What we talk about when we talk about respiratory cultures
A respiratory culture is an attempt to isolate organisms from a patient’s respiratory tract. Because this is all connected to ears, eyes, nose, and throat, the same organisms will be seen in those.
The most difficult part of working up respiratory cultures for new microbiologists is sifting through all the other organisms, the mixed flora, that we see in these cultures. We only want to work up the organisms that are important.
Specimen Collection and Transport
The accuracy of respiratory culture results heavily depends on the quality of the specimen collected. Common types of respiratory specimens include sputum, bronchoalveolar lavage (BAL), tracheal aspirates, and throat or nasopharyngeal swabs. For lower respiratory tract infections, expectorated sputum or BAL samples are preferred. For upper respiratory tract infections, throat or nasopharyngeal swabs are typically collected.
Proper collection techniques must be employed to minimize contamination by oropharyngeal flora. For example, patients are often instructed to rinse their mouths with water before providing a sputum sample to reduce oral contamination. Specimens should be transported to the laboratory as quickly as possible to ensure the viability of pathogens, with refrigeration if necessary. If transport is delayed, certain respiratory pathogens like Streptococcus pneumoniae or Haemophilus influenzae may lose viability, leading to false-negative results.
To tell if the specimen is a good collection, look at the gram stain. If there is a large number to epithelial cells, it is a bad collection. The ideal specimen will demonstrate a large number of white blood cells and no epithelial cells. A recollection may be needed if it is a poor collection.
Media Selection and Culture Setup
Culturing respiratory specimens involves using several different types of agar to optimize the isolation of pathogens. Commonly used media include:
Blood Agar (BA): This is a non-selective medium that supports the growth of most respiratory pathogens, including Streptococcus pneumoniae, Staphylococcus aureus, gram-negative rods. Hemolytic reactions can be observed on blood agar, aiding in the identification of certain organisms.
Chocolate Agar (CHOC): This medium is enriched with heated blood, which releases growth factors like hemin (X factor) and nicotinamide adenine dinucleotide (V factor). CHOC agar is particularly useful for isolating fastidious organisms such as Haemophilus influenzae and Neisseria species.
MacConkey Agar (MAC): A selective and differential medium that supports the growth of Gram-negative bacteria, such as members of the family Enterobacteriaceae and Pseudomonas aeruginosa. MAC agar helps differentiate lactose fermenters, like Escherichia coli, from non-lactose fermenters, like Pseudomonas aeruginosa.
Common Respiratory Pathogens
The BIG THREE
These are the three that we specifically look for in respiratory cultures (and ear/eyes) and we generally don’t see in other types of cultures. They aren’t the most common, but they are the ones that are hard to pick out for new microbiologists.
Streptococcus pneumoniae: A leading cause of bacterial pneumonia, especially in the elderly, young children, and immunocompromised individuals.
Haemophilus influenzae: Often associated with community-acquired pneumonia, bronchitis, and exacerbations of chronic obstructive pulmonary disease (COPD).
Moraxella catarrhalis: Frequently associated with upper respiratory tract infections, particularly in patients with COPD or chronic bronchitis.
The rest of them
These are common pathogens that we see in other types of cultures too, but should be worked up in respiratory cultures
Pseudomonas aeruginosa: Commonly isolated from patients with chronic lung diseases like cystic fibrosis and those on mechanical ventilation. It is known for its multidrug resistance and is a major cause of hospital-acquired pneumonia.
Klebsiella pneumoniae: A Gram-negative bacterium often implicated in hospital-acquired pneumonia, particularly in immunocompromised patients or those with underlying chronic diseases. Other enterics will be seen in respiratory cultures too, such as E. coli and Citrobacter species. As a rule, work up all gram-negative rods.
Staphylococcus aureus (including MRSA): Can cause pneumonia, especially in individuals with weakened immune systems or following influenza infection. Methicillin-resistant Staphylococcus aureus (MRSA) is particularly concerning due to antibiotic resistance.
Stenotrophomonas maltophilia: A gram negative rod that loves oxygen, so we see it in respiratory cultures sometimes as a pathogen.
Fungi: There is a wide range of fungi that can cause respiratory pathologies. This is a topic for another day.
Ones you won’t see in the culture (because they are too small or too slow growing)
Mycoplasma pneumoniae: Atypical bacterium that causes "walking pneumonia" and is more commonly seen in younger adults and in outbreaks in close communities, such as schools or military barracks.
Legionella pneumophila: The causative agent of Legionnaires’ disease, a severe form of pneumonia, often associated with contaminated water sources like air conditioning units or plumbing systems.
Bordetella pertussis: The causative agent of whooping cough, which is more common in children and can lead to severe complications if not promptly treated.
Chlamydia pneumoniae: Causes mild respiratory infections and is often implicated in cases of atypical pneumonia, which can affect both children and adults.
Mycobacterium tuberculosis (TB): The causative agent of tuberculosis, M. tuberculosis is a significant pathogen worldwide, often affecting the lungs. It is highly contagious and requires specialized testing for diagnosis, including acid-fast staining and molecular assays.
Non-tuberculous Mycobacteria (NTM): This group of mycobacteria, which includes species like Mycobacterium avium complex (MAC), can cause chronic lung infections, particularly in individuals with underlying lung diseases like bronchiectasis or cystic fibrosis.
Cystic Fibrosis Cultures
The pathogens found in the respiratory cultures of cystic fibrosis patients are typically chronic and can vary based on the patient's age, antibiotic treatment history, and the progression of their lung disease. Pseudomonas aeruginosa and Staphylococcus aureus are the most common and clinically significant pathogens, particularly as they tend to persist and cause chronic infection. However, other Gram-negative bacteria, fungi, and even viruses can contribute to disease exacerbations. Identifying and managing these pathogens through regular respiratory cultures is critical in the long-term care of CF patients, as timely and appropriate treatments can help slow the progression of lung damage and improve quality of life.
Pseudomonas aeruginosa
Pseudomonas aeruginosa is the most common pathogen found in the lungs of CF patients, particularly as they grow older. This Gram-negative bacterium can cause chronic lung infections due to its ability to form biofilms, which protect the bacteria from the host immune response and antibiotics. Early in CF, infections with P. aeruginosa may be intermittent and more easily eradicated. However, as the disease progresses, P. aeruginosa often becomes mucoid (due to the production of alginate), contributing to its persistence and resistance to treatment. Chronic infections with mucoid P. aeruginosa are associated with more severe lung disease and a decline in lung function over time.
Staphylococcus aureus
Staphylococcus aureus, particularly methicillin-resistant Staphylococcus aureus (MRSA), is commonly found in CF patients, especially in children and young adults. S. aureus is a Gram-positive bacterium that can cause acute exacerbations of lung disease in CF. It is often one of the first pathogens to colonize the airways of CF patients early in life. Methicillin-sensitive Staphylococcus aureus (MSSA) is frequently isolated, but MRSA, which is more difficult to treat due to its resistance to beta-lactam antibiotics, is increasingly prevalent in CF patients and is associated with worse outcomes and lung function decline.
Burkholderia cepacia Complex (BCC)
The Burkholderia cepacia complex (BCC) consists of several closely related species, such as Burkholderia cenocepacia and Burkholderia multivorans. These Gram-negative bacteria are highly pathogenic in CF and are particularly concerning due to their multidrug resistance and potential to cause rapid lung function decline. In some patients, BCC can lead to "cepacia syndrome," a severe, rapidly progressing, and often fatal decline in lung function accompanied by sepsis. Because of its high transmissibility and risk, CF patients infected with BCC are often isolated from other CF patients to prevent cross-infection.
Haemophilus influenzae
Haemophilus influenzae is another early colonizer in CF, particularly in younger patients. It is a Gram-negative bacterium that can cause both acute and chronic respiratory infections. Although it tends to become less frequent as patients age, it can still contribute to exacerbations and chronic lung inflammation in CF patients. H. influenzae infections are often less severe compared to P. aeruginosa and Burkholderia cepacia complex, but they can still exacerbate lung disease if not treated appropriately.
Achromobacter xylosoxidans
Achromobacter xylosoxidans is a Gram-negative bacterium increasingly recognized as an emerging pathogen in CF patients. It has been associated with chronic lung infections and can be difficult to treat due to its intrinsic resistance to many antibiotics. The clinical significance of A. xylosoxidans in CF is still being investigated, but chronic infection with this organism has been linked to poorer lung function and more frequent exacerbations in some CF patients.
Stenotrophomonas maltophilia
Stenotrophomonas maltophilia is a Gram-negative, multidrug-resistant bacterium that can colonize CF lungs, particularly in patients who have been treated with broad-spectrum antibiotics. While S. maltophilia is generally considered less virulent than P. aeruginosa or B. cepacia, its presence can complicate treatment due to its resistance to many commonly used antibiotics. It has been associated with chronic infections and worsening lung function in some patients.
Mycobacterium abscessus Complex
The Mycobacterium abscessus complex is a group of rapidly growing non-tuberculous mycobacteria (NTM) that are increasingly found in CF patients. This group includes Mycobacterium abscessus, Mycobacterium massiliense, and Mycobacterium bolletii. These bacteria are highly resistant to antibiotics and can cause chronic, difficult-to-treat lung infections. Infections with M. abscessus are associated with a more rapid decline in lung function and can complicate lung transplantation due to the risk of post-transplant infections. Treatment of M. abscessus infections requires prolonged courses of multiple antibiotics, and eradication is often challenging.
Aspergillus fumigatus
Aspergillus fumigatus is a fungus that is commonly isolated from CF respiratory cultures, though it does not always cause an active infection. In some CF patients, A. fumigatus can lead to allergic bronchopulmonary aspergillosis (ABPA), a hypersensitivity reaction that results in worsening lung function, wheezing, and bronchiectasis. Chronic colonization with A. fumigatus may also contribute to inflammation and further lung damage in CF, though its role in CF lung disease is still being researched.
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