TABLE 1.

The most common organisms isolated from the respiratory tract and their significance

Site of detection	Organism	Significance
Nasal cavity	Staphylococcus aureus	- colonization of the nasal cavity occurs in about 30% of children and adults - this sometimes leads to impetigo in the nasal cavity, but otherwise is a benign condition - increases the risk of indwelling venous catheter or wound infections with S aureus - a patient with colonization but no infection may require isolation if the organism is methicillin-resistant
Oropharynx/nasopharynx	Group A streptococcus	- present in up to 20% of children (1) - most commonly represents colonization, which is a benign condition - less commonly causes pharyngitis or local suppurative infections, with rheumatic fever being a rare sequelae if untreated - the relationship between Group A Streptococcus invasive disease and pharyngeal colonization is not clear
	Group C/G streptococci	- most commonly represents colonization, but can cause single cases and outbreaks of symptomatic pharyngitis - poststreptococcal glomerulonephritis has been described, but it is not clear that antibiotics decrease the incidence of this rare complication, so treatment is only recommended in the face of persistent symptoms
	Streptococcus pneumoniae	- present in a large percentage of infants and toddlers (range of 6% to 100% [3]) - persists for weeks to months - growth from the oropharynx/nasopharynx is of no significance, but about 15% of children will develop clinical infections within one month of acquiring a new strain (2) - a child who develops a viral upper respiratory tract infection while colonized may develop pneumococcal acute otitis media or sinusitis - colonization can be followed by bacteremia, with the risk being highest soon after acquisition of a new strain - bacteremia may resolve spontaneously but can lead to serious invasive disease (pneumonia, meningitis, septic arthritis)
	Nontypeable Haemophilus influenzae and Moraxella catarrhalis	- present in a large percentage of infants and toddlers - growth from the oropharynx/nasopharynx is of no significance, but a child who develops a viral upper respiratory tract infection while colonized may develop acute otitis media or sinusitis with these organisms
	Neisseria meningitidis	- present in about 5% to 15% of individuals in nonendemic areas (higher in endemic areas or during an epidemic) (4) - growth from the oropharynx/nasopharynx is of no significance, but colonization can be followed by bacteremia, which may resolve spontaneously but more commonly leads to serious invasive disease (septic shock, meningitis, septic arthritis)
	Herpes simplex virus	- can result in vesicular lesions in the oropharynx, but asymptomatic shedding is more common - shedding occurs at times of stress, and therefore is often isolated from the mouth or pharynx of intensive care patients - growth in the absence of lesions is only of significance in an immunocompromised host or in an infant less than 30 days of age
	Candida species	- normal mouth flora - results in thrush if concentration is too high - not thought to be a cause of upper respiratory tract disease except in the immunocompromised host, where laryngitis and tracheitis can occur
Lower respiratory tract	Group A streptococcus	- despite colonization of the pharynx being common, it is rare for lower respiratory tract specimens to be contaminated; therefore, isolation from the lower respiratory tract should usually be treated
	S aureus, S pneumoniae	- common contaminants from the upper respiratory tract (where they are colonizing organisms), but also common causes of lower respiratory tract disease - significance depends on the clinical picture and the results of investigations (Figure 1)
	Nontypeable H influenzae, M catarrhalis, and Enterococcus species	- common contaminants from the upper respiratory tract (where they are colonizing organisms) and rare causes of lower respiratory tract disease in children - usually require no treatment
	N meningitidis	- usually a pathogen if isolated from the lower respiratory tract, therefore, it should be treated
	Enterobacteriaceae and nonfermenting Gram-negative bacilli	- colonize the upper respiratory tract in children who have been in intensive care or have received frequent courses of antibiotics, so often contaminate lower respiratory tract specimens - however, can cause pneumonia, especially in ventilated patients - significance depends on the clinical picture and the results of investigations (Figure 1) - a colonized patient may require isolation if the organism is resistant to multiple antibiotics
	Herpes simplex virus	- rare cause of lower respiratory tract disease, even in immunocompromised hosts - if grown from lower respiratory tract specimens, usually originated in the upper respiratory tract
	Candida species	- usually not from the lower respiratory tract (might originate in the oropharynx, or in the esophagus in an immunocompromised host with fungal esophagitis) - can cause lower respiratory tract disease in immunocompromised hosts
	Aspergillus species	- can be contaminants, but can result in rapidly progressive invasive disease; therefore, lung biopsy is often done if the clinical picture fits
Any respiratory tract site	Viridans group streptococci, Nonhemolyic streptococci, coagulase-negative staphylococci, Nonpathogenic Neisseria species, Corynebacterium species, Lactobacillus species, Micrococcus species, Stomatococcus species, and Bacillus species	- part of normal upper respiratory tract flora and not thought to be causes of lower respiratory tract disease - most laboratories would not report because therapy is not indicated
	Pneumocystis jiroveci (carinii)	- usually a pathogen, but can occasionally be detected in well normal hosts
	Mycoplasma pneumoniae	- usually a pathogen, but carrier state has been described
	Pasteurella species	- can cause sinusitis, bronchitis or pneumonia but can also be part of normal flora - significance depends on clinical picture
	Mycobacterium tuberculosis, Chlamydia pneumoniae, Chlamydia trachomatis, Bordetella pertussis, adenovirus, influenza, parainfluenza virus, respiratory syncytial virus, coronavirus, human metapneumovirus and rhinovirus	- a carrier state has not been described, so identification of these organisms by any means is probably always indicative of active or recent infection, although the spectrum of disease can vary widely