The appropriate use of tests for infectious diseases in 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 appropriate test in the laboratory. Communication between the clinician and the 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 that will perform the test, as practice and test availability may vary among laboratories.
SPECIMEN COLLECTION AND TRANSPORT FOR BACTERIA AND FUNGI
Bacteria and fungi are living organisms that can proliferate or die during specimen transport 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 normal microbiota makes detection of a pathogen less likely (e.g., in stool culture). The time taken for transport to the laboratory should be minimized to reduce death or 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 may be required.1
If it is practical to obtain them, body fluids, tissues, and purulent material are generally preferred to specimens collected on a swab.1 The quantity of material that 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 exceptions 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 that do not survive well during transport even with transport media include Neisseria spp., Streptococcus pneumoniae, Haemophilus influenzae, Campylobacter spp., and obligate anaerobic bacteria.1–3 If these organisms are suspected, transport time to the laboratory should be minimized (<12 hours), or media should be inoculated and incubated immediately after specimen collection. Alternatively, 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 Streptococcus (S. pyogenes), which survives well for 24 hours on either dry swabs or in commercial transport media.1,4
Obligate anaerobic bacteria die in the presence of oxygen, so special transport containers are used for specimens from infections that are likely to include these organisms. Such infections include deep abscesses, fasciitis, and infections that have spread from body sites heavily colonized by anaerobic bacteria, including the oropharynx and intestine. Specimens from the oropharynx, intestine, and vagina generally should not be submitted for anaerobic culture because these body sites are normally colonized by obligate anaerobic bacteria. In addition, superficial skin ...