Respiratory System Microbiology Past Paper PDF 2025

ECUSTA Higher Learning Institute Module: Respiratory System Course: Microbiology Dr. Alem A (PhD, Medical Microbiology) School of Medicine, CHS, Addis Ababa University January, 2025  Respiratory tract infections---Overview 2...

ECUSTA Higher Learning Institute Module: Respiratory System Course: Microbiology Dr. Alem A (PhD, Medical Microbiology) School of Medicine, CHS, Addis Ababa University January, 2025  Respiratory tract infections---Overview 2 The air we inhale contains millions of suspended particles, including microorganisms most of which are harmless a variety of microorganisms live harmoniously in the upper respiratory tract and oropharynx The lower respiratory tract normally lacks microorganisms  Respiratory tract infections---Overview 3 Infections of the upper respiratory tract are a common ambulatory care complaint vast majority of infections are viral and are self-limited some may require hospitalization, particularly in the pediatric population  Lower respiratory tract infections important cause of morbidity and mortality worldwide more severe than infections of the URT 4 5 Mycobacterium tuberculosis Mycobacteria possess a complex, lipid-rich cell wall that is responsible for many of its characteristic properties Acid-fastness; slow growth; resistance to detergents, common antibacterial antibiotics, and the host immune response; antigenicity)  Mycobacterium tuberculosis 6 M. tuberculosis grows slowly it has a doubling time of 18 hours Because growth is so slow, cultures of clinical specimens must be held for 6-8 weeks before being recorded as negative AFB Lowenstein Jensen (LJ) Media  M. tuberculosis… 7 Weakly gram-positive, strongly acid-fast rods M. tuberculosis is an obligate aerobe its predilection for causing disease in highly oxygenated tissues such as the upper lobe of the lung and the kidney The acid-fast property of M. tuberculosis is attributed to long- chain (C78–C90) fatty acids called mycolic acids in the cell wall Cord factor (trehalose dimycolate) is correlated with virulence of the organism  M. tuberculosis… 8 Transmission & Epidemiology M. tuberculosis is transmitted from person to person by respiratory aerosols produced by coughing The source of the organism is a cavity in the lung that has eroded into a bronchus The portal of entry is the respiratory tract, and the initial site of infection is the lung In tissue, it resides chiefly within reticuloendothelial cells (e.g., macrophages)  M. tuberculosis… 9 Transmission & Epidemiology Tuberculosis occurs in only a small number of infected individuals Populations at greatest risk for disease are diabetes (high blood sugar) immunocompromised patients (particularly those with HIV infection) being malnourished tobacco use individuals exposed to diseased patients  M. tuberculosis… 10 Transmission & Epidemiology The WHO estimated that one-fourth of the world’s population is infected with M. tuberculosis In 2022 an estimated 10.6 million people fell ill with tuberculosis worldwide a total of 1.3 million people died from TB  M. tuberculosis… 11 Pathogenesis and Immunity facultative intracellular - lives in both outside and inside M. tuberculosis is an intracellular pathogen able to establish lifelong infection At the time of exposure, M. tuberculosis enters the respiratory airways Few of them penetrate to the alveoli, where they are phagocytized by alveolar macrophages survives and multiplies within a phagosome produces exported repetitive protein → prevents the phagosome from fusing with the lysosome → escape degradative enzymes in the lysosome  M. tuberculosis… 12 Clinical Diseases Although tuberculosis can involve any organ, most infections in immunocompetent patients are restricted to the lungs The patient’s cellular immunity is activated and mycobacterial replication ceases in most patients within 3-6 weeks after exposure to the organism Approximately 5% of patients exposed to M. tuberculosis progress to having active disease within 2 years 5-10% experience disease sometime later in life The likelihood that infection will progress to active disease is a function of both the infectious dose and the patient's immune competence  M. tuberculosis… 13 Clinical Diseases Pulmonary tuberculosis Patients typically have nonspecific complaints of malaise, weight loss, cough, and night sweats Sputum may be scant or bloody and Purulent Extra-pulmonary tuberculosis occur as the result of the hematogenous spread of the bacilli during the initial phase of multiplication Ghons complex- Hilar lymphadenopathy + granulomatous lesion  M. tuberculosis… 14 Diagnosis Tuberculin skin test and interferon (IFN)-γ release tests sensitive markers for exposure to the organism Microscopy: Acid fast staining Culture: gold standard, but take longer Nucleic acid amplification tests PCR Xpert MTB/RIF Identification most commonly made using species-specific molecular probes, sequencing, or mass spectrometry  M. tuberculosis… 15 Treatment, Prevention, and Control Prolonged treatment with multiple drugs is required to prevent development of drug-resistant strains Isoniazid (INH), ethambutol, pyrazinamide, and rifampin for 2 months followed by 4-6 months of INH and rifampin or alternative combination drugs Control of disease through active surveillance prophylactic and therapeutic intervention careful case monitoring  M. tuberculosis… 16 Multidrug-resistant TB (MDR-TB) MDR-TB is a form of TB caused by bacteria that do not respond to isoniazid and rifampicin MTB drug resistance emerges when TB medicines are used inappropriately incorrect prescription by health care providers poor quality drugs patients stopping treatment prematurely MDR-TB is treatable and curable by using second-line drugs (expensive and toxic) 17 Streptococcus pyogenes Sore throat (pharyngitis)  Streptococcus pyogenes 18 General characteristics Gram +ve cocci arranged in chains Grow best in enriched media under aerobic or anaerobic Conditions (facultative) Form β-hemolytic colonies on blood agar  Streptococcus pyogenes 19 Physiology and Structure A. Group-specific carbohydrate (Lancefield group A antigen) constitutes ~10% of the dry weight of the cell used to classify group A streptococci and distinguish them from other streptococcal groups B. Capsule Some strains of S. pyogenes have an outer hyaluronic acid capsule antigenically indistinguishable from hyaluronic acid in mammalian connective tissues protect the bacteria from phagocytic clearance encapsulated strains are more likely to be responsible for severe systemic infections  Streptococcus pyogenes 20 C. M protein major type- specific protein associated with virulent strains anchored in the cytoplasmic membrane  Streptococcus pyogenes 21 C. M protein subdivided into class I and class II both classes can cause suppurative infections & glomerulonephritis S. pyogenes with class I M proteins cause rheumatic fever Epidemiologic classification of S. pyogenes is based on sequence analysis of the emm gene that encodes the M proteins Inactivates C3b → antiphagocytic Strains of S. pyogenes that do not produce M protein are nonpathogenic  Streptococcus pyogenes 22 S. pyogenes produce several enzymes & toxins Streptokinase (fibrinolysin) activates plasminogen to form plasmin, which dissolves fibrin in clots, thrombi, and emboli Streptolysin O (oxygen-labile) is a hemolysin and antigenic (induces ASO) Streptolysin S (oxygen-stable) hemolysin but not antigenic Pyrogenic exotoxin A it is a superantigen responsible for most cases of streptococcal toxic shock syndrome  Streptococcus pyogenes 23 Streptococcal pharyngitis (strep throat) S. pyogenes is the most common bacterial cause of pharyngitis (sore throat) develops 2 to 4 days after exposure to the pathogen abrupt onset of sore throat, fever, malaise, and headache The posterior pharynx can appear erythematous with an exudate cervical lymphadenopathy can be prominent If untreated, spontaneous recovery often occurs in 10 days, but rheumatic fever may occur  Streptococcus pyogenes 24 Streptococcal pharyngitis (strep throat) Untreated pharyngitis may extend to the middle ear (otitis media) the sinuses (sinusitis) the mastoids (mastoiditis) the meninges (meningitis) Complication: Acute Rheumatic Fever  Streptococcus pyogenes 25 Laboratory Diagnosis of S. pyogenes Microscopy: gram-positive cocci in pairs and chains in association with leukocytes Culture S. pyogenes is susceptible to bacitracin β-hemolytic Antibody Detection ASO test: measuring antibodies against streptolysin O for confirming rheumatic fever or acute glomerulonephritis Treatment: Penicillin, cephalosporins 26 Streptococcus pneumoniae Pneumonia  Streptococcus pneumoniae (Pneumococci) 27 Pneumococci are gram-positive lancet-shaped cocci arranged in pairs (diplococci) or short chains oval with somewhat pointed ends rather than being round On blood agar, they produce α- hemolysis In contrast to viridans streptococci, they are lysed by bile or deoxycholate, and their growth is inhibited by optochin >94 serotypes  Streptococcus pneumoniae… 28 Virulence factors Polysaccharide capsules interfere with phagocytosis and favor invasiveness elicits primarily a β-cell (i.e., T-independent) response Specific antibody to the capsule opsonizes the organism, facilitates phagocytosis Teichoic acid: activates complement and induces inflammatory cytokine production Pneumolysin: a cytotoxin similar to the streptolysin O in S. pyogenes, binds cholesterol in the host cell membrane and creates pores IgA protease: enhances the organism’s ability to colonize the mucosa of the upper respiratory tract by cleaving IgA  Streptococcus pneumoniae… 29 Transmission Humans are the natural hosts for pneumococci → there is no animal reservoir common inhabitant of the throat and nasopharynx in healthy people, with colonization more common in children than in adults not considered to be communicable Pneumococcal disease occurs when organisms colonizing the nasopharynx and oropharynx spread to the lungs (pneumonia) MOPS paranasal sinuses (sinusitis) meningitis ears (otitis media) Otitis media meninges (meningitis) pneumonia sinusitis  Streptococcus pneumoniae… 30 Clinical Diseases Pneumonia often begins with a sudden chill, fever, cough, and pleuritic pain Sputum is a red or brown “rusty” color. Sinusitis and Otitis Media Bacteremia occurs in 25% to 30% of patients with pneumococcal pneumonia and in more than 80% of patients with meningitis Meningitis  Laboratory Diagnosis Microscopy Elongated pairs of gram-positive cocci surrounded by an unstained capsule Quellung (German for “swelling”) reaction polyvalent anticapsular antibodies are mixed with the bacteria the mixture is examined microscopically A greater refractiveness around the bacteria is a positive reaction for S. pneumoniae An alternative test Mix a drop of bile with a suspension of bacteria Bile will dissolve S. pneumoniae and no organisms will be seen in the Gram stain 31  Laboratory Diagnosis 32 Culture Specimen: Sputum, Blood, CSF etc α-hemolytic colonies on blood agar The colonies are bile-soluble (i.e., are lysed by bile) inhibited by optochin PCR  Treatment and prevention 33 Treatment Drug of choice for severe pneumococcal infections is penicillin G, for mild infections oral penicillin V Erythromycin or one of its long-acting derivatives (e.g., azithromycin) can be used for Penicillin-allergic patients Vancomycin is the drug of choice for the penicillin-resistant pneumococci Prevention 13-valent pneumococcal conjugate vaccine (Prevnar 13) for children causes IgG response Unconjugated 23-valent pneumococcal vaccine (Pneumovax 23) for adults causes IgM response 34 Bordetella pertussis Whooping cough (pertussis)  Bordetella pertussis 35 Characteristics first described by Bordet and Gengou in 1906 extremely small (0.2 to 0.5 × 1 μm), strictly aerobic, gram-negative coccobacillus 14 Bordetella species are currently recognized, with four species responsible for human disease A. B. pertussis: responsible for pertussis or whooping cough B. B. parapertussis: responsible for a milder form of pertussis C. B. bronchiseptica: responsible for respiratory disease in dogs, swine, laboratory animals, and occasionally humans D. B. holmesii: an uncommon cause of sepsis  Bordetella pertussis 36 Transmission and Epidemiology Pertussis is a human disease with no other recognized animal or environmental reservoir B. pertussis is transmitted by airborne droplets produced during the severe coughing episodes The organisms attach to the ciliated epithelium of the upper respiratory tract but do not invade the underlying tissue Pertussis is a highly contagious disease that occurs primarily in infants and young children and has a worldwide distribution. The number of cases has declined due to vaccine Historically, pertussis was considered a pediatric disease Significant proportion of infections in adolescents and adults  Bordetella pertussis 37 Pathogenesis and Immunity Infection with B. pertussis and the development of whooping cough require exposure to the organism → bacterial attachment to the ciliated epithelial cells of the respiratory tract → proliferation of the bacteria → production of localized tissue damage and systemic toxicity A. Attachment to ciliated epithelial cells Mediated by pertactin, filamentous hemagglutinin, and fimbria  Bordetella pertussis 38 Pathogenesis and Immunity… B. Pertussis toxin stimulates adenylate cyclase → increase in cAMP → edema of the respiratory mucosa →contributes to the severe cough of pertussis has a domain that mediates its binding to receptors on the surface of respiratory tract epithelial cells It is an A-B subunit toxin Pertussis toxin also causes a striking lymphocytosis in the blood of patients with pertussis Inhibit lymphocytes entry to lymphoid tissues; e.g spleen and lymph nodes  Bordetella pertussis 39 Pathogenesis and Immunity… C. Adenylate cyclase when taken up by phagocytic cells, can inhibit their bactericidal activity Bacterial mutants that lack cyclase activity are avirulent D. Tracheal cytotoxin is a fragment of the bacterial peptidoglycan that damages ciliated cells of the respiratory tract appears to act in concert with endotoxin to induce nitric oxide, which kills the ciliated epithelial cells  Bordetella pertussis 40 Pathogenesis and Immunity… Recovery from whooping cough is followed by immunity that is not lifelong Second infections may occur but are usually milder Reinfections occurring years later in adults may be severe It is probable that the first defense against B. pertussis infection is the antibody that prevents attachment of the bacteria to the cilia of the respiratory epithelium Antibodies to Pertussis toxin (PT) are highly immunogenic  Bordetella pertussis 41 Clinical Findings After 7-10 days of incubation period, the classical presentation of pertussis proceeds through three stages a. Catarrhal stage The first stage resembles a common cold, with serous rhinorrhea, sneezing, malaise, anorexia, and low-grade fever Because the peak number of bacteria is produced during this stage and the cause of the disease is not yet recognized, patients in the catarrhal stage pose the highest risk to their contacts  Bordetella pertussis 42 Clinical Findings b. Paroxysmal stage begins after 1 to 2 weeks ciliated epithelial cells are extruded from the respiratory tract, and the clearance of mucus is impaired Characterized by the classic whooping cough paroxysms (i.e., a series of repetitive coughs followed by an inspiratory whoop) Mucus production in the respiratory tract is common and is partially responsible for causing airway restriction Paroxysms are frequently terminated with vomiting and exhaustion A marked lymphocytosis is also prominent during this stage  Bordetella pertussis 43 Clinical Findings c. Convalescent stage Occurs after 2 to 4 weeks the paroxysms diminish in number and severity Secondary complications can occur Clinical presentation of Bordetella pertussis disease  Bordetella pertussis 44 Laboratory Diagnosis B. pertussis is extremely sensitive to drying and do not survive unless care is taken during collection and transport of the specimen to the laboratory Culture Specimen: nasopharyngeal swabs taken during the paroxysmal stage Suitable culture medium: Bordet-Gengou medium Polymerase chain reaction (PCR) rapid, specific, and highly sensitive and should be used if available Serologic tests Isolation of the organism in patients with a prolonged cough is often difficult → serologic tests are preferred  Bordetella pertussis 45 Treatment, control and prevention Treatment for pertussis is primarily supportive Antibiotics can ameliorate the clinical course and reduce infectivity Macrolides (i.e., erythromycin, azithromycin, clarithromycin) are effective in eradicating the organisms However, this effect has limited value because the illness is usually unrecognized during the peak of contagiousness Azithromycin and clarithromycin are generally better tolerated and are the preferred macrolides Trimethoprim-sulfamethoxazole or fluoroquinolones can be used in patients unable to tolerate macrolides trimethoprime-sulfamethoxazole (cotrimoxazole)  Bordetella pertussis 46 Treatment, control and prevention There are two types of pertussis vaccines: acellular & Killed 1. Acellular vaccine (children, adult doses) contain purified proteins from the organism; i.e. inactivated pertussis toxin, filamentous hemagglutinin, pertactin and fimbriae types 2 and 3 Inactivated pertussis toxin (pertussis toxoid) The main immunogen in this vaccine inactivated genetically by introducing two amino acid changes→ eliminates its ADP-ribosylating activity but retains its antigenicity It is the first vaccine to contain a genetically inactivated toxoid  Bordetella pertussis 47 Treatment, control and prevention 1. Acellular vaccine (children, adult doses) Pediatric vaccine: administered to children at the ages of 2, 4, 6, and 15-18 months, with the 5th dose b/n 4 and 6 years Adult vaccine: administered at 11 or 12 years of age, and then again between the ages of 19 and 65 has fewer side effects than the killed vaccine but has a shorter duration of immunity  Bordetella pertussis 48 Treatment, control and prevention II. Killed vaccine contain inactivated B. pertussis organisms various side effects, including postvaccine encephalopathy at a rate of about one case per million doses administered Still in use in several countries, mainly developing countries Azithromycin is useful in prevention of disease in exposed, unimmunized individuals 49 Corynebacterium diphtheria Diphtheria  Corynebacterium diphtheriae Corynebacterium diphtheriae—Gram stain 50 Properties Looks like Chinese handwriting gram-positive rods that appear club- shaped (wider at one end) are arranged in V- or L-shaped formations are aerobic or facultatively anaerobic, nonmotile, and catalase positive The rods have a beaded appearance. The beads consist of granules The granules stain metachromatically The genus Corynebacterium contains 150 species and subspecies  Corynebacterium diphtheriae 51 Transmission and Epidemiology Diphtheria is a disease found worldwide Humans are the only natural host of C. diphtheriae C. diphtheriae is maintained in the population by asymptomatic carriage in the oropharynx or on the skin of immune people Transmission by airborne droplets can also infect the skin at the site of a preexisting skin lesion  Corynebacterium diphtheriae 52 Pathogenesis and Immunity Diphtheria toxin the major virulence factor of C. diphtheriae The tox gene is introduced into strains of C. diphtheriae by a lysogenic bacteriophage, β-phage Is an A-B exotoxin Inhibits protein synthesis by interfering with elongation factor-2 (EF-2) Affects all eukaryotic cells regardless of tissue type but not prokaryotic cells  Corynebacterium diphtheriae 53 Pathogenesis and Immunity The host response to C. diphtheriae infection 1) A local inflammation in the throat, with a fibrinous exudate that forms the tough, adherent, gray pseudomembrane characteristic of the disease 2) Antibody that can neutralize exotoxin activity by blocking the interaction of the binding domain with the receptors, thereby preventing entry into the cell  Corynebacterium diphtheriae 54 Clinical Findings The clinical presentation of diphtheria is determined by the Site of infection Immune status of the patient, and Virulence of the organism Diphtheria toxin produced at the site of the infection disseminates through the blood to produce the systemic signs of diphtheria  Corynebacterium diphtheriae 55 Clinical Findings Respiratory Diphtheria Develop after 2-4 days of incubation period Organisms multiply locally on epithelial cells in the pharynx or adjacent surfaces → localized damage as a result of exotoxin activity The onset is sudden, with malaise, sore throat, exudative pharyngitis, and a low-grade fever The exudate evolves into a thick pseudomembrane that can cover the tonsils, uvula, and palate The pseudomembrane firmly adheres to the underlying tissue difficult to dislodge without making the tissue bleed (unique to diphtheria) As the patient recovers after ~1-week course of the disease, the membrane dislodges and is expectorated  Corynebacterium diphtheriae 56 Clinical Findings Cutaneous Diphtheria acquired through skin contact with infected persons The organism colonizes the skin and gains entry into the subcutaneous tissue through breaks in the skin A papule develops first and then evolves into a chronic, nonhealing ulcer, sometimes covered with a grayish membrane  Corynebacterium diphtheriae 57 Laboratory Diagnosis Clinical diagnosis for quick patient management Microscopy: Gram stained smear of throat swab Culture: Loeffler’s medium, a tellurite plate, blood agar plate Treatment The treatment of choice is antitoxin → to neutralize unbound toxin in the blood Treatment with penicillin G or erythromycin is also recommended Antibiotics inhibit growth of the organism, reduce toxin production, and decrease the incidence of chronic carriers Prevention: immunization with diphtheria toxoid (usually given as DTP) 58 Klebsiella pneumoniae  Klebsiella 59 Characteristics Are non-motile Gram-negative rods colonizes human mucosal surfaces, including the GIT Also exist in the soil and water have a prominent capsule that is responsible for the mucoid appearance of isolated colonies and the enhanced virulence of the organisms  Genus Klebsiella 60 There is global increase in Klebsiella strains resistant to all β-lactam antibiotics including the carbapenems, as well as most other classes of antibiotics Isolates from hospital-acquired infections are frequently resistant to multiple antibiotics The management of patients with Klebsiella infections is a major clinical challenge Medically important species include K. pneumoniae and K. oxytoca → pneumonia K. granulomatis → granuloma inguinale (donovanosis)  Klebsiella pneumoniae 61 K. pneumoniae is carried in the respiratory tract of about 10% of healthy people prone to pneumonia if host defenses are lowered cause community-acquired or hospital-acquired primary lobar pneumonia Pneumonia caused by Klebsiella species involves necrotic destruction of alveolar spaces formation of cavities production of blood-tinged sputum  K. pneumoniae 62 Laboratory Diagnosis Specimen: sputum Culture Treatment Choice of drug depends on the results of sensitivity testing An aminoglycoside (e.g., gentamicin) and a cephalosporin (e.g., cefotaxime) are used empirically until the results of testing are known 63 Legionella pneumophila Pneumonia (Legionnaires’ disease)  Legionella pneumophila 64 The genus is named after the famous outbreak of pneumonia among people attending the American Legion convention in Philadelphia in 1976 (Legionnaires’ disease) Members of the genus Legionella are slender-shaped, pleomorphic, gram-negative rods (coccobacilli) needs silver stain to be visualized Gram staining There are 61 species and 3 subspecies of Legionella L. pneumophila is the cause of 90% of all infections Dieterle silver stain  Legionella pneumophila 65 Properties… Legionellae are facultative intracellular bacteria multiply in free-living amebae in nature, and in alveolar macrophages, monocytes, and alveolar epithelial cells in infected hosts Legionellae are obligate aerobic and nutritionally fastidious They require media supplemented with l-cysteine, and growth is enhanced by iron Legionellae are associated chiefly with environmental water sources such as air conditioners and water-cooling towers  Legionella pneumophila 66 Pathogenesis and immunity Legionellae can infect and survive in alveolar macrophages, monocytes, and alveolar epithelial cells Inhibit phagolysosome fusion Infected macrophages release chemokines and cytokines that stimulate a robust inflammatory response (characteristic of infections with Legionella) The organisms proliferate in their intracellular vacuole and produce proteolytic enzymes (phosphatase, lipase, and nuclease) that eventually kill the host cell when the vacuole is lysed Immunity to disease is primarily cell mediated Production of IFN-γ is critical for elimination of Legionella organisms  Legionella pneumophila 67 Clinical Findings mild influenza-like illness to a severe pneumonia Cough is common with scanty and nonpurulent sputum Hyponatremia (serum sodium ≤130 mEq/L) is an important laboratory finding that occurs more often in Legionella pneumonia than in pneumonia caused by other bacteria Legionellosis is an atypical pneumonia Most cases resolve spontaneously in 7 to 10 days, but in older or immunocompromised patients, the infection can be fatal  Legionella pneumophila 68 Laboratory diagnosis Sputum Gram stains: reveal many neutrophils but no bacteria Culture The organism fails to grow on ordinary media in a culture of sputum or blood it grows on charcoal-yeast agar, a special medium supplemented with iron and cysteine Serology: 4-fold increase in antibody titer using indirect immunofluorescence assay Detection of L. pneumophila antigens in the urine is a rapid means of making a diagnosis.  Legionella pneumophila 69 Treatment and prevention Azithromycin or erythromycin (with or without rifampin) is the treatment of choice The organism frequently produces β-lactamase, and so penicillins and cephalosporins are less effective Prevention reducing cigarette and alcohol consumption eliminating aerosols from water sources, and reducing the incidence of Legionella in hospital water supplies by using high temperatures and hyperchlorination There is no vaccine 70 Mycoplasma pneumoniae “atypical” pneumonia  Mycoplasma pneumoniae 71 Characteristics Mycoplasmas are the smallest free-living organisms; many are as small as 0.3 μm in diameter wall-less organisms; i.e. their outer surface is a flexible cell membrane → can assume a variety of shapes Not affected by antibiotics that inhibit cell wall synthesis (e.g., penicillins and cephalosporins) only bacterial membrane that contains cholesterol grow slowly on artificial media and require at least one week to form a visible colony (“fried-egg” shape) Mycoplasma pneumoniae is the major pathogen  Mycoplasma pneumoniae 72 Pathogenesis & Epidemiology Mycoplasma pneumoniae is a pathogen only for humans Transmitted by respiratory droplets Ciliary motion is inhibited and necrosis of the epithelium occurs Produce hydrogen peroxide, which contributes to the damage to the respiratory tract cells Mycoplasma pneumoniae has only one serotype Immunity is incomplete, and second episodes of disease can occur During M. pneumoniae infection, autoantibodies are produced against red cells (cold agglutinins) and brain, lung, and liver cells  Mycoplasma pneumoniae 73 Pathogenesis & Epidemiology Mycoplasma pneumoniae infections occur worldwide, with an increased incidence in the winter This organism is the most common cause of pneumonia in young adults It is estimated that only 10% of infected individuals actually get pneumonia Mycoplasma pneumonia accounts for about 5% to 10% of all community-acquired pneumonia  Mycoplasma pneumoniae 74 Clinical Findings Mycoplasma pneumonia the most common type of atypical pneumonia onset is gradual, usually beginning with a nonproductive cough, sore throat, or earache Small amounts of whitish, non-bloody sputum are produced fever, headache, malaise, and myalgias resolves spontaneously in 10 to 14 days  Mycoplasma pneumoniae 75 Laboratory Diagnosis Culture: not usually done, takes up to one week PCR: preferred Serology Treatment The treatment of choice is either a macrolide, such as erythromycin or azithromycin, or a tetracycline, such as doxycycline. The fluoroquinolone levofloxacin is also effective There is no vaccine Chlamydiae pneumoniae & Chlamydiae psittaci 76  Chlamydiae 77 Properties obligate intracellular bacteria Unable to produce sufficient energy to grow independently grow only inside host cells (epithelial cells of the mucous membranes or the lungs) Have a rigid cell wall but do not have a typical peptidoglycan layer Their cell walls resemble those of gram-negative bacteria but lack muramic acid  Chlamydiae 78 Chlamydiae have a replicative cycle different from that of all other bacteria The cycle begins when the extracellular, metabolically inert, “sporelike” elementary body (EB) enters the cell and reorganizes into a larger, metabolically active reticulate body (RB) The RB undergoes repeated cycles of binary fission to form daughter reticulate bodies, which then develop into elementary bodies, which are released from the cell Chlamydiae 79  Chlamydiae 80  C. pneumoniae & C. psittaci 81 Laboratory Diagnosis Gram stain is not useful as the organisms are too small to visualize within the cytoplasm Cytoplasmic inclusions, which can be seen with special stains (e.g., Giemsa stain) PCR ELISA Serology Treatment Tetracyclines, such as doxycycline, and macrolides, such as erythromycin and azithromycin  Chlamydia psittaci 82 Clinical features incubation period: 5 to 14 days usually manifests as headache, high fever, chills, malaise, and myalgias Pulmonary signs include a nonproductive cough, rales, and consolidation Lab Diagnosis complement fixation (CF, 4-fold↑), microimmunofluorescence (MIF) test (confirmatory test) Treatment treated successfully with doxycycline or macrolides 83 Rhinovirus  Rhinovirus Common Cold 84 Properties Member of the Picornaviridae family naked, small (25-30 nm), icosahedral capsid, ss +RNA genome Rhinoviruses are acid labile; optimum growth temp is 33°C Genome is an mRNA, i.e. Naked genome is sufficient for infection Virus replicates in cytoplasm  Rhinovirus 85 Member of the Picornaviridae family Naked, small (25-30 nm), icosahedral capsid, ss +RNA genome There are more than 100 serologic types explains why the common cold is so common They replicate better at 33°C than at 37°C explains why they affect primarily the nose and conjunctiva rather than LRT B/c they are acid-labile, they are killed by gastric acid when swallowed do not infect the gastrointestinal tract, unlike the enteroviruses. The host range is limited to humans and chimpanzees  Rhinovirus 86 Transmission & Epidemiology There are two modes of transmission directly from person to person via aerosols of respiratory droplets indirect mode: respiratory droplets are deposited on the hands or on a surface such as a table and then transported by fingers to the nose or eyes The common cold is supposed to be the most common human infection Rhinoviruses occur worldwide A few serotypes of rhinoviruses are prevalent during one season→replaced by other serotypes during the following season  Rhinovirus 87 Pathogenesis & Immunity The portal of entry is the upper respiratory tract The infection is limited to that region Rhinoviruses rarely cause lower respiratory tract disease, probably because they grow poorly at 37°C Immunity is serotype-specific and is a function of nasal secretory IgA rather than humoral antibody  Rhinovirus 88 Clinical Findings After an incubation period of 2 to 4 days, sneezing, nasal discharge, sore throat, cough, and headache are common The illness lasts about 1 week Other viruses such as coronaviruses, adenoviruses, influenza C virus, and Coxsackie viruses also cause the common cold syndrome Laboratory Diagnosis: PCR, serology not appropriate Treatment: No specific antiviral therapy 89 Coronavirus  Coronavirus 90 2nd most prevalent cause of common cold (next to rhinoviruses) Coronaviruses have caused outbreaks In 2002 an atypical pneumonia called severe acute respiratory syndrome (SARS) in China due to SARS-CoV In 2012 another severe pneumonia called Middle East respiratory syndrome (MERS) in the Middle east due to MERS-CoV In 2019 Another severe pneumonia called Coronavirus disease-19 (COVID-19) emerged in China and distributed worldwide due to SARS-CoV 2  Coronavirus 91 Coronavirus Properties Enveloped RNA virus Helical nucleocapsid Non-segmented, single-stranded, positive-polarity RNA genome No virion polymerase Virions measure 80 to 160 nm in diameter In the electron microscope, prominent club- shaped spikes in the form of a corona (halo) can be seen The receptor for the SARS coronavirus on the surface of cells is angiotensinconverting enzyme 2 (ACE-2)  Coronavirus 92 Transmission & Epidemiology Coronavirus is transmitted by the respiratory aerosol SARS originated in China in November 2002 and spread rapidly to other countries 8300 cases and 785 deaths—a fatality rate of approximately 9% Animal coronaviruses are suspected of being the source of SARS-CoV The horseshoe bat appears to be the natural reservoir for SARS-CoV, with the civet cat serving as an intermediate host  Coronavirus 93 Transmission & Epidemiology MERS An outbreak of serious, often fatal pneumonia in Saudi Arabia and other countries in the region in 2012/13 As of 2017, a total of 1879 cases of MERS have been reported, with a mortality rate of 35% Bats are thought to be a reservoir for MERS-CoV Close contact with camels appears to be the mode of transmission to humans The risk of person-to-person transmission is low but has occurred in hospitals with inadequate infection control MERS-CoV binds to CD-26 on the respiratory mucosa, not to ACE-2  Coronavirus 94 Transmission & Epidemiology COVID-19 An outbreak occurred in China and quickly spread to elsewhere WHO global COVID-19 report Globally, as of April 2024 775,364,261 confirmed cases of COVID-19 7,046,320 deaths a total of 113,593,580,510 vaccine doses have been administered.  Coronavirus 95 Pathogenesis and Immunity Most human coronaviruses have an optimum temperature for viral growth of 33°C to 35°C infection remains localized to the upper respiratory tract. SARS-CoV, SARS-CoV-2 and MERS-CoV, can replicate at 37°C and cause systemic disease in humans Coronaviruses cause cytolytic infections → disrupt the function of ciliated epithelial cells SARS-CoV and MERS-CoV can replicate at body temperatures in epithelial cells, lymphocytes, and leukocytes A combination of viral pathogenesis and immunopathogenesis causes significant lung, kidney, liver, and gastrointestinal tissue damage and depletion of immune cells  Coronavirus 96 Clinical features A. Upper respiratory tract infections Most human coronaviruses cause an upper respiratory tract infection Account for 10% to 15% of URTIs in humans The disease is similar to the common cold caused by rhinoviruses but with a longer incubation period (average, 3 days) The common cold caused by coronavirus is characterized by coryza (rhinorrhea, runny nose), scratchy sore throat, and low-grade fever This illness typically lasts several days and has no long-term sequelae  Coronavirus 97 Clinical features B. Severe acute respiratory syndrome (SARS) A form of atypical pneumonia characterized by high fever (>38° C), chills, rigors, headache, dizziness, malaise, myalgia, cough, or breathing difficulty, leading to acute respiratory distress syndrome Up to 20% of patients will also develop diarrhea Mortality is at least 10% of symptomatic people SARS-CoV is most likely transmitted in respiratory droplets  Coronavirus 98 Clinical features C. Middle East respiratory syndrome (MERS) MERS-CoV also causes acute respiratory distress syndrome, With 50% mortality of those with MERS Most of the cases of MERS have occurred in the Arabian Peninsula Bats and camels are the natural reservoirs of MERS-CoV  Coronavirus 99 Clinical features D. Coronavirus disease-19 (COVID-19) Symptoms may appear 2-14 days after exposure to the virus Anyone can have mild to severe symptoms Fever or chills Cough Shortness of breath or difficulty breathing Fatigue Muscle or body aches Headache New loss of taste or smell Sore throat Congestion or runny nose Nausea or vomiting Diarrhea  Coronavirus 100 Laboratory Diagnosis Laboratory tests are not routinely performed to diagnose coronavirus infections other than for SARS, MERS and COVI- 19 RT PCR: is the method of choice for detection of the viral RNA genome in respiratory and stool samples Virus isolation of the coronaviruses is difficult and for SARS- CoV and MERSCoV requires stringent biosafety level 3 (BSL-3) conditions Serology: for epidemiologic purpose  Coronavirus 101 Treatment, prevention and control Common cold Control of respiratory transmission of the common cold form would be difficult probably unnecessary because of the mildness of the infection SARS-CoV, SARS-CoV-2 and MERS-CoV Strict quarantine of infected individuals screening for fever in travelers from a region with an outbreak Wearing mask Practicing hand hygiene's Keep distance of at least 2m No specific antiviral therapy is available Several vaccines available for COVID-19 102 Influenza virus  Influenza virus 103 Components of the virus segmented ss-RNA genome Helical nucleocapsid Envelope RNA-dependent RNA polymerase Envelope contains Hemagglutinin (HA) & Neuraminidase (NA) Genome (Influenza A and B) − consists of eight different helical nucleocapsid segments − each segment contains a negative-sense RNA associated with the nucleoprotein (NP) and RNA polymerase  Influenza Viruses… 104 Hemagglutinin (H1-16) → H1, H2, H3, H5, H7 − viral attachment protein→bind to sialic acid on epithelial cells − Promotes fusion of envelope with cell membrane − Hemagglutinates RBCs − elicits protective neutralizing antibody response Mutation-derived changes in HA are responsible for antigenic drift and shift  Influenza Viruses… 105 Neuraminidase (NA1-9) → N1, N2, N9 Cleaves sialic acid on glycoproteins ̶ facilitates release of the virus from infected cells Degrades protective layer of mucus in RT ̶ enhances the ability of the virus to gain access to the respiratory epithelial cells The NA of influenza A virus also undergoes antigenic changes  Influenza Viruses 106 Epidemiology Influenza virus can infect human, animals and birds worldwide 3 types of influenza viruses: Influenza virus A, B, and C Human infection: H1N1, H2N2, H3N2, H5N1, H7N9 Contagion precedes symptoms and lasts for a long time Higher risk group − Children, immunosuppressed people (including pregnant women), the elderly, and people with underlying respiratory problems (e.g. Asthma sufferers and smokers) More than 90% of mortalities occur in patients who are older than 65 years The virus is easily inactivated by dryness, acid, and detergents  Influenza Viruses 107 Pathogenesis and immunity Influenza spread readily via small airborne droplets After inhalation, neuraminidase degrades the protective mucus layer − allowing the virus to gain access to the cells of the upper and lower respiratory tract Virus binds to specific sialic acid receptors through HA → internalized into a coated vesicle (endosome) → viral envelope then fuses with the endosome membrane → Uncoating and delivery of the nucleocapsid into the cytoplasm Unlike other RNA viruses, transcription and replication takes place in the nucleus but assembles and buds from the plasma membrane  Influenza Viruses 108 Pathogenesis and immunity... Influenza initially establishes a local upper respiratory tract infection the virus first targets and kills mucus-secreting, ciliated, and other epithelial cells, causing the loss of this primary defense system If the virus spreads to the lower respiratory tract, the infection can cause severe desquamation (shedding) of bronchial or alveolar epithelium influenza infection promotes bacterial adhesion to the epithelial cells → secondary bacterial infection  Influenza Viruses 109 Antigenic drift − Minor antigenic change resulting from accumulated point mutation of HA and NA genes → virus escapes immune recognition − occurs every 2 to 3 years, causing local outbreaks of influenza A and B infection Antigenic shift − Major antigenic changes resulting from the reasortment of genomes among different strains infecting a single cell − occurs only with the influenza A virus − often associated with the occurrence of pandemics  Influenza Viruses 110 Antigenic drift and shift…  Influenza Viruses 111 Clinical features Asymptomatic infection Uncomplicated Influenza − 1 to 4 days after infection; the "flu syndrome" begins with a brief prodrome of malaise and headache − followed by the abrupt onset of fever, chills, severe myalgias, loss of appetite, weakness and fatigue, sore throat, and usually a nonproductive cough − The fever persists for 3 to 8 days − unless a complication occurs, recovery is complete within 7 to 10 days  Influenza Viruses 112 Clinical features… Pneumonia − Influenza may directly cause pneumonia − More commonly promotes a secondary bacterial super-infection that leads to bronchitis or pneumonia o S. pneumoniae, H. influenza, S. aureus o sputum usually is produced and becomes purulent  Influenza Viruses 113 Laboratory diagnosis Sample: respiratory secretions Cell culture in primary monkey kidney Immunofluorescence, ELISA RT-PCR Treatment Amantadine and rimantadine inhibit an uncoating step of the influenza A virus but do not affect the influenza B and C viruses Zanamivir and oseltamivir inhibit both influenza A and B as enzyme inhibitors of neuraminidase Prevention: vaccine 114 Respiratory syncytial virus (RSV)  Respiratory syncytial virus (RSV) 115 Properties Relatively large enveloped virus with a negative- sense, single-stranded RNA genome in a helical nucleocapsid first isolated from a chimpanzee in 1956 There are two types (A & B) and many different strains of RSV causing the same diseases Its surface spikes are fusion proteins, not hemagglutinins or neuraminidases The fusion protein causes cells to fuse, forming multinucleated giant cells (syncytia), which give rise to the name of the virus most common cause of fatal acute respiratory tract infection in infants and young children  RSV 116 Transmission and Epidemiology Humans are the natural hosts of RSV RSV is very prevalent in young children; almost all children have been infected by 2 years of age RSV infections almost always occur in the winter The virus is very contagious, with an incubation period of 4 to 5 days Transmission occurs via respiratory droplets and by direct contact of contaminated hands, fomites  RSV 117 Pathogenesis & Immunity RSV infection in infants is more severe and more often involves the lower respiratory tract The infection is localized to the respiratory tract; viremia does not occur Most individuals have multiple infections caused by RSV, indicating that immunity is incomplete The reason for this is unknown not due to antigenic variation of the virus  RSV 118 Clinical Findings RSV is an important cause of bronchiolitis and pneumonia in infants RSV is also an important cause of otitis media in young children In older children and young, healthy adults, RSV causes RT infections such as the common cold and bronchitis In the elderly (>65 years of age) and in adults with chronic cardiopulmonary diseases, RSV causes severe LRT disease, including pneumonia  RSV 119 Laboratory Diagnosis RT-PCR detecting the RNA of RSV in respiratory tract specimens Rapid Antigen Test detects the presence of RSV antigens in respiratory secretions Cell culture cytopathic effect in cell culture is characterized by the formation of multinucleated giant cells Serologic test: fourfold or greater rise in antibody titer Treatment and Prevention Aerosolized ribavirin (Virazole) is recommended for severely ill hospitalized infants There is no vaccine 120 Parainfluenza Viruses  Parainfluenza Viruses 121 Large virion consists of a negative-sense RNA genome in a helical nucleocapsid surrounded by an envelope Infection is limited to the respiratory tract upper respiratory tract disease is most common, but significant disease can occur with lower respiratory tract infection There are four serologic types that can infect human Types 1, 2, and 3 are 2nd only to RSV as important causes of severe LRT infection in infants and young children are especially associated with laryngotracheobronchitis (croup) Type 4 causes only mild URT infections in children and adults  Parainfluenza Viruses 122 Epidemiology and Transmission Parainfluenza viruses are ubiquitous, and infection is common The virus is transmitted by person-to-person contact and respiratory droplets Primary infections usually occur in infants and children younger than 5 years Reinfections occur throughout life, indicating short-lived immunity  Parainfluenza Viruses 123 Clinical syndromes Parainfluenza viruses 1, 2, and 3 may cause mild coldlike URT infection (coryza, pharyngitis, mild bronchitis, wheezing, and fever) Bronchiolitis Pneumonia A parainfluenza virus infection in infants may be more severe than infections in adults causing bronchiolitis, pneumonia, and most notably croup (laryngotracheobronchitis) Croup results in subglottal swelling that may close the airway Most children recover within 48 hours  Parainfluenza Viruses 124 Laboratory diagnosis Rapid RT-PCR techniques are the method of choice Similar to other paramyxoviruses, the virions are labile during transit to the laboratory and cannot be frozen at −20° C Treatment and Prevention Treatment of croup consists of the administration of nebulized cold or hot steam No specific antiviral agents are available No effective Vaccine 125 Pneumocystis Pneumocystis jiroveci  Pneumocystis 126 Pneumocystis jirovecii (formerly P. carinii) classified as a yeast on the basis of molecular analysis, but it has many characteristics of a protozoan causes infection almost exclusively in debilitated and immunosuppressed patients, especially those with HIV infection It is the most common opportunistic infection among individuals with AIDS  Pneumocystis 127 Pneumocystis is acquired by inhalation of airborne organisms into the lungs Malnourished, debilitated, and immunosuppressed patients, especially AIDS patients with low CD4 counts (