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Exam 1 > Micro Lab Diagnosis > Flashcards

Micro Lab Diagnosis Flashcards

1
Q

what part of gram-negative cell walls contribute to shock

A

lipopolysaccharides, particularly lipid A, which is an endotoxin

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2
Q

stain for mycobacteria

A

acid-fast, gram staining won’t work because of waxy lipid layer

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3
Q

stain for spirochetes

A

wright-giemsa, gram staining won’t work, even though they’re gram negative, because they’re too thin to resolve

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4
Q

culture dependent diagnostic tools

A

microscopy and tissue cultures from a sample off where you think the organism resides

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5
Q

culture independent diagnostic tools

A

serology and molecular biology (nucleic acid detection, viruses)

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6
Q

what are all the places you can collect specimen from

A

sputum, urine, feces, tissue lesion (center and border), pus, blood culture, abscess fluid, CSF, vaginal discharge

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7
Q

what are the tools with which you can collect specimen

A

blood culture and swabs

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8
Q

Normal flora of the upper respiratory tract

A

staphylococcus, streptococcus pneumonia and viridans, haemophilus, and anaerobes

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9
Q

normal flora of the skin

A

staphylococcus, coryneform bacteria or diptheroids, and propionibacterium

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10
Q

normal flora of the GI tract

A

anaerobes, enterococcus, enterobacteriacaea (e coli and klebsiella), streptococcus anginosus, lactobacillus, and candida

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11
Q

normal flora of the GU tract

A

lactobacillus and streptococcus agalactiae

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12
Q

neutrophils on slides look like

A

multi-lobed nuclei

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13
Q

epithelial cells in sputum

A

rejected because heavily contaminated with saliva

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14
Q

selectivity of MacConkey

A

inhibits growth of gram positive organisms, grows gram negative

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15
Q

differentiation of MacConkey

A

distinguishes between those with the ability to ferment lactose (pink), and this without (colorless)

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16
Q

the keys to a good blood culture

A

draw before antibiotics, volume, two bottles of 2 draws for 4 bottles total

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17
Q

alpha hemolytic will appear ___ on blood agar

A

green

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18
Q

beta hemolytic will appear ___ on blood agar

A

cleared

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19
Q

gamma hemolytic will appear ___ on blood agar

A

white/colorless, no clearing

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20
Q

if you see yellow colonies on blood agar, think

A

staphylococcus aureus

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21
Q

if you see red/pink colonies on blood agar, think

A

serratia marcescens

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22
Q

if you see blue/green metallic colonies on blood agar, think

A

pseudomonas aeruginosa

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23
Q

if you see “feet” or projections on a colony, think

A

yeast infection, or candida albicans

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24
Q

if you see mucus on a colony, think

A

klebsiella pneumoniae

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25
Q

if you see swarming off the streak link on blood agar, think

A

proteus vulgaris

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26
Q

know a species is gram positive, what’s the next think you want to know

A

cocci or bacilli?

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27
Q

know your species is a gram positive cocci, what’s the next question?

A

clusters or diplococci/chains?

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28
Q

clusters of gram - cocci indicate

A

staphylococcus

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29
Q

diplococci or chains of gram - cocci indicate

A

streptococci

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30
Q

know you have a streptococci, what’s the next step?

A

aerobic or anaerobic

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31
Q

anaerobic streptococci need to know

A

peptostreptococcus

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32
Q

know you have an aerobic streptococci, what’s the next question?

A

what type of hemolysis does it undergo

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33
Q

alpha hemolytic streptococci

A

S. pneumonia, mutans, and viridans

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34
Q

beta hemolytic streptococci

A

S. pyogenes (group A strep, GAS), and agalactiae (group B strep, GBS)

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35
Q

gamma hemolytic streptococci

A

enterococcus

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36
Q

know you have a gram negative isolate, whats the next question?

A

bacillus/coccobacillus or cocci?

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37
Q

gram negative cocci to know

A

neisseria and moraxella

38
Q

know you have gram negative bacili/coccobacilli, what’s the next question?

A

does it grow on macconkey agar

39
Q

gram negative isolate grows on macconkey agar, what’s the next question?

A

does it ferment lactose (pink) or not (colorless)

40
Q

lactose-fermenting macconkey positive gram negative organisms

A

Escherichia, klebsiella, or enterobacter

41
Q

non lactose-fermenting maconkey positive gram negative organism

A

does it ferment glucose

42
Q

gram negatives that ferment glucose

A

are also lactose non-fermenters, and grow on maconkey agar, and include salmonella, shigella, proteus, serratia

43
Q

gram negatives that don’t ferment glucose

A

also don’t ferment lactose, grow on maconkey agar, and include pseudomonas burkholderia and acinetobacter

44
Q

if your gram negative isolate doesn’t grow on maconkey

A

test its oxygen tolerance

45
Q

oxygen tolerant gram negative isolates

A

campylobacter, helicobacter, vibrio

46
Q

oxygen intolerant gram negative isolates

A

bacteroides, fusobacterium, prevotella, porphyromonas

47
Q

PCR-based susceptibility testing

A

detects genes associated with drug resistence

48
Q

mecA gene

A

associated with methicillin resistance in staph aureus

49
Q

vanA/B genes

A

associated with vancomycin resistance in enterococcus faecium

50
Q

bla KPC gene

A

associated with carbapenem resistance (beta lactamase, bla) in Klebsiella pneumonia carbapenemase (KPC)

51
Q

pros and cons of PCR susceptibility testing

A

fast, sensitive, specific, but expensive and only single target, when resistance may be caused by a combination of many mutations

52
Q

MIC

A

minimal inhibitory concentration, minimum concentration of a drug that will inhibit the growth of an organism

53
Q

culture-dependent phenotypic susceptibility testing

A

agar dilution, broth microdilution, disk diffusion, strip test

54
Q

microbroth dilution

A

broth and increasing concentration of antibiotic in well plate, lowest concentration without bacterial growth is the MIC

55
Q

strip testing (Etest)

A

paper/plastic strip with increasing concentration of a drug, placed in center of a lawn of isolate on a plate, MIC is point of growth inhibition

56
Q

disk diffusion test

A

paper disk with single concentration of antibiotic placed on bacterial lawn on agar, measure zone of inhibition, does not give a MIC

57
Q

PCR test

A

extract nucleic acid from sample, denature, anneal primers, elongate, repeat, fluorescently detect DNA

58
Q

NAAT test

A

single target, multiplex, or broad range amplification and sequencing/detecting

59
Q

single target NAAT

A

uses amplification and detection to identify single organism or resistance marker; most sensitive

60
Q

multiplex NAAT

A

uses amplification and detection to identify a pathogen from a panel of common syndromic options i.e. patient has respiratory symptoms, PCR compared to respiratory pathogen pane, less sensitive than single

61
Q

broad range PCR

A

targets 16S rRNA on any bacterial pathogen, can only prove that you have an infection, last resort, done when all other tests are negative, least sensitive

62
Q

MALDI-TOF MS

A

isolate spotted onto metal plate, coated with protective matrix, laser vaporizes bacteria, travel up to analyzer, mass spec profile compared to database

63
Q

current use of MALDI TOF MS

A

identification of cultured bacteria

64
Q

future use of MADLI TOF MS

A

susceptibility testing, strain typing, direct from sample detection

65
Q

Serology: antigen detection

A

administer a lab generated antibody to detect antigen in specimen, which can be urine, serum, sputum, stool, CSF

66
Q

Serology: antibody detection

A

administer lab generated antigen to detect IgG or IgM, or total antigen-specific patient antibodies, only works for blood serum

67
Q

IgM

A

present in acute infection, detectable within 7 days of infection, wanes after 2-3 months

68
Q

IgG

A

present in chronic disease and immunity, detectable within 14 days, detectable for entire life, indicative of either current, chronic, or past infection

69
Q

agglutination

A

antibody or antigen fixed to latex beads, specimen added, visible clumping is a positive result for the antibody/antigen in question

70
Q

lateral flow immunoassay

A

e.g. pregnancy test, antibodies on conjugate pad, antigen in sample wicked along pad, accumulation of antigen antibody complex detectable s visible line

71
Q

ELISA sensitive or specific?

A

high sensitivity, low specificity, high negative predictive value, so all positive results must be confirmed with a secondary assay, which, if negative, indicates negative result

72
Q

ELISA method

A

antibody or antigen immobilized in well, patient sample added, reporter antibodies/antigen added, substrate for colometric change added, read

73
Q

immunoblot aka western blot

A

antigens printed/transferred onto membrane, incubated with patient serum, bound antibodies detected with secondary antibody and color detection substrate

74
Q

immunodiffusion

A

antigen put in center well of gel matrix patient samples put on periphery, samples diffuse outward during incubation, precipitation complex visible in gel

75
Q

when to use as serology test

A

determining vaccine status, infection with culture-independent organisms, infection with organism cleared too quickly, screening for HIV/HCV/HBV

76
Q

why would you get a false positive with a serology test

A

heterophile antibodies, rheumatoid factor, closely related antigens cross react (especially with IgM), and maternal transfer aka passive immunity (especially of IgGs)

77
Q

why would you get a false negative with a serology test

A

patient is immunocompromised or the test is administered either too soon or too late

78
Q

factors to consider when ordering a lab

A

cost-benefit ratio, time to result, do I know how to interpret, will the result change anything

79
Q

role of bacterial cell wall

A

structural rigidity, shape, osmoregulation, defense

80
Q

drugs that target bacterial cell walls

A

penicillins, monobactams, carbapenems, cephalosporins, vancomydin

81
Q

how do bacteria develop resistance to cell wall attacking drugs

A

enzymatic inactivation, modification of target, porin mutations to reduce permeability, and efflux pumps

82
Q

components of peptidoglycan layer

A

NAG and NAM, NAM tetrapeptide side chain, peptide inter bridge cross-linker

83
Q

steps of building the peptidoglycan layer

A

peptidoglycan polymers exported from cell, transglycosylase attaches them, penicillin binding protein creates transpeptidase crosslinks

84
Q

how do beta lactam drugs work?

A

structurally mimic NAM, bind the enzymatic domain of PBP, preventing peptide crosslinking, leading to weak peptidoglycan wall

85
Q

beta lactamase

A

which cleaves and degrades the beta lactic ring at the N-C=O bond e.g. penicillinase, secreted extracellularly in gram positives and into periplasmic space in gram negatives

86
Q

mechanisms of resistance to beta lactams

A

beta lactamase synthesis, modification of target, porin mutations, efflux pumps

87
Q

modification of target in staph aureus

A

via mecA gene that encodes the PBP2a protein, low affinity for penicillin after it’s been modified, develops resistance

88
Q

ways to check for resistant mega gene

A

targeted molecular testing for mecA, antigen testing for PBP2a, and phenotypic testing for oxacillin resistance

89
Q

what are them most likely causes of culture negative endocarditis

A

recent antimicrobial therapy, fastidious organism

90
Q

opportunities to narrow down your broad spectrum antibiotics

A

3 hours after presentation, direct gram stain reported, take rapid AST, de-escalate

1-2 days after presentation, organism growth and ID reported, take another rapid AST, de-escalate antibiotics if differential further narrowed

finally, when AST report comes back after 2-3 days, narrow antibiotics based on organism resistance

Exam 1 (7 decks)

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