Respiratory Tract Infections (RTI)

Respiratory Tract Infections (RTI)

• Respiratory tract infections are common, especially in children.
• Viruses mainly cause them, bacteria, fungi, and parasites less so.
• Types of RTI include Upper (URTI) and Lower (LRTI) respiratory tract infections.
• LRTIs are typically more severe and have a less viral cause than URTIs

Upper Respiratory Tract Infections (URTI)

• The upper respiratory tract is colonized by normal flora that protect against pathogens.
• URTIs are very common, with a majority of viral etiology.
• Common cold, Sinusitis, Pharyngitis, Epiglottitis are examples of URTIs.

Common Cold

• The common cold (Rhinitis) is an acute infection of the nasal mucosa.
• Mostly caused by viruses like rhinoviruses, coronaviruses, and adenoviruses.
• Symptoms involve nasal discharge/obstruction, sneezing, and possibly a sore throat, without fever.
• It is self-limiting, often not diagnosed by microbiology, complications are rare, but can spread to other parts causing sinusitis or otitis media.

Sinusitis

• Sinusitis involves an acute infection of one or more paranasal cavities.
• It often stems from other URTIs as paranasal sinuses communicate with the upper respiratory tract.
• Viruses mostly cause it, potentially followed by bacteria like Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus, and Streptococcus pyogenes.
• Symptoms: mucus secretion, obstruction, impeded drainage, facial pain, pressure, malaise, and subfebrilia.
• Chronic sinusitis involves purulent nasal discharge.
• Diagnosis needs clinical evidence plus culture of sinus puncture in chronic instances.

Otitis Externa

• Inflammation of the external auditory canal.
• Normal skin flora (Staphylococcus sp., Corynebacterium sp.) causes it, as well as Pseudomonas aeruginosa, especially in summer.
• Manifestations: furuncles, severe pain, obstruction, and hearing loss.
• Diagnosis: clinical findings and inspection of the external canal; cultivation is unnecessary.

Otitis Media

• Infection of the middle ear, following infections in other parts of the upper respiratory tract via the Eustachian tube and is common in children.
• Viruses mostly cause it, though bacteria such as Streptococcus pneumoniae, Hemophilus influenzae, and Moraxella catarrhalis are factors.
• Manifestations: persistent, severe ear pain, perforation of the tympanum with purulent discharge, fever, and nausea.
• Meningitis and brain abscess are potential complications.
• Diagnosis: inspection of the tympanus, cultivation possible using needle aspiration.

Pharyngitis and Pharyngotonsilitis

• Inflammation of the pharynx and lymphoid tissues of the posterior/lateral pharynx.
• Mostly triggered by viruses and bacteria: Streptococcus pyogenes, Staphylococcus aureus, Neisseria gonorrhoeae, Arcanobacterium haemolyticum
• Sore throat is experienced, inflammatory exudate/membranes in bacterial infections, fever, malaise, myalgia, and headache occur.

Streptococcus pyogenes

• A group A Streptococcus that is beta-hemolytic.
• Streptococcus pyogenes is the main bacterial cause of pharyngotonsillitis, also known as strep throat.
• M-protein (surface antigen) determines strain virulence, specific to group A.
• Erythrogenic toxin causes scarlet fever (pharyngotonsillitis with erythema).
• Streptolysin O is cardiotoxic and a diagnostic marker (ASLO).
• Rheumatic fever may develop 2-4 weeks post-untreated infection in 3% of patients.
• It's an inflammatory disease affecting the heart, joints, skin, and brain, treatable with S. pyogenes ATB therapy.
• Testing: Culture tests must be done in all suspected situations of bacterial ethiologies related to pharyngotonsilitis
• Testing: CRP tests differentiate viral from bacterial ethiology.
• A proven S. pyogenes infection means starting ATB therapy with penicillin.

Other Causes of Pharyngitis

• Arcanobacterium haemolyticum is less frequent, can cause scarletinous exanthema, must be differentiated from S. pyogenes.
• Neisseria gonorrhoeae is an STD, causes sore throat symptomatically or asymptomatically.
• Corynebacterium diphtheriae causes diphtheria utilizing toxin production.
• Symptoms varying from mild to severe, featuring ulceration/necrosis, and rare in Europe because of vaccination.

Epiglottitis

• Haemophilus influenzae type b is the causative agent.
• Children up to 6 years of age are susceptible.
• Symptoms: erythema and swelling of the epiglottis and fever, and bacteremia.
• Medical emergency - fulminant and potentially fatal, involves airway obstruction, recently rare in Europe due to vaccination.

Lower Respiratory Tract Infections (LRTI)

• Lower RT lacks resident normal flora; inhaled microbes are removed by the mucociliary elevator.
• LRTIs can follow URTIs.
• Laryngotracheitis, bronchitis, and pneumonia are LRTIs.

Laryngotracheitis (Croup)

• Inflammation of the larynx, trachea, and subglottic area.
• Typically affecting children aged six months to 3 years, about 3% annually.
• Primarily viral etiology following a previous URTI.
• Fever, hoarse barking cough, dyspnea, and inspiratory stridor are manifestations
• Usual duration of symptoms is 3-5 days.
• Differentiating from epiglottitis involves lateral neck radiography in severe stridor cases.

Bronchitis

• Inflammation of the bronchial tree.
• It usually follows a URTI.
• More frequently viruses cause it; bacterial infection typically follows viral (H. influenzae, S. pneumoniae).
• Inflammation damages mucosa and mucociliary function, causing airflow restriction and airway damage.
• In chronic bronchitis, epithelium damage can lead to necrosis.
• Incessant cough, occasional sputum (in the morning), subfebrilia or febrilia are manifestations.
• Bronchiolitis is an infant disease with viral etiology.
• Diagnosed via viral immunology methods and bacterial cultivation.

Pertussis

• Bordetella pertussis is Gram-negative, aerobic coccobacillus
• A highly contagious disease, potentially severe, especially in children.
• Starts as a mild URTI with sneezing and occasional cough then presents with paroxysmal cough, inspiratory whoop, and fainting, coughing may cause vomiting, subconjunctival hemorrhages, or fractures.
• Diagnostics include PCR, cultivation from nasopharyngeal swab.
• Control by vaccination, the incidence of infection has grown in Europe over the last two decades.

Pneumonia

• Pneumonia is an inflammation of the lung parenchyma, that beside infection, may be caused by environmental contaminants, allergy or autoimmune disease.
• Risk factors include asthma, diabetes, cystic fibrosis, chronic obstructive pulmonary disease, smoking, high age, immunocompromised.
• Classification:
  • By course: acute, chronic, recurrent, migrating
  • By pathogenesis: alveolar, intersticial
  • By ethilogy: infectious (viral, bacterial, mycotic, parasitic); non-infectious (polutants inhalation, alergy, drug complications)
  • By epidemiology: community acquired, hospital acquired
• Hospital Acquired Infection: An infection that is acquired in a hospital, or other health care facility (HAI also known as a nosocomial infection).
• Community Acquired Infections: infections contracted outside of a hospital with symptoms diagnosable within forty eight hours.

Bacterial Pneumonia, Community Acquired

• Streptococcus pneumoniae mostly causes this infection (pneumococcal pneumonia).
• Other potential pathogens include Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus, and Legionella pneumophila.
• Manifestations include cough, chest pain, fever, dyspnea (=shortness of breath), alveolar exudate production, and sputum production
• Other symptoms: include tachypnea, tachycardia, headache, abdominal pain, and nausea.

Non-purulent Intersticial Pneumonia

• Commonly called atypical pneumonia or walking pneumonia.
• Infection restricted to small areas with no lobar consolidation, low sputum production, lack of alveolar exudate, and lack of leukocytosis.
• Caused by Chlamydia sp., Mycoplasma pneumoniae, Legionella pneumophila, Francisella tularensis, also viral, protozoan and mycotic.
• Manifestations depend on causative agent, but generally includes dry cough, myalgia, arthralgia, headache, nausea, and subfebrilia.

Bacterial Pneumonia, Hospital Acquired

• Bacteria may cause hospital acquired infection, in addition to community acquired.
• Some bacteria cause hospital acquired pneumonia in increased frequency like Staphylococcus aureus, Enterobacteriaceae of normal flora, Pseudomonas sp., Stenotrophomonas maltophilia and Acinetobacter sp.
• Increased drug resistance in hospital environment strains is common.
• In patients using mechanical ventilation, natural protection is limited, which promotes colonization of bacteria via droplets.

Aspiration Pneumonia

• Lung infection caused by inhaling stomach or mouth material.
• Risks include altered consciousness, swallowing problems, alcoholism, periodontal disease or tube feeding
• Tissue is damaged from digestive enzymes in gastric fluid, causing infection.
• Bacteria and anaerobes are the primary etiology.
• Complications include lung abscess, pus filled cavity with necrotic, dead tissues.

Pneumonia in Immunocompromised Patients

• Pathogens in immunocompromised patients also lead to community acquired pneumonia, plus unusual pathogens.
• Opportunistic infections are caused by pathogens, with low pathogenicity, are bening for people in normal health
• Categories of immunocompromised patients include those with HIV, transplant recipients, cancer and congenital immune system dysfunctions.
• Viruses: HSV, CMV
• Bacteria: Mycobacterium sp., Legionella pneumophila, Nocardia sp.
• Fungi: Pneumocystis jirovecii, Aspergillus sp., Mucor sp., Cryptococcus neoformans

Pneumonia in Immunocompromised Patients: Mycobacterium

• Tuberculosis (M. tuberculosis and M. bovis) reactivation from previously latent infections are common.
• Non-tuberculous mycobacteria are saprophytic or zoonotic.
• Diagnostic methods include selective media cultivation, slow growth, and Ziehl-Neelsen/auramine stains and PCR.

Pneumonia in Immunocompromised Patients: Pneumocystic jirovecii

• Pneumocystic jirovecii is a yeast-like fungus.
• Occurs silently but is Prevalent in humans and animals.
• It is found in Pneumonia of three-quarters of people who had AIDS.
• It is one of the most common causes of death.
• Diagnosed via radiography and PCR.

Pneumonia in Immunocompromised Patients: Aspergillus sp.

• Aspergillus sp. is of a fungi mold, around 200 species.
• Ubiquitous in nature and spread quickly via airborne conidia.
• Pulmonary infection or aspergillosis, typically affects transplant patients.
• Infections spread to Hematogenous CNS and cause bloodstream infections.
• Requires microscopic, sputum, and antigen testing samples.

Diagnostics of Pneumonia: Specimens

• Sputum/induced sputum, use inhalation if the cough is not producing a specimen.
• Broncho-alveolar lavage, BAL, and bronchial aspirate are required for diagnosis of pneumonia caused by bacteria in the upper RT.
• Hemocultures tests for bacteremia.
• Antigen detection in the urine tests for S. pneumoniae and L. pneumophila.
• Antigen detection in the sputum tests for viruses.
• Serology (antibody detection) for viruses, Chlamydia, and Mycoplasma.

Specimens and Testing for Bacterial Causative Agents of RTI: Streptococcus pyogenes

• Microscopy: G+ coccus, formation of chains.
• Cultivation: beta-hemolysis on blood agar.
• Tests: catalase negative using Pyr-test.
• Uses biochemical testing and mass spectrometry for identification.
• Perform Lancefield group identification.

Specimens and Testing for Bacterial Causative Agents of RTI: Staphylococcus aureus

• Gram positive coccus formation in a cluster.
• Beige, yellow, ornage color colony of growth from pigment production on a blood sample
• Catalase and plasmacoagulase are positive, identification is confirmed via mass spectrometry and biochemical.

Specimens and Testing for Bacterial Causative Agents of RTI: Haemophilus influenzae

• Short, gram negative rod.
• Cultivated on either blood agar or in a zone of hemolysis with other bacteria using a line of S. aureus.

Specimens and Testing for Bacterial Causative Agents of RTI: Streptococcus pneumoniae

• Gram positive diplococcus
• Growth on blood agar via hemolysis
• Identified using an optochin test or through biochemical testing

Specimens and Testing for Bacterial Causative Agents of RTI: Pseudomonas aeruginosa

• G- rods.
• Grows on Beta-hemolysis, Endo lactose negative, XLD saccharides fermentation negative colored samples.

Specimens and Testing for Bacterial Causative Agents of RTI: Enterobacteriaceae

• Short, hospital-acquired gram-negative microscopic examination
• A light gray color is observed with slight hemo lysis or none at all.
• On selective agar, endotest is lactose +, and fermentation and saccharides are XLD +.

Specimens and Testing for Bacterial Causative Agents of RTI: Mycobacterium sp.

• Ziehl-Neelsen stains and auramine stain are used for microscopy of cultivation
• Colonies grow selectively
• Slow and must be grown under 4~12 weeks
• Identified by its physical morphology