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*H. influenza*

Gram (-) coccobacillus

Fastidious grower → chocolate agar

Encapsulated form is most invasive → polyribitol phosphate

IgA protease

Vaccine

*Strept. pneumoniae*

Gram (+) diplococci

Catalase (-)

Alpha hemolysis

Optochin sensitivity

Polysaccharide capsule (84 serotypes)

IgA protease

Bile soluble

Urine antigen test

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Staph. aureus

Gram (+) cocci

IV drug users

*Pseudomonas aeruginosa*

Moist environments ie hot tub

Gram (-) rods

Oxidase (+)

Lactose (-)

MacConkey agar – clear but bluish border

Cystic fibrosis patients

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*Klebsiella pneumoniae*

Enteric bacteria

Gram (-) bacillus

Blood and MacConkey agar

Lactose (+)

Endotoxin → toxic and life threatening

Capsule → difficult to treat

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Legionella pneumophila

Bacillus

Organism present in artificial water environments (heating and cooling)

Transmission by inhalation

Silver stain, BCYE agar

Urine antigen test

Predisposing condition: classically organ transplant recipients

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Atypical Pneumonia

*Mycoplasma pneumoniae*

Smallest free-living bacteria

No cell wall

Cold hemagglutinins – RBC clumping

ELISA

PCR

Complications: hemolytic anemia, erythema multiforme, myo/pericarditis

Readily treatable with non-beta-lactam antibiotics

Coxiella burnetii

Q fever

“rickettsia-like”

Giemsa stain

Obligate intracellular

Spore-like structures

Phase 1 and phase 2 antigens

Pneumonia and endocarditis

Streptococcus pyogenes

Gram (+) cocci

Catalase (-)

Beta hemolysis

Sensitive to bacitracin

Capsule contains hyaluronic acid and “M” protein

Toxin causes rashes and lyses RBCs

Superantigen disease

Pharyngitis → rheumatic fever + nephritis

Lysogeny

Strept antigen test, blood agar, ASO

Nocardia

Fungi-like because of hyphae

Gram (+) rod

Partially acid-fast

Cell wall contains peptidoglycan and lipid

Brain abscesses and nodular skin lesions

Cord factor (2x mycolic acids + 1 trehalose)

*Bordetella pertussis*

Gram (-) coccobacillus

Bordet-Gengou media

Catarrhal

Paroxysmal

Convalescent

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Mycobacteria Tuberculosis

Granulomatous inflammation

Caseous necrosis

Facultative intracellular

Acid fast

Lowenstein-Jensen medium

Facultative intracellular – within host cells

Cell wall: mycolic acid + lipids

Does not elicit humoral response

Macrophages are primary cells infected; after 3 weeks, TH1 response (produce IFN-gamma) against organisms occurs which activates macrophages to kill the mycobacteria; TH1 response also develops the granuloma formation and necrosis: hypersensitivity response leads to tissue destruction

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Histoplasma capsulatum

Fungus

Inside histiocyte (macrophages are target of infection)

Fibrocaseous (“tree bark”) nodule

Inhalation of dust particles from soil with bird or bat droppings which contain infectious spores

Latent primary lung involvement, primary usually self limited (may see coin lesion on CXR)

Secondary, chronic, progressive lung disease localized to apices with cough, fever, night sweats; local lesions in extrapulmonary sites

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Blastomyces dermatidis

Fungus

Broad-base budding

Multiple nuclei

Soil, dimorphic fungus

Pulmonary blastomycosis – abrupt illness, productive cough, headache, chest pain, weight loss, fever, abdominal pain, night sweats, chills, anorexia

Suppurative granulomas

Macrophages have limited ability to ingest/kill organisms

Neutrophils recruited

Disseminated and primary cutaneous forms also exist

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Coccidioides immitis

Valley fever

Necrotizing granuloma

Delayed type hypersensitivity to inhaled fungus

SW and Western US

Majority of primary infections are asymptomatic; 10% develop lung lesions, fever, cough, pleuritic pain, erythema nodosum or erythema multiforme (San Joaquin valley fever complex)

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Pneumocystis jiroveci

Extracellular pathogen

Interstitial plasma cell pneumonia

Mild thickening of the aveolar septa → fibrosis

Alveoli fill with foamy vacuolated material

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Aspergillus

Close-packed, branching, septate hyphae

Can invade blood vessels

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Cryptococcus Neoformans

Pneumonia because infection acquired via the respiratory tract

Clear capsule surrounding the pale blue nucleus

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CMV

Large cytomegalic cells

Enlarged nuclei and purple intranuclear inclusion surrounded by a clear halo

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Picornaviruses

  • Small, non-enveloped
  • (+) ssRNA genome
  • Virulence factors
  • Nucleocapsid

1. Enteroviruses

2. Rhinoviruses

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Enteroviruses

  • Poliovirus
  • Echovirus
  • Hepatitis A Virus

  • Replicate optimally at 37 C
  • Stable at low pH (3.0)

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Coxsackievirus

Spherical/icosahedral, naked

(+) ssRNA genome

Nucleocapsid (VP1 – VP4)

Transmission

Stool/respiratory secretions

Clinical Presentation (Hand, Foot & Mouth Disease; Type A)

Rash

Non-specific fever

Headache

herpangina (vesicular pharyngitis)

Complications

Aseptic meningitis

Myocarditis/pericarditis

Paralytic disease

Encephalitis

Treatment

Fluids

Acetaminophen

Pooled Ig for CNS disease

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Rhinoviruses

Replicate optimally at 33 C

Acid labile

Human-only reservoir

Transmission

Person-to-person via respiratory droplets

Infection via nasal epithelium (ICAM-1)

Confined to upper respiratory tract

Clinical Presentation

Sneezing, nasal discharge, nasal obstruction

Sore throat, cough, headache

Complications

Bacterial sinusitis

Bacterial otitis media

Asthma exacerbations in children

Chronic bronchitis exacerbations

Treatment

Antihistamines

NSAIDs

Decongestants (vasoconstrictors)

Cough suppressants (narcotics)

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Adenoviruses

Large, naked icosahedral shape

dsDNA genome

57 serotypes (7 association with respiratory illnesses)

Transmission

Respiratory, water-borne, fomite, fecal-oral

incubation period of 2-9 days

Clinical Presentation

Respiratory illness

Common cold symptoms

Pneumonia

Gastroenteritis

Replication Cycle

Attachment/entry: spike proteins (CAR/coxsackie-adenovirus receptor)

Uncoating

Early transcription: regulatory proteins to suppress INF-α & MHC type I

Late transcription: substrates & machinery

Genome replication + assembly → exit → cell lysis

Diagnosis

PCR

Immunofluorescence tests

Tissue culture

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Influenza virus

Segmented

(+) ssRNA genome

Hemagglutinin spike protein: binds to enter host cell

Neuraminidase spike protein: binds to exit host cell

antigenic drift: spontaneous mutations in viral genome → reassortment → new virus

A: variety of hosts (associated with pandemics)

B: human hosts only

Transmission

coughing, sneezing, talking

Clinical Presentation

Acute respiratory disease, runny nose, fatigue, myalgia, fever, vomiting, diarrhea

Complications

ear infections, sinusitis, bronchitis, pneumonia, exacerbations of asthma + CHF

Diagnosis

RT-PCR

Treatment

Adamantine

Neuraminidase inhibitors (oseltamivir, zanamivir, peramivir)

Interferons, IgA

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Coronavirus

  • (+) ssRNA genome
  • SARS

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Paramyxoviruses

Diagnosis

RT-PCR

↑IgE

Treatment

Ribavirin 

Other Viruses:

Parainfluenza virus

Measles virus

Mumps virus

Respiratory Syncytial Virus

Highly infectious

(-) ssRNA genome

Bronchiolitis, pneumonia

Transmission

Respiratory droplets + contact

Clinical Presentation

Incubation period 3-5 days

Bronchiolitis (distinct clinical syndrome)

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Herpes virus

      • Epstein-Barr virus
      • Cytomegalovirus
      • Varicella-Zoster virus