Colonization and infection of the respiratory tract: What do we know?

Distinguishing colonization from infection is an important factor in making the correct diagnosis in a wide variety of paediatric conditions. For example, in this issue of Paediatrics & Child Health, Al-Mutairi and Kirk (pages 25–30) describe the difficulty in distinguishing bacterial tracheitis from other causes of upper airway obstruction. Part of this difficulty is that growth of bacteria from the trachea can occur because of contamination of specimens by organisms that are colonizing the upper respiratory tract. Colonization implies that the patient has a sufficiently high concentration of organisms at a site that they can be detected, yet the organism is causing no signs or symptoms. This differs from contamination, where the organism was never present in the site from which it has been detected, but was introduced into the specimen from another site or from contamination in the laboratory. A carrier is a person who is colonized with an organism and may transmit the organism to other people. Colonization can persist for days to years, with resolution influenced by the immune response to the organism, competition at the site from other organisms and, sometimes, use of antimicrobials. Table 1 summarizes the most common organisms isolated from the respiratory tract and their significance. The most important factor in determining if a patient is colonized or infected with an organism is the clinical picture. For example, in the upper respiratory tract, up to 20% of children are colonized with group A streptococcus (GAS) (1), with the highest concentration of organisms being in the oropharynx. Throat cultures should only be done in children who have symptoms of GAS pharyngitis (sore throat in the absence of cough, rhinitis or laryngitis) because culturing all children with sore throats results in these carriers being treated with antibiotics that will not improve their symptoms. Antibiotics are far less successful in eradicating the organism in the carrier state than in a patient with symptomatic GAS pharyngitis (1); therefore, their use cannot be justified as a measure to reduce transmission of the organism. The most common organisms isolated from the respiratory tract and their significance - 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 - 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 - 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 - 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) - 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 - 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) - 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 - 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 - 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 - 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) - 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 - usually a pathogen if isolated from the lower respiratory tract, therefore, it should be treated - 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 - 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 - 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 - can be contaminants, but can result in rapidly progressive invasive disease; therefore, lung biopsy is often done if the clinical picture fits - 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 - usually a pathogen, but can occasionally be detected in well normal hosts - usually a pathogen, but carrier state has been described - can cause sinusitis, bronchitis or pneumonia but can also be part of normal flora - significance depends on clinical picture - 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 - 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 - 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 - 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 - 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) - 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 - 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) - 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 - 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 - 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 - 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) - 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 - usually a pathogen if isolated from the lower respiratory tract, therefore, it should be treated - 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 - 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 - 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 - can be contaminants, but can result in rapidly progressive invasive disease; therefore, lung biopsy is often done if the clinical picture fits - 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 - usually a pathogen, but can occasionally be detected in well normal hosts - usually a pathogen, but carrier state has been described - can cause sinusitis, bronchitis or pneumonia but can also be part of normal flora - significance depends on clinical picture - 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 The most common organisms isolated from the respiratory tract and their significance - 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 - 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 - 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 - 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) - 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 - 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) - 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 - 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 - 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 - 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) - 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 - usually a pathogen if isolated from the lower respiratory tract, therefore, it should be treated - 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 - 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 - 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 - can be contaminants, but can result in rapidly progressive invasive disease; therefore, lung biopsy is often done if the clinical picture fits - 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 - usually a pathogen, but can occasionally be detected in well normal hosts - usually a pathogen, but carrier state has been described - can cause sinusitis, bronchitis or pneumonia but can also be part of normal flora - significance depends on clinical picture - 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 - 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 - 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 - 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 - 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) - 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 - 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) - 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 - 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 - 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 - 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) - 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 - usually a pathogen if isolated from the lower respiratory tract, therefore, it should be treated - 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 - 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 - 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 - can be contaminants, but can result in rapidly progressive invasive disease; therefore, lung biopsy is often done if the clinical picture fits - 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 - usually a pathogen, but can occasionally be detected in well normal hosts - usually a pathogen, but carrier state has been described - can cause sinusitis, bronchitis or pneumonia but can also be part of normal flora - significance depends on clinical picture - 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 Bacterial pharyngitis in the developed world is usually due to beta-hemolytic streptococci. However, many other organisms can be present in the pharynx. Infants and toddlers commonly become colonized with Streptococcus pneumoniae, nontypeable Haemophilus influenzae, Neisseria meningitidis and/or Moraxella catarrhalis, with the highest concentration of organisms usually being in the nasopharynx (2). Colonization with these organisms occurs earlier in life if children attend a childcare centre or live in overcrowded conditions (2). Clearance of one serotype of S pneumoniae is often followed by colonization with another serotype, and it has been suggested that children may be colonized with multiple serotypes simultaneously, with the predominant type growing in cultures (3). A small percentage of children will develop invasive disease following colonization with S pneumoniae or N meningitidis. This risk appears to be highest immediately after colonization, likely because the patient has not yet produced antibodies to the organism (2). An inflamed nasopharynx (such as that which occurs with influenza or smoking) may increase the risk of invasive disease following colonization with N meningitidis (4). If a child develops an upper respiratory tract infection while colonized with S pneumoniae, H influenzae or M catarrhalis, they may develop acute otitis media or sinusitis with the colonizing strain. Antibiotics may eradicate the strain, but they may also increase the risk of the child being colonized with a different organism that is resistant to the antibiotic that was chosen (2). Approximately one-third of adults are persistently colonized with Staphylococcus aureus (5), with the highest concentration of organisms in the respiratory tract being in the nasopharynx. Colonization of the skin and the nasophaynx can occur shortly after birth. Colonization with S aureus precedes most invasive diseases caused by S aureus (osteomyelitis, cellulitis or pneumonia), but such conditions are so rare that eradication could never be justified in an attempt to prevent them. Eradication may be useful in preventing infection of indwelling venous catheters or wound infections in patients invasive for eradication are if a care is a carrier of methicillin-resistant S aureus or if an carrier has a disease and is therefore likely to in isolation if they However, the to attempt eradication is for infection because the risk of invasive disease is and can also be detected in the upper respiratory tract. respiratory respiratory and are always if detected in the respiratory tract, although they sometimes result in only signs or symptoms. is that can persist for weeks following acute infection can cause but of this and other such as and can result in asymptomatic shedding in the pharynx and which is of no significance. can be part of normal flora from mouth to with thrush the concentration of organisms in the mouth is of from the upper respiratory tract usually implies that a is with mouth is thought that the lower respiratory tract should be and, therefore, any organism detected is a However, for the of lower of organisms than and it may become that asymptomatic colonization also occurs in the lower respiratory tract. are to from the lower respiratory tract, it is always for to be with organisms that are causing colonization in the upper respiratory tract. is to from paediatric and have the and to be sufficiently such that from adults with bacterial pneumonia only in For patients with pneumonia, is no on the of by or a specimen but all are to lung is done but has been described as a useful in children with bacterial pneumonia The to if an organism is a pathogen is to a lung because contamination of such specimens is However, even that may not a diagnosis if the patient has received or if cultures are not for the correct organism (such as with all is that the is by the that the that is may not be the one with the highest concentration of However, one that to specimens from all lower respiratory is that an organism that is on a is present in concentration than one detected only on therefore, it is more likely to be a because lower respiratory tract infections are it is more likely that the pathogen has been if is growth of a single organism than if is The significance of organisms detected in the lower respiratory tract is in Table of the one the of the that the clinical picture (Figure 1) to if should be of lower respiratory tract infection in the paediatric the in the be in if a child has a lower respiratory tract infection and in of lower respiratory tract infection in the paediatric the in the be in if a child has a lower respiratory tract infection and in The difficulty in means that are with determining the significance of these in respiratory tract A more common is to for respiratory tract isolation are are isolated from persistent otitis media sinusitis bacterial tracheitis and paediatric pneumonia are and they are contaminants or colonizing but treatment should be if they are the predominant organism grown from a or lower respiratory to the significance of an organism isolated from the respiratory tract, one the site from which the organism was the of the the the other organisms isolated from the site and, most the clinical picture.

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