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Medical Microbiology > Systems of Pathogen Detection I > Flashcards

Systems of Pathogen Detection I Flashcards

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Biology 101 flashcards USMLE® Step 1 flashcards
1
Q

Why is taxonomy better than standard naming for pathogens?

A

Names only imply capacity for pathogenicity

They do not include an assessment of virulence

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2
Q

Outline the taxonomy of TB

A 
Domain 	Eubacteria 
Kingdom Procaryote 
Phylum 	Gram positive 
Class 	Actinobacteria 
Order 	Actinomycetales 
Family 	Mycobacteriaceae 
Genus 	Mycobacterium 
Species 	Mycobacterium tuberculosis 
Strain 	Beijing 
Type 	IIa6B1 
Isolate 	Sputum
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3
Q

Of the myobacterium genus which are pathogenic to humans?

A

148 current species - Only three are obligate human pathogens:

  • M .tuberculosis
  • M .leprae
  • M .ulcerans
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4
Q

Define a pathogen

A

A microbe capable of causing a specific degree of host damage

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5
Q

What is a commensal non pathogen (in host)?

A

PRESENT but NOT CAPABLE of causing disease in the host
eg. E.coli Bacteroides thetaiotaomicron
‘good bacteria’

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6
Q

What is a Zoonotic Non pathogen (in carrier)?

A

PRESENT but only CAPABLE of causing disease in ANOTHER host

eg. E.coli O157:H7 is subclinical in cattle

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7
Q

What is a commensal opportunist (in host)?

A

PRESENT and CAPABLE of causing disease in the host but only in certain circumstances
eg. Bacteroides fragilis Coagulase Negative Staphylococcus (CNS)

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8
Q

Why does a positive sample not confirm disease?

A

Being infected / presented with disease doesn’t guarantee active disease

Majority people presented with a pathogen don’t develop infection at all or it becomes latent and activated later on in life

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9
Q

What determines how good a test result is?

A

A test result is only as good as the sample provided

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10
Q

Describe the requirements of a sterile testing site

A

Sterile sites must be free from contamination

e.g. Skin flora in blood cultures

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11
Q

How must non-sterile sites of testing be prepared?

A

Non sterile sites require decontamination of normal flora

e.g. Faeces, Mouth, Skin

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12
Q

Why are some samples concentrated?

A

Samples with high volume or relatively low infected pathogen load require concentration (centrifugation, filtering)
e.g. CSF, Ascites, 24 hr Urine

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13
Q

Why do we culture pathogens?

A

Culturing the bacteria proves it’s presence

But don’t always require culturing but knowing which specific pathogen you’re looking for makes identification a lot easier

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14
Q

How is a culture prepared?

A

enrichment
purification
amplification

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15
Q

How is a direct sample prepared for identification?

A

concentrated and treated

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16
Q

What identification techniques are used to identify pathogens in a sample?

A

Molecular DNA/RNA
Microscopy: gross morphology
HPLC MassSpec: chemical Composition

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17
Q

Which pathogens are visible via direct light microscopy?

A

Larger pathogens

  • Trichomonas vaginalis
  • Schistosoma mansoni
  • Entamoeba histolytica
  • Strongyloides (thread worm)
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18
Q

When is Electron microscopy used?

A

Smaller sized samples
Mainly used for viruses
Used when PCR and culturing isn’t an option

> not used for diagnostics

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19
Q

Which pathogens are viewed using electron microscopy?

A
  • Rotavirus (faeces)
  • Rabies lyssavirus (brain tissue)
  • Hepatitis B (liver)
  • Tonsilitis adenovirus - nasal secretion
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20
Q

When are samples stained?

A

Stain direct bacterial samples to identify using light microscopy

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21
Q

What does staining show us?

A

Can identify:

  • Gram stain
  • Shape
  • Features (flagella etc.)
  • Gram +/-
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22
Q

What is the significance of bacterial staining?

A

We can also use this staining to identify capsulated organisms as these are more likely to be pathogens

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23
Q

Give examples of capsulated bacteria

A
  • streptococcus pneumoniae

Bacterial spores also present in Bacillus anthracis and Clostridium perfringens (food poisoning)

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24
Q

How is immunofluorescent staining done?

A

Immunofluorescent staining with pathogen specific conjugated antibody

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25
Q

Which pathogens are seen using immunofluorescence?

A

Treponema pallidum in gastric syphilis

Measles virus Infected into a lab Vero cell line then stained with fluorescent antibody

26
Q

What are the advantages of microscopy evaluation?

A
  • Easy to perform
  • Rapid screening
  • Some parasites have SPECIFIC morphology
    eg. Schistosoma mansoni
  • Specific Immunofluorescence staining possible
27
Q

What are the disadvantages of microscopy evaluation?

A
  • Not Sensitive
    eg. Mycobacterium tuberculosis
    screening sputum smears requires at least 10,000 orgs per ml to be visualised
  • General stains are not specific
  • Labour intensive (expensive)
  • Requires specialist interpretive expertise (more expensive)
28
Q

What does a bacterial culture depend upon?

A

Bacteriology relies on ability of the test system to be able to grow the pathogen

29
Q

What media are used for bacterial culturing?

A
  • Non Selective Media eg. Blood Agar
  • Semi Selective Media eg. MacConkey Agar, DCA, CLED
  • Selective growth temperatures eg. Campylobacter species
30
Q

What are the different selective atmospheres?

A
  • aerobic culture
  • anaerobic culture
  • microaerophilic culture
31
Q

Which pathogens favour aerobic atmospheres?

A

espiratory pathogens are adapted to this environment
But these are both facultative anaerobes

Strict (Obligate ) aerobe
eg. Pseudomonas fluorescens, Nocardia asteroides)

32
Q

Which pathogens favour a microaerophilic atmosphere?

A

Respiratory pathogens

  • Neisseria meningitidis
  • Neisseria gonorrhoeae
  • Haemophilus influenzae
  • Brucella melitensis
33
Q

Why do certain pathogens require an anaerobic environment?

A

Some pathogens are unable to survive in aerobic conditions due to the effects of oxygen on their metabolism

34
Q

Which pathogens favour anaerobic conditions?

A
  • Clostridium tetani
  • Clostridium botulinum
  • Clostridium difficile
  • Bacteroides fragilis
35
Q

Describe the effects of clostridium perfringens

A

Clostridium perfringens on Blood agar Grown in ANAEROBIC atmosphere

Aerotolerant anaerobe producing spores in environmental conditions and exotoxins in humans causing Food poisoning (gut) and Gas gangrene

36
Q

Describe the structure of clostridium perfringens

A

Gram +ve spore forming anaerobic rod/bacillus shaped

37
Q

Which pathogen has selective atmosphere and temperature?

A

E.g. Campylobacter (found in cows) only grows in the following conditions:

  • 42°C
  • 10% CO₂
38
Q

What are the 2 types of specific haemolysis pathogens cause?

A

β- haemolysis

𝛂-haemolysis

39
Q

Which pathogens cause βhaemolysis?

A

streptococcus sp. Group A

40
Q

Which pathogens undergo 𝛂-haemolysis ?

A

Mucoid: optochin sensitivity with gram stain microscopy and colony morphology - diagnostic for streptococcus pneumoniae

41
Q

Outline the different environments and pathogens of bacteriology

A

Environment

  • O₂ E. coli
  • CO₂ Haemophilus influenzae
  • ANO₂ Clostridium perfringens
42
Q

What info does bacteriology provide us?

A

Quantification, Identification, Antibiogram

Colony morphology, Colour, Haemolysis 
Colony Count 
Colony Identification 
Systematic identification 
Colony Resistance to antibiotics
43
Q

What is the purpose of metabolic testing?

A

Can identify Catalase enzymes

Can cleave indole from tryptophan (indole test)

44
Q

How is bacteriology classified?

A

Specific patterns associated with certain pathogens - allows identification
> taxonomically identified

45
Q

Give examples of some of the patterns used to classify pathogens

A

Metabolic function and sugar utilisation tests for identification of Enterobacteriaceae
Eg. Salmonella, Shigella, E.coli

Bacteria are particularly susceptible to phages (bacteriophages)
∴ some systems are used to phage type bacteria particularly E.coli

46
Q

When is antibiotic sensitivity plate testing carried out?

A

Only done if organism is able to be grown quickly

47
Q

What does an E test show?

A

Determines how much antibiotic to administer

48
Q

Which bacteria can cause food poisoning?

A

Can be caused by:

  • Shigella
  • Campylobacter
  • Salmonella
49
Q

What are the symptoms of food poisoning?

A

All these organisms produce similar illnesses : diarrhoea, vomiting, fever etc.

50
Q

How is the pathogen causing food poisoning identified?

A

Fecal samples are taken and tested in aforementioned ways to establish which pathogen is causing disease

51
Q

How is viral culture and microscopy conducted?

A 
Requires permissive cell lines 
E.g. Vero cells (kidney epithelial)
        For Herpes Simplex
Cytopathic effect
Immunofluorescent staining of culture
52
Q

What are the methods of viral classical culture and identification?

A

Culture & Microscopy

Direct Antigen Detection

53
Q

What direct antigen test is used to identify viruses?

A

Rapid ELISA for fluA antigen = 15 mins ELISA for Flu Antibody

54
Q

How is viral cytopathic effect seen?

A

Through culture of permsisive cell lines
Staining allows us to see cytopathic effects of virus - enables identification

Not v. common anymore
V. long and difficult to conduct

55
Q

Why is electron microscopy not enough to identify viruses?

A

Electron microscopy can see this virus but not identify it as ‘swine flu’ Culture takes 3-10 days

56
Q

Describe the outer protein structure of Influenza virus

A

The flu virus contains RNA on inside and 2 types of protein coat the outside (H and N)

57
Q

Outline how an ELISA for flu is conducted

A
  1. Produce antibodies against H + N proteins
  2. Place antibodies on a microtiter plate f
  3. Capture virus and add to antibody + conjugate
  4. Conjugate itself has enzyme attached that binds to substrate (virus) to fluoresce / colour
58
Q

What is a titre in serological ELISA?

A

dilution of sample that gives a signal equal or greater than the positive control cut off

59
Q

What are the advantages of classical culture and identification?

A
  • Cheap simple, reliable reagents
  • Sensitive; single organisms grown and identified
  • Validated specificity; ‘Gold Standards’ w/ multiple parameters
  • Direct in vivo measurement of effectiveness of therapy
    eg Antibiotic sensitivity
  • Easily archived; epidemiology
60
Q

Outline disadvantages of classical culture and identification

A
  • Some pathogens cannot be grown eg. Mycobacterium leprae
  • Some pathogens aren’t well differentiated by biochemistry alone
  • Slow: culture requires at least overnight incubation:
    Viral = 3-10 days
    Mycobacterial = 6-12 weeks
  • Some pathogens grow too slowly to aid rapid diagnosis
    eg. Mycobacterium tuberculosis
  • Labour intensive (expensive)
  • Requires specialist interpretive expertise (more expensive)

Medical Microbiology (15 decks)

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