Clinical microbiology Flashcards
1
Q
requirements of disease
A
Portals of entry, establishment, avoiding host defences, damaging the host
2
Q
portals of entry
A
mucous membranes
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
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.
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
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.
7
Q
primary lymph organs
A
thymus and the bone marrow
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
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)
10
Q
lactenin
A
nitrogenous substance present in milk. It has antimicrobial properties.
11
Q
mastitis
A
inflammation of the mammary glad
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
13
Q
what secretions are antimicrobial in stomach
A
gastric acid
14
Q
what secretions are antimicrobial in intestine
A
-pancreatic enzymes, bile, intestinal enzymes, GALT, peristalsis
15
Q
what secretions are antimicrobial in large intestine
A
- shedding of columnar epithelial cells
- secretory IgA
- normal microbiota
- Paneth cells
16
Q
paneth cells in the large intestine produce
A
lysozyme and cyptins
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.
18
Q
examples of antimicrobial peptides
A
defensives, cationic peptides, bacteriocins
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
20
Q
where are defensives found
A
neutrophils, intestinal Paneth cells and intestinal and respiratory epithelial cells
21
Q
function of defensives:
A
(1) defend from pathogens
(2) shape microbiota
(3) protect stem cells
22
Q
cationic peptiden example
A
Cathelicidin
23
Q
cathelicidin
A
produced by a variety of cells e.g. neutrophils and respiratory epithelial cells
24
Q
bacteriocins
A
peptides produced by bacteria including normal microbiota. lethal to closely related species
25
examples of bacteriocins
e.g. Colitis produced by E.coli e.g. Saracens produced by lactobacilli
26
establishment of bacteria in host cell
attachment is usually far away and then tightens
27
mechanism of adherence of Mycoplasma pneumoniae
forms a protein rich tip organelle
28
mechanism of adherence of streptococcus pneumoniae
Riga, Pillin tip protein; PsaA
29
mechanism of adherence of Neisseria meningitidis
adhesion complex protein ACP: FBP
30
mechanism of adherence of Treponema pallidum
FBP and LBP in genitourinary tract
31
mechanism of adherence of Neisseria gonorrhoeae
Type IV pilli
32
mechanism of adherence of Shigella species
mechanism not known
33
mechanism of adherence of Escheichia coli
bundle forming pilli
34
mechanism of adherence of Vibrio cholerae
OmpU
35
adherence factors are associated with
establishment of infection
36
the bacterial cell wall: gram positive
thick peptidoglycan level, with lipoteichoic acid and wall techie acid
37
the bacterial cell wall: gram negative
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.
38
glycocalyx
made of polysaccharide and proteins. If loosely attached referred to as a slime layer
39
if the glycocalyx is highly ordered
known as a capsule
40
capsules
important in preventing phagocytosis edna allowing the infection process to continue
e.g. encapsulated Klebsiella anthraces and Strep are not infectious if un-encapsulated
41
Fimriae and pilli
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
42
s pilli
secreted fragments that soak up antibody
43
flagella and axial filaments
- protrudes far beyond cell wall and glycocalyx
- aids in movement to distal tissues
- H.pylori uses flagella to penetrate through gastric mucous
44
axial filaments
can oriduce a rotational movement of the whole organism
45
plasma membrane
target for therapeutic strategies, colistin and polymyxin B
46
DNA
spread of antibiotic resistance eon plasmids- target of antibiotic therapy
47
ribosomes
large for antibiotics
48
two enzymes which help to evade the hosts dences
Leukocidins and Coagulase
49
Leukocidins
kill white blood cells including neutrophils and macrophages- produced by Staphylococcal and streptococcal spp.
- causes apotosis
50
what secrete Leukocidins
Staphylococcal and streptococcal spp.
51
coagulase
causes fibrin clots to form in the blood of host- advantageous for bacterial evasion
52
types of exotoxins
neurotoxin, enterotoxin, cytokines
53
neurotoxin
causes paralysis e.g. tetanus
54
enterotoxins
causes sickness and diarrhoea
55
cytokins
causes cell death
56
bacteria secretes sederophore
which rips iron away from the host cells
57
most endotoxins are
gram positive
58
exotoxins
- extracellular - polipeptide, unstable (denatured above 60 degrees). no fever production. useful as an antigen. lethal dose is small.CHEMICALLY CONVERTED TO TOXOID FORM
59
why are exotoxins useful as antigens
long lasting immunity conferred
60
exotoxin infections include
Botulism, gas gangrene, tetanus, diphtheria, cholera, plague, scarlet fever, staphylococcal food poisoning
61
endotoxins
-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
are endotoxins useful as antigens
weak and no immunity conferred
63
endotoxin infections include
salmonella,typhoid, tularemia, meningococcal meningitis, endotoxi shock
64
how is the cause of infection determined (50
(1) rapid test and immunoassays
(2) microscopy
(3) culture
(4) biochemical test
(5) molecular testing
65
Rapid test and immunoassays
Biochemical identification: bacteria and fungi. ELISA- bacteria, fungi, protozoa and viruses
66
light microscopy used to identify
bacteria, fungi and protozoa
67
electron microscopy used to see
viruses
68
you can culture
bacteria and fungi- identification and sensitivity
69
stains for microscopy
Acid fast stain for tuberculosis and PAS
70
acid fast stain for tuberculosis
Diehl- Neelson stain
| -specific, no need for culture- performed directly on sputum
71
PAS
periodic acid-shift
| - stains for glycoproteins, often used for fungi. Disadvantage: high background
72
how is the cause of an infection determined?
(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
the correct medium must be used to grow..
microorganisms
74
which medium is used to isolate Staphylococci
Mannitol salt agar
75
what inhibits the rowht of gram positive bacteris
Bile salts and crystal violet
76
what carbon source is used
lactose
77
6 methods of determining antibiotic resistance/ susceptibility
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
ETest strip in determining antibiotic resistance
Antibiotic present at a gradient of conc
79
Clinical microbio in determining antibiotic resistance
- Molecular methods: NATs and NGS
| - Mass spec methods: MALDI TOF, ESI
80
molecular method in determining antibiotic resistance
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
bacteria and fungi need to be
purified and amplified
82
which structures have direct clinical relevance
cell wall, glycocalyx, fimbriae, pili, axial filaments, flagella
83
which structures do not have direct clinical relevance
plasma membrane, DNA, ribosome
84
which structures are a target for antibiotics
cell wall, plasma membrane, DNA, ribosomes
85
which structures are not a target for antibiotics
glycocalyx, fimbriae, pili, axial filaments, flagella
86
Next generation sequencing of whole bacterial sequencing in determining antibiotic resistance
- culture dependent currently
- species identification
- wealth of info
- becoming cheaper
87
Next generation sequencing- metagenomics and community profiling in determining antibiotic resistance
- 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
molecular methods of determining antibiotic resistance
- MALDI-TOF
- ESI
- cheaper than sequencing
- reliant on databases of known patterns.
89
MALDI-TOF
matrix assisted laser desorption ionisation- time of flight
| -potential tool for microbial identification and diagnosis
90
how does MALDI TOF work
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
ESI
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
aggulation assays
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
lack of agglutination in some assays is the
measure of infection
94
basic agglutination process
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
agglutination and blood type
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
direct and indirect ELISA
comprising a positive versus negative reaction- basis for HIV screening
97
what is the basic for HIV screening
indirect ELISA
98
ELISA process
(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
capture or antibody sandwich ELISA method
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
carbohydrate fermentation
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
casein hydrolysis
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
catalase
detects row present of catalase- which converts hydrogen peroxide to water and oxygen. Diff streptococcus from staph and bacillus from clostridium
103
citrate utilisation
when citrate is used as the sole carbon source, this results in arlkalinization of the medium- used to identify enter bacteria
104
coagulase
detects the presence of coagulase- coagulase causes plasma to clot
105
decarboxylates (arginine, lysine, ornithine)
the decarboxylation of amino acid releases CO2 and amine- enteric bac
106
esculin hydrolysis
tests for the cleavage of glycoside- used to differentiate between Staphylococcus aureus, Streptococcus mites and others.
107
B-galactosidase (ONPG) test
demonstrates the presence of an enzyme that cleaves lactose to glucose and galactose- separate enteric ( citrobacter and salmonella and to identify pseudomnads.
108
what is MALT populated by
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
what is being considered a target for antibiotics in gram positive bacteria
-the teichoic acid- targeted for S.aureus and C. difficile due to high levels of antibiotic resistance
110
what aspect of Mycobacterium tuberculosis prevents many antibiotic and host effects
mycelia acid- thick
111
if glycocalyx is loosely attached
slime layer
112
if glycocalyx is highly ordered
capsule
