Normal Respiratory Microbiota in Health and Disease
Serious respiratory infections are a risk for all hospitalized patients, but are particularly common in the intensive care unit (ICU). Patients admitted to the (ICU) are at a greater risk of developing nosocomial pneumonia than patients admitted to other wards in the hospital, and ventilated patients are at a 3-10 times increased risk of developing nosocomial pneumonia compared with those who are not ventilated. This is in part because many ICU patients require ventilator support to help with obstructed pathways or other conditions that prevent them from breathing on their own. Ventilation involves placing an endotracheal tube down the windpipe to deliver oxygen directly to the lungs, which is a life-saving procedure but not one without risks. For many reasons, mechanically ventilated patients are especially susceptible to developing pneumonia. In fact, pneumonia is the second most common nosocomial infection affecting critically ill patients in the ICU.
Ventilator-Associated Pneumonia and The Role of Normal Respiratory Flora
Patients are at most at risk of developing ventilator-associated pneumonia (VAP) in the first 48 hours after an endotracheal tube has been placed. The placement of the tube disrupts the normal anatomy of the respiratory tract, and prevents the patient from swallowing, coughing or clearing mucus and other secretions normally. As these secretions pool in the oropharynx, bacteria that live in the respiratory tract can begin to accumulate along the endotracheal tube. If the patient aspirates these bacteria, they may cause infection within the lungs.
Organisms that normally live within the respiratory tract may end up being the same organisms that cause pneumonia in these patients. Understanding that a single organism may be either normal microbiota or a pathogen encourages the microbiologist and clinician to consider other key factors when making a VAP diagnosis such as which organisms constitute normal respiratory flora and what makes some members of the respiratory microbiota more pathogenic than others.
Commensal Organisms Have The Potential to Cause HarmLike all human skin and mucosal surfaces, the respiratory tract is colonized with commensal bacteria that protect the host from disease, increase epithelial cell renewal rates, and promote production of mucosal immunoglobulins. The difficulty in diagnosing the cause of VAP comes from the fact that many of these organisms have the potential to cause disease. Are organisms present simply colonizing the endotracheal tube and surrounding airway without causing harm, or are they the cause of infection? Table 1 lists the organisms most commonly isolated from the respiratory tract and the roles they may play in both harmless colonization and disease.
Commonly Isolated Organisms by Site of Detection
Group C or G Streptococci
- Most commonly represents colonization, but can cause isolated cases and outbreaks of symptomatic pharyngitis.
- Colonizes up to 20% of children.
- Less commonly: causes pharyngitis or localized respiratory infections.
- The relationship between Group A Streptococcus invasive disease and pharyngeal colonization is not clear.
- A large range (6% to 100%) of infants and toddlers are colonized.
- Approximately 25% of children between 3 months and 4 years of age are colonized, and 5-10%% of older and younger people.
- Can persist for weeks to months at this site.
- Growing S. pneumoniae from a culture of the oropharynx/nasopharynx is of no significance, but about 15% of children will develop clinical infections within one month of acquiring a new strain.
- A child who develops a viral upper respiratory tract infection while colonized may develop acute otitis media or sinusitis.
- A large percentage of infants and toddlers are colonized.
- Growth of these organisms from a culture of the oropharynx/nasopharynx is of no significance, but children with upper respiratory infections can develop secondary infections like otitis media or sinusitis if they are colonized.
- 5 to 30% of the population is colonized, with the highest percentage representing adolescents and young adults.
- Growing this organism from a culture of the oropharynx or nasopharynx is of no significance, but colonization can lead to bacteremia, meningitis or septic arthritis.
- Common contaminant from the upper respiratory tract (where this is a colonizing organism), but also a common cause of lower respiratory tract disease. The significance of the presence of this organism in culture will rely heavily on the clinical picture, other diagnostic testing and predominance in culture.
- Approximately one-third of adults are colonized with S. aureus in their upper respiratory tracts. This organism is one of the most common causes of VAP, and serious disease with S. aureus is almost always preceded by colonization.
Nontypeable Haemophilus influenzae, Moraxella catarrhalis and Enterococcus species
- Rarely cause lower respiratory infections or VAP. If they are grown in culture from the lower respiratory tract, it is likely they represent contamination from upper respiratory tract colonization.
Enterobacteriaceae and nonfermenting gram-negative bacilli
- These organisms are among the most common causes of VAP.
- Colonize the upper respiratory tract in children who have been in intensive care or have received frequent courses of antibiotics. These may become the new “normal microbiota” of ventilated children in the ICU and their presence in culture may not always indicate infection.
- Significance of these organisms in culture relies heavily on the clinical picture, other diagnostic testing and predominance in culture.
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 microbiota and not associated with clinical disease.
Many respiratory pathogens live normally in the host without causing disease. Identifying one of these organisms as the cause of infection must be done in the context of clinical signs and symptoms of pneumonia*. Treating all organisms identified from respiratory tract cultures can lead to antibiotic overuse and encourage the development of antibiotic resistant organisms. What makes these seemingly normal bacteria so dangerous, and how can they live within humans and not cause disease most of the time, but occasionally cause lethal infections? It is important to understand how some of the most common causes of pneumonia transition from colonizers to opportunistic pathogens. Below are 3 major bacteria associated with VAP and the traits that allow them to do so.
Streptococcus pneumoniae as a Lower Respiratory Tract PathogenStreptococcus pneumoniae is a normal colonizer of the respiratory tract, yet it is the leading cause of pneumonia mortality globally. The World Health Organization (WHO) estimates that this organism is responsible for killing half a million children worldwide each year.
Virulence trait: Polysaccharide capsule.
- Helps the bacterium evade host defenses.
- Capsule, which is negatively-charged, allows the bacterium to avoid getting stuck in mucous, reach and attach to epithelial cells.
- Encourage and promote attachment.
- Promote biofilm production so that more organisms can attach and proliferate.
Pseudomonas aeruginosa as a Lower Respiratory Tract PathogenPseudomonas aeruginosa is not commonly part of the microbiota of the respiratory tract, but it can become a colonizer in patients who have been admitted to the hospital for an extended period of time. This is also true for other Gram-negative rods including the Enterobacterales. In a hospitalized patient, particularly an intubated patient, it is not safe to assume that the presence of P. aeruginosa in a respiratory culture automatically equals infection. That said, in patients with confirmed VAP, P. aeruginosa is the most common bacterial cause. If P. aeruginosa is the predominant organism growing in a tracheal aspirate culture from a ventilated patient with symptoms of pneumonia, it is likely the causative pathogen.
The effect P. aeruginosa has on an intubated patient will differ depending on serotype:
- Isolates with the serotypes O6 and O11 colonize humans more often than other serotypes but 60% of patients resolve VAP infections with these serotypes.
- Serotypes O1 and O2 are less common and are associated with higher mortality.
Staphylococcus aureus as a Lower Respiratory Tract PathogenNearly one-third of adults are colonized with Staphylococcus aureus in their respiratory tracts. While many people will never develop complications as a result of their S. aureus colonization, adults who are colonized and intubated are at a 15-fold greater risk of developing S. aureus pneumonia as compared to those who were not colonized. Additionally, S. aureus is responsible for >20% of VAP cases, 50% of which are caused by MRSA.
Virulence trait: bacterial surface proteins, particularly Protein A, are essential for the organism to be able to cause pneumonia-related mortality.
While these numbers are frightening, it is important to remember that a large portion of the population is colonized with this organism, and the presence of it in culture does not immediately suggest infection.
Respiratory Commensals as Pathogens: All Things ConsideredThe relationships between humans and bacteria are immensely complex. Normal respiratory microbiota can play a key role in human health, but can also play a part in severe respiratory disease. Understanding these relationships can help the clinical microbiology and infectious disease community better understand how to decipher diagnostic results when it comes to hospital-acquired pneumonia.
*How can a clinical microbiologist make a diagnosis in the context of clinical signs and symptoms? Be sure to catch the next article in this series which will discuss the challenges and benefits of pneumonia diagnostics.