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Infectious Diseases > Week 1 > Flashcards

Week 1 Flashcards

1
Q

What are the 3 components of a taxonomy?

A

Classification, nomenclature, identification.

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2
Q

Define classification

A

Orderly grouping of microorganisms.

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3
Q

Define Nomenclature.

A

Naming of microorganisms.

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4
Q

Define identification

A

The correct naming of microorganisms

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5
Q

Who developed Binomial Noemclature?

A

Carl Linnaeus

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6
Q

What is the name of the structure that causes the heirarchy of binomial nomenclature?

A

The Linnaean System

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7
Q

Outline the order of binomial naming as per the Linnaean system.

A

Life, Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species

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8
Q

Which part of a organisms name is capitalised in binomial nomenclature?

A

The genus only

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9
Q

Which part of an organisms name is italicised in binomial nomenclature?

A

The genus and the species, but not common names etc.

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10
Q

Are subspecies italicised in binomial nomenclature?

A

Yes

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11
Q

What are phenotypic methods of bacterial identification based on?

A

Observable characteristics of an organism.

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12
Q

In terms of phenotypic bacterial identification, are genes or gene products analysed?

A

Gene products

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13
Q

Name some examples of phenotypic methods of bacterial identification.

A
  • Microscopic morphology and staining characteristics
  • Macroscopic colony morphology and pigmentation
  • Environmental requirements for growth
  • Resistance or susceptibility to antimicrobial agents
  • Nutritional requirements and metabolic capabilities
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14
Q

Describe genotypic bacterial identification.

A

Involves characterisation of a portion of the organism’s genome using molecular techniques.

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15
Q

Give an example of a method of genotypic bacterial identification.

A

DNA or RNA analysis.

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16
Q

Which method of bacterial identification is most specific and sensitive?

A

Genotypic

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17
Q

What is the aim of the diagnostic microbial library.

A

To correctly identify the pathogen, provide a diagnosis and advise on an appropriate therapy.

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18
Q

What is the purpose of bacterial typing.

A

Allows for differentiation of one bacterial strain from another.

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19
Q

What is the difference between bacterial identification and bacterial typing.

A

Identification just gives a name, whereas typing states relation between different organisms.

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20
Q

Why do we collect and process microbiological samples?

A

Aim is to correctly identify the pathogen, provide a diagnosis and advise an appropriate therapy.

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21
Q

What is achieving a useful microbiological outcome dependent on?

A

The quality of the specimen.

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22
Q

Define contamination in terms of microbiology.

A

Contamination is a microorganism that wasn’t present in the original samples, but has got into the sample during collection, transport or during processing.

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23
Q

Define pathogen.

A

A pathogen is an organism that has the ability to grow in the body and initiate disease.

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24
Q

What are the effects of contamination on microbiological outcomes?

A

Contamination is a microorganism that wasn’t present in the original samples, but has got into the sample during collection, transport or during processing.

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25
Q

What are the issues with contamination of microbiological samples leading to inappropriate treatment?

A

Inappropriate treatment is not good in terms of the whole population and antibiotic resistance. Antimicrobials also have individual risks which may affect the patient.

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26
Q

Are commensals contaminants? Explain

A

Commensals are not seen as contaminants given they do not cause any issues and are not pathogens in situations where they are commensals.

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27
Q

Name some methods of avoiding contamination in terms of microbiology.

A
  • Cleaning the collection site, e.g. use of alcohol based disinfectant on the skin before blood collection
  • Only trained staff collecting samples, e.g. phlebotomist taking blood.
    o Reduces chances of contamination.
  • An appropriate sample being collected, e.g. mid-stream urine (MSU)
  • Using only sterile, approved specimen containers
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28
Q

What is the importance of timing of collecting microbiological samples?

A

Sample must be taken at an appropriate time to maximise the change of organism recovery

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29
Q

Why must some samples be collected before antibiotics are administered?

A

o If antibiotics are present, it will be harder to isolate the organism in question.

30
Q

How many samples of blood should be supplied? Describe

A

o Two blood samples (one aerobic, one anaerobic) should be supplied

31
Q

How many orthopaedic tissue samples should be supplied in microbiology and why?

A

o Multiple orthopaedic tissue samples should be taken.
 This is to ensure a reliable diagnosis. (You don’t know where the infection is, so you increase the chances of detecting it). (If you get the same organism from the multiple samples, you increase the reliability of the diagnosis ).

32
Q

If you have a patient with possible bacterial pneumonia, what samples would you collect and why?

A
  • Sputum sample (puss and mucus collected from deep within the lungs of the patient ). This gives the greatest chance of detecting any fungal or bacterial pathogen from within the lungs. - Pneumonal bacteria may also be commonly found in the blood stream so blood culture samples may be taken.
33
Q

What are the issues with bacterial sputum samples?

A

Take a long time to have results because it needs to be processed.

34
Q

What are the benefits of blood sampling in microbiological diagnosis?

A

Fast results as they do not need processing.

35
Q

Why must a specific quantity of blood be taken in terms of microbiological diagnosis?

A

o Not enough blood = reduce possibility of detecting organism because fewer organisms present.
o Too much blood = false positives caused by metabolic processes.
- Overly full containers can lead to contamination of outside surfaces.
o (This is often common with faecal material. Organisms in the sample may produce gas. When the lid of the sample is taken off, the sample may start to ooze out of the container and cause contamination).

36
Q

When may a microbiological sample be stored at 4 degrees celcius and why?

A

4 degrees may be used if the sample is delayed. This prevents increase in growth of the organism which could alter results in terms of concentration. The concentration found will therefore still be representative and give an appropriate diagnosis

37
Q

Which type of microbiological sample requires rapid processing?

A

CSF (Cerebrospinal fluid)

38
Q

Define a category ‘A’ infectious substance.

A

An infectious substance transported in a form that, when exposure to it occurs, is capable of causing permanent disability, life threatening or fatal disease in otherwise healthy humans.

39
Q

Define a category ‘B’ infectious substance.

A

An infectious substance which does not meet the criteria for inclusion in category A

40
Q

How are microbiological specimens separated?

A

Specimens are separated by specimen type: e.g. urine, blood cultures, fluids, tissues and swabs.

41
Q

Why is microscopy not always useful in microbiological diagnosis.

A

Microscopy is sometimes not very useful.
- For example using a gram stain wouldn’t be useful when a lot of commensal flora are present. These commensal bacteria may also have the same observation as with the pathogen you are looking for (this is likely in faecal samples).

42
Q

In what type of samples are concentrations of commensal bacteria hgih?

A

Faecal samples

43
Q

Why is microscopy with gram staining useful in microbiological diagnosis?

A

Microscopy using a gram stain is useful when a sample should be sterile because anything you see is likely to be pathogenic.

44
Q

Sometimes microscopy alone can be diagnostic. When might this be the case?

A
  • When there is normally a sterile sample (CSF/ blood sample)
    o In a CSF sample, Gram +ve cocci is sufficient to diagnose meningitis and treatment must be urgent.
  • Where the appearance of the organism is diagnostic (Gram -ve diplococci from a vaginal swab = sufficient for treatment for Gonorrhoea).
  • Mycobacterium Tuberculosis is not a commensal so even if only one bacillus stained with Zn stain in the Sputum, that is sufficient to start treatment.
45
Q

Why do you inoculate agar plates?

A
  • To see if there is an organism present
  • To see if there is more than one organism present
  • To obtain a presumptive identification based on the phenotype
  • Have an isolate available to perform additional identification and susceptibility tests

You inoculate media to allow individual colonies to be observed via a streak plate.

46
Q

What is the aim of inoculating agar plates?

A

To isolate single colonies. This allows detection of mixed cultures, single colonies can be observed to aid identification, single colonies can be ‘picked off’ for further testing

47
Q

Why use more than one agar type to test a sample?

A
  • Not all organisms have the same growth requirements
    o Some are fastidious and require growth factors
  • Some agars are selective
    o They contain antibiotics or other inhibitors of growth to prevent the growth of some thus aiding growth of a target pathogen
  • Enrichment media ‘impair’ the growth of some organisms, but boost the growth of the target organisms
  • Some agars are differential
    o They allow the distinction of different organisms based on biochemical reactions
  • Others allow a presumptive identification to be made; e.g. chromogenic media
48
Q

What are the purposes of selective media?

A

Allows background organisms that colonise the sample, which you are not interested in, to be removed. This allows the pathogens to be isolated a lot more easily.

The selective mediums used prevent the growth of these background organisms so that fewer organism are present on the agar plate and therefore the pathogen can be identified a lot more easily.

49
Q

Describe how MacConkey Agar is differential.

A

The MacConkey agar makes Lactose fermenting organisms appear pink on the agar plate. Allows differentiation between lactose fermenting and non-lactose fermenting organisms.

50
Q

What is the purpose of Chromogenic media?

A

Allow differentiation of common UTI pathogens by causing them to show up very different colours. This helps to distinguish between different organisms in a sample.
(The colours can vary with different manufacturers).

51
Q

Outline the order of media that would be used to test a microbiological sample.

A 
-	Media without inhibitors
o	Blood agar
-	Media with indicators
o	Chromogenic agar
-	Media with inhibitors or selective agents 
o	DCA or MSA
-	Fluid Media
o	Cooked meat broth (this is non-selective but enhances the growth of organisms. Often used in tissue which should be sterile but appears to have organisms growing in it). 
-	Smears or films for microscopy
52
Q

Why is the order of inoculating media important?

A

If you have an organism which is susceptible to an inhibitor, you don’t want to contaminate the swab by inoculating these plates first.
Start by initially inoculating the plates which have no factors in them that could affect the organisms. Then move through the ones that become progressively more inhibitory to the organisms.

53
Q

What are the specific requirements for handling infectious organisms named?

A

Containment levels

54
Q

Describe organisms in hazard group 1 and the containment level these are handled with.

A
  • A biological agent unlikely to causes disease
  • Handled by containment level 1 – open lab
  • (e.g. environmental soil organism)
  • Not relevant to diagnostic microbiology labs, as by definition samples are not thought to contain pathogens.
55
Q

Describe organisms in hazard group 2 and the containment level these are handled with.

A

A biological agent that can cause human disease and may be a hazard to employees; it may present a risk of spreading to the community, but there is usually effective prophylaxis or treatment available.
- Handled at containment level 2
- The stand for diagnostic microbiology labs
- (E.g. S, aureus and E.coli).
- PPE Required
o Lab coats, gloves, eye protection, appropriate clothing)

56
Q

Describe organisms in hazard group 3 and the containment level these are handled with.

A

A biological agent that can cause severe human disease and presents a serious hazard to employees; it may present a risk of spreading to the community, but there is usually effective prophylaxis or treatment available.
- Organisms are handled at containment level 3
o Labs require additional safety features;
 Microbiological safety cabinet
 High efficiency particular air filtration of exhaust air
 The lab is sealable to allow disinfection
 Use of dedicated lab coats and disposable aprons
 Authorised personalle access only
o Diagnostic labs usually have these facilities (e.g. for sputum analysis where there is possibility of M.Tuberculosis).
- E.g. Mycobacterium tuberculosis, Salmonella Typhi

57
Q

Describe organisms in hazard group 4 and the containment level these are handled with.

A

A biological agent that causes severe human disease and presents a serious hazard to employees; it is likely to spread to the community and there is usually no effective prophylaxis or treatment available.
- Only viruses in this group (e.g. Ebola)
- Containment level 4 labs
o Specialised units
o People wear suits with their own air supply

58
Q

Describe Class I Microbial Safety Cabinets , what this protects and what level of hazard group organisms it is safe for.

A
  • An open fronted cabinet through which air is drawn at a sufficient rate to minimize aerosol escape
  • The air is filters by a high efficiency particular air (HEPA) filter and is discharged to the exterior
  • The worker but not the work is protected
  • Suitable for work with hazard group 2 pathogens and most hazard group 3 pathogens
59
Q

Describe Class II Microbial Safety Cabinets , what this protects and what level of hazard group organisms it is safe for

A
  • Open fronted cabinet where the working space is flushed with a down-flow of sterile air which is HEPA filtered and re-circulated
  • Some air is drawn in through the front of the cabinet and a corresponding amount discharged to the outside through a HEPA filter
  • Both work and worker are protected (worker not as protected as in MSC Class I).
  • Suitable for hazard group 2 pathogens and, in some circumstances, for hazard group 3
60
Q

Describe Class III Microbial Safety Cabinets , what this protects and what level of hazard group organisms it is safe for

A
  • A totally-enclosed cabinet where the operator is separated from the work by gloves attached to ports and the incoming and outgoing air is HEPA filtered.
  • Gives a high degree of protection to the work and worker
  • Suitable for Hazard groups 3 and 4
61
Q

Describe how Mannitol Salt Agar is selective and what it is selective for.

A
  • High salt concentration which inhibits the growth of many bacteria but not Staphylococci, which can tolerate the salt concentration.
  • Selective for Staphylococci
62
Q

Name the pH indicator in Mannitol Salt Agar and describe how and when this may change.

A
  • Contains pH indicator phenol red.
    o Red at neutral pH
    o Yellow at acidic pH when fermentation of mannitol occurs
  • Specimen that show yellow on MSA agar are probably mannitol-fermenting species of Staphylococcus
  • Specimen that remain red on MSA agar are probably non mannitol fermenting species of staphylococcus. (No acid produced by mannitol fermentation).
63
Q

What are the categories observed when describing bacterial colonies?

A

Colony Morphology – The appearance of colonies of a bacterial culture.

1) Size
2) Shape
3) Colour
4) Any other distinguishing features (e.g. colony surface appearance – glossy, slimy, smooth, dry).

64
Q

What is alpha haemolysis? (In terms of blood agar)

A

Partial degradation of the red blood cells

65
Q

What is beta haemolysis? (In terms of blood agar)

A

Complete degradation of the red blood cells.

66
Q

Unlike qualitative research, quantitative research starts with questions that are formulated into testable hypotheses which are then investigated. True or False?

A

True

67
Q

Scientific Observations must be recorded as numbers. True or false?

A

False

68
Q

Qualitative research involves the collection of objective numerical data. True or false?

A

False

69
Q

Unlike quantitative research, qualitative research is studied in “everyday” settings without intervention by the experimenter. True or false?

A

Tru

70
Q

Qualitative research involves deductive reasoning whereas quantitative research involves inductive reasoning.

A

False

Infectious Diseases (9 decks)

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