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

FINAL: DETECTION & ID OF MICROORGANISMS Flashcards

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Biology 101 flashcards
1
Q

Routine
- colony morphology
- enzyme/pigment production
- carbohydrate fermentation patterns

A

Phenotypic

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2
Q
  • genome, transcriptome, proteomes
A

Molecular

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3
Q
  • Designed to avoid contamination from environments that may yield FALSE POSITIVES
  • equipment and reagents are utilized
A

Specimen collection

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4
Q

Complete set of RNA molecules

A

Transcriptome

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5
Q

Complete set of proteins

A

Proteome

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6
Q

SAMPLE PREP
- dependent to microorganisms

A

Lysis procedure

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7
Q

Difficult to lyse due to THICK cell wall

A

Mycobacteria and fungi

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8
Q

Gram + bacteria has _____ cell wall compared to gram -

A

THICKER

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9
Q

This microorganisms has NO PLASMA

A

Mycoplasma

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10
Q

Concentration of microorganisms is done through

A

Centrifugation

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11
Q

SAMPLE PREP
- removal and inactivation should be included
Removal of RNAses for RNA analysis

A

Presence of inhibitors

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12
Q

SPECIMEN: BLOOD
- Removal of Hemoglobin in blood
samples
because Hgb inhibits ____ which causes _______

A

DNA pol
- causes FALSE NEGATIVE

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13
Q

SPECIMEN: BLOOD
WBC separation by?

A

Ficoll- Hypaque

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14
Q

SPECIMEN: BLOOD
______ & __________ can also be sources of microorganisms

A

SERUM (no clotting factors) & PLASMA (contains clotting factors & proteins)

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15
Q

SPECIMEN:
For Respiratory Tract infections(RTI)

A

SPUTUM

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16
Q

SPECIMEN: SPUTUM
Removal of ________ as it inhibits DNA pol

A

Acidic polysaccharides

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17
Q

SPECIMEN: URINE
- Centrifugation
- Inhibitors of DNA Pol:

A

o nitrate, crystals, hemoglobin,
o beta-human chorionic
gonadotropin

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18
Q
  • Ensures accuracy
  • integrity of specimens are critical
  • Ensure the absence of inhibitors in
    the sample
A

 Quality control

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19
Q

CONTROLS:
- Ensures that assay system is working properly
- 2 Positive controls:
o LOWER and UPPER limit

A

Positive controls

20
Q

CONTROLS:
- Should always yield NEGATIVE results
- All reagents except the target

A

Reagent Blank/contamination
controls

21
Q

CONTROLS:
- For studies with NONTARGET organisms
- identify the presence of UNDESIRED TARGETS while avoiding any reaction with the desired target.

A

Negative template control

22
Q

CONTROLS:
- Rule out amplification failure
- To confirm TRUE NEGATIVE result
- Ex. Housekeeping genes
o groEL, rpoB, recA, gyrB, ẞ -
actin, interferon-y, human
mitochondrial DNA

A

Amplification control

23
Q

CONTROLS:
- Amplification controls that monitors particular step of amplification
method
- Can be:
o homologous extrinsic
o heterologous extrinsic
o heterologous intrinsic

A

Internal controls

24
Q
  • Target derive with a non target derived sequence

o homologous extrinsic
o heterologous extrinsic
o heterologous intrinsic

A

Homologous extrinsic

25
Q
  • Non-target derived

o homologous extrinsic
o heterologous extrinsic
o heterologous intrinsic

A

Heterologous extrinsic

26
Q
  • Non-target that are present in sample

o homologous extrinsic
o heterologous extrinsic
o heterologous intrinsic

A

Heterologous intrinsic

27
Q
  • Carry over of samples
  • Antimicrobial therapy
    o To avoid: test 3-6 weeks after therapy
A

False positives

28
Q

HOW TO AVOID FALSE POSITIVES

A

test 3-6 weeks after therapy

29
Q
  • Nucleic acid degradation
  • Inhibition of amplification procedures
  • Inhibitors in Amplification
A

False negatives

30
Q
  • Inhibitors in Amplification
A

o Hemoglobin
o Lactoferrin
o Heparin
o Sodium polyanethol sulfonate
o Polyamines

31
Q

SELECTION OF SEQUENCE TARGETS
 Microorganisms share similar sequences

TRUE OR FALSE?

A

TRUE

32
Q

MOLECULAR DETECTION OF
MICROORGANISMS

A
  • AGAROSE GEL
    ELECTROPHORESIS
  • AMPLIFICATION METHODS
  • SEQUENCING
  • IMMUNOASSAYS
  • WESTERN BLOTS
  • MASS SPECTROMETRY
33
Q
  • Non-molecular methods: lack
    sensitivity and time-consuming
  • Bordetella, Legionella
  • Mycobacteria, Chlamydia, and
    Streptococcus spp.

WHAT TYPE OR BACTERIA?

A

RESPIRATORY

34
Q

Respiratory BACTERIA
- Upper respiratory tract
- Whooping cough
- specimen source: nasopharyngeal

A

Bordetella pertussis

35
Q

Respiratory BACTERIA
- Lower respiratory tract
- 3RD MOST COMMON CAUSE OF COMMUNITY ACQUIRED PNEUMONIA
- Legionnaires’ disease
- specimen source: deep respiratory secretions, serum, buffy coat, urine

A

Legionella pneumophila

36
Q

Respiratory BACTERIA
- 10% of community-acquired pneumonias
- implicated in atherosclerosis &
coronary artery disease
- specimen source: respiratory, throat, atherosclerotic lesions

A

Chlamydophila pneumoniae

37
Q

Respiratory BACTERIA
- TB: contagious infection disease primarily affecting the lungs
- Detection (Traditional)
o Smear and culture
o Kinyoun and Ziehl Neelsen
stains -
o Flurochromess

  • qPCR
    o Targets rRNA internal
    transcribe spaces (ITS)
  • specimen source: sputum, bronchoalveolar lavage, bronchial washings, gastric aspirators
A

Mycobacterium tuberculosis

38
Q

Respiratory BACTERIA
- damages living of respiratory system (throat, lungs, trachea)
- specimen source: bronchoalveolar lavage,
DETECTION:
- multilocus variable-number
tandem-repeat (VNTR) analysis
- multilocus sequence typing.
- matrix-assisted laser desorption
ionization time-of-flight mass spectrometry (MALDI-TOF MS).

A

Mycoplasma pneumoniae

39
Q

Respiratory BACTERIA
- Major/LEADING cause of community-acquired
pneumonias.
- significant cause of MENINGITIS
- can cause BACTEREMIA which can lead to SEPTICEMIA
- specimen source: bronchoalveolar lavage,

A

Streptococcus pneumoniae

40
Q
  • Organisms
    o Neisseria gonorrhoeae
    o Chlamydia trachomatis
  • Cervical swabs. Urine, transport
    vials for PAP smears
  • Culture can be performed along
    with molecular methods
A

BACTERIA in the Urogenital tract

41
Q

BACTERIA in the Urogenital tract
- gonorrhea
- specimen source: urine, urethral, cervical, thin preparation vials/ transport vials for PAP smears
- Traditional diagnostic method: culture
- DETECTION: PCR

A

Neisseria gonorrhea

42
Q

BACTERIA in the Urogenital tract
- MOST COMMON STI
- CHLAMYDIA
- specimen source: urine, urethral, cervical, thin preparation vials/ transport vials for PAP smears, conjunctiva
- Traditional diagnostic method: culture, EIA, direct fluorescent anti-body (DFH)

A

Chlamydia trachomatis

43
Q

BACTERIA in the Urogenital tract
o Agent of syphilis
o A spirochete
o Cannot be grown in vitro
- Stages:
o PRIMARY- formation of hard
chancre in site
o SECONDARY- disseminated rash
o LATENT- asymptomatic
o TERTIARY- CNS and CV
- Laboratory diagnosis of Syphilis
o Serologic
- Hemaglutination
- EIAS (fluorescent treponemal
antibody absorption FTA-ABS)
- Detection of cardiolipin
 Rapid Plasma Reagin
(RPR)
 Venereal disease
laboratory (VDRL)
o PCR assays
- specimen source: GENITAL ULCERS, BLOOD, BRAIN TISSUE, CSF, amniotic fluid, placenta, umbilical cord, fetal tissue, serum

A

Treponema pallidum subsp. Pallidum

44
Q

Agents of nongonococcal
urethritis
TRADITIONAL METHOD: CULTURE

A

Mycoplasma hominis, Mycoplasma
genitalium, Ureaplasma
urealyticum and Haemophilus ducreyi

45
Q

Agents of nongonococcal
urethritis
- causes CHANCROID, STI characterized by painful genital ulcers
- specimen sources; samples collected from the ulcers

A

Haemophilus ducreyi

MOL. BIO LAB (9 decks)

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