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MT6319 > 03 Unit 7: Molecular Diagnosis of Infectious Diseases > Flashcards

03 Unit 7: Molecular Diagnosis of Infectious Diseases Flashcards

1
Q

Ideal primer targets for amplification from all bacterial species

A

Conserved regions

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2
Q

In using the sequences, the degree of divergence is observed within ___ rRNA molecule

A

16s

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3
Q

In the diagnosis with sequencing, the small-subunit rRNA molecule is a fragment with a sedimentation coefficient of 16s and is encoded by a roughly ___-bp gene

A

1542

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4
Q

Targets for detection used in Bartonella spp. in RT-PCR

A
  • mtRNA ssRA
  • 16S-13S internal transcribed spacer ITS
  • B-subunit of RNA polymerae rpoB
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5
Q

T/F: In the identification of Bartonella spp., the use of qPCR is more definitive and specific compared to the molecular characterization of isolates from cultures

A

False

qPCR is less definitive and specific, but is also less time-consuming

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6
Q

The use of RT-PCR in the identification of Bartonella spp. is faster, but has many ___

A

interfrences

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7
Q

Recently applied technique for Borellia spp.

A

NGS & proteomic approaches

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8
Q

C. trachomatis identification

Molecular genotyping of ___ can be performed by using restriction fragment length polymorphism on PCR products from culture isolates, but also directly from clinical specimens

A

ompA

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9
Q

C. trachomatis identification

The nine polymorphic membrane protein genes, ___ to ___, can be used for typing but the discriminating capacity is limited

A

pmpA to pmpI

A, B, C, D, E, F, G, H, I

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10
Q

C. trachomatis identification

The highly conserved genome can be used for ___

A

multilocus target systems

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11
Q

C. trachomatis identification

Analysis of variable numbers of tandem repeats in three loci combined with ___ can bring a significantly diversity index than by using ___ alone

A

ompA sequencing
ompA

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12
Q

C. difficile identification

RT-PCR target toxin genes

A
  • tcdA
  • tcdB
  • tcdC117
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13
Q

C. difficile identification

Multiplex PCD for the detection of ___, ___, and the binary toxin ___ gene is a one-step, rapid, specific screening method for C. difficile

A
  • tcdA
  • tcdB
  • cdtA/cdtB
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14
Q

C. difficile identification

___ ___-dependent amplification for the detection of toxigenic C. difficile has been developed

A

Isothermal helicase

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15
Q

M. pneumoniae identification

___ and ___ have been used to detect M. pneumoniae RNA

A

Conventional & real-time NAATs

these can be used in monoplex and multiplex format

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16
Q

M. pneumoniae identification

LAMP assay has been applied using ___ sequences for primers in direct comparison to RT-PCR

A

P1

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17
Q

C. difficile identification

A multiplex real-time PCR assay can be used to detect point mutations in all three positions of the ___ that are related to the macrolide resistance on all clinical samples that are positive for M. pneumoniae in the ___ RT-PCR assay

A

23s rRNA gene (2063, 2064, 2617)
repMp1

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18
Q

S. aureus identification

___ and ___ are the main genes responsible for the resistance of MRSA to most of the B-lactam antibiotics

A

MecA
MecC

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19
Q

S. aureus identification

___ is considered to be the best molecular diagnostic tool for MRSA detection, confirming ___ gene

A

PCR
mecA

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20
Q

S. aureus identification

Duplex PCR assay detecting ___ and ___ genes can be very useful

A

mecA
femB/nuc

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21
Q

S. aureus identification

A triplex PCR targeting ___, ___, and ___ genes can reach 98% accuracy within 6h of visible growth detection

A

16s rRNA
mecA
nuc

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22
Q

S. aureus identification

The latest development in direct MRSA detection and identification is that of ___

A

RT-PCR

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23
Q

S. pneumoniae identification

PCRs have been employed with varying degrees of success, using primers specific to repetitive regons and genes encoding rRNA

A
  • pneumococcal surface adhesion A molecule (psaA)
  • pneumolysin (ply)
  • penicillin binding protein (PBP)
  • autolysin (lytA)
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24
Q

S. pneumoniae identification

RT-PCR has improved diagnostics by analyzing sputum through RT-PCR with the targets at ___

A

lytA

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25
Q

S. pyogenes identification

One of the molecular diagnosis - the __ identifies rRNA sequences in pharyngeal specimens by a single-stranded chemiluminescent nucleic acid probe

A

GASDirect test

applied for primary testing and is used as a backup to (-) antigen test

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26
Q

S. agalactiae identification

Types of PCR used

A
  • Conventional
  • RT-PCR
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27
Q

S. agalactiae identification

The LAMP method can amplify target nucleotide sequences at ___ conditions (give the temp) within 90 mins using probes targeting ___ gene

A

isothermal
60-65C
cfb gene

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28
Q

S. agalactiae identification

Targets for GBS-PCR include which genes? (4)

A
  • sip
  • cfb
  • scpB
  • ptsl
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29
Q

S. agalactiae identification

Gene that codes for immunogenic protein

A

sip

30
Q

S. agalactiae identification

Gene that codes for Christie-Atkins-Munch Petersen factor

A

cfb

31
Q

S. agalactiae identification

Gene that codes for the C5a peptidase

A

scpB

32
Q

S. agalactiae identification

Gene that codes for phosphotransferase

A

ptsl

33
Q

Give the target fungi for this target gene:

Actin

A

Aspergillus

34
Q

Give the target fungi for this target gene:

B-tubulin

A
  • Phaeacremonium
  • Aspergillus
  • Pseudallescheria
35
Q

Give the target fungi for this target gene:

Calmodulin

A
  • Aspergillus
  • Pseudallescheria info
36
Q

Give the target fungi for this target gene:

Chitin synthase 2

A

Lacazia loboi

37
Q

Give the target fungi for this target gene:

Cytochrome b

A
  • Aspergillus
  • Trichosporon
  • Rhodotorula
38
Q

Give the target fungi for this target gene:

D1-D2

A

most fungi

39
Q

Give the target fungi for this target gene:

Elongation factor 1a

A

Fusarium spp.

40
Q

Give the target fungi for this target gene:

ITS

A
  • medically significant yeasts
  • fungi
41
Q

Give the target fungi for this target gene:

26S

A

medically relevant Fusarium and Scedosporium

42
Q

Nested PCR formats can be used to detect ___ and ___

A

Aspergillus and Candida

43
Q

For direct sequencing, the ___ and ___ fragments can be used for PCR amplification

A

26S and 28S

44
Q

For differentiation between strains of the same fungal species, ___ sequence typing of ___ genes should be used

A

multilocus
house-keeping

45
Q

Molecular detection of Aspergillus

___ is highly sensitive and specific for the DNA and RNA

A

NAAT

46
Q

Molecular detection of Aspergillus

Amplification of DNA by PCR has been the most widely applied ___ method

A

NAAT

47
Q

Molecular detection of Aspergillus

___ can be used to optimize sensitivity

A

Nested PCR protocols

48
Q

Molecular detection of Aspergillus

Multiplex PCR detection methods coupled with ___ is commonly used

A

fluorescently labeled probes

49
Q

Molecular detection of Aspergillus

___ can be used to quantify fungal burden

A

RT-PCR

50
Q

Molecular detection of Aspergillus

___ allow for the differentiation of larger numbers of pathogenic species

A

Multiplex arrays

51
Q

Molecular detection of Aspergillus

Most common target of assays designed for direct detection in clinical specimens because of the presence of highly conserved and variable regions

A

rDNA gene cluster

highly conserved: 18S & 28S rDNA
variable: ITS & D1/D2

52
Q

Molecular detection of Aspergillus

In general, genus level assay designs often target ___

A

18S

53
Q

Molecular detection of Aspergillus

A. fumigatus-specific assays target ___, ___, ___, or ___

A
  • ITS-1
  • mitochondrial DNA
  • alkaline protease
  • Aspergillus collagen-like (acl) genes
54
Q

Molecular Detection of Human Papillomavirus

Refers to the dominant promoter

A

P97

55
Q

Molecular Detection of Human Papillomavirus

The majority of molecular diagnoses are designed to detect nucleic acids of the ___ carcinogens

A

12 IARC HPV group 1

HPV16, -18, -31, -33, -35, -39, -45, -51, -52, -56, -58, -59

56
Q

Molecular Detection of Human Papillomavirus

Multiplex real-time PCR and nucleic acid hybridization with four different fluorescent reporter probes cn be used to concurrently detect the ___ gene of HPV16 and HPV18

A

L1

57
Q

Molecular Detection of Human Papillomavirus

Detection of ___ oncogene mRNA in cervical cells is an alternative to detection of HPV DNA

A

HPV E6/E7

58
Q

Molecular Detection of Human Papillomavirus

Detection of overexpression of E6/E7 mRNA might be more directly associated with ___

A

disease progression

59
Q

Molecular detection of Hepatitis virus

PCR-based assays, coupled with ___ technology, would allow for the simultaneous detection an genotyping of several viruses, including blood borne pathogens, respiratory viruses, and adenoviruses

A

oligonucleotide microarray

60
Q

Molecular detection of Hepatitis virus

Multiplex qpCR assay use the ___ region representing all the strains/variants for detection of the hepatitis viral genome in body fluid

A

most conserved

61
Q

Molecular detection of Hepatitis virus; give the conserved region

HAV

A

5’ UTR

62
Q

Molecular detection of Hepatitis virus; give the conserved region

HBV

A

S-gene
X-gene

63
Q

Molecular detection of Hepatitis virus; give the conserved region

HCV

A

5’ UTR

64
Q

Molecular detection of Hepatitis virus; give the conserved region

HDV

A

Ribozyme-1

65
Q

Molecular detection of Hepatitis virus; give the conserved region

HEV

A

ORF 2
ORF 3

66
Q

Molecular detection of Hepatitis virus; give the conserved region

HGV

A

5’ UTR

67
Q

Molecular detection of Hepatitis virus

A ___ allows for an early diagnosis and timely treatmennt of patients with viral hepatitis

A

single-step multiplex qPCR

68
Q

Detection of HBV

___ is regarded as the best test for quantitative cccDNA detection

A

southern blotting

69
Q

Detection of HBV

To reduce rcDNA contamination, a chimeric sequence composed of segments A and B increases specificity. Give the actions of these segments

specificity is compromised in the presence of abundant rcDNA

A
  • segment A: complementary to HBV DNA plus strand from nt1615 to 1604
  • segment B: consensual to the HIV long terminal repeat (LTR) region
70
Q

Two types of MALDI-TOF

A
  • Linear
  • Reflective

MT6319 (7 decks)

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