Microbiology lecture note terminology

Virus summary





Diagnosis/ Treatment/ control




class IVa


year round infection

110 serotypes

Binds ICAM. Endocytosed. Goes to URT and rarely LRT.

Nonspecific PH. No vaccine


Class IVb

Human only. Peak incidence in winter, spring.

Unknown serotypes

URT only. Low grade fever, rhinorrhea, cough, sneezing, runny nose.


vaccination not practical




Class I

> 100 serotypes

2 antigenic determinants

fibre has a specific HA determinant

respiratory + fecal transmission

worldwide, temperate zones.

ARD transmitted by resp droplets

Pharynx and tonsils. Fever, cough, vomiting, coryza, diarrhea, meningeal signs and pulmonary infiltrates.

Antibodies against Serotypes 1, and 2 by age 2

pharyngo-conjuntival fever (PCF) (serotypes 3, 7)

Topical alpha-interferon

vaccines for serotypes 3,4,7,21



class V

Pharynx and tonsils



Class V

Pharynx and tonsils

Bacterial infections

URT defenses

Lysozyme, lactoferrin, sIgA. Mucociliary escalator

LRT defenses

IgA and IgG, complement components, macrophages, Mucociliary escalator (not in alveoli)

Uncommon infections

C. diphteriae, K. pnemoniae, Pseudomonas spp., E. coli, C. albicans (is present in URT)

Predisposing factors

Damage to mucociliary cleaning mechanisms, irritants, intubation or other by-passing of normal defenses, general anaesthesia, inherited factors (cystic fibrosis), age

Professional pathogens

Capable of infecting healthy RT, adhere to normal mucosa, interfere w/ action of cilia, evade removal, damage local tissue

Secondary pathogens

Require impaired host defenses. Initial damage to RT, Chronic bronchitis, depressed immune response, or depressed resistance --> impared defenses.

URT infections

Conjunctivits, otitis media, sinusitis, Streptococcal pharyngitis, epiglottitis, diphtheria, bronchitis

LRT infections

Pneumonia, whooping cough, bronchitis?? pg 25-4 and 25-1 conflict

Eye defenses

Washing effect of tears (contain lysozyme)

Eye infection transmission

Poor hygiene, fomites, use of poor contact lens hygiene

Eye infection symptoms

Sore itchy eyes, purulent discharge, reddened conjunctiva

Eye infection pathogens

H. influenzae, S. pneumoniae, S. aureus

Eye infection treatment

Antibiotic drops and ointments

Otitis media

Mostly children 6-36 months. Edema and blockage of eustachian tube w/ impaired drainage of middle war fluid. Caused by S. pneumoniae, H. influenzae, S. aureus, beta-hemolytic streptococci. H. influenzae is MOST COMMON

Otitis media symptoms

Fever, headache, reddened bulging eardrums, if untreated -> drum perforation and purulent discharge.

Chronic otitis media

Fluid persists for weeks to months “glue ear”

Acute otitis media

form Common as a complication of thinovirus infection because normal flora become trapped in middle ear

Otitis media diagnosis

Gram stain & morphology. Catalase production – streps from staphs. Chocolate agar w/ C and V factors (H. influenzae)

Acute sinusitis

Range of secondary bacterial invaders same as for other URTIs. Blockage of eustachian tubes or openings of sinuses --> no mucociliary clearance --> local accumulation of inflammatory bacteria --> more swelling. H. influenzae is the MAJOR CAUSE in CHILDREN. Pneumococci also can cause it

Sinusitis diagnosis

Clinical features, microscopy and culture of aspirated pus (sinus puncture not usually carried out).

Sinusitis treatment

Elevation of head and decongestants

Acute epiglottitis

Most serious. Can be rapidly fatal. Destruction of airways due to swelling of epiglottis and surrounding structures. Most common in young children. Characterized by acute inflammation, edema and neutrophil infiltration. Initial low grade fever --> elevated temperature (39.5), sudden onset of breathing difficulties. H. influenzae is the most common cause. Severe invasive disease particularly associated w/ capsular ype B. Others of the 6 capsules can be present as local flora

Haemophilus influenzae in epiglotittis

Common component of URT microflora. G- coccobacillus. Facultative anaerobe. Polysaccharide capsue, IgA protease, naturally competent (transformation), produces catalase. Vaccine available. Diagnosis by culture on chocolate agar. Detection of capsular antigen (latex agglutination), radioimmunoassay. Can be prevented via vaccine, polyribose-ribitol phosphate coupled to protein carrier, T-cell response, can induce T-cell response in children as young as 2 months


Pharyngitis is the most common type of S. pyogenes infection. Can also be caused by C. diphtheriae, H. influenzae, N. gonorrhea. Severe purulent inflammation of oropharynx and tonsils. White exudate; enlarged erythematous tonsils, swollen anterior cervical nodes. Throat discomfort, malaise, fever, and headache. Complications include scarlet fever, rheumatic fever and acute glomerulonephritis, and invasive group A streptococcal diseasse

Scarlet fever

Complication of pharyngitis. Punctuate erythematous rash (sunburn-like) on neck, trunk and extermities. Spread of erythrogenic toxin

Group A Streptococci

S. pyogenes. Lancefield classification according to cell wall carbohydrate. Virulence factors streptokinase, hyaluranidase, hemolysins. Pharyngitis most common infection. Diagnosis on blood agar. Characteristic small opalescent colonies. Beta-hemolytic, bacitracin sensitive, optochin resistant. Antigen detection kits available. Rapid eradication of organism can prevent development of rheumatic fever.


Corynebacterium diphteriae. Vaccination makes this rare. Early diagnosis is critical. Block ADP-ribosylation of EF-2. 1B:1A toxin. Symptoms: swollen “bull” neck, temporary facial and neck paralysis, Greyish pseudomembrane, enlarged cervical lymph nodes. Heart, muscle, kidney, liver and other organ irregularities. Only toxin producing strains are virulent. Foreigners and unvaccinated people susceptible. Presence of a pseudomembrane.

Tinsdale agar

Contains potassium tellurite which inhibits growth of RT flora other than diphteria

Precipitate bands

Elek immunodiffusion test. Sterile filter paper impregnated w/ diptheria antitoxin is imbedded in agar. Isolates of C. diphteria streaked across plate. If toxin present, toxin diffuses away from bacteria and reacts w/ antitoxin --> lines of precipitin


Whooping cough. Caused by Bordetella pertussis. Exclusively human. Highly infectious. Adults provide main reservoir. Highly communicable amongst susceptible infants. Life threatening in infants w/ cardiac or pulmonary disease. Complications: CNS anoxia, exhaustion, secondary pneumonia. Incubation period of 1 to 3 weeks

Neurologic sequelae

Can be caused by pertussis

B. pertussis

Gram negative rod. Inhaled in respiratory droplets coughed by infected individuals. Bind to cilia of epithelial cells. Mediated by Fha (filamentous haemagglutinin). Number of virulence factors: pertussis toxin (1A:5B). Tracheal cytotoxin (inhibits ciliated epithelial cells). Diagnosed w/ FA test


Inflammation of the tracheobronchial tree. Increase in mucus-producing goblet cells. May see impairment of mucociliary mechanisms. Can be of bacterial or viral origin. Acute and chronic forms. Acute: cough is most prominent symptom. Chronic: cough and excessive mucous.

Chlamydia pneumoniae

Small, obligate intracellular parasite. Community acquired respiratory tract infections. 50% of adults in US have antibodies to this organism. Infections of both upper and lower RT. Rarely causes invasive disseminated infections. Serologic tests and culturing usually not available. Use giemsa stain, immunofluorescence, FA stain, ELISA and DNA hybridization.

Mycoplasma pneumoniae

Increased incidence in late fall and winter. Virulence factor: P1 cytoadhesion. Culture on supplemented agar: small, “mulberry” shaped colonies (corrected from notes). Diagnosis via culture requires 8-15 days. Serologic test more frequently used. Complement fixation. 4 fold rise in tites. False positives can result from infectious mononucleosis, rubella, influenza, adenovirus, listeria infections

Croup v. epiglottis

Croup vs. epiglottitis




Prodormal period 1-7 days

Rapid: 4-12 hours

Seasonal occurance

Late autumn and early winter


Typical age

3 months to 3 years

1 to 6 years

Clinical manifestations

Barking, seal like cough, coryza, low-grade fever, insipiratory and expiratory stridor

Dysphagia, drooling, muffled voice, high fever, inspiratory stridor

Treatments for various infections





Penicillin G

Resistance not yet observed in S. pyogenes



Rifampcin for close contacts. prevention = Hib vaccine


Erythromycin, penicillin G

Antitoxin. Vaccine = DPT vaccine

Otitis media



Ampicillin, amoxycillin



C. pneumoniae (bronchitis)

Doxycycline or azithromycin

M. pneumoniae (bronchitis)

Doxycycline or erythromycin

Whooping cough symptoms


Incidence in adults


Protracted paroxysmal coughing (worse at night)



SOB during coughing



Tingling sensation in throat



Sleep disturbed by cough



Whoop soung with cough



Cyanosis with cough





Infection of the lung paranchyma. Most common cause of infection related death. Overwhelming inflammatory response (which gives pathology). Influx of fluid into the lung alveoli. Interferes w/ gas exchange.


Fever, general feeling of sickness, chest pain – frequently pleuritic, cough (productive/non-productive), SOB, rapid respiration, poor colour, cyanosis, rales, shadowy infiltrate on CXR.


Chest X-ray

Systemic effects

Fever, shock, wasting

Local effects

Interference of lung function

Pneumococcal pneumonia

Can heal w/ no scar formation.

G- rods

Permanent lung tisse destruction

Anaerobic bacteria

Permanent lung tisse destruction

Anatomical involvement

Lobar v. bronchopneumonia

Lobar pneumonia

Most commonly pneumococci than with Staphylococci

Epidemiological markers

Hospital/nursing home, chronic lung disease, elevated neutrophil count = bacterial infection, age, onset and course, anatomical involvement (lobar or bronchiole)

Streptococcus pneumoniae

CAP. Follows URTI. Occasional cause of pneumonia. Normal flora in 5-40% of healthy individuals. Causes lobar pneumonia. Spreads between the alveoli until contained by anatomical barriers. Highest incidence in children < 5 years of age and adults > 40. high incidence in African Americans and native americans. Penicillin resistant (altered target).

Mycoplasma pneumoniae

CAP, young adults, summer & fall. Gradual onset, nonspecific symptoms. Flu like symptoms progessing to Dry/scantily productive cough. Earache, CXR: patchy, diffuse bronchopneumonia (involves > 1 lobe). No gram stain (no cell wall). Nucleic acid hybridization test. Culture may require 7-10 days. **ELISA is prefered choice. Complement fixation also possible. Does not have “Fried egg” colonies, but mulberry shaped colonies. Probably won't be sick enough to require hospitalization.

Haemophilus influenzae

G- bacilli (is actually pleiomorphic). CAP, Follows URTI. Part of normal flora. Also causes epiglotittis, otitis media, and meningitis. DOES NOT CAUSE INFLUENZA. Type b (capsule) most virulent. Median age of infection is 1 year. False-negatives and false-positives common. Component of normal flora. Diagnosis via chocolate agar w/ X and V factors. IF detection of capsular antigens.

Chlamydia pneumoniae

CAP. Lobar pneumonia. Small gram -. obligate intracellular parasite. General symptoms: Headache, fever, cough (non-productive), mialgia. Chronic infections associated w/ cystic fibrosis, lung cancer, and asthma. Can not gram stain. Giemsa stain for intracytoplasmic inclusions. **Complement Fixation (CF) test is most widely used. ELIA and Fluorescent antibodies also available.

Staphylococcus aureus

CAP & NAP. Associated w/ influenza. Part of normal flora. Necrotizing pneumonia

Klebsiella pneumoniae

CAP & NAP. Chronic alcoholics, diabetes, COPD. Necrotizing pneumonia. Carried by 5% of healthy individuals. Has a large capsule. See a lot of damage to lung tisse. Most damage due to endotoxin. Positive to V-P reaction and citrate reaction. Culture is pink, very viscous, muccoid colonies.

Moraxella catarrhalis

CAP & NAP. Pre-existing lung disease

Escherichia coli


Legionella pneumophila

CAP & NAP. Exposure to contaminated source. Multi-system symptoms. Develops in 1-5% of people exposed to common source. Early symptoms non-specific: fever, myalgia, malaise, anorexia. System ic effects: Watery diarrhea (25-50% of cases), nausea, vomiting. Severity and range of associated symptoms varies widely. Much of local damage due to host inflammatory response. Virulence factors:intracellular growth, possibly endotoxin , and possibly extracellular protease. Can be picked up from water fountains or from tap water, showers, air conditioners. Predisposing factors: men, immunocompromised, age, heavy alcohol consumption, debilitation, exposure to contaminated source.

Pathogenesis of pneumococcal pneumonia

S. pneumoniae infection --> outpouring of fibrinous edema fluid into alveoli, early (red) consolidation (red cells and leukocytes) (good growth medium for bacteria) --> late (grey) consolidation (consolidation of portions of lung (alveolar walls remain intact) macrophages and cell debris) --> resolution.

S. pneumoniae virulence factors

Capsular polysaccharide (85 serotypes... now 90). IgA protease, or no toxin

Pneumococcal pneumonia diagnosis

Initially dry cough --> purulent, blood-streaked or rusty sputum. Diagnosis by nasopharyngeal swab: culture on blood agar: G+; pairs. Alpha-hemolytic, growth inhibited by optochin, Quellung test, coagulase negative

Vaccination against pneumococcal pneumonia

polyvalent” capsular polysaccharide vaccine. Immunizes against 23 (85-90% of infections) of the most common serotypes. Heptavalent conjugate vaccine: 7 pneumococcal antigens conjugated to CRM197.


Mutant non-toxic diphteria toxin. Can be bound to pneumococcal antigens for vaccination

Chlamydia psittaci

Causes pneumonia following contact w/ sick birds. Can get pneumonia from this organism. Bird handlers.

Differentiating L. pneumophila

Gram stain to demonstrate neutrophils. Gimenez stain (intracellular). Culture from RT. Buffered charcoal yeast extract agar (BYCE). Supplement w/ L-cysteine; low sodium. Detection: all approaches have limited sensitivity. DFA test. Radioimmunoassay (antigen in urine)

Necrotizing pneumonia

>1 area of lung parenchyma replaced by cavities filled with debris. Large % of cases involve anaerobic bacteria and can be polymicrobial (grow in the center of biofilm). Aspiration of oropharyngeal contents into lungs (occurs w/ seizure, drug overdose, and excessive alcohol intake). Breathe has putrid smell. Fever of several weeks duration. Cough.

Pseudomonas aeruginosa

Gram – rod. Common oppurtunistic pathogen widely distributed. Culture in simple media: produces pyocyanin (yellow-green pigment). Oxidase positive.