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MOL. BIO LAB > FINAL: DETECTION & ID OF MICROORGANISMS II > Flashcards

FINAL: DETECTION & ID OF MICROORGANISMS II Flashcards

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1
Q

TRADITIONAL DIAGNOSTIC METHODS FOR VIRUS

A
  • antibodies against the virus (INDIRECT)
  • presence or absence of viral antigens
  • growth of a virus in a culture system
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2
Q
  • Produced the host for immune response
  • Retrospective indication for infection
  • Paired sera
    o 1 from Acute phase
    o 1 from Recovery Phase
  • 4x rise from acute phase
    o Acute stage of virus
A

ANTIBODIES

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3
Q

best evidence for the presence of virus

A

IgM

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4
Q
  • Igm may be low detection limit
  • px is infected and infectious
A

WINDOW PERIOD

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5
Q
  • Produced/expressed by the pathogen/virus
A

ANTIGENS

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6
Q

DETECTION OF ANTIGENS

A

EIA/DIRECT IMMUNOFLUORESCENT ASSAYS

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7
Q
  • Tissue/cell culture
    o Monolayer of cells
    o Virus is inoculated to the culture
    o Observation of CYTOPATHIC EFFECT microscopically
A

Growth of viruses

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8
Q

Culture is Gold standard for

A

Adenovirus, enteroviruses, CMV, influenza, and HSV

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9
Q

Disadvantages OF CULTURE:

A

o Time-consuming
o Some viruses do not present cytopathic effect
o Must be collected on acute phase

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10
Q

Genomes of Viruses
- Detection via:

A
  • Detection via:
    o Target amplification
     PCR
     RT-PCR
     qPCR
     TMA
    o Signal amplification
     bDNA
     hybrid capture
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11
Q
  • RNA VIRUS; Has Reverse Transcriptase
  • Rapidly mutates, creates multiple subtypes//clades
A

Human Immunodeficiency virus (HIV)

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12
Q

Human Immunodeficiency virus (HIV) TYPE:
- More pathogenic

A

Type 1/ HIV-1

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13
Q

Human Immunodeficiency virus (HIV) TYPE:
- Minor isolate

A

Type 2/HIV-2

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14
Q

SUBTYPES OF HIV:
- 95% around the world
- Further divided into 8 clades
- A, B, C, D, E, F, G, H, J

A

GROUP M (MAJOR)

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15
Q

SUBTYPES OF HIV:
- West Africa

A

GROUP O (OUTLIER)

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16
Q

SUBTYPES OF HIV:
- Cameroon

A

GROUP N (NON - M & NON - O)

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17
Q

SUBTYPES OF HIV:
- RAREST, Cameroon

A

GROUP P

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18
Q

_________ & _________ of HIV interact with CD4- fusion

A

gp120 & gp41

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19
Q

How important are helper T cells?

A

They help to coordinate the immune response by communicating with and activating other immune cells

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20
Q

Structural genes:
- 1 envelope
- Attachment and fusion to cell
- Gp160
o Gp120
o Gp41

A

Env

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21
Q

Structural genes:
- Group Antigen gene
- Found in nucleocapsid
- p55
o P15, p17, p24
o 1st antibody to emerge in HIV

A

Gag

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22
Q

Structural genes:
- Polymerase gene
- Reverse Transcriptase
o RNA to DNA
- Integrase
o Inserts viral DNA to host DNA

A

Pol

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23
Q

HIV DIAGNOSIS:
- for antibodies produced

A

EIA = ENZYME IMMUNOASSAY

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24
Q

HIV DIAGNOSIS:
standard screening

A

ELISA = ENZYME - LINKED IMMUNOSORBENT ASSAY

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25
Q

HIV DIAGNOSIS:
- standard confirmatory test

A

Western Blot

26
Q

HIV DIAGNOSIS:
- is applied after HIV diagnosis
- for determination of viral loads

A

Nucleic acid amplification

27
Q

CDC criteria for western blot

A

2 out of 3 bands to p24, gp41 and gp120/160

28
Q

Nucleic acid amplification:
- goal of Antiretroviral therapy

A

50 copies/ml of blood

29
Q

Nucleic acid amplification:
- reduced AIDS development

A

10,000 copies/ml

30
Q
  • To know when to start ART
  • Monitor efficacy of treatment
A

RT-PCR

31
Q

Herpes virus has how many members?

A

25 members

32
Q

Herpes simplex virus
- 2 main types
 Cold sores and fever
blisters

A

HSV-1

33
Q

Herpes simplex virus
- 2 main types:
 Genital herpes

A

HSV-2

34
Q

HSV DIAGNOSIS

A
  • EARLY METHODS: CULTURE,ANTIGEN & ANTIBODY
  • WESTERN BLOT TEST
  • qPCR
35
Q
  • Can reactivate and found in saliva of infected persons
A

Epstein-Barr virus (Kissing Disease)

36
Q

Epstein-Barr virus (Kissing Disease) DIAGNOSIS?

A
  • Immunohistochemistry (IHC)
    o EBV-encoded RNA (EBER)
  • Antibodies for EBV
  • EBV nuclear antigen (EBNA)
  • Southern Blot
  • qPCR
  • Downey cells in blood smears
37
Q
  • May also reactivate
  • typically ASYMPTOMATIC, but can cause complications in people w/ weakened immune system
    -qPCR: CMV polymerase (UL54) or
    glycoprotein B (gB) gene
A

CYTOMEGALOVIRUS (CMV)

38
Q
  • Varicella Chicken pox
  • Zoster - Shingles (reactivated)
  • ELISA and PCR w/ hybridization/ gel electrophoresis
A

Varicella Zoster /Herpes Zoster virus

39
Q

Varicella Zoster /Herpes Zoster virus SPECIMEN SOURCES?

A
  • LESION SWAB, BLOOD, CSF, TISSUE BIOPSY, THROAT SWAB
40
Q
  • ssRNA virus,
    Flaviviridae
  • viral hepatitis & cirrhosis, associated w/ causing hepatocellular carcinoma
  • Parenteral transmission
  • serology: detection of antibodies (specify western blot)
  • RT - PCR, TMA, bDNA
A

HEPATITIS C VIRUS (HCV)

41
Q
  • dsDNA virus, Oncogenic
  • Five genotype groups (α, β, y, μ, and v)
  • detection: hybridization, amplification (PCR & hybrid capture), direct sequencing methods
A

Human Papilloma Virus (HPV)

42
Q

HPV Five genotype groups:
- largest, 64 types
- Anogenital cancers

A

α

43
Q

HPV Five genotype groups:
- >50 types
- Nonmelanoma squamous cell carcinomas

A

β

44
Q

HPV Five genotype groups:
- Benign diseases

A

y, μ, and v

45
Q
  • dsDNA virus
  • BK - renal diseases
  • JC -Progressive Multifocal Leukoencephalopathy/ PML
    o qPCR kits
A

Human Polyomavirus

46
Q
  • multiple species in a single analyses creatinine PCR for influenza A, B, & RSV
  • melt - curve analysis (2009 influenza H1N1 virus)
  • NASBA/ Nucleic Acid Sequence Based Amplification = (RSV) - Respiratory Syncytial virus
  • BEAD ARRAY TECHNOLOGY = (RSV, influenza H, nonspecific A, H1, H3, Influenza B, parainfluenza 1, 2, 3, metapneumovirus)
A

RESPIRATORY VIRUS

47
Q
  • ssRNA virus w/ spike proteins, responsible for COVID - 19 pandemic
  • novel coronavirus that emerged in late 2019 in Wuhan, China causing pandemic
  • symptoms vary: fever, cough, difficulty breathing, w/ severe cases potentially leading to pneumonia, acute respiratory diseases syndrome (ARDS), organ failure and death
  • DETECTION: RT- PCR (gold standard), qRT - PCR, rapid antigen test, antibody test
A

SARS COV - 2

48
Q

FUNGI:
CONVENTIONAL?

A

SMEAR, MICROSCOPY, CULTURE

49
Q

FUNGI:
MOLECULAR?

A
  • SEQUENCING & PCR: mold
  • GENE PROBES: Histoplasma, Blastomyces, Coccidioides & Cryptococcus neoformans
  • BROAD RANGE PCR & SUBSEQUENT ANALYSIS: Candida, Aspergillus, Rhizopus, other zygomycetes, HIstoplasma
  • REAL - TIME PCR: Aspergillus, Pneumocystis carinii
  • DIRECT PROBE HYBRIDIZATION: blastomycetes, coccidiosis immitis, histoplasma capsulatum
  • PFGE: yeasts
50
Q

PARASITES DETECTION:
CONVENTIONAL?

A

MORPHOLOGY BY MICROSCOPY

51
Q

PARASITES DETECTION:
MOLECULAR?

A
  • PCR METHODS: Trypanosomes, Plasmodium, Toxoplasma, Entamoeba & Cryptosporidium
  • MULTIPLEX PCR to simultaneously detect multiple parasites: intestinal parasite in stool sample
  • REAL - TIME PCR: Babesia, Trichomonas microti, Encephalitozoon spp. , Microsporidia, Trichomonas vaginalis
52
Q

ANTIMICROBIAL AGENTS
2 types:
- Inhibit growth

A

Static (Bacteriostatic/fung
Istatic)

53
Q

ANTIMICROBIAL AGENTS
2 types:
- Kill organisms

A

Cidal (Bacteriocidal/fungi cidal)

54
Q
  • A single nucleotide variant in a drug
    target or transport protein can result
    in resistance.
    o Resistant
     Staphylococcus
     Pseudomonas
     Klebsiella spp.
A

RESISTANCE TO ANTIMICROBIAL AGENTS

55
Q

DETECTION OF RESISTANCE:
- Gold standard for validation of phenotype
- PCR, quantitative PCR, Multiplex PCR

A

Molecular methods

56
Q

MOLECULAR EPIDEMIOLOGY:
- Affects many unrelated individuals at the same time
- rapidly spreading outbreak

A

Epidemic

57
Q
  • disease that sweeps across a WIDE geographical area
A

Pandemic

58
Q
  • acquired in a healthcare setting (hospital/clinic acquired)
A

Nosocomial infections

59
Q
  • Acquired from the actions of physicians (medical intervention/ treatment, surgical procedures/ use of medical devices
A

iatrogenic infections

60
Q

MOLECULAR STRAIN TYPING METHODS

A

 PLASMID ANALYSIS
 PULSED-FIELD GEL ELECTROPHORESIS
 RESTRICTION FRAGMENT LENGTH
POLYMORPHISM ANALYSIS
 ARBITRARILY PRIMED PCR
 AMPLIFIED FRAGMENT LENGTH POLYMORPHISM (AFLP) ASSAY
 INTERSPERSED REPETITIVE ELEMENTS
 INTERNAL TRANSCRIBED SPACER
ELEMENTS
 SPA TYPING
 MULTILOCUS SEQUENCE TYPING
 MASS SPECTROMETRY

MOL. BIO LAB (9 decks)

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