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Clinical microbiology Flashcards

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USMLE® Step 1 flashcards Biology 101 flashcards
1
Q

requirements of disease

A

Portals of entry, establishment, avoiding host defences, damaging the host

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2
Q

portals of entry

A

mucous membranes

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3
Q

how are mucous membranes protected

A

(1) washing with secretions .e.g tears, saliva, mucus, and urine
(2) filtet hairs in nasal passages prevent entry of large particles
(3) cilia in respiratory tract pushes mucous and microbes upwards

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4
Q

non specific innate mechanisms: mechanical factors

A

keratinized surface of skin- touch- acts a barrier against entry i.e. mechanical barrier to microbial invasion.

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5
Q

mucous membranes

A

forma protective covering that resists penetration and traps many microbes. often bathed in antimicrobial secretions which contain a variety of antimicrobial substances

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6
Q

Mucosal associated lymphoid tissue(MALT)

A

is a diffuse system of small concentrations of lymphoid tissue found in various submucosal membrane sites of the body, such as the gastrointestinal tract, thyroid, breast, lung, salivary glands, eye, and skin.

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7
Q

primary lymph organs

A

thymus and the bone marrow

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8
Q

antimicrobial secretions

A

many body fluids e.g. the blood are not suitable;e for microbial growth due to the presence/ absence of various factors

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9
Q

why some body fluids aren’t suitable for microbial growth

A

1) normal iron is not bioavailable in blood or breast milk
2) long chains of fatty acid (oleic acid) occur in slight acidic secretions of the skin (pH4-6) and these ar lethal to many bacteria
3) lactenin- proteins present in breast milk which are selectively bactericidal for streptococcus pyogene, protect against mastitis (inflammation of the mammary gland)

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10
Q

lactenin

A

nitrogenous substance present in milk. It has antimicrobial properties.

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11
Q

mastitis

A

inflammation of the mammary glad

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12
Q

what do lysozyme do

A

hydrolyse bonds connecting sugars in peptidogylcans- action of lysozyme on the cel wall of Gram +ve bacteria. Peptidoglycan backbone , B(1-4) bonds connecting alternating N-acetylgucosamine and N-acetylmuramic acid (NAM) residues

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13
Q

what secretions are antimicrobial in stomach

A

gastric acid

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14
Q

what secretions are antimicrobial in intestine

A

-pancreatic enzymes, bile, intestinal enzymes, GALT, peristalsis

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15
Q

what secretions are antimicrobial in large intestine

A
  • shedding of columnar epithelial cells
  • secretory IgA
  • normal microbiota
  • Paneth cells
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16
Q

paneth cells in the large intestine produce

A

lysozyme and cyptins

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17
Q

what protects the genitourinary tract

A
  • low pH of urine and vaginal epithelia
  • urea and other toxic metabolic end products in urine.
  • hypetonic nature of kidney medulla.
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18
Q

examples of antimicrobial peptides

A

defensives, cationic peptides, bacteriocins

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19
Q

defensins

A

peptides that are open ended, rich in arginine and cycsetine and disulphide linked (quaternary structure).
- they are highly hydrophobic and hydrophilic regions

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20
Q

where are defensives found

A

neutrophils, intestinal Paneth cells and intestinal and respiratory epithelial cells

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21
Q

function of defensives:

A

(1) defend from pathogens
(2) shape microbiota
(3) protect stem cells

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22
Q

cationic peptiden example

A

Cathelicidin

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23
Q

cathelicidin

A

produced by a variety of cells e.g. neutrophils and respiratory epithelial cells

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24
Q

bacteriocins

A

peptides produced by bacteria including normal microbiota. lethal to closely related species

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25
Q

examples of bacteriocins

A

e.g. Colitis produced by E.coli e.g. Saracens produced by lactobacilli

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26
Q

establishment of bacteria in host cell

A

attachment is usually far away and then tightens

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27
Q

mechanism of adherence of Mycoplasma pneumoniae

A

forms a protein rich tip organelle

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28
Q

mechanism of adherence of streptococcus pneumoniae

A

Riga, Pillin tip protein; PsaA

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29
Q

mechanism of adherence of Neisseria meningitidis

A

adhesion complex protein ACP: FBP

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30
Q

mechanism of adherence of Treponema pallidum

A

FBP and LBP in genitourinary tract

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31
Q

mechanism of adherence of Neisseria gonorrhoeae

A

Type IV pilli

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32
Q

mechanism of adherence of Shigella species

A

mechanism not known

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33
Q

mechanism of adherence of Escheichia coli

A

bundle forming pilli

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34
Q

mechanism of adherence of Vibrio cholerae

A

OmpU

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35
Q

adherence factors are associated with

A

establishment of infection

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36
Q

the bacterial cell wall: gram positive

A

thick peptidoglycan level, with lipoteichoic acid and wall techie acid

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37
Q

the bacterial cell wall: gram negative

A

Lipid A anchors LPS to the outer phospholipid bilayer. Release of this leads to a heightened immune reaction- endotoxin.
-O-antigen is highly variable and recognised by the immune system- can be used in typing.

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38
Q

glycocalyx

A

made of polysaccharide and proteins. If loosely attached referred to as a slime layer

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39
Q

if the glycocalyx is highly ordered

A

known as a capsule

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40
Q

capsules

A

important in preventing phagocytosis edna allowing the infection process to continue
e.g. encapsulated Klebsiella anthraces and Strep are not infectious if un-encapsulated

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41
Q

Fimriae and pilli

A

Involved in adherence e..g bundle forming pili from E.coli. Typically found on gram negative bacteria. Aids in motility, so is therefore a potential vaccine candidate

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42
Q

s pilli

A

secreted fragments that soak up antibody

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43
Q

flagella and axial filaments

A
  • protrudes far beyond cell wall and glycocalyx
  • aids in movement to distal tissues
  • H.pylori uses flagella to penetrate through gastric mucous
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44
Q

axial filaments

A

can oriduce a rotational movement of the whole organism

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45
Q

plasma membrane

A

target for therapeutic strategies, colistin and polymyxin B

46
Q

DNA

A

spread of antibiotic resistance eon plasmids- target of antibiotic therapy

47
Q

ribosomes

A

large for antibiotics

48
Q

two enzymes which help to evade the hosts dences

A

Leukocidins and Coagulase

49
Q

Leukocidins

A

kill white blood cells including neutrophils and macrophages- produced by Staphylococcal and streptococcal spp.
- causes apotosis

50
Q

what secrete Leukocidins

A

Staphylococcal and streptococcal spp.

51
Q

coagulase

A

causes fibrin clots to form in the blood of host- advantageous for bacterial evasion

52
Q

types of exotoxins

A

neurotoxin, enterotoxin, cytokines

53
Q

neurotoxin

A

causes paralysis e.g. tetanus

54
Q

enterotoxins

A

causes sickness and diarrhoea

55
Q

cytokins

A

causes cell death

56
Q

bacteria secretes sederophore

A

which rips iron away from the host cells

57
Q

most endotoxins are

A

gram positive

58
Q

exotoxins

A
  • extracellular - polipeptide, unstable (denatured above 60 degrees). no fever production. useful as an antigen. lethal dose is small.CHEMICALLY CONVERTED TO TOXOID FORM
59
Q

why are exotoxins useful as antigens

A

long lasting immunity conferred

60
Q

exotoxin infections include

A

Botulism, gas gangrene, tetanus, diphtheria, cholera, plague, scarlet fever, staphylococcal food poisoning

61
Q

endotoxins

A

-almost all gram negative
- part of the pathogen cell wall and released when cell dies. Stable, can withstand 60 degree heat for hours. Weak toxicity, but fatal in high doses. Non-specific and can cause fever, aches and possible shock.
NO CONVERSION TO TOXIS FORM

62
Q

are endotoxins useful as antigens

A

weak and no immunity conferred

63
Q

endotoxin infections include

A

salmonella,typhoid, tularemia, meningococcal meningitis, endotoxi shock

64
Q

how is the cause of infection determined (50

A

(1) rapid test and immunoassays
(2) microscopy
(3) culture
(4) biochemical test
(5) molecular testing

65
Q

Rapid test and immunoassays

A

Biochemical identification: bacteria and fungi. ELISA- bacteria, fungi, protozoa and viruses

66
Q

light microscopy used to identify

A

bacteria, fungi and protozoa

67
Q

electron microscopy used to see

A

viruses

68
Q

you can culture

A

bacteria and fungi- identification and sensitivity

69
Q

stains for microscopy

A

Acid fast stain for tuberculosis and PAS

70
Q

acid fast stain for tuberculosis

A

Diehl- Neelson stain

-specific, no need for culture- performed directly on sputum

71
Q

PAS

A

periodic acid-shift

- stains for glycoproteins, often used for fungi. Disadvantage: high background

72
Q

how is the cause of an infection determined?

A

(1) stain based methods for classification of microscopic morphology to support early diagnostic decisions
(2) microbial culture for propagation of the offending organism on agar or liquid medium
(3) biochemical or antigenic techniques for subsequent analysis and phenotypic analysis leading to microbe identification
(4) antimicrobial susceptibility testing to confirm therapeutic choices

73
Q

the correct medium must be used to grow..

A

microorganisms

74
Q

which medium is used to isolate Staphylococci

A

Mannitol salt agar

75
Q

what inhibits the rowht of gram positive bacteris

A

Bile salts and crystal violet

76
Q

what carbon source is used

A

lactose

77
Q

6 methods of determining antibiotic resistance/ susceptibility

A

1) test strips
2) moden clinical microbiology
3) molecular methods (nucleic acid based)
4) Next generation sequencing of whole bacterial genome
5) Next generation sequencing- metagenomics and community profiling
6) molecular methods

78
Q

ETest strip in determining antibiotic resistance

A

Antibiotic present at a gradient of conc

79
Q

Clinical microbio in determining antibiotic resistance

A
  • Molecular methods: NATs and NGS

- Mass spec methods: MALDI TOF, ESI

80
Q

molecular method in determining antibiotic resistance

A

Single and multiplex PCR

  • often no need for culture
  • doesnt detect live or dead
  • cheap
  • sensitive
  • no gold standard for comparison
  • prone to error in set up
81
Q

bacteria and fungi need to be

A

purified and amplified

82
Q

which structures have direct clinical relevance

A

cell wall, glycocalyx, fimbriae, pili, axial filaments, flagella

83
Q

which structures do not have direct clinical relevance

A

plasma membrane, DNA, ribosome

84
Q

which structures are a target for antibiotics

A

cell wall, plasma membrane, DNA, ribosomes

85
Q

which structures are not a target for antibiotics

A

glycocalyx, fimbriae, pili, axial filaments, flagella

86
Q

Next generation sequencing of whole bacterial sequencing in determining antibiotic resistance

A
  • culture dependent currently
  • species identification
  • wealth of info
  • becoming cheaper
87
Q

Next generation sequencing- metagenomics and community profiling in determining antibiotic resistance

A
  • culture independent
  • total DNA isolated from a sample of metagenomics
  • certain regions such as 16s rRNA sequenced in community profiling
  • culturomics born out of limitations
88
Q

molecular methods of determining antibiotic resistance

A
  • MALDI-TOF
  • ESI
  • cheaper than sequencing
  • reliant on databases of known patterns.
89
Q

MALDI-TOF

A

matrix assisted laser desorption ionisation- time of flight

-potential tool for microbial identification and diagnosis

90
Q

how does MALDI TOF work

A

intact cells or cell extracts are turned into ions. then using spectroscopy ions abundance and type can be determined- diff in all species.
-rapid, sensitive m and economic

91
Q

ESI

A

electrospray ionisation microscopy
-method used to proceed ions using an electrospray in which high voltages applied to a liquid to produce an aerosol. “soft ionisation”- reduces fragmentation- analysis of biological macromolecules

92
Q

aggulation assays

A

does require culture- used frequently in the detection of viral infections.
- immunolatex covered in antigens is added to a specificc antibody (testing of a specific pathogen) and a precipitate will be formed if infection present.

93
Q

lack of agglutination in some assays is the

A

measure of infection

94
Q

basic agglutination process

A

Agglutination is commonly used as a method of identifying specific bacterial antigens, and in turn, the identity of such bacteria. Because the clumping reaction occurs quickly and is easy to produce, agglutination is an important technique in diagnosis.

95
Q

agglutination and blood type

A

The blood will agglutinate if the antigens in the patient’s blood match the antibodies in the test tube. A antibodies attach to A antigens - they match like a lock and key - and thus form a clump of red blood cells. In the same way B antibodies attach to B antigens and Rh antibodies to Rh antigens.

96
Q

direct and indirect ELISA

A

comprising a positive versus negative reaction- basis for HIV screening

97
Q

what is the basic for HIV screening

A

indirect ELISA

98
Q

ELISA process

A

(1) known antigen is adsorbed to well
(2) serum samples with unknown antibodies
(3) well is ringed to remove unsound (nonreactive antibodies)
(4) indicator antipodi linked to enzyme attaches to any bound antibody
(5) well are rinsed to remove unbound indicator- colorised the substrate for enzyme is added
(6) enzymes linked to indicator Ab hydrolyse the substrate, which releases a dye.
(7) wells which develop colour are positive for the antibody: colourless wells are negative

99
Q

capture or antibody sandwich ELISA method

A

antigen is trapped between two antibodies. This test is used to detect haunt virus and measles

(1) antibody is adsorbed to well
(2) test antigen is added, if complementary, antigens binds to antibody.
(3) Enzyme- linked antibody specific for test antibody then binds to another antigen, forming a sandwich
(4) Enzymes substrate is added and reaction produces a visible colour change.

100
Q

carbohydrate fermentation

A

acid or gases are produced during fermentative growth with sugars or sugar alcohols. Used to differentiate enteric bacteria as well as the genera or species

101
Q

casein hydrolysis

A

detects presence of caseinase, an enzyme that hydrolyses the milk protein casein. Bactria that use appear as colonies surrounded by clear zones.
Used to differentiate aerobic actinomycetes based on casein utilisation e.g. streptomycin uses casein and Nocardia does not

102
Q

catalase

A

detects row present of catalase- which converts hydrogen peroxide to water and oxygen. Diff streptococcus from staph and bacillus from clostridium

103
Q

citrate utilisation

A

when citrate is used as the sole carbon source, this results in arlkalinization of the medium- used to identify enter bacteria

104
Q

coagulase

A

detects the presence of coagulase- coagulase causes plasma to clot

105
Q

decarboxylates (arginine, lysine, ornithine)

A

the decarboxylation of amino acid releases CO2 and amine- enteric bac

106
Q

esculin hydrolysis

A

tests for the cleavage of glycoside- used to differentiate between Staphylococcus aureus, Streptococcus mites and others.

107
Q

B-galactosidase (ONPG) test

A

demonstrates the presence of an enzyme that cleaves lactose to glucose and galactose- separate enteric ( citrobacter and salmonella and to identify pseudomnads.

108
Q

what is MALT populated by

A

MALT is populated by lymphocytes such as T cells and B cells, as well as plasma cells and macrophages, each of which is well situated to encounter antigens passing through the mucosal epithelium

109
Q

what is being considered a target for antibiotics in gram positive bacteria

A

-the teichoic acid- targeted for S.aureus and C. difficile due to high levels of antibiotic resistance

110
Q

what aspect of Mycobacterium tuberculosis prevents many antibiotic and host effects

A

mycelia acid- thick

111
Q

if glycocalyx is loosely attached

A

slime layer

112
Q

if glycocalyx is highly ordered

A

capsule

Medical and general microbiology (36 decks)

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