Chapter 1

The appropriate use of tests for infectious diseases of children is critical to determining the correct diagnosis. The keys to successful testing are collection and transport of an appropriate specimen to the laboratory and correct performance of the right test in the laboratory. Communication between the clinician and laboratory staff is important in diagnostic testing, particularly if a rare or fastidious organism is suspected. General guidelines for specimen collection and transport are included in this chapter, but it is important to seek guidance from the laboratory which will be performing the test, as practice varies between laboratories.

Because bacteria and fungi are living organisms, they can proliferate or die during transportation of the specimen to the laboratory. Survival of the pathogen is required for culture, however, growth of organisms during transport is undesirable, if the quantity of bacteria is important in making a diagnosis (e.g., in urine culture) or if overgrowth by flora makes detection of a pathogen less likely (e.g., in stool culture). The time for transport to the laboratory should be minimized to reduce death or excessive growth of organisms. When transport time exceeds 1–2 hours, as in the outpatient office where transport times of up to 24 hours are sometimes required, use of specialized transport media is essential for most specimens.

If it is practical to obtain them, body fluids, tissues, and purulent material are generally preferred to specimens collected on a swab. The quantity of material, which can be collected on a swab, is small and bacteria may remain trapped on the swab, where they cannot be detected. Throat and genital specimens for bacterial culture are an exception to this rule and adequate specimens can be collected from these sites using swabs. If swabs must be submitted, submit one swab for each stain or culture ordered.

Many commercial transport systems include a swab and transport media in a tube. These systems work well for most medically important bacteria and fungi. Organisms, which do not survive well during transport (even with transport media), include Neisseria spp., Streptococcus pneumoniae, Haemophilus influenzae, Campylobacter spp., and obligate anaerobic bacteria. If these organisms are suspected, transport time to the laboratory should be minimized (<6–12 h) or media should be inoculated and incubated immediately after specimen collection or nonculture methods of detection should be used. Submission of swabs without transport media to the microbiology laboratory should be avoided, except for throat cultures for group A streptococci (Streptococcus pyogenes), which survives well for 24 hours on either dry swabs or in commercial transport media.

Obligate anaerobic bacteria are killed by the presence of oxygen, so special transport systems are used for specimens from infections that are likely to include these organisms. These include deep abscesses, fasciitis, and infections which have spread from sites heavily colonized by anaerobic bacteria, such as the oropharynx and intestine. Specimens from the oropharynx, intestine, and vagina, which are normally colonized by obligate anaerobic bacteria, generally should not be submitted for anaerobic culture, because the growth of these organisms is expected and susceptibility testing is not typically performed on anaerobic bacteria. In addition, superficial skin and wound infections are unlikely to include ...

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