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Molecular Biology Lecture > 4: Diagnosis of Infectious Diseases > Flashcards

4: Diagnosis of Infectious Diseases Flashcards

1
Q

These are conditions or
associated with pathogens

A

Infectious diseases

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2
Q

These are conditions or
associated with pathogens

A

Infectious diseases

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3
Q

These are microorganisms or microbes
which has the capability to cause diseases

A

Pathogens

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4
Q

Pathogens present in the environment that cause certain diseases which may also cause certain infections are?

A
  1. Bacteria
  2. Fungi
  3. Virus
  4. Parasites
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5
Q

Molecular techniques are also referred to as?

A

GENOTYPE ASSAYS or GENOTYPE TESTING or GENOTYPING

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6
Q

HOW TO IDENTIFY THAT A CONDITION IS CAUSED BY AN INFECTIOUS AGENT

Identify whose role:
Diagnosis?

A

Physician

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7
Q

HOW TO IDENTIFY THAT A CONDITION IS CAUSED BY AN INFECTIOUS AGENT

Identify whose role:
Isolates the pathogen
from different clinical specimens?

A

MT

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8
Q

HOW TO IDENTIFY THAT A CONDITION IS CAUSED BY AN INFECTIOUS AGENT

Identify whose role:
Isolates the pathogen
from different clinical specimens?

A

MT

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9
Q

HOW TO IDENTIFY THAT A CONDITION IS CAUSED BY AN INFECTIOUS AGENT

Summary of the process of identifying diseases?

A

ISOLATE the PATHOGEN (clinical specimens) → MICROBIOLOGY section → IDENTIFY (Genus and Species) ‘name’ → BASIS of TREATMENT

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10
Q

HOW TO IDENTIFY THAT A CONDITION IS CAUSED BY AN INFECTIOUS AGENT

The actual name of microbe/pathogen?

A

Genus and the species

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11
Q

HOW TO IDENTIFY THAT A CONDITION IS CAUSED BY AN INFECTIOUS AGENT

T or F

Identifying isolated genus and species is important since it will be the basis of treatment

A

T

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12
Q

HOW TO IDENTIFY THAT A CONDITION IS CAUSED BY AN INFECTIOUS AGENT

T or F

treatment associated to your pathogen is universal to other genus and speciest

A

F (treatment associated to your pathogen is SPECIFIC for its genus and species)

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13
Q

HOW TO ISOLATE THE PATHOGEN?

What classical,traditional,usual or routine method is used to identify microorganism?

A

phenotyping analysis (microscopic analysis)

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14
Q

HOW TO ISOLATE THE PATHOGEN?

Focuses more on the physiological or physiologic properties of microorganism

A

Phenotype

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15
Q

HOW TO ISOLATE THE PATHOGEN?

2 Common methods of phenotype analysis?

A
  1. See through naked eye
  2. Microscope
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16
Q

HOW TO ISOLATE THE PATHOGEN?

A Common way of identifying presence of microorganisms in phenotype analysis?

A

staining procedures

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17
Q

HOW TO ISOLATE THE PATHOGEN?

T or F

Staining procedures identifies both the presence/absence of microorganism as well as the name (genus and species)

A

F (PRESENCE OR ABSENCE OF MICROORGANISM ONLY)

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18
Q

HOW TO ISOLATE THE PATHOGEN?

Before identifying specific name of microogranism in phenotype analysis, this should be done

A

Culture the specimen

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19
Q

HOW TO ISOLATE THE PATHOGEN?

Before identifying specific name of microogranism in phenotype analysis, this should be done

A

Culture the specimen

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20
Q

HOW TO ISOLATE THE PATHOGEN?

grow the microorganism outside the body using artificial environment

A

Culture

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21
Q

HOW TO ISOLATE THE PATHOGEN?

majority of the microorganisms will grow during the span of these hours

A

24-48 hours

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22
Q

HOW TO ISOLATE THE PATHOGEN?

Denote the presence or growth of bacteria or pathogen, specifically if the one we isolated is clinically significant.

A

colonies

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23
Q

HOW TO ISOLATE THE PATHOGEN?

After presence of colonies, to specifically know the genus and species what dhould be done as a follow up?

A

Follow-up testing through biochemical testing

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24
Q

HOW TO ISOLATE THE PATHOGEN?

T or F

One biochemical test is enough to know genus and species of microogranism

A

F (series of biochem test)

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25
Q

What are the 2 ways of detection of pathogen/diagnosis?

A
  1. Diagnosis using NAATS
  2. Diagnosis using SEQUENCING
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26
Q

WAYS OF DETECTION OF PATHOGENS

→Most common method of diagnosis
→Amplify small amount of nucleic acid

A

Diagnosis using NAATS

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27
Q

WAYS OF DETECTION OF PATHOGENS: NAATS

→Among all the Amplification assays, this is the most common (very popular method)

A

PCR based amplification techniques

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28
Q

WAYS OF DETECTION OF PATHOGENS: NAATS

what are the PCR based amplification techniques?

A

qPCR, RT-PCR, real time PCR, multiplex, duplex PCR, enzyme-based PCR,

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29
Q

WAYS OF DETECTION OF PATHOGENS: NAATS

T or F

when we perform or do a nucleic acid amplification technique, it is important to know the specific target sequence or location or position of the gene

A

T

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30
Q

WAYS OF DETECTION OF PATHOGENS: NAATS

Common target sequence of genes for bacteria?

A

16S rRNA or 23S rRNA (have varying degrees)

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31
Q

WAYS OF DETECTION OF PATHOGENS: NAATS

Common target sequence of genes for fungi?

A

18S rRNA (have varying degrees)

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32
Q

WAYS OF DETECTION OF PATHOGENS: NAATS

T or F

Identifiers and sequences (like the 16s rrNA) does not matter

A

F (it does since these will be used as a basis for designing primers)

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33
Q

WAYS OF DETECTION OF PATHOGENS

→sequencing in detecting pathogens.

A

DIAGNOSIS WITH SEQUENCING

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34
Q

WAYS OF DETECTION OF PATHOGENS: DIAGNOSIS WITH SEQUENCING

Most common sequencing tests for sequencing?

A

NGS or next generation sequencing technique.

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35
Q

WAYS OF DETECTION OF PATHOGENS: DIAGNOSIS WITH SEQUENCING

Under NGS, one of the most important things to know is the part of the gene/commonly sequenced is the?

A

16S rRNA

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36
Q

WAYS OF DETECTION OF PATHOGENS: DIAGNOSIS WITH SEQUENCING

Under NGS, one of the most important things to know is the part of the gene/commonly sequenced is the?

A

16S rRNA

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37
Q

WAYS OF DETECTION OF PATHOGENS: DIAGNOSIS WITH SEQUENCING

Why is 16s rRNA the most common target to use for nGS?

A

it contains alternating sequence with conserved regions which contains the signature sequence and makes the organism unique, making it
also highly specific.

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38
Q

IDENTIFY THE SPECIES: MOLECULAR DETECTION OF BACTERIA

→ belongs to the Fastidious microorganisms or Fastidious bacterium

→Arthropod borne

→ Serology is most common method of diagnosis

→ Screening assay is qPCR/real time PCR

→ Confirmatory assays are enzyme-based PCR, microarray techniques, ISH, Blotting techniques

A

BARTONELLAE SPECIES

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39
Q

IDENTIFY THE SPECIES: MOLECULAR DETECTION OF BACTERIA

is fastidious meaning it very selective in such a way that it requires a special environment or special requirement or special procedures before you can grow it.

A

BARTONELLAE SPECIES

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40
Q

IDENTIFY THE SPECIES: MOLECULAR DETECTION OF BACTERIA

T or F

Molecular techniques is performed for BARTONELLAE since it is difficult to grow in the lab as it requires a lot of special requirements.

A

T

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41
Q

IDENTIFY THE SPECIES: MOLECULAR DETECTION OF BACTERIA

T or F

Isolation using classical bacteriological methods is easy to do since it requires minimum requirements

A

F (Isolation using classical bacteriological methods is laborious and requires specific conditions and prolonged incubation periods)

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42
Q

MOLECULAR DETECTION OF BACTERIA

Most commonly used method of diagnosis for bacteria that looks for antibody production when infected with species

A

SEROLOGY

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43
Q

MOLECULAR DETECTION OF BACTERIAL BARTONELLA SPECIES

T or F

Serological assay is diffucult for bartonellae since it contain lots of species – more than 30 which cannot be differentiated

A

T

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44
Q

MOLECULAR DETECTION OF BACTERIA: BARTONELLAE SPECIES

To screen presence of Bartonellae in an infection or condition, the most commonly used assay is?

A

real-
time PCR techniques (qpcr)

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45
Q

MOLECULAR DETECTION OF BACTERIA: BARTONELLAE SPECIES

After screening through qPCR, waht should be followed?

A

molecular confirmatory assays targeting several loci

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46
Q

MOLECULAR DETECTION OF BACTERIA: BARTONELLAE SPECIES

Familiarize the confirmatory assays under bartonellae

A

enzyme-based PCR, microarray techniques, ISH, Blotting techniques

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47
Q

IDENTIFY THE SPECIES: MOLECULAR DETECTION OF BACTERIA

→ arthropod borne

→ genus is under the group of Spirochetes

→ One of its most common arthropod or insect associated with it are ticks

A

BORELLA SPECIES

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48
Q

MOLECULAR DETECTION OF BACTERIA: BORELLA

→ refer to bacteria that have spiral shape, a feature for BORELLA

A

Spirochetes

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49
Q

IDENTIFY THE SPECIES: MOLECULAR DETECTION OF BACTERIA

Common insects associated with BORELLA

A

Ticks

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50
Q

MOLECULAR DETECTION OF BACTERIA: BORELLA

Characteristic symptoms for BORELLA?

A

Bull’s eye rash

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51
Q

MOLECULAR DETECTION OF BACTERIA: BORELLA

Classical microbiology method or traditional method for diagnosing bacterial isolate, Borella species ?

A

Blood Smear preparation

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52
Q

MOLECULAR DETECTION OF BACTERIA: BORELLA

T or F

Blood smear detection analysis is ideal since it gives early diagnostics

A

F (blood smear can only detect bacteria if it is high enough; meraning the patient is already highly infectious, therefore NOT IDEAL)

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53
Q

MOLECULAR DETECTION OF BACTERIA: BORELLA

Instead of blood smear, what molecular techniques can be used to give early diagnosis?

A
  1. PCR
  2. NGS
  3. Proteomic Approaches
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54
Q

MOLECULAR DETECTION OF BACTERIA: BORELLA

→ gives the highest viable diagnostic approach specifically during the early stages/acute phases

→ valuable diagnostic approach in acutely ill
patients

early diagnosis thorugh molecular technqiues

A

PCR

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55
Q

MOLECULAR DETECTION OF BACTERIA: BORELLA

most recently applied techniques for detecting Borella species

early diagnosis thorugh molecular technqiues

A

NGS and PROTEOMIC APPROACHES

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56
Q

This bacterium is an important cause of Sexually Transmitted Diseases (STD) specifically in the United States (US)

A

CHLAMYDIA TRACHOMATIS

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57
Q

Chlamydia Trachomatis - T or F

when an individual presents with an infection associated with it, the said infected individual presents as symptomatic

A

F - Asymptomatic (Majority of cases)

have signs of
symptoms but are very mild

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58
Q

what should be done for patients that are suspected with Chalmydia Trachomatis?

A

Early diagnosis or
Early screening test

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59
Q

What is the most concernincg factor of Chlamydia Trachomatis?

A

When missed out, it can easily spread

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60
Q

What ate the three main target genes in chlamydia trachomatis?

A
  • Cryptic plasmid
  • Genomic sequences
  • rRNA (16S rRNA and 23S rRNA)
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61
Q

in chlamydia what was considered the best target gene specifically for the AMPLIFICATION TECHNIQUES?

also commonly used

A

cryptic plasmid

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62
Q

CHLAMYDIA TRACHOMATIS

What does the cryptic plasmid contains

A

introns or the intracellular sequences which can be amplified via a multicopy.

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63
Q

Reasons and applications of typing Chlamydia
trachomatis?

A

detecting the transmission pattern or
pattern of spread

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64
Q

Reasons and applications of typing Chlamydia
trachomatis? - FORENSIC PRUPOSES

A

typing for
cases associated with sexual assault

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65
Q

In typing the chlamydia trachomatis, it is based
mainly on the discrimination of?

A

** 15 different serovars** encoded by the ompA (omp1) gene

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66
Q

CHLAMYDIA TRACHOMATIS

What encodes the 15 different serovars?

A

ompA (omp1) gene

main focus of its sequencing

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67
Q

CHLAMYDIA TRACHOMATIS

 Main advantage when we do typing:

A

differentiate, which can identify diff serovars (Strains)

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68
Q

A microorganism that is difficult to grow using the classical method because an anaerobe.

A

CLOSTRIDIUM DIFFICILEA

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69
Q

For an anaerobic microorganism to grow? what is the pre-requisite

A

NO OXYGEN in the environment

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70
Q

an important cause of nosocomial type
of diarrhea

A

Clostridium Difficilea

clue: DIFFI = DIFFICATE (natae rawr)

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71
Q

CLOSTRIDIUM DIFFICILEA

what does nosocomial Diarrhea means

A

hospital-acquired or antibiotic-associated diarrhea

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72
Q

CLOSTRIDIUM DIFFICILEA

Main responsible for hospitalacquired diarrhea.

A

Nosocomial Diarrhea

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73
Q

is Clostrodium Difficilea are photogenic? TOF

A

F (Pathogenic)

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74
Q

What is the relative activity of Clostrodium Difficilea when it can be considered pathogenic?

A

Once it release toxic

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75
Q

Best method for detect Clostrodium Difficilea and why?

A

TISSUE CULTURE CYTOTOXIN ASSAY – bcos its pathogenic and in this assay we culture the toxic release

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76
Q

In Clostrodium Difficilea what is the target toxin genes of real time PCR?

A

(1) tcdA
(2) tcdB
(3) tcdC117

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77
Q

C. Difficile

What method besides tissue culture cytotoxin assay and Real time pcr can be used?

A

Multiplex PCR - one-step, rapid, and specific screening method for C. difficile toxin genes

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78
Q

bacterium which is commonly missed out because it is not quick to be identified since it is the only bacteria that has no cell wall—therefore does not retain any dye

A

MYCOPLASMA PNEUMONIAE

79
Q

Almost all the bacteria are observable under the microscope as long as we stain it, except

A

mycoplasma pneumoniae

80
Q

Why is Mycoplasma pneumoniae not microscopically observable?

A

does not retain
any dye or stain

bcos it lacks CELL WALL

81
Q

one of the most common
causes of community-acquired type of
pneumonia

A

Mycoplasma pneumoniae

82
Q

TOF

M. pneumoniae is easily
transmitted from one individual
to another via vehicle
droplets.

A

F - Respiratory

83
Q

What are the molecular techiniques can be used in mycoplasma pneuomoniae

A

PCR

84
Q

Gene targets of mycoplasma pneumoniae

A

(1) 16S rRNA
(2) P1
(3) Tuf
(4) parE
(5) dnak
(6) pdhA
(7) ATPase operon
(8) CARDS toxin gene (mpn372)
(9) repMp1

85
Q

what is the target gene that is commonly used for mcyoplasma pneomoniae

A

P1 gene, there is the
unique signature sequence of
mycoplasma pneumoniae

86
Q

What are the two types of Rickettsia Species?

A

arthropod-borne insects or Bacteria

87
Q

What is its difference of rickettsia specied from other
arthropod-borne infections?

A

Early treatment should be provided when the physician suspected the patient with Rickettsia species

infection associated with Rickettsia is considered lifethreatening

88
Q

How the physician suspects that the patient’s condition is associated with Rickettsia?

Clue: 3 unique manifestation

A

(1) Fever
(2) Rash
(3) Presence of Eschar

89
Q

How do we diagnose Rickettsia through
Molecular Techniques

A

Mainly through PCR-BASED ASSAY

90
Q

if u see this card

A

study the table specimen used in rickettsia detection

91
Q

Among all the specimens, the best to use for rickketseria are?

A
  • skin or eschar biopsy
  • autopsy organ tissue.

there is high amount of bacterium present,

92
Q

Rickettsia

Molecular detection is based mainly on recognition of sequences from different targets

what specific genes are these

A

(1) 16S rRNA
(2) Protein-coding genes

93
Q

most common isolates
in the laboratory

A

STAPHYLOCOCCUS AUREUS

94
Q

TOF

Staphylococcus auerus causes a wide variation of disease?

A

T

It does not only infect the skin but also the other organs.

95
Q

An invasive, life-threatening infection
associated with Staphylococcus aureus

A

Methicillin Resistant Staphylococcus Aureus (MRSA)

96
Q

this is the strain of S. aureus due to MUTATION OF MecA and MecB gene

A

 Methicillin Resistant Staphylococcus Aureus (MRSA)

97
Q

TOF

MRSA is life-threatening
because S. aureus is almost
resistant to all beta lactum
drugs/antibiotics

A

F (Lactam)

it aint milk tf

98
Q

best molecular diagnostic tool for MRSA
detection

A

PCR

99
Q

Among the latest development in the direct
MRSA detection and identification,

A

REAL-TIME PCR

100
Q

S. Aureus

Method that could be used to predict resistance, assess virulence, and type isolates at the highest possible resolution

A

Whole Genome Sequencing (WGS)

101
Q

What are the molecular techniques of S. Aureus?

A
  • PCR
  • Real-time PCR
  • Whole Genome Sequencing
102
Q

 Causative agent of pneumonia

A

Streptococcus pneumoniae

103
Q

when under microscope this genus is identified with an arrangement like a LINE

A

Streptococcus pneumoniae

104
Q

What prier can be used with Streptococcus pneuminae?

A

specific to repetitive regions

105
Q

Streptococcus Pneumoniae

 Primers used in PCR testing are specific to REPETITIVE REGIONS and genes encoding:

A
  • rRNA
  • Pneumococcal surface adhesion A molecule (psaA)
  • Pneumolysin (ply)
  • Penicillin binding protein
  • Autolysin (lytA)
106
Q

TOF Streptococcus Pnuemininadifaw

the best na ginagamit ng majority ng laboratory targets Autolysin (lytA) gene (the focus of majority of different techniques).

A

True

107
Q

Other name: Group A Streptococcus (GAS)

A

Streptococcus pyogenes

108
Q

Molecular test for Strptococcus pyogenes

A

GASDirect test

109
Q

Streptococcus pyogenes

Identifies specific rRNA sequences of
Streptococcus pyogenes in pharyngeal
specimens by a single-stranded
chemiluminescent nucleic acid probe f

A

 GASDirect test

110
Q

what are the specimen used in Streptococcus pyogenes?

A

pharyngeal
specimens

111
Q

what are the probe for identification used in Streptococcus pyogenes

A

single-stranded
chemiluminescent nucleic acid probe

112
Q

Main application/advantages of GASDirect test for Streptococcus pyogene

A
  • Applied for primary testing
  • Use as a backup test to negative
    antigen/serology tests
    Batch screening test of throat cultures
113
Q

Other name: Group B Streptococcus (GBS)

A

Streptococcus agalactiae

114
Q

Clinically significant to neonates/newborn because
it is a very important cause of a highly life-threatening
condition termed as neonatal meningitis.

A

Streptococcus agalactiae

115
Q

Group B Streptococcus (GBS)

Clinically significant to neonates/newborn because
it is a very important cause of a highly life-threatening
condition termed as

A

neonatal meningitis.

116
Q

What is the detection for Streptococcus agalactiae

A

Screen the pregnant mother
during the 35th
-37th week of gestation - can be seen in VAGINA or RECTUM

117
Q

Where does the colonization of GBS SEEN

A

vaginal area or it can be in rectal area too

118
Q

How is the GBS passed to new born?

A

during normal delivery, bacterium is transferred to baby

119
Q

Streptococcus agalactiae

Using the classical method in microbiology, it can be
identified/screened via

A

culture method

120
Q

only bacterium that produces a
pattern of growth – arrow head zone of hemolysis:

A

Group B Streptococcus (GBS)

Streptococcus agalactiae

121
Q

arrow head zone of hemolysis is caused
by GBS releasing the so-called?

A

CAMP factor
(due to one gene).

122
Q

Main disadvantage of this culture technique for GBS?

A

matagal siyang gawin (at least
2 days or 24-48 hours)

123
Q

what is the solution for slow TAT culture for GBS?

A

conventional or real-time PCR assays (mol bio)
may be used

124
Q

Streptococcus agalactiae

Target genes for PCR or Conventional

A
  • sip
  • cfb - common
  • scpB
  • ptsl genes
125
Q

Streptococcus agalactiae

s one of most common targets
because it is responsible for the release
of CAMP factor

A

cfb gene

126
Q

what are the other method for detection of GBS besides culture, and pcr methods?

A

LAMP Method

 Maximum time of detection is within 90 minutes

127
Q

Most common method in detecting Fungi

A

PCR or amplification techniques

128
Q

Why is it important to have unique probes and formats in the molecular formats of Fungi detection?

A

bc it will help in the identification

129
Q

MOLECULAR DETECTION OF FUNGI

Enumerate DNA targets

A
  • rDNA,
  • cytochrome b,
  • β-tubulin,
  • calmodulin,
  • enolase,
  • chitin synthase, and
  • heat shock protein
130
Q

MOLECULAR DETECTION OF FUNGI

DNA target to be used depends on what?

A

Genus of the Fungi

131
Q

MOLECULAR DETECTION OF FUNGI

Identify the Target Fungi: Actin

A

Aspergillus

132
Q

MOLECULAR DETECTION OF FUNGI

Identify the Target Fungi: beta - Tubulin

A

Phaeacremonium
Aspergillus
Pseudallescheria

133
Q

MOLECULAR DETECTION OF FUNGI

Identify the Target Fungi: Calmodulin

A

 Aspergillus
 Pseudallescheria info

134
Q

MOLECULAR DETECTION OF FUNGI

Identify the Target Fungi: Chitin synthase 2

A

Lacazai loboi

135
Q

MOLECULAR DETECTION OF FUNGI

Identify the Target Fungi: Cytochrome b

A

Aspergillus,
Trichosporon, and
Rhodotorula

135
Q

MOLECULAR DETECTION OF FUNGI

Identify the Target Fungi: D1-D2

A

Most Fungi

136
Q

MOLECULAR DETECTION OF FUNGI

Identify the Target Fungi: Elongation factor 1a

A

Fusarium species

137
Q

MOLECULAR DETECTION OF FUNGI

Identify the Target Fungi: ITS

its what?

A

Medically significant yeasts
& fungi

138
Q

MOLECULAR DETECTION OF FUNGI

Identify the Target Fungi: 26S

A

Medically relevant Fusarium and Scedosporium

139
Q

Molecular Detection of Fungi

Among all medically important fungi, what is the most common target gene

A

Internally transcribed spacer (ITS)

Note: it le universal target gene

140
Q

Molecular Detection of Fungi

Among all the medically important fungi, majority focuses on what genus?

A

Aspergillus

141
Q

Molecular Detection of Fungi:

List molecular techniques employed in detecting Aspergillus

A
  • Nucleic Acid Amplification Test (NAAT)
  • In situ hybridization (ISH) techniques
141
Q

Molecular Detection of Fungi

Identify the molecular technique used in identifying Aspergillus:
Provides rapid and accurate diagnosis

A

NAAT

142
Q

Molecular Detection of Fungi

Identify the molecular technique used in identifying Aspergillus:
used in fresh and formalin-fixed, paraffin-embedded (FFPE) tissues without requiring nucleic acid extraction or amplification

A

In situ hybridization (ISH) techniques

142
Q

Molecular Detection of Virus

Human Immunodeficiency Virus (HIV),,, Identify:
* Family
* Genus
* Types

A

Fam: Retroviridae
Genus: Lentivirus
Types: HIV 1 and 2

143
Q

Molecular Detection of Virus

globally; majority causative agent of HIV infections; most virulent

A

HIV 1

144
Q

Molecular Detection of Virus

Commonly isolated in the West and Central part of Africa

A

HIV 2

145
Q

Molecular Detection of Virus

In performing molecular detections, what are the 3 main targets in detecting HIV?

A
  • gag
  • polymerase (pol)
  • envelope (env)
146
Q

Molecular Detection of Virus

Identify the Viral Gene Products of the gene: GAG

A

p24, p18, and p15

147
Q

Molecular Detection of Virus

Identify the Function of the Gene: gag

A

Codes for core structural CHON

arrangement/shape seen under the microscope

148
Q

Molecular Detection of Virus

Identify the viral gene products of the gene: pol

A
  • Reverse Transcriptase
  • RNAse
  • Protease
  • Integrase
149
Q

Molecular Detection of Virus

Identify the function of the gene: pol

A
  • Transcribes RNA into DNA
  • Degrades RNA
  • Makes HIV particles into complete and functional HIV virus
  • Inserts viral DNA into host DNA
150
Q

Molecular Detection of Virus

Identify the viral gene product of the gene: env

A

gp120

151
Q

Molecular Detection of Virus

Identify the function of the gene: env

A

binds CD4 receptor

152
Q

Molecular Detection of Virus

Identify the function of the viral gene product: gp41

A

Viral fusion of the cell

153
Q

Molecular Detection of Virus

Among the 3 genes identified in HIV, what gene is the main focus in detection?

A

gag

specifically the viral gene product: p24

154
Q

Molecular Detection of Virus

Target of drugs or treatment for HIV

anong gene/s?

A

pol and env genes

155
Q

Molecular Detection of Virus

Among all techniques in molbio, what technique/s do they use for HIV?

clue: HIV is an RNA type of Virus

A

RT PCR

reverse transcription

156
Q

Molecular Detection of VIrus

The methods of its identification can be detected in HIV through?

A

antigen, antibody, and
DNA/RNA of the virus.

157
Q

Molecular Detection of VIrus

Most of the time, the ____ is commonly detected

A

HIV Antibody

157
Q

If u see this card, review mo table ng HIV diagnostics table

A

yes

158
Q

Molecular Detection of Virus

One of the most commonly used technique for HIV Diagnostics

confirmatory test

A

Western blot

159
Q

Molecular Detection of Virus

it is method that focuses on detecting the protein of the extracted sample from the assay.

A

Western blot

159
Q

Molecular Detection of Virus

This group of virus contains lots of strains which
causes different wide varying types of infection.

A

Human Papillomavirus

160
Q

Molecular Detection of Virus

most clinically significant strain which causes cancer in humans

A

Human Papillomavirus

ewan q kung nagkamali k p dyan

161
Q

Molecular Detection of Virus

the most popular HPV that causes cancer. The causative agents of cervical CA.

A

HPV 16/18

162
Q

Molecular Detection of Virus

Strains of HPV are based on what

A

numbers

review the major clinical association of genital tract and other mucosal

….HPV; I dont make the rules

163
Q

MOLECULAR DETECTION OF VIRUS

medically important genes detected for HPV 16&18

A

E6 and E7

164
Q

Molecular Detection for Virus

Hepatitis virus is caused by allat of viruses. Now, what is the common target of these types?

A

Liver cells

165
Q

MD of Virus (pagoda na)

Enumerate the types of Hepatitis virus

A

HAV, HBV, HCV, HDV, HEV, HGV

166
Q

MD of Virus (pagoda na)

ONE OF THE MOST WIDELY USED ASSAY FOR HEPA VIRUS

A

qPCR

167
Q

TOF. targets for qPCR depends on the family of the virus

A

F (type)

168
Q

MD of Virus

review the Hepa V regions used as qPCR templates

TW: next page

review mo nalang din sa table

A

HAV: 5’ UTR
HBV: S-gene & X-gene
HCV: 5’ UTR
HDV: Ribozyme -1
HEV: ORF 2 and 3
HGV: 5’ UTR

left Virus; right Conserved Regions

169
Q

MD of Virus

Among the types of hepa v, which of them most commonly use molecular techniques?

A

HBV

170
Q

MD of Virus

Type of Hepa V which causes life threatening complications, such as Liver CA and Liver Cirrhosis

A

HBV

171
Q

MD of Virus

what is detected and targeted in detecting HBV using nucleic acid based testing?

A

cccDNA minichromosome

172
Q

MD of Virus

  • covalently closed circular DNA.
  • It is produced during its life cycle.
  • Molecular techniques take advantage of
    this for detection purposes.
A

cccDNA

173
Q

An emerging technique in Microbiology used
for identification of genus and species of
microorganisms (e.g. bacteria).

A

Matrix Assisted Laser Desorption Ionization – Time of Flight Mass Spectroscopy.

MALDI-TOF MS

174
Q

It is an automated method for the identification
of the genus and species of bacterium.

A

MALDI-TOF MS

175
Q

PRINCPIPLE OF MALDI-TOF MS

From ________, put a sample on a test tube where the assay will be mixed.

1st step

A

bacterial culture

176
Q

PRINCIPLES OF MALDI-TOF MS

The matrix/reagents used in this method is composed of what?

A

SATURATED LOW IONIC ORGANIC MASS

in short, BIOMASS

177
Q

PRINCIPLE OF MALDI-TOFF MS

After mixing reagents with the samples, you transfer it to the
________________________

A

MALDI-TOF MS PLATE

178
Q

PRINCIPLE OF MALDI-TOF MS

TOF. After mixing samples and transferring it to the MALDI-TOF MS plate, next step is to analyze it in the microscope

A

F. automated identification

179
Q

What is the defining feature of MALDI-TOF MS as compared to other molecular techniques?

A
  • extracts purified proteins
  • extraction method is already mixed into the matrix (specifically extracts protein of the bacterial sample)
180
Q

PRINCIPLE OF MALDI-TOF MS

TOF. Bacterial sample/Clinical sample at first has no charge/it is in neutral charge

A

T

181
Q

MALDI-TOF MS PRINCIPLE

What provides the charge to the samples?

A

Matrix (satured low ionic organic mass/ biomass)

provides protons

182
Q

PRINCIPLE OF MALDI-TOF MS

measures the net charge produced during the procedure.

A

Ionization process

183
Q

PRINCIPLES OF MALDI-TOF MS

MAIN PRINCIPLE OF MALDI-TOF

A

SOFT IONIZATION

184
Q

MALDI TOF

SOFT IONIZATION IS MEASURED THRU?

A

MS PROFILE (PATTERNS)

185
Q

MALDI TOF

TOF. MS profiles of each bacterium is identical from one organism to another

A

f (unik)

186
Q

In MALDI-TOF assay, the most important
consideration during the procedure is

A

sample preparation

187
Q

MALDI-TOF SAMPLE PREP

main consideration in the prep of sample?

A

isolate a purified protein

188
Q

MALDI-TOF

protein can be purified by mixing what?

A

specific reagents

eme formic acid

sabi nila depends on bacterium pero formic acid parin naman gamit

189
Q

MALDI-TOUGH

TOF. for better extraction, methanol is added

A

F (-m)

Molecular Biology Lecture (17 decks)

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