Revision of Microbiology for Respiratory module-Summer 2024 PDF

Final Revision of Microbiology for Respiratory module- Summer2023  Respiratory Tract Infections 18-Jul-24 Medical microbiology and immunology department- MTI  Respiratory Tract Infections Disease Important patho...

Final Revision of Microbiology for Respiratory module- Summer2023  Respiratory Tract Infections 18-Jul-24 Medical microbiology and immunology department- MTI  Respiratory Tract Infections Disease Important pathogens Common cold Rhinoviruses, coronaviruses Croup Parainfluenza virus Epiglottitis Haemophilus influenzae type B (the most common cause). Pharyngitis Streptococcus pyogenes, Corynebacterium diphtheriae. Adenovirus (Pharyngoconjunctival fever) Otitis media Streptococcus pneumoniae, Haemophilus influenzae Bronchiolitis Respiratory syncytial virus Pneumonia Bacterial, viral, and fungal causes  Pharyngitis Inflammation of throat caused primarily by viruses. Streptococcus FUNGI BACTERIA Adenovirus. Candida pyogenes. VIRUSES Influenza virus. albicans (oral Parainfluenza viruses. Corynebacterium thrush) Rhinovirus. diphtheriae. Coronavirus. Borrelia vincentii, Coxsackie A virus. Fusobacterium Epstein–Barr virus. (Vincent’s angina) Cytomegalovirus. 18-Jul-24 Medical microbiology and immunology department- MTI  Streptococcus pyogenes Gram-positive cocci arranged in chains. Catalase negative. 18-Jul-24 Medical microbiology and immunology department- MTI  Clinical manifestations Streptococcal pharyngitis Scarlet fever Post streptococcal diseases Throat pain & high fever. Erythrogenic toxin -Approximately 2 weeks after On examination: producing strains result streptococcal infection (pharyngitis), rheumatic fever may develop. inflamed throat and in Scarlet fever with -Due to cross-reaction between tonsils with a yellowish rash& characteristic antibodies to streptococcal M proteins exudate and tender strawberry tongue. and heart tissue. cervical lymph nodes. -It is an autoimmune disease, exacerbated by recurrence of streptococcal infections. 18-Jul-24 Medical microbiology and immunology department- MTI  Laboratory Diagnosis Specimen: Throat swab. I-Direct smear: Gram positive cocci arranged in chains. II-Isolation and identification: by Culture on blood agar. Gram-stained smear. β-Hemolytic colonies. Catalase negative. Sensitive to bacitracin (Group A streptococci). III-Rapid detection of group A streptococcal antigens in throat swabs by ELISA or latex agglutination. 18-Jul-24 Medical microbiology and immunology department- MTI  Adenovirus Transmitted by respiratory droplets, fecal–oral, direct inoculation of conjunctiva by eye equipment or fingers. Adenoviruses infect the mucosal epithelium: of several organs (e.g. the respiratory tract, GIT, conjunctiva). Adenovirus cause: Acute infection: leading to death of the cells. Latent infection: particularly in the adenoidal and tonsillar tissues. 18-Jul-24 Medical microbiology and immunology department- MTI  Clinical manifestations 18-Jul-24 Medical microbiology and immunology department- MTI  Coxsackie virus ❑Single-stranded, positive sense RNA genome. ❑Nonenveloped with icosahedral nucleocapsid. ❑Classified into group A & group B viruses. ❑Group A–Specific Diseases: ✓ Herpangina: fever, sore throat and tender vesicles in oropharynx. ✓ Hand, foot and mouth disease: mainly in children, a vesicular rash on the hands and feet with ulcerations in the mouth. 18-Jul-24 Medical microbiology and immunology department- MTI  Corynebacterium diphtheriae Gram positive club-shaped bacilli (Chinese letter). Virulence factor: Diphtheria toxin: inhibits protein synthesis (necrotic and neurotoxic effects). Produced by lysogenized strain = Virulent strain. The organism causes local inflammation in the throat & forms thick adherent gray pseudomembrane on the tonsils and throat with sore throat, low grade fever & cervical adenopathy. The exotoxin is produced locally and spread by bloodstream to distant organs. Complications: ✓ Extension of the membrane into the larynx and trachea causing airway obstruction. ✓ Myocarditis. ✓ Nerve weakness or paralysis (especially of the cranial nerves), Peripheral neuritis affecting the18-Jul-24 muscles of the extremities. Medical microbiology and immunology department- MTI  Laboratory Diagnosis (Isolating the organism and demonstrating toxin production) Based on clinical impression and antitoxin treatment cannot wait for the laboratory results. Specimen: throat swab. I-Direct smear: Finding of many tapered Gram-positive bacilli can be suggestive. II-Culture: Loeffler’s serum, Blood tellurite medium. III-Toxin production: Elek’s test. PCR for the presence of the toxin gene.  Treatment I-Diphtheria antitoxin: Neutralize the unbound toxin in the blood before it irreversibly binds to cells. The antiserum is made in horses (precautions should be taken to manage anaphylaxis, Serum sickness may occur). II-Treatment with penicillin G or erythromycin antibiotics: Inhibit growth of the organism. Reduce toxin production. Decrease the incidence of chronic carriers. 18-Jul-24 Medical microbiology and immunology department- MTI  Prevention Diphtheria toxoid is given in 1-Diphtheria, combination with tetanus Tetanus, toxoid and killed pertussis killed vaccine. pertussis Diphtheria toxoid is prepared vaccine (DPT): by treating the exotoxin with formaldehyde. Diphtheria toxoid is given in 2- Diphtheria, combination with tetanus toxoid Tetanus, and acellular pertussis vaccine. acellular Vaccine is given at 2, 4,6 pertussis months. A booster at 1.5 years, vaccine (DTaP): at school age and every 10 years are recommended. 18-Jul-24 Medical microbiology and immunology department- MTI  Otitis media Clinical Manifestations Ear pain and pressure. Decreased hearing and fever. In some cases, On examination: the may bulge & tympanic membrane is erythematous then rupture. Diagnosis Clinically. A sample of the exudate if present analyzed by Gram stain & culture. 18-Jul-24 Medical microbiology and immunology department- MTI  Streptococcus pneumoniae Gram positive cocci (lancet shaped) arranged in pairs and have polysaccharide capsule. The most common cause of community-acquired Pneumonia. Upper respiratory tract infections: otitis media, mastoiditis and sinusitis. 18-Jul-24 Medical microbiology and immunology department- MTI  Haemophilus influenzae Small, pleomorphic Gram-negative bacilli (coccobacillus) with a polysaccharide capsule. Capsular serotype b causes most of the invasive diseases. Uncapsulated strains usually causes the non-invasive diseases. Invasive diseases: in young children (6 months-6 years) e.g. epiglottitis. Non- Invasive: Upper respiratory tract infections (otitis media, sinusitis). Pneumonia. 18-Jul-24 Medical microbiology and immunology department- MTI  Influenza Influenza virus is the only member of the orthomyxoviruses family. A segmented single-stranded negative sense RNA genome. A helical nucleocapsid and an outer lipoprotein envelope. The envelope is covered with two different types of spikes: hemagglutinin & neuraminidase. 18-Jul-24 Medical microbiology and immunology department- MTI  Influenza Antigenic Structure: 1.Group-specific antigen: The internal ribonucleoprotein that distinguishes influenza A, B, and C viruses. 2.Type-specific antigens: The hemagglutinin & neuraminidase located on the surface.  Type-specific antigens Binds to the cell surface receptor to initiate infection Hemagglutinin of the cell. Target of neutralizing antibody. Cleaves neuraminic acid to release progeny virus from the infected cell. Neuraminidase Degrades the protective layer of mucus in the respiratory tract. 18-Jul-24 Medical microbiology and immunology department- MTI  Types of Influenza Viruses Infects humans & animals. Undergoes continuous antigenic variations (Antigenic shift & drift). Many animal species have their own influenza A virus Influenza A (aquatic birds, chicken, pigs and horses). Causes worldwide epidemics (pandemics) of influenza. Pigs & birds play an important role in influenza epidemics and pandemics. Infects human only. Causes major outbreaks of influenza. Influenza B Undergoes antigenic variations only by antigenic drift. Causes mild respiratory tract infections. Influenza C Does not cause outbreaks of influenza. 18-Jul-24 Medical microbiology and immunology department- MTI  Antigenic Variation Antigenic Antigenic shift drift 18-Jul-24 Medical microbiology and immunology department- MTI  Antigenic Variation Antigenic Antigenic shift drift ✓ Major change. ✓ Minor change. ✓ Reassortment of segments of the ✓ Mutations in the genome RNA genome RNA encoding for envelope resulting in change of amino acid of glycoproteins. envelope glycoproteins. ✓ Entire segments of RNA are exchanged ✓ The current strain must be included in and new strain of the virus is produced. the new version of influenza vaccine ✓ Pigs serve “mixing bowl” within which each year. human, avian & swine viruses reassort. Occurs only in influenza A Occurs in influenza A & B (wide host range) Variants appear infrequently Variants appear every year 18-Jul-24 Medical microbiology and immunology department- MTI  Pathogenesis & Clinical manifestations The virus is transmitted by respiratory droplets. The infection is limited to respiratory tract. ✓Severe myalgias+ Respiratory symptoms= Influenza. Complications: 1-Pneumonia: influenzal or bacterial (S. aureus, S. pneumoniae). 2-Reye’s syndrome. 18-Jul-24 Medical microbiology and immunology department- MTI  Drugs for BOTH the treatment & prevention of influenza Oseltamivir (oral), zanamivir (inhalation) Neuraminidase inhibitors acting by inhibiting the release of virus from infected cells. ✓ Reducing the spread of virus from one cell to another. ✓ Effective against both influenza A & B. ✓ Avian & swine influenza are sensitive to both drugs. ✓ These drugs must be given within 48 Amantadine and rimantadine hours of the onset of symptoms. ✓ Act by inhibition of uncoating. ✓ Effective ONLY against influenza A. ✓ Avian and swine influenza are resistant to 18-Jul-24 Medical microbiology and immunology department- MTI both drugs.  Prevention (Immunization is the most reliable mode of prevention) ✓ Quadrivalent vaccine containing two A strains (H1N1 and H3N2) and two B strains. ✓ The vaccine is usually reformulated each year to contain the current antigenic strains. 18-Jul-24 Medical microbiology and immunology department- MTI  Prevention I-killed vaccine II-Live attenuated vaccine Preparation Contains purified protein subunits of the Contains temperature-sensitive mutants virus (hemagglutinin and neuraminidase). of influenza A&B viruses that can The virus is inactivated with formaldehyde. replicate in cooler nasal mucosa (33˚C), but not in warmer lower respiratory tract (37˚C). Route of administration IM or ID shortly before the flu season. Given by nasal spray. (Protection is short lived, Yearly boosters (provide mucosal, humoral and cell are recommended). mediated immunity). Immunoglobulin produced IgG IgA & IgG Recommendation for use Should be given to all persons 6 months -Recommended for children. and older. -Should not be given to pregnant women It is especially recommended for: or immunocompromised individuals. -Persons with chronic diseases. -Health care personnel. 18-Jul-24 -Pregnant woman. Medical microbiology and immunology department- MTI  Prevention III- Recombinant vaccine: Inserting the gene encoding the viral hemagglutinin into a vector that is propagated in cell culture and contains purified hemagglutinin as the immunogen. 18-Jul-24 Medical microbiology and immunology department- MTI  Croup (Acute laryngotracheobronchitis) Causative agents: Parainfluenza viruses (the most common cause). Respiratory syncytial virus. Influenza virus. Clinical Manifestations Inspiratory stridor (key finding), together with a barking cough and a hoarse voice. Diagnosis: Clinically (Mainly), Radiography. Treatment: Symptomatic. 18-Jul-24 Medical microbiology and immunology department- MTI  Parainfluenza virus A member of the paramyxovirus family. Nonsegmented single stranded negative sense RNA with Helical nucleocapsid and an outer envelope. The surface spikes: hemagglutinin, neuraminidase and fusion proteins. The fusion protein mediates the formation of multinucleated giant cells. There are four types (1,2,3,4). Parainfluenza viruses 1 and 2 are major causes of croup. 18-Jul-24 Medical microbiology and immunology department- MTI  Pneumonia Pneumonia is an inflammation of the lung affecting the alveoli. Pneumonia classified according to Presenting symptoms & Source of infection causative organism Community acquired Hospital-acquired Typical Atypical (acquired outside of the (48 hrs. or more after pneumonia pneumonia hospital) admission to hospital) 18-Jul-24 Medical microbiology and immunology department- MTI  Causative agents ❑S. pneumoniae: the most common cause. Influenza virus: the most ❑ K. pneumoniae common viral cause. BACTERIA ❑ H. influenzae Respiratory syncytial virus. VIRUSES ❑ P. aeruginosa in cystic fibrosis Parainfluenza virus. Coccidioides patients, and S. aureus in patients Adenovirus. immitis. with influenza. Human metapneumovirus. Histoplasma FUNGI ❑Wool sorter’s disease: a Corona viruses. capsulatum pneumonia caused by Bacillus anthracis. Pneumocystis In patients with reduced cell- mediated immunity: jiroveci in AIDS ❑Mycoplasma pneumoniae. herpesviruses, e.g. herpes patients. ❑Legionella species, simplex virus, varicella-zoster ❑Chlamydia pneumoniae, virus and cytomegalovirus, Chlamydia psittaci, Coxiella can cause life-threatening burnetii pneumonia. 18-Jul-24 Medical microbiology and immunology department- MTI  Typical pneumonia VS Atypical pneumonia ▪ Rapid onset, severe symptoms, ▪ Causative bacterium can’t be isolated on productive cough. routine media or the disease does not resemble pneumococcal pneumonia. ▪ Radiologic pattern: Dense ▪ Gradual onset, less severe symptoms, uniform consolidation of one or nonproductive cough. more lobes. ▪ Radiologic pattern: patchy interstitial pattern. Causative agents: Causative agents: ✓ S. pneumoniae. ✓ Mycoplasma pneumoniae. ✓ Legionella pneumophila. ✓ H. influenzae. ✓ Chlamydia pneumoniae. ✓ K. pneumoniae. ✓ Chlamydia psittaci. ✓ P. aeruginosa. ✓ Coxiella burnetii. ✓ Viruses and fungi. 18-Jul-24 Medical microbiology and immunology department- MTI  Clinical Manifestations ✓Cough (productive of sputum, “Rusty” in pneumococcal pneumonia, “Currant jelly” by Klebsiella. ✓Fever, chills, chest pain. ✓Shortness of breath. ✓Physical examination: tachypnea and rhonchi. ✓If the lung is consolidated (dullness to percussion may be detected). 18-Jul-24 Medical microbiology and immunology department- MTI  Diagnosis ✓The gold standard for diagnosis is an infiltrate on a plain chest radiograph. ✓Clinical data may be helpful. ✓Microbiological: Sputum analysis for Gram stain and culture are optional in an outpatient setting (therapy is empiric). Diagnosis = Radiologic + Clinical 18-Jul-24 Medical microbiology and immunology department- MTI  Streptococcus pneumoniae Gram positive cocci (lancet shaped) arranged in pairs and have polysaccharide capsule. The most common cause of community-acquired Pneumonia. Upper respiratory tract infections: otitis media, mastoiditis and sinusitis. 18-Jul-24 Medical microbiology and immunology department- MTI  Virulence factors IgA protease The Capsule Cleaves IgA, so enables the 1) Antiphagocytic. organism to attach to the 2) Antigenic: mucosa of upper respiratory ✓ Serologic grouping. tract. ✓ Aids in diagnosis (rapid detection in CSF). ✓ Preparation of vaccine. Pneumolysin 1) Released by autolysis. 2) Antiphagocytic. 18-Jul-24 Medical microbiology and immunology department- MTI  Prevention 13-valent pneumococcal conjugate vaccine: -The immunogen in is the The unconjugated 23-valent pneumococcal polysaccharide of the 13 pneumococcal vaccine: should be given most prevalent serotypes conjugated to to healthy individuals age 50 years or carrier protein (diphtheria toxoid). older. -Given to immunocompromised (especially splenectomized) patients & children