Lab Testing and Pneumonia

 Pneumonia is a type of infection that occurs in the lower respiratory tract. It is caused by fungi, viruses, and bacteria. This infection may cause symptoms that range from moderate all the way up to life-threatening. The Centers for Disease Control and Prevention (or CDC) reports that over one million adults and children in the United States are admitted into a hospital every year for pneumonia. The World Health Organization reports that worldwide, 2.7 million people per year are killed by pneumonia, which is more than all other infectious diseases, and it is the leading cause of death for children younger than 5 years old. Although pneumonia occurs at all times of the year, the highest numbers of cases are seasonal during the flu (influenza) season, which typically runs from the late fall through to early springtime.  

Although people of all ages can get pneumonia, it develops most often in people who have weakened immune systems (immune-compromised), individuals over 65 years old, and very young children. Women who are pregnant, and individuals who have underlying conditions like damaged lungs due to smoking or cystic fibrosis are at higher risk to develop pneumonia as well. That includes people who have had an organ donation and those who have undergone chemotherapy or are on mechanical ventilation. Individuals with AIDS are highly susceptible to getting pneumonia.  

Fungi, viruses, and bacteria are microbes that may cause lower respiratory tract infections. Most often, pneumonia is caused by microbes that have gotten past the immune defenses of the body and are residing deep inside the lungs in alveolar sacs, which are tiny structures. The second most common cause of pneumonia is viruses, and the most common is bacteria.  

Bacteria 

In adults, the most common cause of pneumonia is bacteria, but in young children it is uncommon. Pneumonia can be caused by many different kinds of bacteria, while some are more common than other ones. At times, people, especially those who have health problems or who are elderly, will get bacterial pneumonia after they have had a viral respiratory infection.   

Those microbes can be spread to other people via microscopic respiratory secretion droplets that become airborne whenever an infected individual sneezes or coughs. Airborne drops settle onto surfaces like phone receivers, keyboards, and countertops in the area or inhaled directly by another person. The microbe gets spread whenever someone touches a surface that is contaminated and then touches her or his mouth or eyes or some of their other mucous membranes. Pneumonia may also be caused by normal bacteria in food, saliva, or vomit whenever an individual gags or chokes and breathes their own fluids in accidentally.  

To cause pneumonia, it takes more than just being exposed to a potential pathogen. Microbes are constantly present within the environment, and sources of infection are encountered by people every day. The lungs are able to handle these assaults in most cases. There are various layers of immune defense in the respiratory system, beginning with the hair-like structures and mucous that trap and eliminate numerous pathogens out of the airways. Pathogens that are able to make it past those initial defense systems then get subjected to an attack of a range of immune system cells that find and engulf pathogens that are identified as being foreign to the human body. Pneumonia takes place whenever these defenses are damaged or weakened or whenever the invading pathogens are severe enough to evade or overcome them.  

A broad range of bacteria, viruses, and fungi (less commonly) may cause pneumonia. However, most cases are caused by just a few of them. The microbes that are most likely to cause a specific pneumonia case will depend on the health status and age of the affected individual as well as the time of year to some degree. People who have weakened immune systems, and individuals who have traveled to certain parts of the world, might develop pneumonia due to the microbes being more unusual. 

The following familiar terms describe some of the general types of pneumonia:  

Double pneumonia is a type of infection where both lungs are affected.  

Lobar pneumonia is a type of disease that affects a part of a lung (lobe). 

Walking pneumonia is a mild type of the disease that usually doesn’t require any bed rest. This is often caused by mycoplasma pneumoniae (a virus).  

Aspiration pneumonia is a type of pneumonia that is caused by a person inhaling food particles or gastric juices and can be harder to treat. In these cases, it might be more challenging to identify the pathogens causing the infection. Therefore, health practitioners might need to do additional testing to be able to prescribe the right antibiotic. Individuals who have gastroesophageal reflux disease (or GERD) or people who have difficulties swallowing from other circumstances have a higher risk of this kind of pneumonia. Sometimes aspiration pneumonia is referred to as anaerobic pneumonia since the bacteria that cause it normally is beneficial bacteria living in the digestive tract, and oxygen is not required for them to live.  

The place where pneumonia is acquired determines the most likely cause of pneumonia, the most effective way of spreading the infection, and helps to guide the proper treatment.  

Healthcare-associated and hospital-acquired microbes are more likely to be able to resist first-line antimicrobials. It is also more likely for community-acquired pneumonia to occur due to the fact that bacteria are susceptible to antibiotics that are commonly prescribed or seasonal viruses where antimicrobial drugs are not the right treatment.  

Healthcare-associated pneumonia – whenever an individual is infected while they are in a healthcare-associated environment, like a dialysis clinic or nursing home.  

Ventilator-acquired pneumonia – takes place when an individual is connected up with a ventilator machine.  

Hospital-acquired pneumonia – occurs when a person develops an infection while in the hospital for a different illness.  

Community-acquired pneumonia – occurs whenever an individual becomes infected outside of a healthcare setting during daily activities.     

There is some bacterial pneumonia that is fairly rare but might be found in some geographic areas and in certain populations. People who immigrated from certain countries and travelers might be infected with bacteria that are not as common in the United States. Also, people who have pre-existing conditions like weakened immune systems or decreased lung function might be more vulnerable to kinds of bacteria that are not present within the general population.  

The following is the most common bacterial pneumonia cause that is contracted outside of a healthcare or hospital setting (community-acquired): 

Streptococcus pneumoniae pn-eumococcal pneumonia can be caused by these bacteria, which are spread easily through regular social contact. S. pneumoniae has many serotypes so you could get repeat infections from various kinds. There is a vaccine that is available for the most common S. pneumoniae serotypes to help prevent pneumonia as well as other types of serious infections, including blood infections (septicemia) and meningitis. 

Some of the other less common causes can include the following:  

  • Pseudomonas aeruginosa – Those who have reduced lung function from cystic fibrosis are often affected 
  • Streptococcus agalactiae (also called Group B strep) – The female vagina may be colonized with it, and it may be passed to a baby from a pregnant mother during childbirth.  
  • Klebsiella pneumoniae – This can cause pneumonia in individuals who are weakened by disease, commonly within a hospital setting.  
  • Staphylococcus aureus – Recently, this has become more common within hospital settings from drug-resistant strains such as methicillin-resistant S. aureus (or MRSA) or after influenza (flu) infection.  
  • Moraxella catarrhalis – his is more commonly a middle ear infection source in children  
  • Haemophilus influenzae (type B Hib) – Causes pneumonia most often but also can cause other types of invasive infections like septicemia and meningitis. Hib vaccinations have made infections less common. However, infections might occur with other kinds of H. influenzae bacteria that the Hib vaccine does not cover.   

Atypical pneumonias are a type of bacterial lung infection. They do not respond to many antibiotics that are commonly prescribed.

Examples include: 

  • Mycobacterium tuberculosis – Causes tuberculosis (or TB), as well as nontuberculous Mycobacteria (M. kansasii, M. avium-intracellulare, and other mycobacteria species), are not as common in the United States but can be found in people with AIDS, prison populations, and in travelers, among others.  
  • Legionella pneumophila – this causes Legionnaires’ disease; an infection can occur whenever a person inhales airborne droplets, mist, or steam that is contaminated with the bacteria. This infection doesn’t spread from one individual to the next. Legionella infections frequently require hospitalization, and the death rate is significant.  
  • Chlamydophila pneumoniae – This causes around 10% of all community-acquired types of pneumonia. It occurs most commonly in people 65 to 79 years old.  
  • Mycoplasma pneumoniae – This commonly causes upper respiratory infection. Every year in the U.S., there are around 2 million cases, and they are responsible for 15% to 20% of community-acquired pneumonia cases. It causes “walking pneumonia,” which is a less serious infection. Typically, people under 40 years are affected.   

Viruses 

In the United States, around one-third of the total pneumonia cases every year are caused by viruses infecting the respiratory system. They are the most common cause of pneumonia in babies and account for around 90% of lower respiratory infections. Fewer than 20% of pneumonia is viral in adults under 60 years old. Viral causes are becoming increasingly common in people over 60-65 years old.   

Viral pneumonia is frequently mild, and only supportive care is required. However, hospitalization might be required for more serious cases. After a primary viral infection, secondary bacterial pneumonia sometimes can develop.  

The most common viral pneumonia causes are:  

  • Adenoviruses – these are common viruses that frequently cause respiratory illness. The infections are usually not serious. However, for people who have weakened immune systems, they can be serious.  
  • Respiratory syncytial virus (or RSV) – in children under one-year-old, this is the most common cause of pneumonia. 
  • Parainfluenza virus– this often causes respiratory infections in young children and infants. It can progress into pneumonia.  
  • Influenza virus – in adults, this is the most common viral pneumonia cause. 

The following are some other less common causes:  

  • Rhinoviruses – these viruses cause the common cold in adults and children. It might infect the lower respiratory tract occasionally and cause pneumonia in the elderly and young children. 
  • Varicella (chickenpox) – this is caused by a varicella-zoster virus (or VZV) infection, which belongs to the herpes virus family. A majority of cases resolve without any serious complications. An uncommon complication is pneumonia.  
  • Measles – or rubeola, is a highly contagious viral infection transmitted via respiratory secretion. A majority of individuals recover within a few weeks. However, up to 20% of people can develop complications, including pneumonia.  
  • Cytomegalovirus (or CMV) – can cause serious developmental and physical problems whenever women are infected for the very first time (primary infection) while they are pregnant and pass the infection on across the placenta to their developing baby.  
  • Human metapneumovirus – in 2001, the virus was initially identified. It is believed to cause around 5% to 15% of hospitalizations for lung infections. 
  • Adenoviruses – these are common viruses that frequently cause respiratory illness. However, they normally are not serious.  

Fungi 

Pneumonia that is caused by fungi is fairly rare. Some fungi do cause pneumonia in individuals with weakened immune systems. Those people include those who have AIDS, individuals on chemotherapy regimens, and organ transplant recipients taking immunosuppressive drugs.

They are referred to as “opportunistic” fungi and include the following:  

  • Cryptococcus neoformans – can infect anyone, but in the U.S. the highest prevalence is with individuals who have HIV/AIDS.  
  • Candida species – yeasts that are part of regular human flora. Within the body’s moist mucous membranes, infections can occur. 
  • Aspergillus species – may cause fungal masses and aspergillosis in the lungs and sinuses. 
  • Pneumocystis jiroveci – in the U.S., it is most common in individuals with AIDS. It was called P. carinii formerly. Pneumonia that this organism cause is still sometimes referred to as PCP or Pneumocystis carinii pneumonia. 

There are some fungi that are pathogenic. This means they may cause pneumonia in individuals no matter what their health status is. Individuals become infected by breathing in fungal spores. Usually, these types are only found in certain parts of the world and/or the U.S.: 

  • Blastomyces dermatididis – this is found in the midwestern, southeastern, and south-central US.in decaying leaves and wood as well as moist soil. 
  • Coccidioides immitis – this causes Valley Fever or coccidioidomycosis, also called Valley Fever; it is often found in parts of California and in Arizona. 
  • Histoplasma capsulatum – this causes histoplasmosis. It is found in soil that has been contaminated with bird or bat droppings. It is commonly found in Mississippi and Ohio river valleys. 

Complications, Symptoms, and Signs  

Pneumonia symptoms can vary widely, depending on the health status and age of the affected person and which microbe has caused the infection. The elderly might experience confusion. Very young babies might be lethargic and irritable, breathe rapidly, wheeze, and grunt. Bacterial pneumonia can emerge after a viral infection and might be view as a worsening or lingering bout of flu or a cold.  

The following are some of the most common symptoms of pneumonia:  

  • Feeling worse after the flu or a cold  
  • Vomiting and nausea 
  • Chest pain 
  • Muscle aches 
  • Headache 
  • Shortness of breath 
  • Fatigue 
  • Chills and fever 
  • Cough  
  • Complications 

Some of the complications that may arise with pneumonia include sepsis, respiratory failure, lung tissue scarring (which could result in recurrent infections), fluid buildup inside the lungs, and rarely, lung abscesses (pus pockets inside the lung tissue).

When it comes to testing, the goals are determining which microbe is causing pneumonia, limiting its spread to other individuals, determining how severe the pneumonia is, and to help guide treatment. In many cases, determining acute pneumonia’s exact cause is not possible. Treatment will be based on the person’s medical history and clinical presentation, the experience of a health practitioner, microorganisms that are likely present within the community, like influenza, and on guidelines that have been established for caring for lower respiratory infections. If the symptoms of a person do not resolve, then other tests might need to be conducted to help diagnose the causes of pneumonia that are less common.  

Laboratory Tests 

There are a number of different laboratory tests that might be performed to make a diagnosis depending on the affected individual’s medical history as well as the symptoms and signs that are present during the physical exam.  

General laboratory tests can include the following:  

Blood gases – these tests measure the carbon dioxide (or CO2), oxygen (or O2), and pH present in a blood sample. Usually taken from an artery to evaluate lung function. 

Basic metabolic panel (or BMP) – blood tests for potassium, sodium, as well as other chemistries in order to determine how severe the illness is.  

Complete blood count (or CBC) – evaluates the number and type of white blood cells. Test results can indicate whether or not there is an infection. 

Suspected bacterial pneumonia tests include the following:  

Legionella testing – this is a molecular or culture test for diagnosing a suspected Legionella infection or blood test for a certain antigen. 

Mycoplasma testing – this is a special culture or blood test for diagnosing a mycoplasma infection. 

Blood culture – used for detecting septicemia whenever it is suspected that an infection has spread to the blood from the lungs or from the lungs to the blood.  

AFB testing -These tests are ordered when a nontuberculous or tuberculous mycobacteria infection is suspected.  

Susceptibility testing – this is conducted on pathogenic bacteria that are grown within a culture. Testing is used to identify it and is used for guiding treatment. 

Gram stain and bacterial sputum culture — these are primary tests that are ordered and used for detecting and identifying bacterial pneumonia causes.  

Tests that are used when viral pneumonia is suspected include the following:  

Viral culture – used for growing a number of different viruses that might cause infections  

RSV testing – these tests are conducted throughout the RSV season in order to help with diagnosing the infection in individuals with lower respiratory tract involvement and moderate or severe symptoms. The tests are mainly ordered for the elderly, infants (six months to two years old), and people who have compromised immune systems like those with an organ transplant or with pre-existing lung disease.  

Influenza tests – these tests are used to help with diagnosing an influenza infection and to help with documenting influenza present in a community at times. Testing might also be used for identifying the strain and/or type of influenza that is causing an infection.  

Fungal tests – these tests might be ordered for a suspected fungal infection. Examples include the following:  

Fungal cultures – These are used for identifying specific fungi. Fungi are often slow-growing, so to get results can take weeks. Susceptibility testing that is conducted on fungi that are isolated from the culture can help with determining which is the best antifungal to use as a treatment. 

Tests for fungal antibodies and antigens – used for determining if a person has, or recently had a certain fungal infection. Compared to fungal cultures, these are more rapid. However, they test only for a certain fungal species. Therefore, healthcare practitioners need to know which fungal organism needs to be tested for. Since many individuals have fungal antibodies from being exposed to a fungus in the past, a single antibody test might not confirm a current infection or presence of the fungus. Blood samples are sometimes collected 2-3 weeks apart (convalescent and acute samples) and then tested to find out whether the antibody levels (titers) have changed. It can take several weeks to evaluate the results.  

Molecular tests – Used for identifying the presence of viruses, fungi, and/or bacterial within a respiratory sample through detecting the microbes’ genetic material (RNA, DNA). Usually, these kinds of tests are very specific and sensitive and especially helpful in detecting microorganisms that are hard to culture.  

There are some tests that look for a specific microbe like Mycoplasma pneumoniae. PCR (or polymerase chain reaction) is a common method.  

There are newer methods that can test simultaneously for several viruses, fungi, and/or bacterial. Those methods include DNA microarrays and multiplexed PCR.  

Pleural fluid analysis – when there is an accumulation of fluid in the space between the chest wall and lung, the fluid might be tested so that the cause of the infection can be determined.