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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
# *S. pyogenes* identification One of the molecular diagnosis - the __ identifies rRNA sequences in pharyngeal specimens by a single-stranded chemiluminescent nucleic acid probe
GASDirect test | applied for primary testing and is used as a backup to (-) antigen test
26
# *S. agalactiae* identification Types of PCR used
* Conventional * RT-PCR
27
# *S. agalactiae* identification The LAMP method can amplify target nucleotide sequences at ___ conditions (give the temp) within 90 mins using probes targeting ___ gene
isothermal 60-65C cfb gene
28
# *S. agalactiae* identification Targets for GBS-PCR include which genes? (4)
* sip * cfb * scpB * ptsl
29
# *S. agalactiae* identification Gene that codes for immunogenic protein
sip
30
# *S. agalactiae* identification Gene that codes for Christie-Atkins-Munch Petersen factor
cfb
31
# *S. agalactiae* identification Gene that codes for the C5a peptidase
scpB
32
# *S. agalactiae* identification Gene that codes for phosphotransferase
ptsl
33
# Give the target fungi for this target gene: Actin
*Aspergillus*
34
# Give the target fungi for this target gene: B-tubulin
* *Phaeacremonium* * *Aspergillus* * *Pseudallescheria*
35
# Give the target fungi for this target gene: Calmodulin
* *Aspergillus* * *Pseudallescheria info*
36
# Give the target fungi for this target gene: Chitin synthase 2
*Lacazia loboi*
37
# Give the target fungi for this target gene: Cytochrome b
* *Aspergillus* * *Trichosporon* * *Rhodotorula*
38
# Give the target fungi for this target gene: D1-D2
most fungi
39
# Give the target fungi for this target gene: Elongation factor 1a
*Fusarium spp.*
40
# Give the target fungi for this target gene: ITS
* medically significant yeasts * fungi
41
# Give the target fungi for this target gene: 26S
medically relevant *Fusarium* and *Scedosporium*
42
Nested PCR formats can be used to detect ___ and ___
*Aspergillus* and *Candida*
43
For direct sequencing, the ___ and ___ fragments can be used for PCR amplification
26S and 28S
44
For differentiation between strains of the same fungal species, ___ sequence typing of ___ genes should be used
multilocus house-keeping
45
# Molecular detection of *Aspergillus* ___ is highly sensitive and specific for the DNA and RNA
NAAT
46
# Molecular detection of *Aspergillus* Amplification of DNA by PCR has been the most widely applied ___ method
NAAT
47
# Molecular detection of *Aspergillus* ___ can be used to optimize sensitivity
Nested PCR protocols
48
# Molecular detection of *Aspergillus* Multiplex PCR detection methods coupled with ___ is commonly used
fluorescently labeled probes
49
# Molecular detection of *Aspergillus* ___ can be used to quantify fungal burden
RT-PCR
50
# Molecular detection of *Aspergillus* ___ allow for the differentiation of larger numbers of pathogenic species
Multiplex arrays
51
# 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
rDNA gene cluster | highly conserved: 18S & 28S rDNA variable: ITS & D1/D2
52
# Molecular detection of *Aspergillus* In general, genus level assay designs often target ___
18S
53
# Molecular detection of *Aspergillus* *A. fumigatus*-specific assays target ___, ___, ___, or ___
* ITS-1 * mitochondrial DNA * alkaline protease * *Aspergillus* collagen-like (acl) genes
54
# Molecular Detection of Human Papillomavirus Refers to the dominant promoter
P97
55
# Molecular Detection of Human Papillomavirus The majority of molecular diagnoses are designed to detect nucleic acids of the ___ carcinogens
12 IARC HPV group 1 | HPV16, -18, -31, -33, -35, -39, -45, -51, -52, -56, -58, -59
56
# 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
L1
57
# Molecular Detection of Human Papillomavirus Detection of ___ oncogene mRNA in cervical cells is an alternative to detection of HPV DNA
HPV E6/E7
58
# Molecular Detection of Human Papillomavirus Detection of overexpression of E6/E7 mRNA might be more directly associated with ___
disease progression
59
# 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
oligonucleotide microarray
60
# 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
most conserved
61
# Molecular detection of Hepatitis virus; give the conserved region HAV
5' UTR
62
# Molecular detection of Hepatitis virus; give the conserved region HBV
S-gene X-gene
63
# Molecular detection of Hepatitis virus; give the conserved region HCV
5' UTR
64
# Molecular detection of Hepatitis virus; give the conserved region HDV
Ribozyme-1
65
# Molecular detection of Hepatitis virus; give the conserved region HEV
ORF 2 ORF 3
66
# Molecular detection of Hepatitis virus; give the conserved region HGV
5' UTR
67
# Molecular detection of Hepatitis virus A ___ allows for an early diagnosis and timely treatmennt of patients with viral hepatitis
single-step multiplex qPCR
68
# Detection of HBV ___ is regarded as the best test for quantitative cccDNA detection
southern blotting
69
# 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
* segment A: complementary to HBV DNA plus strand from nt1615 to 1604 * segment B: consensual to the HIV long terminal repeat (LTR) region
70
Two types of MALDI-TOF
* Linear * Reflective

MT6319 (7 decks)

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