Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Study Materials > Molecular Microbiology > Flashcards

Molecular Microbiology Flashcards

1
Q

HCV

A

Hepatitis C Virus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Virus type for HCV

A

single-stranded RNA virus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Primary transmission routes for HCV

A

intravenous drug use and through blood products

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Abbott HCV RNA assay

A

real-time PCR to amplify the 5’ noncoding region of HCV. Able to detect genotpyes 1-6. internal control is introduced to each specimen at the beginning of sample preparation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Specimen requirements for Abbott HCV RNA assay

A

whole blood or plasma

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Limit of detection for the Abbott HCV RNA assay

A

12 copies/mL with 0.5 mL sample volume.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is the linear range, upper and lower limits of quanitation for the Abbott HCV RNA assay

A

upper: 100 million copies/mL
lower: 12 copies/mL

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What are some transmission routes of HIV

A

sexual contact, exposure to infected blood or blood products, transmision from infected mother to fetus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the methodology behind the Abbott HIV1 RNA viral load assay?

A

in vitro reverse transcription PCR followed by real-time PCR. Partially double-stranded flluorescent probe design allows detection of diverse group M subtypes and group O isolates. Internal control is added to the sample prior to isolation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

HIV

A

Human immunodeficiency virus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Virus type for HIV

A

lentivirus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Specimen types for Abbott HIV1 RNA assay

A

blood or plasma

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is the LOD claim for the Abbott Real-Time HIV1 assay?

A

40 copies/mL

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is the linear range, upper and lower limits of quanitation for the Abbott Real-Time HIV1 assay?

A

upper: 10 million copies/mL
lower: 40 copies/mL

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is the inter-assay standard deviation of the Abbott Real-Time HIV1 assay?

A

0.25 log copies/mL in samples containing HIV1 RNA concentrations between 5 million and 500 copies/mL.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

MecA

A

gene encoding the altered penicillin binding protein, PBP2a or PBP2’, which has a low binding affinity for methicillin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Which of the following gene would be analyzed to determine whether an isolate of Staphylococcus aureus is resistant to oxacilllin?

a. mecA
b. gyrA
c. inhA
d. vanA

A

a. mecA
Explanation: mecA S. aureus developed resistance to antibiotics that target its penicillin-binding protein (PBP1) by replacing PBP1 with PBP2a encoded by the mecA gene. PBP2a found in methicillin-resistant S. aureus (MRSA) has a low binding affinity for methicillin.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Which of the following is a genotypic method used to compare two isolates in an epidemiological investigation?

a. Biotyping
b. Serotyping
c. Ribotyping
d. Bacteriophase typing

A

c. ribotyping
Explanation: There are many laboratory methods that can be used to determine the relatedness of multiple isolates, both phenotypic (e.g. by serology and antimicrobial susceptibility patterns) and genotypic (e.g. pulsed field gel electrophoresis and ribotyping)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

For which of the following organisms must caution be exercised when evaluating positive PCR results because the organism can be found as normal flora in some patient populations?

a. Neisseria gonorrhoeae
b. HIV
c. Chlamydophila pneumoniae
d. Streptococcus pneumoniae

A

d. Streptococcus pneumoniae.
Explanation: Although PCR is specific for S. pneumoniae, the clinical significance of a positive PCR assay is questionable because a significant portion of the population (especially children) is colonized with the organism and PCR cannot discern between colonization and infection.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Which of the following controls are critical for ensuring that amplification is occurring in a patient sample and that the lack of PCR product is not due to the presence of inhibitors?

a. reagent blank
b. sensitivity control
c. negative control
d. amplification control

A

d. amplification control. The amplification control should always generate a product, even in the absence of the target.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

A PCR assay was performed to detect Bordetella pertussis on sputum obtained from a 14-yo girl who has had a chronic cough. The results reveal two bands, one consistent with the internal control and the other consistent with the size expected for amplification of the B. pertussis target. How should these results be interpreted?

a. false-positive for B. pertussis
b. The girl has clinically significant B. pertussis infection.
c. B. pertussis detection is more likely due to colonization
d. invalid because two bands were present

A

b. The girl has clinically significant B. pertussis infection.
Explanation: Molecular-based assays are used almost exclusively for analysis of microorganisms such as N. gonorrhoeae, C. trachomatis, and B. pertussis.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Which of the following is a disadvantage of molecular-based testing?

a. results stay positive longer after treatment than do cultures
b. results are available within hours
c. only viable cells yield positive results
d. several milliliters of specimen may be submitted for analysis

A

a. results stay positive longer after treatment than do cultures
Explanation: Molecular-based results can detect both living and dead organisms. A positive result due to a dead or dying organism can complicate interpretation of treatment efficacy.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

A molecular-based typing method that has high typing capacity, reproducibility, and discriminatory power, moderate ease of performance, and good-to-moderate ease of interpretation is:

a. repetitive elemets
b. PFGE
c. plasmid analysis
d. PCR-RFLP

A

b. PFGE

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

A patient has antibodies against HCV and a viral load of 100,000 copies/mL. What is the next test that should be performed on this patient’s isolate?

a. ribotyping
b. PCR-RFLP
c. hybrid capture
d. inno-LiPA HCV genotyping

A

d. inno-LiPA HCV genotyping.
Explanation: The viral load and the HCV genotyping are used to determine the therapeutic protocol, both type of drug(s) as well as duration. Methods available in the laboratory for HCV genotyping are PCR with RFLP analysis and reverse hybridization (Inno-LiPA, Bayer), and direct DNA sequencing (HCV DupliType, Quest; TruGENE, Bayer; and ViroSeq, Celera).

25
Q

A positive result for HPV type 16 indicates:

a. a high risk for antibiotic resistance
b. low risk for cervical cancer
c. high rise for cervical cancer

A

c. high risk for cervical cancer
Explanation: Of the sexually transmitted types of HPV, 12 to 15 oncogenic genotypes have strong association with cervical cancers and are considered high-risk (HR) HPV types.

26
Q

Which of the following is used to type molds?

a. sequence-specific PCR
b. microarray
c. ITS sequencing
d. flow cytometry

A

c. ITS seuqencing

Explanation: Molds are typed by PCR and sequencing of Internal Transcribed Spacers (ITS) regions of 28S rRNA.

27
Q

Give six reasons why molecular tests might be developed for microorganisms.

A
  1. difficult and/or time consuming to develop (mycobacterium tuberculosis)
  2. hazard with which to work in the clinical laboratory (Histoplasma, coccidioides)
  3. reliable micro tests are lacking (HIV, HCV)
  4. received in high volumes (NG/CT)
  5. antibiotic resistance (vanA, vanB, vanC - Enterococcus resistance to vancomycin)
  6. characterize genotypes (HPV, HCV, HIV)
28
Q

What makes HIV unique among the RNA viruses?

A

It is a retrovirus that makes a DNA copy of genomic RNA using virally encoded reverse transcriptase.

29
Q

Which HIV subgroup causes 95% of infections around the world?

a. Group A
b. Group C
c. Group J
d. Group M

A

d. Group M

30
Q

Which HIV clade within group M is most often found in the United States and Europe?

a. Clade A
b. Clade B
c. Clade C
d. Clade D

A

b. Clade B

31
Q

Describe the conditions under which patients have a 10x more likelihood of progressing to AIDS within 5 years.

a. viral load above 10,000 copies/mL within 6 months of seroconversion.
b. viral load above 100,000 copies/mL within 6 months of seroconversion
c. viral load above 10,000 copies/mL within 3 months of seroconversion
d. viral load above 100,000 copies/mL within 3 months of seroconversion

A

b. viral load above 100,000 copies/mL within 6 months of seroconversion

32
Q

What is the goal of antiretroviral therapy?

a. 500 copies/mL in blood
b. 100 copies/mL in blood
c. 50 copies/mL in blood
d. 10 copies/mL in blood

A

c. 50 copies/mL in blood

33
Q

Patients that maintain ______ viral levels during the early stages of the infection are at a decreased risk of progression to AIDS.

a. 100,000 copies/mL
b. 10,000 copies/mL
c. 500 copies/mL
d. 50 copies/mL

A

b. 10,000 copies/mL

34
Q

Patient effectively treated with antiretroviral therapy will see a significant reduction in HIV viral load after ______ of therapy initiation.

a. one week
b. two weeks
c. one month
d. six months

A

a. one week

35
Q

HAART stands for ____.

A

Highly Active Anti-Retroviral Therapy

36
Q

Describe the components of Highly Active Antiretroviral Therapy.

A

Consists of two reverse transcriptase inhibitors combined with a protease inhibitor or a nonnucleoside reverse transcriptase inhibitor.

37
Q

HIV viral load testing should be done in conjunction with ____ counts.

a. CD8
b. CD4
c. CD34
d. CD53

A

b. CD4

CD4 is a surface marker for helper T-cells. This is a way to monitor the strength of the immune system.

38
Q

Slight variations in HIV viral load quantity that are normal include:

a. 0.2 log10 units
b. 0.3 log10 units
c. 0.5 log10 units
c. 1.0 log10 units

A

b. 0.3 log10 units

39
Q

Genotyping HIV is appropriate:

a. after 5 years on HAART therapy
b. viral load starts to trend upwards
c. before starting therapy
d. every year

A

b. viral load starts to trend upwards

40
Q

HIV viral load should be determine every ___ to ____ weeks after therapy initiation?

a. 1-2 weeks
b. 3-4 weeks
c. 2-8 weeks
d. 10-12 weeks

A

c. 2-8 weeks

41
Q

HIV viral load should be monitored every ___ to assess therapeutic effectiveness?

a. 1-2 months
b. 3-4 months
c. 6 months
d. 1 year

A

b. 3-4 months

42
Q

What is the CDC-recommendation for reporting HIV viral load?

A

The CDC recommends reporting HIV viral load in integers (copies/mL or IU/mL) and log-transformed copies (log IU/mL).

43
Q

Name the advantages and disadvantages of testing HIV viral load by bDNA.

A

Advantages: high throughput, broad dynamic range, applicable for group M subtypes A-G.
Diadvantages: no internal control and false-positive results reported

44
Q

Name the advantages and disadvantages HIV viral load testing by Amplicor RT-PCR.

A

Advantages: internal control, good specificity
Diadvantages: limited dynamic range

45
Q

What are the advantages and disadvantages to HIV viral load testing by NASBA?

A

Advantages: broad dynamic range and performed on many specimen types and volumes
Disadvantages: does not detect all non-B subtypes

46
Q

What is the standard specimen for testing quantitative HIV-1 RNA?

a. whole blood
b. plasma
c. sorted cells
d. bone marrow

A

b. plasma

47
Q

Which of the following genes would be analyzed to determine whether an isolate of Staphylococcus aureus is resistant to oxacillin?

a. mecA
b. gyrA
c. inhA
d. vanA

A

a. mecA S. aureus developed resistance to antibiotics that target its penicillin-binding protein (PBP1) by replacing PBP1 with PBP2a encoded by the mecA gene. PBP2a found in methicillin-resistant S. aureus (MRSA) has a low affinity binding for methicllin.

48
Q

Which of the following is a genotypic method used to compare two isolates in an epidemiological investigation?

a. biotyping
b. serotyping
c. ribotyping
d. bacteriophage typing

A

c. ribotyping
There are many laboratory methods that can be used to determine the relatedness of multiple isolates, both phenotypic (e.g. by serology and antimicrobial suseptibility patterns) and genotypic (e.g. pulsed field gel electrophoresis and ribotyping).

49
Q

Which of the following is a phenotypic method used to compare two isolates in an epidemiological investigation?

a. biotyping
b. serotyping
c. ribotyping
d. bacteriophage typing

A

b. serotyping
There are many laboratory methods that can be used to determine the relatedness of multiple isolates, both phenotypic (e.g. by serology and antimicrobial susceptibility patterns) and genotypic (e.g. pulsed field gel electrophoresis and ribotyping).

50
Q

For which of the following organisms much caution be exercised when evaluating positive PCR results because the organism can be found as normal flora in some patient populations?

a. Neisseria gonorrhoeae
b. HIV
c. Chlamydophila pneumoniae
d. Streptococcus pneumoniae

A

c. Streptococcus pneumoniae
Although PCR is specific for S. pneumoniae, the clinical significance of a positive PCR assay is questionable because a significant portion of the population (especially children) are colonized with the organism and PCR cannot discern between colonization and infection.

51
Q

Which of the following controls are critical for ensuring that amplification is occurring in a patient sample and that the lack of PCR product is not due to the presence of inhibitors?

a. reagent blank
b. sensitivity control
c. negative control
d. amplification control

A

d. amplification control

52
Q

A PCR assay was performed to detect Bordetella pertussis on sputum obtained from a 14-yo girl who has had a chronic cough. The results revealed two bands, one consistent with the internal control and the other consistent with the size expected for amplificaiton of the B. pertussis target. How should these results be interpreted?

a. false-positive for B. pertussis
b. the girl has clinically significant B. pertussis infection
c. B. pertussis detection is more likely due to colonization
d. invalid because two bands were present

A

b. the girl has clinically significant B. pertussis infection.
Molecular-based assays are used almost exclusively for analysis of microorganisms such as NG, CT, and B. pertussis.

53
Q

Which of the following is a disadvantage of molecular-based testing?

a. Results stay positive longer after treatment than do cultures?
b. Results are available within hours.
c. Only viable cells yield positive results.
d. Several milliliters of specimen must be submitted for analysis.

A

a. Results stay positive for longer after treatment than do cultures.
Molecular-based results can detect both living and dead organisms. A positive result due to dead or dying organisms can complicate interpretation of treatment efficacy.

54
Q

A molecular-based typing method that has high typing capacity, reproducibility and discriminitory power, moderate ease of performance, and good-to-moderate ease of interpretation is:

a. repetitive elements
b. PFGE
c. plasmid analysis
d. PCR-RFLP

A

b. PFGE
Most molecular epidemiological tests are performed by pulsed field gel electrophoresis (PFGE). For PFGE, DNA is digested with restriction enzymes that cut infrequently, the large fragments are then resolved by PFGE. Banding patterns differ depending on chromosomal DNA sequence of the organism. Band patterns for known organisms are stored as a reference.

55
Q

PFGE

A

pulse field gel electrophoresis

56
Q

What is the most common technique used for molecular epidemiological tests?

A

pulse field gel electrophoresis (PFGE)

57
Q

A patient has antibodies agains HCV and a viral load of 100,000 copies/mL. What is the next test that should be performed on this patient’s isolate?

a. ribotyping
b. PCR-RFLP
c. hybrid capture
d. Inno-LiPA HCV genotyping

A

d. Inno-LiPA HCV genotyping
The viral load and the HCV genotype are used to determine the therapeutic protocol, both the type of drug(s) as well as duration. Methods available in the laboratory for HCV genotyping are PCR with RFLP analysis and reverse hybridization (Inno-LiPA, Bayer) and direct DNA sequencing (HCV DupliType, Quest; Trugene, Bayer; and ViroSeq, Celera)

58
Q

A positive result for HPV type 16 indicates:

a. high risk for antibiotic resistance
b. low risk of cervical cancer
c. high risk for cervical cancer

A

c. high risk for cervical cancer
Of the sexually transmitted type of HPV, 12 to 15 oncogenic genotypes have strong association with cervical cancers and are considered high-risk (HR) HPV types. 16 and 18 are the most common in the US.

59
Q

Which of the following is used to type molds?

a. sequence-specific PCR
b. microarray
c. ITS sequencing
d. flow cytometry

A

c. ITS sequencing.

Molds are typed by PCR and sequencing of Internal Transcribed Spacer (ITS) regions or 28S rRNA.

Study Materials (12 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions