Week 12 Flashcards

1
Q

Naked viruses

A

Naked viruses: nucleocapsid = [genome + capsid]

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2
Q

Enveloped viruses

How are they inactivated?

A
  • Enveloped viruses: nucleocapsid + matrix/tegument + lipid bilayer + glycoprotein spikes
    • Enveloped viruses can be inactivated via drying, detergents, pH, temperature
      • This is because the lipid bilayer is required for infection of cells
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3
Q

DNA Virus Genome Types (5)

A
  • Duplex, open ends: adenovirus and herpesvirus (open = say AH)
  • Duplex, closed ends: poxvirus
  • Duplex, closed circle: polyomarvirus and papillomavirus
  • Duplex, inner strand incomplete: hepadnavirus
  • Single stranded, linear: parvovirus
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4
Q

RNA Virus Genome Types (2)

A
  • Coding strand = positive strand (same polarity as mRNA and functions as mRNA)
  • Template strand = negative strand (opposite polarity of mRNA)
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5
Q

Capsid structures Types

A
  • Capsid structures (protomer → capsomer → capsid)
    • Icosohedral – rigid structure comprised that limits size of enclosed nucleic acid
    • Helical – flexible structure that can accommodate any length of nucleic acid
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6
Q

Matrix/tegument

A

Proteinaceous layer – layer between capsid and envelope containing endogenous proteins/enzymes for viral assembly and initiating new infection

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7
Q

Envelope components

A
  • Lipid bilayer derived from host cell membrane
  • Glycoprotein spikes
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8
Q

DNA Virus

Capsid Structure?

Naked or Enveloped?

(NAME EXCEPTIONS TOO)

A
  • DNA Viruses
    • Capsid: icosahedral
      • Exceptions: Pox
    • Envelope: none
      • Exceptions: Hepatitis B., Herpes viruses, and Pox
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9
Q

RNA Virus

Capsid Structure?

Naked or Enveloped?

(NAME EXCEPTIONS TOO)

A
  • Capsid: icosahedral or helical
  • Envelope
    • Icosahedral: all naked
      • Exceptions: Togaviruses and Flaviviruses
    • Helical: all enveloped
      • Exceptions: none
  • Retroviruses have complex capsid and are enveloped
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10
Q

What are the general steps of virus life cycle?

A
  • Virus Attachment Protein (VAP) binds to non-suspecting receptor on host PM
    • Capsomere on naked virus
    • Glycoprotein spike on envelope virus
  • Virus penetration: release of nucleocapsid is dependent on pH changes → conformational change
    • Endocytosis
    • Fusion
  • Uncoating of genome: release of genome from capsid
  • Cellular Sites of Replication
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11
Q

Cellular Sites of Replication

RNA vs. DNA

(EXCEPTIONS?)

A
  • RNA viruses: occurs in cytoplasm
    • Exceptions: influenza and retroviruses (only virus to have 2 exact copies of its genome)
  • DNA viruses: occurs in nucleus
    • Exceptions: Pox and Hepatitis B
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12
Q

GENOME REPLICATION

RNA+ vs. RNA -

A
  • Genome Replication: RNA-dependent RNA polymerase functions as replicase and transcriptase
    • Positive Strand Virus: positive strand codes for mRNA to make proteins, one of which is an RNA poly → positive strand acts as template to make negative strand → negative strand serves as template for mRNA and positive genome production
    • Negative Strand Virus: negative strand acts as template to make positive strand → positive strand serves as mRNA and as template for negative genome production
      • Comes with RNA-dependent RNA polymerase in the virion
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13
Q

Protein production in DNA viruses

Three regulatory classes?

A
  • Immediate-Early: regulatory proteins
  • Early: genome replication
  • Late: structural proteins
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14
Q

Provide examples of how viruses alter cell functions and appearance, intracellular defenses, and viral countermeasures.

A
  • Evelopment: budding process of enveloped viruses to exit infected cells
  • Cytopathology: host cell may be destroyed in process of evelopment
  • Intracellular defenses: cells release interferon to activate immune response against infected cell
  • Viral countermeasures: interrupt interferon signaling or encode anti-apoptotic proteins
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15
Q

Permissive vs. Non-permissive

A
  • Permissive cells: allow for complete viral life cycle including release of virus
  • Non-permissive cells: do not allow the viral life cycle to complete
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16
Q

Virus-Cell Interactions (5 TYPES)

A
  • Lytic infection – virus production with cell death
  • Abortive infection – infection of non-permissive cells with no infectious virus production
  • Persistent infection – long-term virus-cell association with cell survival
    • Chronic: virus replicates
    • Latent: no replication but some viral gene expression
  • Recurrent infection: has latent and lytic periods
  • Transformation: oncogenic conversion caused directly by viral gene activities
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17
Q

Tropism

A

Tropism – a particular disease may be caused by several viruses that have a common tissue preference

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18
Q

Virulence factors

A

Virulence factors – required for pathogenicity and/or survival in the host; may not include factors required for viral growth

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19
Q

Attenuation

A

Attenuation – loss of virulence factors

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20
Q

Explain the differences between local and systemic viral infections with respect to replication sites, target organs, and disease manifestations.

A
  • Local infection – virus replication at site of entry and spreads to adjacent cells
  • Systemic infection
    • Entry into host → primary replication → primary viremia → secondary replication → secondary viremia → disease → shedding (transmission to new host/cell)
    • Primary is low viral load
    • Secondary is high viral load
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21
Q

What if primary site of infection is target site of virus?

A
  • If primary site of infection is target site of virus, disease is shorter incubation
    • If secondary site is target tissue, disease is longer incubation
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22
Q

Viral modes of transmission

A
  • Self-inoculation
  • Inhalation
  • Breaks in skin or mucoepithelial membranes
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23
Q

Sites of Entry (6)

Defense Mechanisms?

A
  • Oropharynx – viruses can enter via aerosols or saliva
    • Defense mechanism: mucous
  • Respiratory tract – viruses can enter via inhalation
    • Defense mechanism: temperature and mucociliary transport system
      • Upper RT: 32 degrees Celsius gives rise to common cold
      • Lower RT: 37 degrees Celsius gives rise to adenovirus
  • GI tract – viruses can enter through our food and drink
    • Defense mechanism: bile salts degrade enveloped viruses
  • Skin – viruses can enter through trauma
  • Conjuctiva – viruses enters via direct inoculation
    • Defense mechanism: tears
  • Genitourinary Tract: viruses enter via sex
    • Defense mechanism: mucous, pH, urine
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24
Q

How do viruses causes damage?

A
  • Cell killing by virus replication – budding can cause cell lysis
  • Oncogenesis – can convert cells into tumor cells
  • Immunopathology – activation of immune system to cause disease symptoms
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25
Q

Provide examples of viral counter-measures against host defenses.

A
  • Cross BBB (ABs cannot reach this area)
  • Pass beneath tight junction (restrict access of immune response)
  • Viruses make IL-10 homologue (immunosuppression)
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26
Q

NAME EACH TYPE

A
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27
Q
A
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28
Q

Describe different types of exposure to viruses and provide examples of viruses that are transmitted in each situation.

A
  • Crowded living conditions – rhinoviruses, influenza
  • Certain occupations – HBV, HCV, HIV, HPV
  • Lifestyle – HIV, HPV, herpesvirus
  • Daycare centers – measles, mumps, rubella, rhinoviruses, influenza, herpesvirus
  • Travel – arboviruses, respiratory viruses
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29
Q

Explain how viruses commonly found in healthy individuals and animals can cause disease in humans.

A

Normal Flora

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30
Q

Normal Flora

Sites and Examples

A

Normal Flora

  • Oropharynx and Mouth
    • Adenoviruses and cytomegalovirus (CMV)
  • Large Intestines
    • Adenoviruses and enterovirus
  • Urinary/Reproductive Systems
    • Papillomaviruses
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31
Q

Explain how each of the following affects susceptibility and severity of viral disease: age, immune status, general health, geography, and time of the year.

A
  • Age
    • Children – susceptible because immunologically naïve and small size/physiologic requirements
    • Elderly – susceptible to new viral infections and reactivation due to decline in immune response
  • Immune status – immunosuppressed individuals are at risk
  • General health – poor nutrition leads to compromised immune system
  • Geography – population density can spread disease
  • Time of year – individuals spend more time inside during winter so higher concentration of air droplets
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32
Q

Explain the differences between outbreak, epidemic, and pandemic.

A
  • Outbreak – introduction of a virus into a new area with immunologically naïve population
  • Epidemic – spread of virus to larger geographic region
  • Pandemic – worldwide spread of virus
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33
Q

Define:

Saprophytic, Symbiotic, Parasite, Pathogen

A
  • Saprophytic – feeds on dead or decaying matter
  • Symbiotic – mutually beneficial relationship with host
  • Parasite – lives on or in a host solely to benefit itself
  • Pathogen – when the parasite harms its host, it is called this
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34
Q

How fungi differ from bacteria?

A
  • Fungi are eukaryotic
  • Major sterol in cell membrane of fungi is ergosterol
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35
Q

Characteristics of Yeast

A
  • Yeast
    • Unicellular
    • Mechanisms of division
      • Nuclear fission
      • Budding (blastoconidia or blastospores)
      • Germ tube (pseudohyphae – only occurs with Candida albicans)
36
Q

Characteristics of Molds

A
  • Molds
    • Multicellular
    • Hyphae – tubular structures of cells
      • Septated – partitioned
      • Nonseptated – not-partitioned
    • Mycelium – a mass of hyphae growing (like mold on bread)
    • Conidia/spores – break off of hyphae at septum
37
Q

Characterisitics of Dimorphic

A
  • Dimorphic
    • A mold in environment at 25 degrees Celsius and a yeast in humans at 37 degrees Celsius
38
Q

Fungi Cellular Structure?

A
  • Capsule – polysaccharide coating present on only some fungi (Cryptococcus neoformans)
  • Cell wall – made up of:
    • Mannoprotein
    • Beta glucans
    • Chitin
  • Cell membrane
    • Lipid bilayer with ergosterol
39
Q

List some noninfectious medical problems from fungi.

A
  • Allergies – hypersensitivity to fungi
  • Mycotoxins
    • Aflatoxins – Aspergillus flavus in grain storage
    • Amatoxins/phallotoxins – poisonous mushrooms produce alpha-amanitin, which inhibits RNA Pol II (mRNA)
40
Q

Diagnosostic Test used for Fungi?

A
  • Diagnosis: KOH Prep
    • Positive test indicates a cutaneous/mucosal fungal infection
41
Q

Superficial Mycoses

Characterisitics and Examples (4)

Only 1 for SPM exam, 4 total otherwise.

A
  • Characteristics
    • Involves outer keratinized layer and noninvasive
  • Tinea versicolor (caused by Malassezia fufur)
    • Causes hypo/hyper pigmentated lesions
    • Lipophilic and can infect intravenously through IVs
  • NOT REQUIRED FOR SPM EXAM
    • Tinea nigra – caused by Hortaea werneckii and causes lesions
    • Black piedra – caused by Piedraia hortae and causes dark nodules on hair shafts
    • White piedra – caused by Trichosporon genus and causes white growths around hair of groin
42
Q

Cutaneous Mycoses

Characterisitics and Examples (5)

A
  • Characteristics
    • Involves keratinized layer → inflammation of epidermis and upper dermis
    • Referred to as tinea and named by location on body (not an organism!)
  • Caused by molds called Dermatophytes
    • Itchy, flakey, red lesions
    • Referred to as ringworm
  • tinea pedis – foot (athlete’s foot)
    • Provides portal of entry for Group A Beta Strep (cellulitis)
  • tinea cruris – groin (jock itch)
  • tinea corporis – general body (classic Ringworm)
  • tinua capitis – scalp
  • tinea unguium – nails (called onychomycosis)
43
Q

Subcutaneous Mycoses

Characterisitics and Examples (3)?

A
  • Characteristics
    • Infection of dermis and subcutaneous tissue
    • Develops at site of trauma (i.e. rosebush thorn prick)
  • Sporotrichosis (Rose gardener’s disease)
    • Caused by Sporothrix schenckii (dimorphic)
    • Presents as lymphocutaneous nodules/legions following site of trauma up lymph
      • Similar presentation caused by Mycobacterium marinum (from fish tanks)
  • Chromoblastomycosis
    • Due to various pigmented molds
    • Presents as slow growing cauliflower-like nodules
  • Eumycotic mycetoma – seen in tropics (swelling)
44
Q

Explain the concept of opportunistic infections.

A

Disruption of the normal delicate balance of various factors permits colonization, infection, and disease of opportunistic infections.

45
Q

Describe epidemiology of and clinical syndromes from (3 total syndromes)

Candida (i.e. C. albicans, C. glabrata, C. krusei)

  • Yeast or mold or dimorphic?
A
  • (YEAST)
    • Part of normal flora
    • Pathogenicity occurs endogenously
    • Syndromes
      • Mucosal: thrush – cottage cheese-like coating of mouth
      • Cutaneous: intertrigo – red rash in between skin folds
      • Candidemia: retinitis – fungus in bloodstream seeds in retina (via IV)
      • IMPORTANT: positive respiratory samples never indicate pneumonia
46
Q

Describe epidemiology of and clinical syndromes from…

Cryptococcus (i.e. C. neoformans)

  • yeast or mold or dimorphic?
A
  • (YEAST)
    • Prominent capsule that is identified with India Ink
    • Strictly opportunistic pathogen seen predominately in AIDS
    • Bird feces → lungs → brain
    • Syndromes
      • Cryptococcal Meningitis
47
Q

Describe epidemiology of and clinical syndromes from…

Pneumocystis (fungi but treated as a protozoan)

A

Lacks ergosterol and does not respond to anti-fungals

Strictly opportunistic pathogen seen predominately in AIDS

48
Q

Describe epidemiology of and clinical syndromes from…

Histoplasmosis

  • Mold or yeast or dimorphic
A
  • Endemic Mycoses - DIMORPHIC
    • Epidemiology: Ohio and Mississippi River valleys
    • Transmission: mold grows in soil → infects macrophages → grows as yeast in human
      • Patients not contagious in yeast form
    • Symptoms: infects lungs
    • Diagnosis: histology showing macrophages with many small intracellular yeast
49
Q

Describe epidemiology of and clinical syndromes from…

Blastomycosis

  • yeast or mold or dimorphic?
A
  • Endemic Mycoses - DIMORPHIC
    • Epidemiology: Ohio and Mississippi River valleys
    • Transmission: mold grows in soil → grows as yeast in human
      • Patients not contagious in yeast form
    • Symptoms: infects lungs/cutaneous lesions
    • Diagnosis: histology showing broad-based budding during division
50
Q

Describe epidemiology of and clinical syndromes from…

Coccidioidomycosis

  • yeast or mold or dimorphic?
A
  • Endemic Mycoses - DIMORPHIC
    • Epidemiology: arid Southwestern States (AZ and CA)
    • Transmission: mold grows in soil → inhalation of spores → yeast grows in lungs
    • Symptoms: asymptomatic but disseminated disease is lethal (skin/lung)
    • Diagnosis: large spherules containing endospores
51
Q

Describe epidemiology of and clinical syndromes from…

Aspergillus - most commonly Aspergillus fumigatus (or Aspergillus-like: Pseudallescheria boydii, Fusarium, Penicllium)

  • mold or yeast or dimorphic?
  • 3 total syndromes?
A
  • Invasive Molds
    • Septated hyphae with 45 degree branching
    • Neutropenia is biggest risk
    • Clinical Syndromes
      • Allergic bronchopulmonary aspergillosis (ABPA) – colonization of airways leads to asthmatic symptoms
        • Responds to steroids
      • Invasive aspergillosis (IA) – prolonged neutropenia and causes infarcts
        • Responds to antifungals
      • Aspergilloma (or fungus ball) – in pre-existing lung cavity
        • Responds to surgery
52
Q

Describe epidemiology of and clinical syndromes from…

Mucormycosis – most commonly caused by Mucor (or Zygomyces)

  • mold or yeast or dimorphic?
A
  • Invasive Molds
    • Risk factors: DKA, steroids, neutropenia, iron overload
    • Diagnosis: non-septated hyphae with 90 degree branching
    • Clinical Syndromes
      • Rhinocerebral: black necrotic eschars in nasal passage
53
Q

Non-invasive Molds

A

Dermatophytes (see above)

Trichophyton, Microsporum

54
Q

Flu-like symptoms (fever, coughing, chills, myalgia)

A

Influenza

55
Q

Cold sores/blisters on the genitals or mouth

A

Herpes Simplex virus

56
Q

Chicken pox: red sores all over the skin

Shingles: painful rash on half the body (neural)

A
  • Varicella-zoster virus
    • Varicella – Chicken pox: red sores all over the skin
    • Zoster – Shingles: painful rash on half the body (neural)
57
Q
  • Oral hairy leukoplakia in AIDs
    • White rash on edge of the tongue
A

Epstein-Barr Virus

58
Q

Retinitis – inflammation of the eye

A

Cytomegalovirus

59
Q
  • Family:RNA Viruses
  • Target:Influenza A
  • MOA:M2 inhibitors
  • Clinical:Not used clinically
A

Amantadine/Rimantadine

60
Q
  • Family: RNA Viruses
  • Target: Influenza A & B
  • MOA: Neuraminidase Inhibitor – prevents cleavage of HA and sialic acid à blocking release of virus
  • Clinical:
    • Zanamivir – powder (contraindicated in asthma pts)
    • Oseltamivir – oral
A

Zanamivir/Oseltamivir(Tamiflu)

61
Q
  • Family: DNA Viruses
  • Target: HSV, VZV
    • (EBV – oral hairy leukoplakia in AIDs)
  • MOA:
    • DNA homolog: Acts as a DNA chain terminator
    • Prodrug → active drug via viral thymidine kinase (TK)
  • Clinical:
    • Resistance via TK mutations
    • Drug of choice for HSV encephalitis
A

Acyclovir (IV)

62
Q
  • Family: DNA Viruses
  • Target: HSV, VZV
  • MOA:
    • Prodrug of Acyclovir that are activated in intestinal wall or liver
    • More bioavailable form of Acyclovir
  • Clinical:
    • More Bioavailable than acyclovir in oral form
    • Used for herpes labialis before symptom appear
A

Valacyclovir/Famciclovir (PO)

63
Q
  • Family: DNA Viruses
  • Target: CMV
  • MOA:
    • Triphosphate that inhibits viral DNA synthesis
  • Clinical:
    • IV for therapeutics
    • PO for prophylaxis
    • CMV retinitis
    • Very toxic (bone marrow)
A

Ganciclovir (IV) /Valganciclovir (po)

64
Q
  • Family: DNA Viruses
  • Target: Resistant CMV, HSV, VZV
  • MOA:
    • Pyrophosphate analog that inhibits viral DNA synthesis
  • Clinical:
    • CMV retinitis
    • Very toxic (kidney)
A

Foscarnet (IV)

65
Q
  • Family: Polyenes
  • Target: Cell membrane
  • MOA:
    • Lipophilic molecule that binds to ergosterol
  • Use:
    • Candida, Cryptococcal,
    • Mucormycosis (drug of choice)
    • EXCEPT: Pseudallescheria
  • Clinical:
    • Tx: Meningitis, Neutropenia
    • HIGH nephrotoxicity
    • Less toxic versions available (Lipid versions)
A

Amphotercin (IV)

66
Q
  • Family: misc.
  • Target: n/a
  • MOA:
    • interferes with nucleic acid synthesis
  • Use:
    • Candida, Cryptococcal,
  • Clinical:
    • In meningitis: used with amphotericin initially → fluconazole
    • Toxic to bone marrow
A

Flucytosine (PO)

67
Q
  • Family: Azole
  • Target: Cell membrane
  • MOA:
    • inhibits ergosterol synthesis
  • Use:
    • Candida albicans, Cryptococcal
    • NOT MOLDS
  • Clinical:
    • Candida krusei & glabrata are resistant
    • Tx: esophagitis, candidemia
A

Fluconazole

68
Q
  • Family: Azole
  • Target: Cell membrane
  • MOA:
    • inhibits ergosterol synthesis
  • Use:
    • Sporotrichosis
    • Histo & Blasto
  • Clinical:
    • Pulse therapy for onychomycosis
A

Intraconazole

69
Q
  • Family: Azole
  • Target: Cell membrane
  • MOA:
    • inhibits ergosterol synthesis
  • Use:
    • Aspergillus (drug of choice)
  • Clinical:
    • Visual disturbances
A

Voriconazole

70
Q
  • Family: Azole
  • Target: Cell membrane
  • MOA:
    • inhibits ergosterol synthesis
  • Use:
    • Mucormycosis (not used clinically)
  • Clinical:
    • Prophylaxis
A

Posaconazole

71
Q
  • Family: Azole
  • Target: Cell membrane
  • MOA:
    • inhibits ergosterol synthesis
  • Use:
    • Aspergillus & Mucormycosis
  • Clinical:
    • New drug: expanding role
A

Isavuconazole

72
Q
  • Family: Echinocandins
  • Target: Cell wall
  • MOA:
    • Inhibits synthesis of 1,3-beta-D glucan
  • Use:
    • Candida and Aspergillus
  • Clinical:
    • Tx: esophagitis, candidemia

Last line of defense against Aspergillus

A

Caspofungin (IV)

73
Q

Can you mix 2 or 3 antifungals?

A

Mix 2 or 3 of these Antifungals → Extra toxicity and possible antagonism of MOAs

74
Q

What are Newer Respitory Viruses? (5)

A
  • Hantavirus Pulmonary Syndrome – noncardiogenic pulmonary edema due to inhalation of aerosolized saliva
  • Metapneumovirus – upper and lower respiratory infections caused by paramyxovirus
  • SARS (Severe Acute Respiratory Syndrome) and MERS (Middle East Respiratory Syndrome) – caused by coronviruses
  • Avian Influenza (Bird Flu) – very rare human-to-human transmission caused by Influenza A (H5N1 and H7N9)
    • Can become pandemic once gain human virulence factors
  • H1N1 (Swine Flu) – pandemic that is now in seasonal vaccine
75
Q

Disease: Common Cold

Presentation, Etiology, Treatment?

A

Presentation: Coryza (runny nose)

Etiology: Rhinovirus or coronavirus

Treatment: Let run natural course

76
Q

Disease: Sinusitis / Otitis Media / Mastoiditis

Presentation, Etiology, Treatment?

A

Presentation: Inflammation of ear drum, sinuses

Etiology: Assumed to be bacterial: Strep pneumonia, H. flu, or Moraxella catarrhalis

Treatment: Amoxicillin

77
Q

Disease: Pharyngitis / Tonsillitis / Laryngitis

Presentation, Etiology, Treatment?

A

Presentation: Inflammation of pharynx, tonsils, larynx

Etiology: Viral, usually part of common cold or flu

Treatment: Make sure it’s not bacterial

78
Q

Disease: Epiglottitis (Supraglottitis)

Presentation, Etiology, Treatment?

A

Presentation: In children: cellulitis of supraglottic region (vocal cords); fever; sore throat; drooling

Etiology: Haemophilus influenzae type b

Treatment: Beta-lactamase resistant antibiotic (Cefatriaxone)

79
Q

Disease: Laryngotracheobronchitis (Croup)

Presentation, Etiology, Treatment?

A

Presentation: In children: inflammation of subglottic region (below vocal cords); barking cough; stridor; hoarseness

Etiology: Parainfluenza virus

Treatment: n/a

80
Q

Disease: Tracheobronchitis / Bronchitis

Presentation, Etiology, Treatment?

A

Presentation: Cough

Etiology: Virus

Treatment: Make sure it’s not pneumonia

81
Q

Disease: Whooping Cough (Pertussis)

Presentation, Etiology, Treatment?

A

Presentation: 1- to 3-week incubation; dry short coughs followed by inspiratory gasp or “whoop”; lymphocytosis

Etiology: Bordetella pertussis

Treatment: Macrolides (Azithromycin)

82
Q

Disease: Bronchiolitis

Presentation, Etiology, Treatment?

A

Presentation: Occurs in first two years of life; wheezing; hyperaeration of lungs (air trapping)

Etiology: Respiratory Syncytial Virus (RSV), especially during winter

Treatment: Let run natural course

83
Q

Disease: HAP

Presentation, Etiology, Treatment?

A

Presentation: Fever; cough; sputum; X-ray consolidation

Etiology: Pseudomonas (nosocomial)

Treatment: Sputum sent for Gram stain and culture

84
Q

Disease: CAP

Presentation, Etiology, Treatment?

A

Presentation: Fever; cough; sputum; X-ray consolidation

Etiology:

  • Normal anaerobes from aspiration
  • Typical: Strep pneumoniae
  • Atypical: Mycoplasma pneumoniae, Legionella pneumophila, Chlamydophila pneumoniae

Treatment: Sputum sent for Gram stain and culture

85
Q

Disease: Post-influenza Pneumonia

Presentation, Etiology, Treatment?

A

Presentation: Fever; cough; sputum; X-ray consolidation

Etiology: Staph aureus

Treatment: Sputum sent for Gram stain and culture