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microbiology Flashcards

1
Q

Why is infection important?

A
  • 25% of all consultants in GP are for RTI
  • 5-10% of all patients who come to hospital develop an infection
  • most practice doctors treat infection daily
  • increasing antibiotic resistance means we MUST learn how to use antibiotics wisely.
  • Infectious agent are implicated in an increasing range of diseases
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2
Q

What are the three fundemental divisions of life?

A
  • Eubacteria (bacteria)
  • Archea e.g. viruses, prions
  • Eukaryotes (eukaryia) e.g. fungi, protozoa, parasites
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3
Q

Name the 4 main groups of human pathogens

A
  • protozoa
  • fungi
  • Bacteria
  • Viruses
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4
Q

What are protozoa and which domain of life do they belong to?

A
  • Single celled animals
  • Eukaryotes
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5
Q

Name the most significant protozoa

A

Malaria

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6
Q

What are fungi? Which domain do they belong to?

A
  • higher plant like organisms
  • eukaryotes
  • e.g. mushrooms which are fundementally important in causing the degradation and recycling of materials for ecosystems.
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7
Q

Name the most discussed fungi

A

Candida which is a yeast

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8
Q

What are bacteria and which domain do they belong to?

A
  • Generally small, single celled organisms
  • prokaryotes
  • they are largely associated with causing disease in communities but the collection behaves differently to the single celled organism.
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9
Q

What is a virus? What domain of life is it a part of?

A
  • very small oblogate parasite
  • none, they are non-living
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10
Q

Describe Eukaryotes (fungi and protazoa inc). Provide 8 points

A
  • size 5-50ums
  • complex (compartmental)
  • frequently multi-cellular
  • linear chromosomes + histones
  • introns/exons
  • 80S ribosomes
  • no/flexible cell wall (sterols)
  • cell cycle (mitosis/meiosis)
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11
Q

Describe prokaryotes (inc bacteria). Provide 9 points

A
  • size 0.5-10ums
  • simple (relatively)
  • often single celled
  • single circular chromosome
  • gene structure (introns rare)
  • 70S ribosomes
  • co-transcription/translation
  • rigid cell walls (PG)
  • Rapid cell cycle
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12
Q

Why does the size of bacteria matter?

A
  • small bacteria can remain suspended for longer
  • larger might fall to the ground and find it harder to gain access
  • so different sizes can effect how infectious they are
  • size has implications on dispersal and cleaning
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13
Q

Describe the key components of the structure of eukaryotic cells

A
  • Contains a cell wall
  • contains a nucleus and nucleolus
  • Contains membrane bound organelles including mitochondria
  • some contain cilia and flagellum
  • diameter >5um
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14
Q

Describe the key components of the structure of prokaryotic cells

A
  • large capsule
  • 1 um in width
  • contain DNA lose in cytoplasm- i.e. no nucleus
  • sometimes contain flagella and fimbrae which are important in attachment
  • contain a cytoplasmic membrane and a cell envelope
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15
Q

Why are the outside structures in prokaryotes important?

A
  • they are what the body encounters
  • bacteria try to alter these structures to overcome the immunity and to hide.
  • the capsule can be a large, polymeric substance made of material from the body like polymeric acid so it can hide the material from the body.
  • flagella, fimbrae are important in attachment, etc
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16
Q

State the key components of the cell sturcture in eukaryotic cells

A
  • cell membrane
  • nucleus
  • centriole/centrisome
  • nucleus/ribosomes
  • endoplasmic reticulum (ER)
  • cytosol
  • mitochondria
  • golgi
  • cytoskeleton
  • secretory vesicles, lysosomes
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17
Q

Name the 6 key components of cell structure in prokaryotic cells

A
  • plasma membrane
  • cell wall (peptidoglycan)
  • nucleoid (DNA & associated proteins)
  • ribosomes
  • cytoplasm
  • capsule, flagellar, Pili
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18
Q

Describe the nucleoid in prokaryotic cells

A
  • No membrane, or defined location- not the nucleus
  • DNA & associated proteins- refers to the genetic material and the proteins areound it- histone like proteins, repressors, etc
  • No nuclear membrane
  • chromosomes sinfle circular molecule
  • primitive DNA segregation machinery
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19
Q

As the nucleoid has no nuclear membrane in prokaryotes how does DNA replication occur?

A

Via DNA dependent RNA polymerase, transcription and translation coordinated

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20
Q

The chromosome in prokaryotes is a single circular molecule, how is it organised?

A

By gyrases

  • extra chromosomal replicons often exist i.e. plasmids
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21
Q

Name the steps of prokaryotic protein synthesis which is the target of several antibiotic classes

A
  1. Gene (DNA) TRANSCRIPTION
  2. mRNA (DNA dependent RNA polymerase)
  3. ribosome (tRNA)
  4. Protein TRANSLATION
  5. 2nd, 3rd, 4th structure
  6. export/assembly/processing

As the chromosome isn’t separated off in a membrane bound nucleus some processes are not separated either, here there is co-transcription and translation.

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22
Q

What are the 7 key points of prokaryotic protein synthesis?

A
  • distinct proteins
  • co-transcription/translation
  • cytoplasmic membrane
  • no-polyadenylation of trasncript
  • target for antibitoics
  • 16sRNA identification
  • ribosome is highly conserved
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23
Q

Bacteria are sensitive to disruption of the ________ _____________ by physical or __________ methods.

A
  • plasma membrane
  • chemical
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24
Q

Why is the cytoplasmic membrane important in prokaryotes?

A
  • site of lipid synthesis
  • site of import and export
  • defines the periphery
  • location for the enzymes involved in respiration so it generates energy
  • Basically defines the ability to live
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25
Q

Describe energy generation at the cytoplasmic membrane

A
  • Electrons accumulate in the cytoplasm making the inside of the cell negative
  • electrons are released from high energy compounds in the cytoplasm
  • reach the membrane and are passed through a series of electron acceptors
  • As a consequence protons passed outside the membrane producing a positive charge and a proton gradient across the membrane.
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26
Q

What is the name given to the cell wall in prokaryotes?

A

Peptidoglycan

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27
Q

Describe how a cell wall in prokaryotes is composed

A
  • long sugar molecule that is cross linked through its peptide side chains to form a network or mesh.
  • Repeating subunit which is 2 sugars with a side chain, that by extending it in one direction and cross-linking it in another you can create a cage and that cage is fundementally different in 2 classes of microorganisms.
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28
Q

What are the 2 types of cell wall/peptidoglycan?

A

Gram positive and gram negative

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29
Q

Describe a gram positive cell wall

A
  • rigid layer
  • barrier
  • repeated polysaccharide sturcture
  • thick multi-layer peptidoglycan
  • target of penicillin
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30
Q

Describe a gram negative peptidoglycan

A
  • rigid layer
  • barrier
  • repeated polysaccharide structure
  • outer membrane
  • periplasm- lies between
  • thinner PG layer - cannot deal with the same osmotic pressure.
  • asymmetric so more unstable
  • target of penicillin
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31
Q

What type of bacteria are lipopolysaccharides a key component of?

A

Gram negative, surface is nearly all LPS

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32
Q

What do lipopolysaccharides do within endotoxins/gram negative bacteria?

A

Increase the negative charge of the cell membrane and help stabilize the overall membrane structure.

Antigenic- promote an immune response, relatively unspecific

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33
Q

LPS are glycolipids what does this mean?

A
  • lipid A
  • core polysaccharide
  • O-chain/antigen
  • structural role
  • antigen & bacterial toxin links to sepsis
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34
Q

Is fimbriae a gram negative term?

A

No, it is a gram positive term.

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35
Q

What is a flagellin? What does it do?

A
  • protein unit making up a multi-stranded filament with core.
  • used for attachment, delivering material & info.
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36
Q

What is a fimbriae?

A

A non-flagella protein appendage.

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37
Q

Describe pili

A
  • gram -ve pilus
  • no motor, pilin repeated motor unit
  • length, number, arrangement, shape & functions vary
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38
Q

What is another role of flagella and fimbriae?

A

Adherence and sex- DNA exchange by conjugation

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39
Q

Why is it significant to understand the structure of each of the following:

  1. cytoplasmic or plasma membrane
  2. cell wall
  3. outer membrane & LPS
  4. chromosome
  5. ribosome
  6. Pili, fimbriae & flagella
A
  1. sonication (disruption) & ethanol
  2. penicillun & glycopeptides
  3. antibiotic uptake and inflammation, acts as a barrier
  4. gyrases antibiotic target
  5. protein synthesis inhibitors
  6. Attachment, motility, invasion, HGT, & pathology vaccine targets
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40
Q

What does DNA gyrase do?

A

An essential bacterial enzyme that catalyzes the ATP-dependent negative super-coiling of double stranded closed-circular DNA

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41
Q

What sources of food are needed for prokaryotic growth?

A
  • C source organic e.g. proteins/sugars, inorganic e.g. fix CO2
  • O & H
  • N source, e.g. amino acid, ammonia
  • inorganic salts P,S,K,Mg, Ca, Fe
  • Trace elements Zn, Cu, Mn, Ni, Mo
  • Vitamins (small organic cofactors) e.g. Biotin Folic Acid, Niacin
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42
Q

Some organisms can be very sensitive to temp and fever can interfere with the reproduction of some microorganisms. Which temperatures are suitable for prokaryotic growth?

A

mesophiles- body temp, 37 degrees celcius

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43
Q

Which hydrogen ion concentration is suitable for prokaryotic growth?

A

Human commensals- pH 6.8-7.2

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44
Q

Which osmostic protection is suitable for prokaryotic growth?

A

Human commensals 0.85% NaCl

Gram positives have a much more effective way of coping with high osmotic pressure

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45
Q

How does oxygen supply interfere with prokaryotic growth?

A

Determines:

  • aerobes
  • micro-aerophiles
  • facultative anaerobes- prefer aerobic growth but can switch to anaerbic if needed (most human pathogens)
  • obligate anaerobes
  • capnophilic
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46
Q

Name the 4 growth phases on a bacterial growth curve.

A
  1. lag phase
  2. exponential phase
  3. stationary phase
  4. decline phase
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47
Q

Bacteria can form cooperative communities. Give one example.

A

Biofilms

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48
Q

What are the 4 themes for identification of microorganisms?

A
  1. appearance/structural features (microscopic analysis)
  2. growth requirements
  3. enzyme/metabolic tests
  4. molecular tests
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49
Q

What are 4 factors of microorganisms appearance that can be seen microscopically?

A
  • shape
  • size
  • arrangement
  • cell wall i.e. gram +ve/ gram -ve
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50
Q

what are 3 factors of growth requirements that can be used to classify microorganisms?

A
  • aerobic/anaerobic
  • requirement for blood products
  • sensitivity to inhibitory agents
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51
Q

what are the enzyme/metabolic tests which can be used to identify microorganisms?

A
  • coagulase test
  • haemolysis (streptococci ONLY)
  • biochemical profiling (e.g. carbohydrates metabolised)
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52
Q

What are the three molecular tests used in the identification of microorganisms?

A
  • immunological tests e.g. cell surface antigens
  • DNA sequencing e.g. qPCR or 16sRNA
  • protein profiling e.g. Mass-spec analysis
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53
Q

Give 4 important factors to look at when using microscopy for identification

A
  • is it a pure culture or polymorph (many shapes)
  • shape, size, grouping
  • structures (capsules, flagella, spores)
  • staining (gram, ziehl nielson, fluorochromes)
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54
Q

What are the three common shapes of bacteria?

A
  • cocci- spheres
  • bacilli (rods)
  • spiral-shaped
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55
Q

Name the two most common genera of cocci

A

streptococcus

staphylococcus

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56
Q

What is it called when there is division in one plane to produce two cocci?

A

A diplococcus (found as pairs together)

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57
Q

How are streptococci found?

A

They divide in one plane in parallel to produce chains of 4-20 cocci.

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58
Q

How are staphylococcus found?

A

They divide in three planes to produce clumps.

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59
Q

What do staphylococci and streptococci have in common?

A

They are both gram positive.

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60
Q

Describe bacillus/bacilli and give 2 examples of this genera

A
  • rod-shaped bacteria
    • elongation in one plane
    • parallel cell division
  • chains of bacilli
    • delayed separation of cell wall
    • more common with gram +ve
  • genera include escherichia and bacillus
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61
Q

Describe curved rod bacteria and give an example

A
  • modified structural proteins change shape, e.g. vibrio
  • slightly curved rod
  • some protein in the cytoplasm leads to a curvature as the cell wall is being synthesised
  • gram negative
  • 34 recognised species
  • e.g. vibrio cholerae
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62
Q

what are the 2 types of spiral shaped bacteria and give an example of a common genera

A

rigid spiral bacterium- spirillum

flexible spiral bacterium- spirochaete

e.g. significant pathogens

  • spirillum are not that common but have flagella
  • spirochettes are gram -ve and more relevant, flagella which does not extend out of the cytoplasm e.g. STI’s, peridontal pathogens, limes disease
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63
Q

Describe fusiform bacteria

A
  • long slender rods & species considered emerging pathogens
  • originally associated with throat infections
  • abscesses in the head & neck, peridontal disease
  • can pass through the bloodstream into the placenta
  • not the width, but much longer than a streptococcus
  • impact on host can be linked with the size of an organism so these are large
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64
Q

Give three examples of structures that can characterize species and strains

A
  • flagella
  • pili
  • capsules
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65
Q

On a phase contrast, spores do not soke up stain so reflect light and appear as bright spots. What is the role of the 2 chromosomes involved in sporulation?

A

One carries out the process of ensuring large parts of the spore is produced, the other is silenced and packaged inside the spore.

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66
Q

What are spores? Give one example

A

Inert structures, resistant to physical and chemical challenge

e.g. C.difficile

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67
Q

Why is it a big decision for a cell to produce a spore?

A
  • cell must sacrifice half of its genetic material
  • cytoplasm that could be used to produce 2 daughter cells is taken up to make an inert object, only one structure
  • structure doesn’t immediately go into the growth cycle
  • this happens when cells are starving.
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68
Q

Describe the process of sporulation

A

When a cell runs out of nutrients one chromosome becomes the mother cell and forms the prespore at one end and packages the chromosome into this compartment

Gradually uses some of the genes expressed within the prespore to construct the spore before it is silenced, wrapped in proteins, ribosomes disappear and what you have is an inert package of DNA with one intact chromosome surrounded by a thick, rigid structure- no cell membrane, ribosomes, cell wall.

last a long time and can germinate in the right environment.

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69
Q

What is gram stain?

A

Retention of crystal violet/iodine complex by gram-positive bacteria.

A simple method that distinguishes two major classes of bacteria according to cell wall structure.

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70
Q

Describe the procedure for gram staining

A
  1. prepare a heat fixed film of bacteria on a glass slide.
  2. stain with crystal violet for one min and rinse with water
  3. treat with grams iodine for one min and rinse with water
  4. briefly decolourize with acetone or ethanol (a few seconds depending on the thickness of the film)
  5. counter stain with basic fuchsin or safarin (pink dye) for 1 min and rinse with water.
  6. blot dry and view under oil immersion
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71
Q

What colour do gram positive cells stain?

A

Purple (dark violet)

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72
Q

What colour do gram negative cells stain?

A

pink

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73
Q

Describe the cell wall structure of gram -ve cells

A
  • lipopolysaccharide
  • outer membrane
  • peptidoglycan
  • cytoplasmic membrane
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74
Q

Describe the cell wall of gram +ve cells

A
  • multi-layered peptidoglycan
  • secondary polymer
  • cytoplasmic membrane
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75
Q

What are the limitations of gram stain?

A
  • gram-variable bacteria & microbes that do not stain with crystal violet/iodine complex exist
  • not all organisms stain well with gram stain and other staining methods or diagnostic tests must be used for these infections.
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76
Q

Give 2 examples of organisms which do not stain well with gram stain

A

Mycobacterium tuberculosis

  • the organism that causes TB
  • has a lipid rich/waxy cell wall that does not take up the stain

treponema pallidum

  • a spiroachete organism that causes syphillis, a STI/D
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77
Q

What is the order of linnean classification?

A
  • kingdom
  • phylum
  • class
  • order
  • family
  • genus
  • species
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78
Q

Define each linneage of classification

A
  • kingdom- plant, animal, fungi, protist, monera
  • phylum- third taxonomic ranking, set of defining characteristics, division
  • class- organisms which share a common attribute
  • order- comprised of famailies sharing a set of similar nature or character.
  • family- one or more genera, especially sharing a common attribute
  • genus- group of related species with similar phenotypic and phylogenetic characteristics
  • species- a group of organisms capable of interbreeding and producing fertile offspring.
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79
Q

What are aerobic bacteria?

A

Ones which grow in oxygen/air

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80
Q

What are obligate anaerobes?

A

Ones which REQUIRE oxygen to breath

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81
Q

What are obligate anaerobes?

A

Ones which are killed by oxygen.

  • respiration uses electron acceptor other than oxygen
  • smaller reduction potential than oxygen
  • less proton motive force across membrane (ATP synthase)
  • less energy released per molecules oxidised.
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82
Q

What are facultative anaerobes?

A

Tolerate oxygen

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83
Q

What are capnophillic bacteria?

A

prefer high carbon dioxide to grow.

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84
Q

What is selective media?

A

A media that selects for the growth of specific prokaryotes.

The presence of specific substances permits the growth of one organism over another.

85
Q

Give 2 examples of selective media

A

Mannitol salt agar (MSS)

  • 7.5% salt allows preference and isolation of staphylococci
  • mannitol fermentation produces acid and turns agar/colony yellow

Salmonella shigella (SS)

  • bile salts inhibit coliforms
86
Q

What is differential media?

A

Incorporation of chemicals produces visible changes in colonies that facilitate identification (differentiation)

e.g. presence of a dye is differential

87
Q

Give 2 examples of differential media

A

MacConkay Agar

  • bile salts & crystal violet
  • lactose only C source & neutral red indicates fermentation
  • facilitate identification of enterobacteriaceae

Eosin & Methylene Blue (EMB)

  • lactose salts & two dyes
  • allows identification of lactose fermenters e.g. E.coli
88
Q

What is enrichment media?

A
  • when the type of nutrition on a petri dish supports the organisms you’re interested in
  • most common is blood agar
  • enrichment media usually comes before selective and differentiative
89
Q

How is streptococcus spp. identified?

A

Via haemolysis

90
Q

What are the 3 types of haemolysis?

A

Alpha, beta and gamma

91
Q

Which bacteria show alpha haemolysis?

A

streptococci pneumoniae

Viridans/oral group of streptococci

92
Q

Describe beta haemolysis

A
  • greening is the bleaching of red blood cells
  • a complete lysis of red blood cells in the media around and under the colonies
  • groups G, A and C streptococcus
  • GAS- group A streptococcus
  • colony size large (pyogenic) or small (s.miller)
93
Q

What is gamma haemolysis?

A

If an organism does not induce haemolysis, the agar under and around the colony is unchanged and the organism is non-haemolytic and said to display gamma haemolysis.

94
Q

What are you doing if you are growing a material from a swab or a culture?

A

You are amplifying it.

95
Q

Metabolic processing is a type of ____________ ________________

A

Biochemical characterisation.

96
Q

How is metabolic profiling carried out?

A
  • utilising carbon sources (acid production)
  • utilising amino acids
  • exo-enzyme production
    • catalase (breakdown of hydrogen peroxide)
    • coagulase (clot plasma)
    • hydrolysis of lipid- clostridia species
    • urease (urea converted to ammonia)
97
Q

What can a coagulase test be used to identify?

A

Staphylococcus aureus +ve

98
Q

How are bacterium identified?

A
  • innoculate/resuspend a single colony
  • transfer 100 micro-litres for automated biochemical profiling
  • media you enrich and select with for the organism you’re interested in is what you use when you set up the machine.
99
Q

Describe serological tests

A

Blood samples for the presence of viral and bacterial antigens and antibodies, to help diagnose diseases and check immune status, are tested in serology.

  • Host immune response to Ag by the raising of Abs
  • Ab specific to microbe/virus (polyclonal), or single component (monoclonal)
  • detect presence of specific IgM Ab to virus/microbe.
  • demonstrate in vitro by agglutination (aggregation) reaction
  • rapid detection of viruses (24 hours), even possible to identify stafe of infection using 2 different tests
  • can identify specific serotypes of bacteria
100
Q

What can the specificity shown in agglutination of antigen and antibodies in serology be used for?

A

For the recognition of a particular pathogen

101
Q

Describe PCR and its use

A
  • Specific primers amplify specific pieces of DNA
  • PCR allows you to amplify specific target sections to allow you to detect the presence of a genetic sequence in a properly prepared sample.
  • can take very small amounts
  • need PCR to show the presence of something
  • can use the product as the starting point to figure out the specific sequence of that gene.
102
Q

What are the 2 types of PCR?

A

Real time or qPCR

103
Q

What can successful amplification of DNA target indicate?

A

the presence of an organism or even specific virulence factor.

104
Q

What can DNA sequencing of product from PCR allow?

A

precise identification

  • ribotyping 16S RNA
  • spa typing S.aureus
105
Q

The 16sRNA can be sequenced. This is the most common and oldest approach but it is not perfect and you get far more info sequencing the whole genome. What is the 16sRNA?

A

An RNA component of the holoenzyme/ribosome

106
Q

What does MALDI-TOF stand for?

A

Matrix assisted laser desorption ioniazation time of flight

107
Q

Does malditof look at DNA?

A

No, it looks at the protein components associated with a cell.

108
Q

How does MALDITOF work?

A
  • Analyte is prepared by ionizing and transferring the analyte ions into gas phase.
  • Ionizing radiation moves through a charged gas. so all the peptides derived from the exposure to radiation become volatile, almost gaseous and suspended in the chamber.
  • they are attracted to the detector at the far end.
  • move from the plate to the detector through a chamber
  • depending on their size they move at different rates
  • depending on their charge they will have a different position
  • Hit the detection plate in different places, at different times, giving off a different signal.
  • the amount that hits is also detected
  • need to have a comparator e.g. what would a pure culture do.
109
Q

What is MALDI-TOF used for?

A

detecting peptide components.

  • generates a series of ions from a sample dependent on its constituents
  • separates the ions according to mass and charge
  • detects the spectrum of proteins released from a sample
  • results in characteristic signature.
110
Q

What are the benefits of MALDI-TOF?

A
  • Powerful- 99% correct
  • Rapid- colony tested in 6 mins
  • Precise- species, sub species, sometimes strain level
  • cost-effective- 17-32% the cost of conventional techniques
111
Q

What is MALDI-TOF not so good for?

A

Streptococci and staphylococci

112
Q

Define microbiome

A

The combined genetic material of the microorganisms of a particular environment.

Includes potential pathogens

113
Q

What are the 2 types of microorganisms?

A

endogenous microorganisms

exogenous- not normal flora

114
Q

What is pathogenesis?

A

The parasitic life cycle

115
Q

What are the stages of pathogenesis?

A
  • release/spread
  • (resevoir of pathogens)
  • contact (entry) into the host
  • adhere/colonize and invade
  • evade host defences
  • multiply/complete its lifecycle
  • exit the host (host is damaged)
116
Q

Define virulence

A

The capacity of a microbe to cause damage to the host

117
Q

What is a pathogen?

A

A harmful organism that produces a pathology

118
Q

What does commensal/mutualism/symbiosis mean?

A
  • An organism that is part of the normal flora
  • often mutualistic relationship
  • endogenous

often mutualistic is used as they actually benefit you because they are adapted to your immune system, you likely have antibodies if they’ve potential to cause disease so can protect against other diseases etc.

If you disturb a symbiotic relationship you may loose some beneficial interactions meaning some other harmful organism may enter or neutral oganisms could adapt and become oppertunistic.

119
Q

What is an oppertunistic pathogen?

A

An organism that causes infection when oppertunity/change in natural immunity arises e.g. in an immunocompramised individual.

120
Q

What is a contaminant?

A

An organism that is growing in a culture by accident

121
Q

Why are fungal infections difficult to treat?

A

There is a limited no. of targets for anti-mycotic/fungal drugs.

122
Q

How can fungi evolve in immunocompromised individuals?

A

Bud sites can become elongated and form hyphae or pseudohyphae

123
Q

Name some common examples of fungal infections

A
  • Candida spp.
  • yeast (budding)
  • from skin infections to candidaemia
  • aspergillus spp.
  • moulds
  • infections for immunocompromised
124
Q

What is eukaryote candida and how is it treated?

A

Budding yeast, common example of a fungal infection

You can’t use antibiotics and have to use anti-fungals

125
Q

Name 3 significant protozoan diseases of man

A

Malaria

Toxoplasma

GI infections

126
Q

Briefly describe malaria

A
  • protozoa
  • lives in mosquito
  • can be transmitted in the blood stream
  • Can replicate in RBCs and released entering the liver and causing waves of disease
  • RBCs can become sticky and clot leading to ischaemic events
127
Q

Of the prokaryotic pathogens, name some common gram negative ones in the UK

A
  • Neisseria spp.
  • escherichia spp.
  • klebsiella
  • enterobacter spp.
  • proteus
  • salmonella spp
  • shigella spp
  • haemophilus spp
  • pseudomonas
  • bacteriodes
128
Q

Of the prokaryotic pathogens, name some common gram positive ones

A
  • Streptococcus spp.
  • staphylococcus spp.
  • enterococcus spp.
  • clostridium
129
Q

How do gram negative cocci appear on gram film?

A

Appear in pairs (diplococci)

130
Q

Name 2 pathogenic species of aerobic gram negative cocci

A

Neisseria meningitidis- commonest cause of bacterial meningitis.

Neisseria Gonorrhoea- causes gonorrhoea, a sexually transmitted infection

131
Q

What are the 2 types of gram negative bacteria associated with the GI tract?

A
  • Gut commensal coliforms (normal bowel flora)
  • significant gut pathogens
132
Q

Give 4 examples of gut commensal coliforms

A
  1. Most strains of escherichia coli
  2. klebsiella spp.
  3. enterobacter spp
  4. proteus spp
133
Q

Give 3 examples of significant gut pathogens

A
  1. salmonella spp
  2. shigella spp
  3. verotoxin (VTEC producing E coli)
134
Q

Define enterobacteriacaea

A

A large, heterogenous group of gram negative rods that includes bacteria that naturally inhabit the gut but can also occur and multiply in other environments.

135
Q

What is the term coliform used to describe?

A

sub group of the enterobacteriaceae

term used to describe species of gram negative bacilli that look like escherichia coli (E/coli) on gram film and when cultured on blood agar.

136
Q

In what oxygen conditions do coliforms grow best?

A

aerobically but they can also grow anaerobically

137
Q

Many _________ are part of the normal bowel flora.

A

Coliforms

138
Q

How are coliforms differentiated from each other?

A

By:

  • biochemical reactions
  • antigenic structure of cell wall (serotyping)
  • O antigens (cell wall) and H antigen (flagella)
139
Q

Any coliform that becomes oppertunistic and gets into a normally sterile site can cause serious infection, give 3 examples.

A
  • Urinary tract infection
  • peritonitis
  • biliary tract infection
140
Q

Name the first line antibiotic used for the treatment of infections caused by coliforms

A

Gentamicin

141
Q

Why can people with coliform (gram negative) sepsis become very unwell very quickly?

A

Because of the endotoxin released from the gram negative cell wall when the bacteria die.

142
Q

How would you describe the symmetry of the outer gram negative membrane bacteria?

A

Asymmetric

143
Q

Describe the outer membrane of gram negative bacteria

A
  • asymmetric bacteria
  • lipopolysaccharide (LPS)
  • peptidoglycan
  • lipoproteins
  • bind to receptors on macrophages, B cells, & other cells that stimulates the release of acute phase cytokines.
144
Q

What is another name given to endotoxin shock?

A

systemic inflammatory response syndrome (SIRS)

145
Q

How does endotoxin shock occur?

A

Lipopolysaccharide, referred to as an endotoxin, causes the release of inflammatory cytokines from macrophages and a series of responses. This is linked with sepsis.

146
Q

Sepsis is a host response to severe infection. Describe what happens during sepsis

A
  • small blood vessels become “leaky” and lose fluid into the tissues
  • lower blood volume requires heart to work harder to maintain oxygenation of tissues (increased HR)
  • poor tissue oxygen perfusion means blood supply to less essential organs (skin, kidneys, liver) is shut down to try to maintain blood supply to brain.
  • blood clotting system is activated causing clotting in tiny vessels -> uses up all clotting factors -> increased risk of haemorrhage.
147
Q

State the mechanism of fever production step by step

A
  1. antigen (component of micro-organisms or lipopolysaccharide (endotoxin)) interact with macrophages (WBC)
  2. macrophages release cytokines into the bloodstream
  3. cytokines travel to the anterior hypothalamus (brain)
  4. prostoglandin E is released, which increases the body’s thermal set point.
  5. the body now perceives that it is cold and starts to “shiver” to conserve heat
  6. FEVER
  7. increased survival from infection
148
Q

How is fever defined?

A

Fever is defined as a temp > 38 degrees celcius

149
Q

What is the “normal” core body temperature where most human pathogens grow best?

A

37 degrees celcius, growth starts to slow if temp increases.

150
Q

True or false: raising the core body temperature is an adaptive response and is considered to be beneficial in fighting infection.

A

True

151
Q

Give an example of the fact that harm can also result from fever

A

febrile convulsions in young children

152
Q

What are the 4 escalations of host response to a pathogen?

A
  1. infection
  2. sepsis
  3. severe sepsis
  4. septic shock
153
Q

Give 4 examples of gram positive pathogens

A

Streptococcus

  • pneumonia, GAS, oral streps

Enterococcus

  • enteric infections

Staphylococcus

  • nosocomical & community
  • skin infections & biofilms
  • URT & skin infections

clostridia

  • anaerobic bacilli
154
Q

Why is haemolysis important?

A

For the classification of streptococci.

155
Q

Describe alpha haemolysis

A

Partial haemolysis

Caused by enzymes that denature the haemoglobin inside red blood cells causing greenish discoloration around the colony

156
Q

Describe Beta-haemolysis

A

Complete haemolysis

caused by enzymes that lyse (breakdown) red blood cells causing complete clearing around the colony. the most pathogenic streptococci are beta haemolytic,

157
Q

Describe gamma haemolysis

A

No haemolysis

158
Q

Name the most significant pathogenic streptococci

A

Group A streptococcus (streptococcus pyogenes)

159
Q

Name some of the numerous types of associated diseases to GAS

A
  • streptococcal sore throat (scarlet fever)
  • invasive disease e.g. necrotising fasciitis
  • peurperal sepsis (infection of pregnant & post-natal women)
  • severe skin infections
160
Q

The major species streptococcus pyogenes has a group _ antigen on its surface.

A

Group A, GAS

161
Q

Define pneumonia

A

An acute inflammation of the lungs, often caused by inhaled pneumococci of the species streptococcus pneumoniae. The alveoli and bronchiles of the lungs become plugged with a fibrous exudate.

162
Q

Describe streptococcus pneumoniae

A
  • Gram positive alpha haemolytic cocci- short chains or pairs
  • part of normal upper respiratory tract flora in many people
  • commonest cause of pneumonia-also causes a severe form of meningitis
  • 90+ different capsular types- vaccine available that immunises against commonest 23 types
  • majority of UK strains are still sensitive to penicillin.
163
Q

Name the most important group of non-haemolytic streptococci

A

Enterococci

164
Q

Name 2 types of enterococci

A
  • enterococcus faecalis
  • enterococcus faecium
165
Q

State some key features of enterococci

A
  • non-haemolytic
  • part of the normal bowel flora
  • not particularly pathogenic, but can cause problems if they get into a normally sterile site.
  • e.g. common cause of UTI
  • most strains of E.faecalis are sensitive to amoxicillin (but not penicillin)
  • some very antibiotic-resistant strains of E.faecium
166
Q

What does VRE stand for?

A

Vancomicin resistant enterococci which can cause outbreaks of infections in hospital.

167
Q

Name one gram positive staphylococcus

A

S. aureus

168
Q

Name one gram negative staphylococcus

A

S.epidermidis

169
Q

Describe staphylococci

A
  • gram +ve
  • non-motile
  • irregular grape-like clusters
  • aerobe + facultative anaerobe
  • catalase +ve (usually, common for identification)
  • oxidase -ve
  • coagulase +ve or -ve (ability to coagulate plasma)
  • tolerate 15% NaCl (can tolerate high salt)
170
Q

Define nosicomial

A

Infection associated with a health care setting/hospital

171
Q

What is the commonest cause of skin, soft tissue and wound infection?

A

Staphylococcus aureus

172
Q

Describe the mechanism of s.aureus

A
  • 20% colonisation
  • anterior nares (nostrils) and perineum
  • nosocomial and community
173
Q

Describe the mechanism of S.epidermidis

A
  • 100% colonisation
  • skin and mucous membranes
  • nosocomial infection/immunocompromised- associated with foreign devices e.g. catheters
174
Q

Descrive mRSA

A
  • Mainly nosocomial
  • elderly & immunocompromised
  • ICU
  • burns patients
  • surgical patients
  • Intravenous lines
  • dialysis patients
175
Q

Describe clostridiodes

A
  • gram positive anaerobic bacilli
  • part of normal bowel flora of man and animals- found in faeces and in soil
  • produces spores that can survive outside the body for many months
  • produce exo-toxins that cause severe tissue damage
176
Q

What does clostridiodes difficile do?

A

Causes antibotic associated diarrhoea, esp. in the elderly.

177
Q

What is a virus?

A

A very small, non-cellular microbe. It is an obligate intracellular parasite.

178
Q

Describe viral structure

A
  • Nucleic acid genome (DNA or RNA)
  • protein shell (capsid)
  • sometimes lipid layer too (envelope) associated with virus proteins
179
Q

How does replication of a virus occur?

A

virus genomes direct synthesis of virus proteins and progeny virus genomes using cellular machinery.

180
Q

What is a virion?

A

A virus particle

181
Q

How are viral particles assembled?

A

The virus components produced by the host cell are assembled into progeny virus particles.

182
Q

Where do all materials required by a virus come from?

A

The host cell.

183
Q

What are the 2 fundemental types of virus structure?

A

Enveloped and non-enveloped

184
Q

Give 3 examples of blood born viruses which are icosahedral (20 identical, equilateral triangular faces)

A
  • Adenovirus
  • papillomavoris (HPV)
  • rotavirus
185
Q

Which systems can be affected by viruses?

A

All of them

186
Q

Give 3 examples of viruses which contain ssRNA

A
  • influenza virus
  • Ebola virus
  • Parainfluenza virus
187
Q

Describe SARS-CoV-2

A
  • spike (S)
  • membrane (M)
  • envelope (E)
  • nucleocaspid (N)
  • hemagglutinin-esterase dimer (HE)
  • RNA
    • 4 structural proteins
    • 16 non-structural proteins
  • glycoproteins
188
Q

Describe the genome of a virus

A

The genomes of different viruses are extremely varied

  • chemistry- DNA or RNA (has an influence on if it is positively or negatively charged)
  • structure- double stranded, single stranded, linear, circular
  • size- 3500 bases to 330,000 base pairs
189
Q

What is the role of the protein caspid?

A
  • Protects the genome from the environment
  • delivers genome to the cell
  • functional proteins might be present in the capsid
190
Q

In some viruses the caspid is enveloped. What does the envelope consist of?

A

A lipid bilayer (derived from the host cell) containing viral proteins.

191
Q

Viruses are not alive so they only replicate. What are the stages of the viral growth cycle?

A

Attachment -specifies cells/systems effected, has to attach to a cell to gain entry

Entry-Can use more than one method

uncoating-cytoplasm, releases its genetic components

Synthesis of viral components-proteins, polymerases, all the enzymes, need to be synthsized. need to make copies of the genome to be inserted into a mature virion.

Assembly & release- lysis(destruction) or budding (leaking out)

192
Q

How do enveloped viruses acquire their envelopes?

A

By budding

193
Q

How do viruses cause damage to host cells?

A

By lysis or budding. They damage the cell by hijacking its mechanisms and taking over its function.

194
Q

Name 4 ways a virus can enter into a host

A
  • respiratory tract- inhalation and touch, sexual (URT)
  • Gastro-intestinal tract- ingestion and inhalation
  • urogenitary tract- Sexual transmission
  • blood- vertical(child birth), needles, products, insect vector
195
Q

Name 6 routes of transmission of viruses

A

oral transmission- contaminated food and drink, saliva

direct skin contact

trans-placental

droplet transmittion- inhalation

direct innoculation- injections, trauma, insect bites

sexual transmission

196
Q

What are localised (discrete) infections by viruses?

A

When viruses remain at the site of infection e.g. rhinovirus, molluscum

197
Q

What are the 2 mechanisms of viral spread?

A

Neural spread i.e. invasion of the nervous system e.g. Herpes Simplex Virus (HSV)

Hematogenous spread i.e. in blood (HIV)

198
Q

How do viruses cause damage to the host?

A
  • cell lysis- they destroy the cell
  • cell-cell fusion- fusing cells can disrupt the function and viability and impair movement of material across membranes
  • inhibition of host cell transcription, translation
  • alteration of host cell cycle, proliferation.
199
Q

What host factors can cause damage when there is a virus present?

A
  • apoptosis (cell ‘suicide’)
  • lysis of infected cells by immune cells
  • inflammation
200
Q

Describe how viral pathology is specific

A
  • cells in different tissues have different properties (including receptors)
  • viruses are heavily dependent on the host cell for their replication.
  • viruses can only replicate in cells that have the right properties for that virus
  • in many cases impact on host is via impairing the function of specific systems
201
Q

How does immune response to infection effect viruses?

A

adaptive immune response can prevent entry, mark virions for destruction & destroy infected cells.

  • neutralising antibodies e.g. IgG, IgM- virus surface proteins specify what cells it can enter, so if antibody binds to this it can block entry
  • cytotoxic T response- promotes destruction of infected cell
202
Q

What are some of the problems posed by viral infections?

A
  • latency- period where person has been infected but is not producing the virus so may be asymptomatic e.g. herpes, varicella-zoster
  • chronic/persistant infections e.g. HIV and Hepatitis C
  • Transformation of host cells
  • Evolution-numbers of replication cycles, RNA, Zoonotic (can go in and out of different organisms), recombination.
  • Treatment options- vaccines, passive immunisation, anti-viral drugs
203
Q

How are viral infections controlled? Give some examples

A
  • isolation and quarantine
  • antibodies harvested from donor/tissue culture
  • vaccines
  • anti-viral drugs
204
Q

Name some anti-viral drug targets

A
  • viral nucleic acid polymerases
  • viral enzymes involved in viral nucleic acid replication or in protein synthesis- integrase, protease
  • uncoating
  • attachment/entry
  • release
205
Q

What are the 4 types of vaccines?

A
  • live attenuated-take strains that showed no disease characteristics in humans but could be grown in labs or had very limited replication so it doesn’t produce a virus in a human but initiates an immune response
  • inactivated
  • sub-unit-take small sections like a small surface protein
  • toxin- kind of subunits applied to bacteria
206
Q

What are the 2 ways to diagnose a viral infection?

A
  • Detect the virus
  • Detect the host response/serology
207
Q

How can viruses be detected?

A

PCR

  • qPCR (quantitative, done in real time)- isolation of genetic material and its amplification
  • loop-mediated idothermal amplification (LAMP)

Antigen

  • blood/saliva/swab
  • host cells
  • fluorescent antibody staining
208
Q

How can the host response to a virus be detected?

A

Antibodies- IgM, IgG

You can take an antibody specific to the viral particle and fluorescently tag it to screen the material- fluorescent antibody staining.

Principles (10 decks)

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