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Clinical Micro > Lecture 2 diagnostic clinical microbiology > Flashcards

Lecture 2 diagnostic clinical microbiology Flashcards

1
Q

State the 9 step diagnostic template

A 
1- request
2- sample collection
3- transport samples
4- reception of samples 
5- safety issues
6- non culture methods
7-culture methods
8- ID and sensitivity 
9- result to clinician
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2
Q

Name 5 sterile sites

A 
Blood/bone marrow
CSF
Tissue
Bladder
Lower respiratory tract
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3
Q

Name 5 non sterile sites

A

Upper respiratory tract - c. Albicans, streptococci
Skin - s. Epidermidis
GI tract - coliforms, anaerobes, faecal flora
Vagina - lactobacilli, anaerobes
Urethra tip - skin and faecal flora

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4
Q

Name the main types of specimens received in an NHS micro lab

A 
Mid stream urine
Blood
Urethral swab
Faeces 
Toe nail clippings 
Sputum
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5
Q

What can toe nail clippings be used to identify

A

Fungal and dermatophyte (cause ringworm) infection

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6
Q

What can urethral swabs be used to identify

A

STI

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7
Q

What can faeces be used to identify

A

Diagnose for enteropathogenic bacteria,, campylobacter or parasites

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8
Q

What is the most common sample received

A

Mid stream urine

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9
Q

Why must specimen be collected before antibiotics are given

A

May killbacteria and give a false negative.

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10
Q

Do fastidious organisms need to be transported to the lab quickly

A

Nutrient demanding otherwise will die in transport

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11
Q

What is important to consider when viewing sputum samples

A

Sputum must travel through upper respiratory tract which isn’t sterile so must know normal flora

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12
Q

What is Stuart’s media used for

A

Bacteria swab transportation

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13
Q

What does Stuart’s medium contain and why

A

Nutrient gel

Charcoal to inactivate toxic byproducts from metabolism of nutrient gel.

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14
Q

On what circumstances will a swab need to be refrigerated during transportation?

A

If there is a delay but no more than 24 hrs

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15
Q

What is the transport media used to transport viral swabs

A

Viral transport media

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16
Q

What does viral transport media contain

A

Buffered salt solution containing serum and contain antimicorbials to control overgrowth to prevent contaminating bacteria and fungi

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17
Q

What differs chlamydial transport media from VTM

A

No antimicrobials which are toxic to chlamydia

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18
Q

What transport media is used for parasitic transportation

A

Merthiolate-iodine-formalin preserves ova and cysts but kills bacteria. Not suitable for protozoal trophozites

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19
Q

What are the main roles of reception

A

Check specimen and form details filled in properly
Allocate unique lab number
Macroscopic appearance - discard unsuitable ones (DIARRHOEA get solid stool

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20
Q

What are the key safety issues to consider with patient samples

A

Patient may have HIV or hep b

Category of organism 1,2,3,4.

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21
Q

How do lafu keep lab staff safe

A

Negative pressure

HEPA FILTER

22
Q

What are the ACDP categorisation of biological agents

A

Cat 1 - saphrophytic
Cat 2- biological agent cause disease hazardous in lab but not likely to spread in community, effective treatment (s. Aureus, c. Diff, n. Gonorrhoeae, streptococcus pneumoniae)
Cat 3- biological agent cause severe human disease, serious hazard to employees , risk to spread in community, effective treatment
(Mycobacterium tuberculosis )

Cat 4- severe human disease and serious hazard to emploYees. Likely to spread in the community with no effective treatment.
(Ebola)

23
Q

Name 4 non culture techniques

A

Direct microscopy
antigen detection
NAAT (molecular micro)
Serological response

24
Q

What is the gold standard for diagnosis

A

Culture on solid agar

25
Q

What is beneficial about antigen detection

A

Bacteria doesn’t need to be alive to detect antigen

26
Q

Which common STI causing bacterium is commonly identified using serological response testing

A

Treponema pallidum cause syphilis Look for IgM and IgG response.

27
Q

What are nucleic acid amplification tests for

A

Useful for slow growing or difficult microrogansims (hep b/c, HIV, mycobacteria)

Also for MRSA screening

28
Q

Why are NAAT methods better than serological

A

Greater sensitivity

29
Q

Name some examples of NAAT

A

Polymerase chain receptor (PCR)
Ligase chain reaction (LCR)
Nucleic acid sequence-based amplification (NASBA)
Strand displacement amplification (SDA)

30
Q

What does ligase chain reaction involve

A

Hybridisation of two oligonucleotide probes at adjacent positions on a strand of target DNA which are then joined by thermostable ligase enzyme.

31
Q

What does nucleic acid sequence based amplification involve

A

Use RNA as a target and utilise 3 enzymes simultaneously: reverse transcriptase, RNAase H and DNA-dependent RNA polymerase

32
Q

What does strand displacement amplification involve

A

Utilise oligonucleotide primers containing a restriction enzyme site, DNA polymerase and a restriction enzyme at constant temp to produce exponential amplification of the target

33
Q

When would you use a wet preparation

A

View parasite ova and cysts (faeces)

34
Q

Name a common fluorescent stain used to detect mycobacterium tuberculosis in clinical specimens

A

Auramine

35
Q

Name 3 organisms that can be identified using the non culture technique, antigen detection

A

Haemophilus influenzae
Streptococcus pneumoniae
Neisseria meningitidis

36
Q

What is the benefit of antigen detection

A

Bacteria don’t need to be alive

37
Q

What does antigen detection involve

A

Bacteria e.g n. Meningitidis in CSF
Latex beads have specific antibody for bacteria bound
Agglutination of carrier particles

38
Q

Antigens can only be detected using co-agglutination. True or false?

A

FALSE.
Immunofluorescence for influenza virus or RSV respiratory sample
ELISA for chlamydia trachomatis for urogenital specimens
Enzyme immunoassay (EIA) for s.pnuemoniae for urogenital specimens/ C. difficile toxin in faeces

39
Q

Name 4 different types of agar

A

Basic e.g nutrient
Enriched - take nutrient and add horse blood
Selective e.g contain antimicrobial
Differential e.g, MSA, s aureus yellow, s epidermidis white

40
Q

What percentage of horse blood agar is horse blood

A

5-7%

41
Q

How is chocolate agar made

A

Heat blood and add to agar so x and v factors are released.

H. Influenzae and n gonorrhoeae are grown on this

42
Q

Name an example of selective media

A

CCFA (cycloserine, cefoxitin fructose agar) for C. difficile detection

Cycloserine and cefoxitin are antimicrobial and selective for c diff as kill normal faecal commensals.

43
Q

Give an example of differential agar

A

CLED (cystine lactose electrolyte deficient agar)
Look for E. coli ferment lactose which produce acid, turn bromothymol blue to yellow.
Differentiation of enterobacteriaceae

44
Q

State the 4 levels of ID

A

Stage 1 Basic microscopic e,g, gram stain (e,.g gram neg rod)
Stage 2 generic basic tests such as macroscopic and microscopic (e,g enterobacteriaceae/coliforms)
(Most clinical specimens) Stage 3 full - Basic ID plus additional tests e,g. API/MALDI-TOF (e.g. E.coli)
Stage 4 (for outbreaks) full plus genetic fingerprinting ( ecoli 0157)

45
Q

What haemolysis does s pyogenes do on blood afar

A

Beta haemolytic (1mm, entire edge)

46
Q

Benefit of MALDI TOFF (mass spec) over API

A

API takes 24 to 48 hrs

MALDI toff can take few mins

47
Q

How can genetic fingerprinting/molecular typing be done

A

Pulsed field gel electrophoresis (PFGE)

Restriction enzymes chop up whole bacterial genome, and can compare the bands on a gel to identify strain

48
Q

Which methodology is followed for sensitivity testing

A

EUCAST

EUROPEAN COMMITTEE ON ANTIMICROBIAL SUSCEPTIBILITY TESTING

49
Q

What is sensitivity testing for

A

To identify sensitivity or resistance of clinical pathogens, provides national standardised sensitivity / resistance data, epidemiologically useful

50
Q

What machines do labs use to perform antimicrobial sensitivity testing

A

VITEK 2. Strips contain antibitoics so put bacteria into the strip and put into a machine

Sensitivity patterns in 30 mins.

Can use disc susceptibility methodology using agar.

Clinical Micro (9 decks)

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