Microbiology review week 6

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Microbiology reviewweek 6

• efking_at_u.washington.edu

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On the docket

• Wrap up fungus
• Superficial
• Subcutaneous
• Systemic
• Viral general info
• Retroviruses
• HIV
• HTLV
• Hepatotropic viruses

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Superficial mycoses

• Dermatophytes
• Can digest keratin, live in skin/hair/nails
• Infections - Tinea
• barbae beard
• capitis scalp
• cruris jock itch
• corporis ringworm
• pedis atheletes foot
• unguium nails

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Dermatophytes

• Host response - cell-mediated immunity
• Strong inflammatory response, early clearing of
  infection
• Zoophilic spp grow on animals
• Geophilic spp grow in soil
• Mild, chronic inflammatory response
• Anthropophilic spp grow on people
• Dx KOH of scrapings culture on mycologic media

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Dermatophytes

• Be able to recognize name of bug as dermatophyte
• Microsporum canis - zoophilic
• Trichophyton
• T. rubrum - anthropophilic
• T. tonsurans - anthropophilic most common cause
  of tenia capitis
• T. mentagrophytes, verrucosum - zoophilic
  associated with animal husbandry
• Epidermophyton floccosum - anthropophilic
• Rx tolnaftate, griseofulvan, terbinafine or
  azoles

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More superficial mycoses

• Malassezia furfur - tinea versicolor
• Altered pigmentation, scaling in tropics
• Phaeoannellomyces werneckii - tenia nigra
• Black macules on hands and feet mimics melanoma
• Trichosporon beiglii - white piedra
• Nodules on body hair r/o louse eggs
• Piedraia hortae - black piedra
• Nodules on body hair

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SubQ mycoses

• Invasion of skin (through punctures), subQ tissue
  causing chronic, localized lesion due to
  inappropriate immune response
• Sporothrix schenckii
• Dimorphic fungus
• Found worldwide
• Rose gardeners disease
• Skin ulcer at entry site
• Chain of nodules tracking along lymph vessel
• Rx KI, azole

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More subQ mycoses

• Chromoblastomycosis
• 3 important spp can cause
• Tropics, subtropics
• Infection following puncture of feet
• Verrucous, disfiguring lesions
• Dx sclerotic bodies
• Rx excision, itraconazole or terbinafine
  long-term

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And another

• Mycetoma
• Caused by a number of bacteria, fungi (including
  Nocardia, Pseudoallescheria boydii)
• Tropics, subtropics
• Chronic, swollen skin/subQ lesions
• Begin at hand/foot
• Can involve bone
• Draining sinuses may develop
• Dx collect material within sinus tract
• Rx debulking surgery drugs
• Actinomycetoma bactrim up to 6 months
• Eumycotic itra/fluconazole or ampho B 10 months

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Systemic mycoses

• Dimorphic fungi (yeast in vivo, mold in vitro)
• Saprophytes
• Infection begins with inhalation of conidia
• Majority of infections are asymptomatic or
  subclinical, self-limited
• Disseminated disease in immunocompromised
  populations often fatal

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Histoplasma capsulatum

• Worldwide in US, Mississippi and Ohio river
  valleys
• Lives in bird-poop enriched soil
• Histoplasmosis
• Primary infection pulmonary
• Disseminated AIDS
• Reticuloendothelial organs (liver, spleen, lymph,
  BM)
• Dx collect BM, tissue Bx
• Wright Geimsa stain, as live inside macros
• Culture mold - white, cottony colonies spiked
  macroconidia
• Also ID with DNA probe
• Rx itraconazole/ampho B for pulmonary/disseminate
  d

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Coccidioidomycosis

• SW US - San Joaquin Valley
• Soil organism flourishes during rains
• Primary infection pulmonary
• Most asymptomatic acute pneumo in 1/3,
  nodules/cavitary lesions in 5
• Disseminated disease with immunosuppression (not
  seen much in AIDS)
• Bone, skin, CNS
• Dx collect sputum, pus, urine, tissues
• Visualize thick-walled spherules with KOH
• Culture grows rapidly into cottony colony
• ID by DNA probe
• Rx itra/fluconazole, ampho B for disseminated
  disease

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Blastomycosis

• Mississippi, Ohio, St. Lawrence river valleys
• Saprophyte
• Primary infection pulmonary
• Asymptomatic or mild pneumonia can be chronic
• Disseminated disease - infrequent
• Chronic cutaneous most common
• Bone, male UG
• Dx sample sputum, prostatic fluid, subQ tissue
• serology
• Fungal stain - broad based buds
• Culture cottony colonies
• Rx itra/fluconazole or Ampho B for severe
  pulmonary/disseminated disease

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Paracoccidioidomycosis

• S and Central America - tropics, subtropics
• Saprophyte, lives in soil
• Primary pulmonary
• Subacute pneumonia, occaional progression to
  chronic pulmonary/disseminated disease
• Dissemination
• Severe, chronic mucocutaneous disease
• Dx sputum, pus, tissue Bx
• Mariners wheel on fungal stains
• Culture white/tan colonies
• ID no DNA probe tough
• Rx itra/ketoconazole, ampho B for disseminated

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The subcutaneous mycosis one is most likely to
see in the USA

• Actinomycotic mycetoma
• Sporotricosis
• Chromoblastomycosis
• Eumycotic mycetoma

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The subcutaneous mycosis one is most likely to
see in the USA

• Actinomycotic mycetoma
• Sporotricosis
• Chromoblastomycosis
• Eumycotic mycetoma

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Of the following classes of fungi, which is
composed primarily of saprophytes that have
little/no ability to cause human disease?

• Zygomycetes
• Basidiomycetes
• Ascomycetes
• deutromycetes

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Of the following classes of fungi, which is
composed primarily of saprophytes that have
little/no ability to cause human disease?

• Zygomycetes
• Basidiomycetes
• Ascomycetes
• deutromycetes

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Which of the following is the most sensitive and
specific rapid Dx test for cryptococcal
meningitis that is generally available to the
clinician?

• Cryptococcus PCR on CSF
• India ink prep on CSF
• Gram stain of CSF
• Ag detection in CSF by latex agglutination
• Ag detection in urine by latex agglutination

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Which of the following is the most sensitive and
specific rapid Dx test for cryptococcal
meningitis that is generally available to the
clinician?

• Cryptococcus PCR on CSF
• India ink prep on CSF
• Gram stain of CSF
• Ag detection in CSF by latex agglutination
• Ag detection in urine by latex agglutination

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viruses
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Basics

• Obligate intracellular parasites - no organelles
• Reproduce via assembly of components
• Virion structure
• Genome - RNA OR DNA, not both
• ss or ds, linear or circular, segmented or
  continuous strands
• ssRNA
• sense - ready to translate
• - sense - must carry RNA-dependent RNA polymerase
• structural proteins, enzymes (ex. reverse
  transcriptase)
• Capsid protein coat
• Capsomere subunits - icosoahedral or helical (RNA
  only)
• resistant to drying, acid detergents
• lipid bilayer envelope - acquire by budding
• Requires aqueous environment

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Replication

• Early phase
• Adsorption binding of viral attachment proteins
  on capsid to host cell receptors - tissue/host
  specificity
• Penetration endocytosis/membrane fusion/
  translocation
• Uncoating nucleic acid is released into nucleus
  or cytoplasm
• Start of eclipse phase where little/no infectious
  virus is detectable in cell

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Replication (2)

• Late phase
• Macromolecular synthesis
• RNA most replicate in cytoplasm if - sense,
  must encode own replicative enzymes
• DNA most replicat in nucleus use host RNA
  polymerase, transcription factors
• Early translation of proteins for DNA
  replication
• Late translation of structural (capsid) proteins
• Virion assembly
• Marks end of eclipse phase, beginning of
  maturation phase
• Release of mature virions
• Enveloped - bud from golgi/nuclear membrane/PM
• Naked - cell lysis or exocytosis

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Host cell outcomes

• Death of cell
• Cell function shuts down as virus comandeers
  protein synthesis
• Lytic infections
• Immune reaction to infection - CD8 cells, NK
  cells
• Latent infection
• Virus survives in dormant state no clinically
  overt infection. Can be reactivated
• Chronic slow infection
• Transformation

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Viral genetics

• Mutations spontaneously, readily occur
• Poor fidelity of viral polymerase no
  proofreading
• Rapid rate of replication
• Can result in attenuated mutations, host range
  mutations
• Recombination - exchange of genes between viruses
  or virus host
• Reassortment - viruses with segmented genomes
• Complementation - rescue of defective viruses

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Stages of viral infection

• Transmission
• Route depends on
• Tissue source of virus
• Ability of virus to endure environment
• Presence/absence of envelope
• With envelope - relatively fragile, must stay wet
• Infection - success depends on viral and host
  cell factors
• Cell
• Nonpermissive - doesnt allow replication of a
  particular virus
• Semipermissive - inefficient/incomplete support
  of replication
• Permissive - cell provides all machinery needed
  by virus
• Virus
• Mutation in virus can result in abortive
  infection

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Stages of viral infection (2)

• Incubation period
• Virus is replicating but has not yet reached
  target tissue or caused enough damage to produce
  symptoms
• Prodrome
• Non-specific Sx preceding characteristic Sx

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Transformation

• Stable integration into host genome can activate
  or introduce oncogenes - uncontrolled cell
  growth
• Can be initiating event in carcinogenesis not
  sufficient for malignancy by itself
• RNA viruses retroviridae
• Not usually cytocidal (notable exception HIV
  CD4)
• Transforming gene product is not essential to
  viral reproduction
• DNA viruses
• Transforming gene product is essential to viral
  reproduction
• In permissive cells primarily cytocidal
  surviving cells may be transformed
• Nonpermissive cells higher rate of
  transformation

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Retroviruses

• Family of viruses that
• carry reverse transcriptase (RTase) and replicate
  through DNA provirus intermediate
• Many carry integrase - can integrate into host
  genome
• Replication
• ssRNA - dsDNA via RTase (error prone)
• Viral DNA has sticky ends - integrates,
  replication as part of host cell genome -
  transcription to mRNA
• mRNA - translated to protein and incorporated
  into new virions as genomic material
• Oncoviridae carry oncogenes, can cause malignant
  transformation
• Lentiviridae exogenous transmission, generally
  cytopathic (ex. HIV)

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HIV

• Envelope
• Major antigenic component lots of Ag variation
• gp160 - 2 parts
• gp120 binds CD4, coreceptor
• Coreceptor CXCR4 on T cells, CCR5 on macrophages
• gp41 may bind coreceptor
• Capsid
• p24 core protein - 1st Abs made to this
• ssRNA genome
• 5 cap, ployA tail, flanked by LTRs (RQ for
  integration)
• gag - capsid proteins
• pol - RTase, protease, integrase
• env - envelope glycoproteins
• tat - transactivator, regulates virion
  production
• nef - positive regulator of virus production,
  down-regulates CD4

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Cellular HIV infection

• Virus binds to CD4 coreceptor
• Macrophages can be persistently infected -
  trojan horse that carries virus to CNS, male
  GU, lymph nodes
• CD4 cells
• Latent infection provirus is integrated into
  cell
• When these cells are activated, produce
  infectious virions
• Established early in course of infection
• Dendritic cells- virions stick to them, infect
  T cells when interact with DCs
• Some brain cells also have CD4, can be infected

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Primary HIV infection

• Acute infection
• May be asymptomatic
• Fever, pharyngitis, malaise, lymphadenopathy,
  occasional meningitis
• Wide dissemination and organ seeding,
  establishment of latent reservoirs
• Contained by CD8 response subsides in a few
  weeks
• Establishment of viral load steady state by 4-6
  months post infection
• Persistent replication from infection - death
• Level of this viral load influences long term
  course - get it low with early detection,
  antiretroviral Rx

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HIV

• Latency
• Clinically asymptomatic
• Highly variable - may last for many years
• Some may have generalized lymphadenopathy
• Progressive destruction of CD4 cells
• memory cells selectively depleted
• Eventually gets low enough that start to get
  infections
• AIDS
• Defined as CD4
• Fever, weight loss, night sweats
• Opportunistic infections candida, PCP, Kaposis
  sarcoma, histoplasmosis, toxoplasmosis, CMV

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Hairy leukoplakia
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Kaposis sarcoma
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HIV

• Acquired by sexual contact, parenterally,
  vertically
• Low efficency of transmission
• Some people innately resistant or acquire
• Post-exposure prophylaxis reduces maternal-fetal,
  needlestick transmission
• Dx
• ELISA screening test - detects Abs lots of false
  
• Western Blot - detects p24, gp120
• Viral load - measure RNA copies in plasma
• Rx RTase inhibitors (nucleoside and
  non-nucleoside), protease inhibitors - combo Rx

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Oncoviridae

• ssRNA (diploid)
• HTLV-1
• See in S Pacific, W africa, Caribbean African
  populations
• adult T-cell leukemia
• Most are smoldering, some acute
• Skin lesions, hepatosplenomegaly
• tropical spastic paraparesis
• Insidious onset of spinal cord demyelination
• HTLV-2 no known disease (yet)
• More common than -1 see in IVDA, Native Americans

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HTLV-1

• Pathogenesis
• Transmitted by breast milk, sex, transfusions
• Causes immortalization of CD4 cells
• Binds, integrates genome via RTase, integrase
• tax - activates transcription, promotes growth
  of infected cell
• rex - promotes structural mRNA synthesis
• Speeds progression of AIDS
• Dx serology, PCR
• Rx AZT, prevention by screening blood organs

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Hepatitis A

• ssRNA, no envelope, icosahedral capsid
• Picrornavirus
• Hepatitis
• Incubates 14-40 days
• Fever, vomiting, RUQ pain, jaundice
• Many asymptomatic or mild (especially kids)
• Rarely fulminant
• No chronic carriers or carcinoma
• Pathogenesis
• Fecal - oral transmission
• Migrates to liver via portal circulation,
  replicates in hepatocytes Kupffer cells
• Cell-mediated and humoral immunity needed to
  clear

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Hep A

• Epidemiology
• Epidemics related to food handlers, families,
  shellfish
• Dx
• IgM - marker of acute infection persists 4-5
  months
• IgG - marker of old infection lifelong immunity
• Viral Ag in stool
• Monitor LFTs
• Pre-exposure prophylaxis with killed vaccine
• Post-exposure prophylaxis during incubation
  period with immune serum globulin

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Hepatitis B

• dsDNA, circular genome, enveloped
• Hepadnaviridae
• Virion contains DNA polymerase with RTase
  activity
• acquisition
• Lives in body fluids - semen, saliva, urine,
  blood, breast milk
• Very contagious with parenteral contact
• Vertical - majority are perinatal

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Possible outcomes of infection
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Hep B

• Pathogenesis
• Virus enters liver cell - DNA circularizes,
  moves to nucleus
• May become integrated into DNA - chronic
  infection
• Transcription to mRNA - back to cytoplasm,
  packaged into capsid
• Virions released by exocytosis
• Liver injury due to cell mediated immune response
• Dx serology
• HBsAg- marker of live virus present 6 months
  defines chronic infection
• Anti-HBsAg - indicates immunity
• Anti-HBeAg - marker for high infectivity
• Rx
• Recombinant HBsAg vaccine for prophylaxis
• Immune globulin
• Antiviral meds for chronic active/persistent
  infection

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Hepatitis D

• Viroid with ssRNA, circular, helical capsid
• Parasite of HBV - steals HBsAg, envelope
• Coinfection with or superinfection of HBV
• Increase incidence of acute fulminant hepatitis
• More rapid cirrhosis
• Parenteral acquisition
• IVDAs in US
• Dx serology - IgG or IgM
• Rx prevent with HBV vaccine

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Hepatitis C

• ssRNA, enveloped, icosahedral capsid
• Flaviviridae
• Pathogenesis
• Parenteral transmission (maybe sexual)
• Does not integrate persists in hepatocytes,
  macrophages, latent in WBCs
• Ag variation of envelope - immune escape
• Damage due to cell-mediated immunity
• Dx serology, RNA assay, liver Bx
• Rx no vaccine IFN for chronic active disease

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Hepatitis C disease spectrum
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Hepatitis E

• ssRNA, naked
• Calcivirus
• Self-limiting hepatitis, like HAV
• Incubates 6-9 weeks
• High fatality in pregnant women
• No chronic carriers
• Epidemic water-borne disease
• Fecal - oral transmission
• Uncommon in US

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Hepatitis G

• ssRNA, enveloped, no visible capsid
• Flavivirus
• No known disease
• Parenteral transmission
• May decrease rate of HIV progression

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Which of the following statements is FALSE?

• Viruses do not have protein synthetic machinery
• Viruses contain DNA or RNA
• Both viruses and cells encode polymerase to copy
  their genomes
• Eukaryotic cells always have multiple
  chromosomes, whereas all viruses only have one
• Viruses are unable to generate their own ATP

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Which of the following statements is FALSE?

• Viruses do not have protein synthetic machinery
• Viruses contain DNA or RNA
• Both viruses and cells encode polymerase to copy
  their genomes
• Eukaryotic cells always have multiple
  chromosomes, whereas all viruses only have one
• Viruses are unable to generate their own ATP

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Hepatitis B uses reverse transcription in the
cell nucleus to initiate protein synthesis of the
hepatitis B surface antigen.

• True
• False

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Hepatitis B uses reverse transcription in the
cell nucleus to initiate protein synthesis of the
hepatitis B surface antigen.

• True
• False

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A 3 month old child presents to your office with
thrush. He is in foster care there is a hx of
IVDA in biological mother. You are concerned
about HIV infection. What do you do?

• Order a test for HIV antibody by western blot
• Order a CD4 T cell count to define if
  antiretroviral therapy is needed
• Order a test for HIV-1 RNA in plasma or HIV DNA
  in blood cells
• Treat the thrush with fluconazole and order an
  HIV antibody assay on a revisit in 2 weeks

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A 3 month old child presents to your office with
thrush. He is in foster care there is a hx of
IVDA in biological mother. You are concerned
about HIV infection. What do you do?

• Order a test for HIV antibody by western blot
• Order a CD4 T cell count to define if
  antiretroviral therapy is needed
• Order a test for HIV-1 RNA in plasma or HIV DNA
  in blood cells
• Treat the thrush with fluconazole and order an
  HIV antibody assay on a revisit in 2 weeks

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