Untitled Quiz

Microbiology: Basic and Clinical Principles - Chapter 16

• Chapter 16 covers Respiratory System Infections
• Presented by Janet Dowding, Ph.D., St. Petersburg College
• A clinical case, "The Case of the Suffering Spelunker" is introduced, asking students to visit the Mastering Microbiology study area for details.

Overview of the Respiratory System

• Students should be able to describe the parts of the upper and lower respiratory system.
• Factors that limit respiratory infections should be described.
• Common terminology associated with respiratory system inflammation and infection should be defined.
• The location of normal flora in the respiratory system and examples of respiratory flora should be stated.

The Respiratory System as a Portal of Entry

• The respiratory system brings oxygen into the body and removes carbon dioxide.
• It's the most common microbial portal of entry, with varied impact and destination based on the pathogen.
• The respiratory tract is divided into upper and lower divisions.

Upper Respiratory Tract Anatomy and Related Infection Terms

• Paranasal sinuses are four interconnected hollow cavities lined with mucous membranes. Specialized cells and glands secrete mucus, warming and humidifying inhaled air and trapping microbes and debris. Cilia sweep debris and mucus toward the nose and mouth.
• Sinusitis is inflammation and swelling of the sinus membranes, often aggravated by infectious agents and inhaled allergens. Drainage of mucus is blocked, accumulating in hollow chambers, putting pressure on surrounding structures. Trapped mucus can serve as a breeding ground for bacteria.
  • A significant percentage of antibiotic prescriptions are for sinusitis, but viruses and allergens are the more common causes, making antibiotics ineffective.
• The pharynx is the end of the upper respiratory tract and gatekeeper between the respiratory and digestive tracts.
• Pharyngitis is inflammation of the pharynx caused by bacteria, viruses, or allergens.
• The epiglottis is a cartilage structure that seals off the airway during swallowing to prevent food and drinks from entering the lungs. Epiglottitis is a medical emergency caused by infections such as Haemophilus influenzae type b, characterized by inflammation and swelling of the epiglottis. This can block the airway.

Lower Respiratory Tract Anatomy and Related Infection Terms

• The mucociliary escalator is a ciliated mucous membrane lining the lower respiratory tract. It traps inhaled debris and sweeps it toward the mouth to prevent entry into the lungs.
• Alveolar macrophages reside in the alveoli to clear out debris and pathogens.
• Inhaled allergens and microbes cause inflammation in lower respiratory tract tissues. This can lead to laryngitis (inflammation of the larynx), which may cause temporary voice loss. Tracheitis is inflammation of the trachea; Bronchitis is inflammation of the bronchi and/or bronchioles; Croup is inflammation of the larynx, trachea, bronchi, and bronchioles, mainly caused by viruses. Pneumonia is inflammation of the lung tissue, potentially life-threatening due to oxygen imbalance. Signs and symptoms include coughing, stridor, dyspnea (shortness of breath), fatigue, sneezing, sore throat and fever.

Clinical Vocabulary

•  Sinusitis: inflammation and swelling of the sinus membranes.
• Pharyngitis: inflammation of the pharynx (throat).
• Epiglottitis: inflammation and swelling of the epiglottis, potentially blocking the airway.
• Laryngitis: inflammation and swelling of the larynx; causing temporary voice loss.
• Tracheitis: inflammation and swelling of the trachea.
• Bronchitis: inflammation and swelling of the bronchi and/or bronchioles.
• Croup: laryngotracheobronchitis (combined inflammation of the larynx, trachea, bronchi, and bronchioles).
• Stridor: wheezing or loud breathing associated with a blocked or narrowed airway.
• Pneumonia: inflammation of the alveoli (small air sacs in the lungs where gas exchange occurs).
• Dyspnea: shortness of breath.

Respiratory Tract Microbiome

• Many microorganisms colonize the respiratory tract.
• Healthy lungs were previously thought to be sterile but now known to be colonized by normal microbiota.
• Microbial profiles resemble those found in the mouth.
• Resident microbiota are helpful as they compete with potential pathogens and secrete antimicrobial peptides to limit the growth of potential pathogens.
• Profiles vary between individuals and between those with healthy lungs and those with underlying health conditions (e.g., asthma, COPD, cystic fibrosis, and lung cancer).
• The healthy respiratory microbiome has a high diversity of species, mainly dominated by bacteria from the phyla Bacteroides, Firmicutes, Actinobacteria, Proteobacteria, and Fusobacteria.

Viral Infections of the Respiratory System

• Hundreds of different viruses can infect the respiratory tract.
• General symptoms of viral respiratory illnesses often overlap, with severity and prognosis depending on the infectious agent and patient factors (e.g., age, general health).
• Vaccines are available for some viral respiratory illnesses, including those caused by RSV, HPIV, Adenoviruses, influenza, SARS-CoV-2.
• Antigenic shift—major genetic change—plays a crucial role in influenza pandemics, like the 1918 "Spanish flu".

Colds

• The common cold, clinically known as acute respiratory infection (ARI), is caused by over 200 genetically distinct viruses from different genera.
• It's usually self-limiting but can have an economic impact due to lost productivity and healthcare expenditures.
• Serovars of rhinoviruses and coronaviruses cause 60–80% of all colds. 
• Other viruses causing colds include parainfluenza viruses, adenoviruses, and nonpolio-type enteroviruses (more common in warmer months).
• Colds spread through personal contact and respiratory droplets as well as through fomites (e.g., doorknobs, cell phones).
• Symptoms can include sudden onset sore throat, runny nose, coughing, sneezing, fatigue, general body achiness, loss of appetite, low-grade fever (common in children), and thickened/discolored mucus in later stages.
• Adults typically experience ~3 colds per year, while children average ~6.
• In about 1 in 200 colds, secondary bacterial infections can develop that may progress to sinus infections, ear infections, or lower respiratory tract infections. 
• Doctors typically prescribe antibiotics if symptoms persist for more than 10 days without improvement.

Respiratory Syncytial Virus (RSV) Infections

• Respiratory syncytial virus (RSV) infections are caused by an enveloped RNA virus in the Paramyxoviridae family, with subtypes A and B.
• RSV is a major cause of acute lower respiratory tract infections in children under 5 worldwide and is the leading cause of bronchitis and pneumonia in infants under 1 year old.
• Most children have encountered this virus by their second birthday.
• Globally, it's estimated that there are 33 million cases, 3 million hospitalizations, and 66,000 deaths each year associated with RSV infections.
• Prevention is currently in clinical trials, and expensive antibody preparations are available for high-risk patients; however, treatment typically involves monthly injections.

Human Parainfluenza Virus (HPIV) Infections

• Human parainfluenza virus (HPIV) infections involve a single-stranded RNA virus of the Paramyxoviridae family, distinct from influenza viruses.
• There are four types of HPIV. HPIV-1 and HPIV-2 are the most common cause of croup in children, and HPIV-3 often leads to bronchiolitis, bronchitis, and pneumonia. HPIV-4 causes mild, cold-like symptoms.
• HPIV is responsible for up to 30% of respiratory infections in children under the age of 5. Transmission occurs via respiratory droplets and fomites, with infections usually occurring in fall, spring, and summer.
• In developing nations, a significant risk for death can be found among healthy preschool children due to complications from these infections. Treatment typically involves supportive therapies.
• Currently, a vaccine is in clinical trials for preventive measures.

Adenovirus Infections

• Adenovirus infections are caused by nonenveloped DNA viruses.
• More than 50 types of adenoviruses can infect humans.
• Adenoviruses are responsible for up to 10% of respiratory illnesses in children, and common symptoms include infection of the respiratory tract, characterized by a sore throat and cold-like symptoms.
• Certain types of adenoviruses might also cause viral conjunctivitis, gastroenteritis, cystitis, bronchitis, pneumonia, and croup.
• A vaccine against adenovirus types 4 and 7 is administered in the U.S. military.

Influenza

• Influenza ("the flu") is caused by influenza viruses, and commonly causes symptoms resembling a severe cold.
• Most influenza strains initially infect ciliated cells of the upper respiratory tract or in some cases, can directly affect the lungs; leading to pneumonia and fatality in those with underlying conditions. 
• Types A and B are significant causes of human epidemics, while Type C is less impactful. 
• The pathogenicity of this virus is impacted by mutations/shifts impacting the glycoproteins hemagglutinin (HA) and neuraminidase (NA)
  • These subtypes are numerically designated.
  • Hundreds of subtypes of HA and NA are possible and can impact infection rates and outcomes.
  • Emergence of new strains, via mutations or possible mixing of RNA segments, are not uncommon and may include new strains. 
• Disease and death rates vary each year, as different strains circulate.
• Several different influenza vaccines are available.

Novel Coronaviruses

• Coronaviruses are a large and diverse family of enveloped RNA viruses, including those causing SARS-CoV-1, MERS-COV, and SARS-CoV-2(which caused COVID-19).
• SARS-CoV-2 has an enveloped single-stranded RNA genome, encoding for 29 proteins. 
• SARS-CoV-2 spreads via respiratory droplets and aerosols by binding to ACE2 on host cells causing symptoms within 2–14 days.
• Serious outcomes such as Acute respiratory distress syndrome (ARDS) can result from infection.
• Viral variants, as result of RNA mutation, are now being categorized based on their potential risk, including those of interest, concern, and high consequence.

Hantavirus Pulmonary Syndrome (HPS)

• Hantavirus pulmonary syndrome (HPS) is an acute, often fatal, respiratory illness caused by certain hantaviruses, including 25 located in North and South America. In the United States, the deer mouse is the most common carrier, transmitting through airborne dust particles, including those found in animal urine, feces and/or birth products. Symptoms can include a progressive respiratory illness that may lead to pulmonary edema, typically accompanied by a high mortality rate(30–40%).

Bacterial Infections of the Respiratory System

• Viruses are a frequent cause of respiratory infections.
• Bacterial infections are often a secondary complication of viral infections. 
• Causes of otitis media (e.g., Streptococcus pneumonia, Moraxella catarrhalis).
• There are various infectious agents causing bacterial atypical pneumonia, including Chlamydia pneumonia, Mycoplasma pneumoniae, Legionella pneumophila, Chlamydophila psittaci, Coxiella burnetii, and Francisella tularensis. 

Streptococcus Pyogenes (Strep Throat)

• Streptococcus Pyogenes can cause strep throat, often characterized by inflammation of the throat, swollen lymph nodes, low-grade fever, exudates, and the absence of a cough.
• The disease is transmitted through respiratory droplets, often occurring in the winter and early spring.
• Complications from strep throat can include otitis, sinusitis, and invasive pneumonia. 
• Treatment typically involves penicillin, or macrolides for those allergic to penicillin.

Scarlet Fever

• Scarlet fever is a bacterial infection caused by Streptococcus Pyogenes strains that produce an erythrogenic toxin.
• It often presents with a red "sandpaper"-like rash, beginning on the face and neck, progressing down the body.
• A characteristic symptom of scarlet fever is a red, "strawberry-like" tongue. 

Autoimmune Complications of S. pyogenes Infection

• Certain M proteins can trigger host antibodies that target Streptococcus Pyogenes but may also cause an inappropriate response against heart valves, kidney and/or joints. 
• Rheumatic fever results from this immune response and is associated with potentially fatal heart complications (i.e. Rheumatic Heart Disease).

Corynebacterium Diphtheriae (Diphtheria)

• Diphtheria is caused by Corynebacterium diphtheriae, a gram-positive rod.
• Common in children under age 5.
• Transmission occurs via respiratory droplets.
• Symptoms initially include cold-like symptoms (fever, sore throat), cough (hoarseness). The organism can form a leathery pseudomembrane in the upper airways within 3 days.
• Complications are potentially fatal: Untreated cases can be fatal due to a pseudomembrane formation. The organism also can spread A-B exotoxins through the bloodstream, affecting protein synthesis.
• Treatment and prevention rely on antibiotics, antitoxin, and DTaP vaccine (diphtheria and tetanus toxoids and acellular pertussis vaccine).

Clinical Vocabulary (Additional Terms)

• Exudate: fluid discharge (can be pus-like or clear).
• Paroxysm: sudden/violent attack (e.g., coughing).
• Convalescent: recovering from sickness.
• Latent infection: infectious agent is present, but not actively causing symptoms.
• Induration: hardening of tissue often due to inflammation. 

Pertussis (Whooping Cough)

• Pertussis, or whooping cough, is an acute infection of the respiratory tract caused by Bordetella pertussis, a Gram-negative bacteria.
• The disease progresses in three stages, characterized by cold-like symptoms (First/Catarrhal phase), severe coughing fits (Second/Paroxysmal phase), and less frequent coughing spells (Third/Convalescent phase).
• Complications may include vomiting, fractured ribs, and loss of bladder control in children and babies. Severe cases may lead to hypoxia, bleeding behind the eyes, and brain damage.
• Tdap vaccine, a diphtheria and tetanus toxoids, and acellular pertussis vaccine, is highly recommended for preventing disease and maintaining immunity. 

Reemergence of Pertussis

• Immunity from the routine DTaP vaccine is not long lived. 
• Adolescents and adults are encouraged to receive a booster shot (Tdap).
• Tdap is highly recommended for pregnant women, childcare workers, healthcare providers, parents, and grandparents. 

Pneumonia

• Pneumonia involves inflammation of the lower respiratory tract, primarily alveoli.
• Caused by a variety of agents including bacteria, viruses, fungi, and protists.
• Pneumonia can be classified as typical and atypical. 
  • Typical Pneumonia: Characterized by the presence of consolidation (fluid in the lungs), examples include pneumococcal pneumonia caused by Streptococcus pneumoniae, and Haemophilus influenzae.
  • Atypical Pneumonia: Characterized by a lack of consolidation, examples include walking pneumonia (Mycoplasma pneumoniae), Chlamydophila pneumonia, Legionnaires' disease, Psittacosis, Q fever, and Tularemia.
• Types of Pneumonia that can be healthcare-acquired include Healthcare acquired pneumonia (HCAP), Hospital acquired pneumonia (HAP), and Ventilator-associated pneumonia (VAP).
• Community acquired pneumonia (CAP), where a patient has not recently been hospitalized or admitted to a healthcare facility, represents another frequent type of pneumonia. 

Pneumococcal Pneumonia

• Pneumococcal pneumonia is a gram-positive, encapsulated diplococcus (Group B streptococcus).
• Humans are the only known natural source. 
• PCV-13 (Prevnar 13®) and PPSV-23 (Pneumovax®) are pneumococcal conjugate vaccines recommended for preventing infection, especially for people over 65.
• Infection typically begins with colonization of the nasopharynx, and can spread to the middle ear to cause otitis media, or to the lungs to cause pneumonia.
  • Complications, potentially leading to bacteremia and meningitis, can result if pneumonia progresses to the bloodstream.

Haemophilus Influenzae (Hib) Pneumonia

• Caused by gram-negative bacteria.
• Typable strains based on analyses of polysaccharide capsules (6 types a-f).
• Non-typable types lack polysaccharide capsules. 
• Though often found in children under the age of 6, non-typable strains are the leading cause of community-acquired pneumonia in adults.

Atypical Bacterial Pneumonia

• Includes various infectious agents, classified as zoonotic or non-zoonotic. 
  • The zoonotic causative agents include Q fever and Tularemia.
  • Non-zoonotic atypical pneumonia is caused by pathogens such as Chlamydia pneumoniae, Mycoplasma pneumoniae, and Legionella species. 
• Walking pneumonia is typically caused by Mycoplasma pneumoniae, an extremely small bacterial agent lacking a cell wall.

Psittacosis

• Psittacosis, or ornithosis, is a Gram negative bacterial infection, zoonotic disease, arising from, and transmitted to humans through inhalation of dust from dried bird droppings. 
• This infection is primarily found in birds, including birds of the psittacine family, and zoonotic contact.

Q Fever

• Q fever, or Query fever, is caused by Coxiella burnetii, a highly infectious Gram-negative bacteria.
• This pathogen is primarily found impacting livestock, with ticks as a major transmission vector. 
• Human infection often occurs by inhaling contaminated dust/aerosol (feces, urine, and birth products), or consuming unpasteurized milk products. 

Tularemia

• Tularemia is a Gram-negative bacterium (Francisella tularensis) affecting mostly rural Northern America, Europe, and Northern Asia. This illness affects a variety of different hosts, including animals, birds and humans. This is a zoonotic illness primarily transmitted via inhalation of aerosols or dried grasses contaminated with infected carcasses; it can also be transmitted through skinning or butchering these animals.

Fungal Respiratory System Infections

• Mycoses are rare infections relative to bacterial and viral respiratory infections. 
• Mycoses are becoming more common due to deforestation, increased urbanization, and increased number of immune-compromised individuals. 
• Fungal infections are further categorized into endemic (specific geographic locations) and ubiquitous (varied climates).
  • Endemic fungi are often categorized as true pathogens.
  • Ubiquitous fungi are part of the normal flora of various environments. 
• Mycoses are contracted by inhaling fungal spores.

Blastomycosis (Chicago Disease)

• Blastomycosis is an endemic mycosis caused by the dimorphic fungus Blastomyces dermatitidis primarily impacting the Mississippi and Ohio River valleys, the Great Lakes region, and parts of Canada and the Great Lakes and St. Lawrence Seaway.
• Blastomycosis arises from inhalation of conidia spores that develop into a yeast-like form in the lungs as a result of environmental disturbances (e.g., digging, construction).
• Disseminated blastomycosis is a possible complication and leads to higher mortality rates in immune-compromised patients.
• Treatment usually involves antifungal drugs (e.g., amphotericin B, fluconazole, itraconazole, ketoconazole). 

Coccidioidomycosis (Valley Fever)

• Coccidioidomycosis (Valley Fever) is an endemic mycosis.
• Coccidioides immitis and Coccidioides posadasii are the causative fungal agents, and the illness is commonly found in the southwestern United States, parts of Central and South America, and northern Mexico.
• The illness arises from inhalation of the arthroconidia spores from disturbed soils. Spores develop into spherules, which rupture and release endospores. The spherules release fungal endospores. 
• Symptoms include body aches, fever, cough, headache, and rash, with a higher risk in individuals exposed to environments with high spore concentrations, and those with compromised immune systems.
• Treatment typically involves antifungal drugs (e.g., fluconazole, itraconazole, ketoconazole, or amphotericin B). 

Histoplasmosis

• Histoplasmosis is an infection resulting from the inhalation of spores of the dimorphic fungus Histoplasma capsulatum.
• The fungus is primarily found in soil enriched with bat and bird droppings.
• Symptoms are generally less severe and only occur in about 5% of exposed individuals. Immune compromised patients are at higher risk for developing the disseminated form. 
• Treatment typically involves antifungal drugs (e.g., itraconazole).

Ubiquitous Fungi

• Some ubiquitous fungi have the potential to cause serious infections in immune-compromised patients.
• These types of infections are typically rare in healthy individuals.  Examples include those caused by aspergillosis, mucormycosis, and PCP. 

Aspergillosis

• Invasive aspergillosis results from the inhalation of spores of Aspergillus species, such as A. fumigatus, a common soil fungus throughout the world.
• This infection most commonly impacts immune-compromised patients. 
• Complications and high mortality risk accompany the infection. Microscopic observation/culture is used to identify the organism for confirmatory diagnosis. Treatment typically involves voriconazole. 

Mucormycosis

• Mucormycosis results in infection through inhalation of spores of Rhizopus arrhizus, a fungal agent commonly found in decaying soil.
• The infection is rare in the general population and commonly impacts immune-compromised patients

Pneumocystis Pneumonia

• Pneumocystis pneumonia (PCP), resulting from Pneumocystis jirovecii, is not considered a fungus, but a parasite of eukaryotic cells or a type of protist.
• It arises from the inhalation of spores in environmental systems and in those with compromised immunity. 
• Symptoms potentially include fever, fatigue, dyspnea (shortness of breath), and nonproductive cough. 
• Treatment involves low doses of trimethoprim–sulfamethoxazole. 

Visual Summary of Respiratory System Infections

• A visual summary is provided with different types of respiratory infections categorized by their cause(viral/bacterial/fungal), and the most common agents, symptoms, and treatment options for those diseases are provided).
• This summary is intended to aid in the identification of an infection's etiology in clinical diagnostics.

Think Clinically: Respiratory System Infection Case Studies

• Case studies are provided for further clinical reasoning practice on various potential respiratory infections.