsis or septic shock; venous thrombosis; metastatic foci or important abscess formation). Guidance as to when to consider transition to oral therapy includes a good clinical response and consideration of the following: afebrile for 48-72 hours; normalization of inflammatory markers or decrease in CRP by 50%; absence of complications or metastatic foci; and negative blood culture if culture was initially positive.

Urine cultures are the most frequently ordered microbiologic test, with the majority of specimens submitted from asymptomatic patients. Urine cultures should only be ordered if patients have symptoms localizing to the urinary tract such as acute dysuria, urgency, frequency, suprapubic or flank pain or fever without an obvious alternate source. Outside of these specific symptoms, positive cultures indicate asymptomatic bacteriuria and frequently result in antimicrobial therapy that is of no benefit and is potentially harmful. Cloudy or malodorous urine are not specific findings of urinary tract infection and should not prompt culture unless acute urinary tract symptoms are present. Delirium is not considered a symptom of cystitis in non-catheterized patients. In catheterized patients with fever or delirium, a positive urine culture may still represent asymptomatic bacteriuria unless alternate sources have been excluded. Laboratories should consider supplementing educational efforts to reduce collection of urine cultures from asymptomatic patients with analytical interventions that reduce processing of low-value specimens.

Only liquid stool specimens should be collected or processed for C. difficile detection, as a positive test in the absence of diarrhea likely represents C. difficile colonization. Diagnostic gains are minimal with repeat C. difficile nucleic acid amplification testing within 7 days of a negative test. Repeat C. difficile toxin testing by enzyme immunoassay within 7 days of a prior negative test is also of little incremental diagnostic yield but may be warranted in select cases. Test of cure in patients with recent C. difficile infection is also not recommended. Prior investigations have shown that the use of hospital information systems to restrict ordering of repeat tests for these reasons resulted in a 91% reduction in repeat testing.

All wounds are colonized with microorganisms. Cultures should not be obtained from wounds that are not clinically infected (i.e., absence of classical signs of inflammation or purulence or increasing pain). For wounds that are clinically infected, the ideal specimens for culture are deep specimens that are obtained through biopsy or deep curettage following cleansing/debridement of the wound. Laboratories should consider use of screening criteria to reject such swabs without proceeding to culture. For superficial swab specimens that are processed/cultured, interpretation of the results should be correlated with the Gram stain.

Although nucleic acid amplification testing is the modality of choice for determining the viral etiology of meningitis/encephalitis, it should not be requested routinely on all cerebrospinal fluid specimens. The routine use of these tests in patients without compatible clinical syndromes can result in unnecessary empiric antiviral treatment, additional care, and prolonged length of hospitalization for patients awaiting testing results. Additionally, routine testing may result in depletion of cerebrospinal fluid needed for other diagnostic purposes. In cases where nucleic acid testing is requested for adults, laboratories should have policies for when testing will be performed if the cerebrospinal fluid cell count and protein are normal.

Fluids and tissue specimens can usually be obtained in the controlled setting of the operating room and represent higher quality specimens than swabs. Culture of swab specimens is associated with increased false negative results, as they are inferior in recovering anaerobic bacteria, mycobacteria and fungi, and provide inadequate volumes to perform all necessary diagnostic tests. To encourage collection of fluid and/or tissue samples, consideration should be given to making swabs unavailable in the operating room without specific request.