FINAL: DETECTION & ID OF MICROORGANISMS

Question 1

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

Answer 1

Phenotypic

Question 2

• genome, transcriptome, proteomes

Answer 2

Molecular

Question 3

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

Answer 3

Specimen collection

Question 4

Complete set of RNA molecules

Answer 4

Transcriptome

Question 5

Complete set of proteins

Answer 5

Proteome

Question 6

SAMPLE PREP
- dependent to microorganisms

Answer 6

Lysis procedure

Question 7

Difficult to lyse due to THICK cell wall

Answer 7

Mycobacteria and fungi

Question 8

Gram + bacteria has _____ cell wall compared to gram -

Answer 8

THICKER

Question 9

This microorganisms has NO PLASMA

Answer 9

Mycoplasma

Question 10

Concentration of microorganisms is done through

Answer 10

Centrifugation

Question 11

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

Answer 11

Presence of inhibitors

Question 12

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

Answer 12

DNA pol
- causes FALSE NEGATIVE

Question 13

SPECIMEN: BLOOD
WBC separation by?

Answer 13

Ficoll- Hypaque

Question 14

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

Answer 14

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

Question 15

SPECIMEN:
For Respiratory Tract infections(RTI)

Answer 15

SPUTUM

Question 16

SPECIMEN: SPUTUM
Removal of ________ as it inhibits DNA pol

Answer 16

Acidic polysaccharides

Question 17

SPECIMEN: URINE
- Centrifugation
- Inhibitors of DNA Pol:

Answer 17

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

Question 18

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

Answer 18

 Quality control

Question 19

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

Answer 19

Positive controls

Question 20

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

Answer 20

Reagent Blank/contamination
controls

Question 21

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

Answer 21

Negative template control

Question 22

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

Answer 22

Amplification control

Question 23

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

Answer 23

Internal controls

Question 24

• Target derive with a non target derived sequence

o homologous extrinsic
o heterologous extrinsic
o heterologous intrinsic

Answer 24

Homologous extrinsic

Question 25

- Non-target derived o homologous extrinsic o heterologous extrinsic o heterologous intrinsic

Answer 25

Heterologous extrinsic

Question 26

- Non-target that are present in sample o homologous extrinsic o heterologous extrinsic o heterologous intrinsic

Answer 26

Heterologous intrinsic

Question 27

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

Answer 27

False positives

Question 28

HOW TO AVOID FALSE POSITIVES

Answer 28

test 3-6 weeks after therapy

Question 29

- Nucleic acid degradation - Inhibition of amplification procedures - Inhibitors in Amplification

Answer 29

False negatives

Question 30

- Inhibitors in Amplification

Answer 30

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

Question 31

SELECTION OF SEQUENCE TARGETS  Microorganisms share similar sequences TRUE OR FALSE?

Answer 31

TRUE

Question 32

MOLECULAR DETECTION OF MICROORGANISMS

Answer 32

- AGAROSE GEL ELECTROPHORESIS - AMPLIFICATION METHODS - SEQUENCING - IMMUNOASSAYS - WESTERN BLOTS - MASS SPECTROMETRY

Question 33

- Non-molecular methods: lack sensitivity and time-consuming - Bordetella, Legionella - Mycobacteria, Chlamydia, and Streptococcus spp. WHAT TYPE OR BACTERIA?

Answer 33

RESPIRATORY

Question 34

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

Answer 34

Bordetella pertussis

Question 35

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

Answer 35

Legionella pneumophila

Question 36

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

Answer 36

Chlamydophila pneumoniae

Question 37

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

Answer 37

Mycobacterium tuberculosis

Question 38

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).

Answer 38

Mycoplasma pneumoniae

Question 39

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,

Answer 39

Streptococcus pneumoniae

Question 40

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

Answer 40

BACTERIA in the Urogenital tract

Question 41

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

Answer 41

Neisseria gonorrhea

Question 42

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)

Answer 42

Chlamydia trachomatis

Question 43

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

Answer 43

Treponema pallidum subsp. Pallidum

Question 44

Agents of nongonococcal urethritis TRADITIONAL METHOD: CULTURE

Answer 44

Mycoplasma hominis, Mycoplasma genitalium, Ureaplasma urealyticum and Haemophilus ducreyi

Question 45

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

Answer 45

Haemophilus ducreyi