1. 2017/2018

2. Microbiology Phase 2a Wrap-up Session Krishanth Ganesan 24/1/19
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3. Microbiology Objectives Cover things you actually need to know
Various tests for each organism
Approach to antibiotics
Resources
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4. How to study Study microbiology by condition, not the organism
Eg study infective endocarditis and its associated organisms, not staph aureus, strep pyogenes etc
The things that they might test you with regards to organisms is recognising them on microscope (described in text eg gram –ve diplococci) or tests to identify a certain bug (+ve optochin test)
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5. Approach to bacteria Determine if it is: Gram +ve or –ve
Cocci, bacilli or others
In clusters or chains
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6. Bacteria - shapes Cocci Bacilli
Spirochaete – eg Treponema pallidum (syphilis), borrelia burgdorferi (Lyme disease)
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7. Bacteria – gram +ve or -ve
Gram +ve: Purple
Contains peptidoglycan that is stained by crystal violet
Gram –ve: pink
Has a lot less peptidoglycan that is not stained, by instead stained by safranin
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8. Bacteria – staph vs strep
Staph in clusters
Strep in chains
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9. Bacteria – Gram +ve cocci in clusters
Catalase test:
H2O2  + Staphylococci → Gas bubbles
+ve = staph
-ve = non staph
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10. Bacteria – Gram +ve cocci in clusters
Now that you know it’s a staph.. Is it staph aureus?
Coagulase test
+ve = staph aureus since it produces coagulase that converts fibrinogen to fibrin
-ve = coagulase –ve staph
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11. Bacteria – Gram +ve cocci in clusters
Eg of coag –ve staph = staph epidermis
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12. Bacteria – Gram +ve cocci in chains
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13. Bacteria – Gram +ve cocci in chains
Blood agar can undergo 3 types of haemolysis depending on the organism
Beta haemolysis: complete
Alpha: partial
Gamma: none
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14. Bacteria – alpha haemolytic strep
Alpha haemolytic strep – only 2 important bugs, you want to know if it is strep pneumoniae
If optochin +ve = strep pneumoniae (clear demarcated ring around optochin disc)
Optochin resistant = strep viridians
Strep pneumo on microscopy =
Gram +ve diplococci
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15. Bacteria – beta haemolytic strep
Lancefield test – groups bacteria based on carbohydrate composition of bacterial antigen on cell wall, normally for beta-haemolytic strep
A: Streptococcus pyogenes
B: Streptococcus agalactiae
D: Enterococcus, Strep bovis (group D is not beta- haemolytic)
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16. Bacteria – gram +ve bacilli
Gram +ve bacilli that are important
Listeria monocytogenes
Propionibacterium acne – acne
Clostridium difficile – diarrhoea from antibiotic overuse (those starting with C)
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17. Bacteria – gram –ve bacilli
MacConkey agar:
Contains bile salts, lactose & neutral red (pH indicator)
Identifies bacteria that can ferment lactose (normally gram-ve enteric bugs)
Ferment lactose -> produce acid -> pH drop <6.8= pink, or if pH>6.8, remains normal colour
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18. Bacteria – gram –ve bacilli
Yellow - non fermenters - salmonella, shigella, pseudomonas aeruoginosa, proteus mirabilis
Pink - fermenters - e.coli, klebisella pneumoniae
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19. Bacteria – gram –ve bacilli
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20. Bacteria – gram –ve bacilli
Done macconkey, it’s yellow:
Perform oxidase test:
Black/purple = +ve = pseudomonas or Neisseria(note it is cocci not bacilli)
Additional anti-pseudomonal sensitivity tests required to identify pseudomonas
Colourless = -ve = shigella, salmonella, proteus
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21. Bacteria – gram –ve bacilli
Proteus mirabilis:
Swarms on many agars, difficult to identify other bacteria growing (normally urinary tract)
CLED is used to inhibit proteus
To identify proteus: urease test +ve
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22. Bacteria – gram -ve cocci
Neisseria meningitidis, gonorrhoea
Moraxella catarrhalis
Any Neisseria on microscopy: gram –ve diplococci
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23. Bacteria – gram -ve other rods
Comma/curved shaped:
Vibrio cholera – rice water stool
Helical shape:
Campylobacter jejuni – bloody diarrhoea
Helicobacter pylori – gastric and duodenal ulcer
Coccobacilli:
Haemophilus influenza
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24. Bacteria – gram -ve other shapes
Haemophilus influenza
Gram –ve coccobacilli, requires factor X and V to grow
Fastidious bacteria: requires chocolate agar which is blood agar but with lysed RBCs due to heating to 80 deg C (haem from factor X)
Neisseria meningitidis also requires chocolate agar
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25. Mycobacteria Most important = m. tuberculosis
Can get bovine TB from m. bovis from cows
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26. Mycobacteria
Takes long to culture, have to be cultured with Löwenstein–Jensen medium
mycolic acid in the cell wall does not absorb normal gram-staining: requires Ziehl-Neelsen stain to identify acid-fast bacilli
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27. Approach to antibiotics
Learn mechanism of antibiotics
Much better to learn the empirical antibiotics used for each condition than trying to learn specific antibiotics for certain bugs
Eg CURB65 - pneumonia
Empirical antibiotics may differ from trust to trust when you start working
Learn side effects of TB drugs
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28. Approach to antibiotics
Some bugs have definite antibiotics, such as:
Vancomycin for MRSA
Metronidazole for entamoeba histolytica, giardia
Co-trimoxazole for PCP
CURB65 score for pneumonia and their respective antibiotic regimens
Vancomycin/metronidazole for C. difficile
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29. Approach to antibiotics
Important side effects:
Folate antagonist eg trimethoprim and pregnancy
Aminoglycoside such as gentamicin – ototoxicity, renal impairment
C drugs for C.diff
Carbapenems
Ciprofloxacin (Quinolones)
Co-amoxiclav (Penicillins)
Cephalosporins (especially 2nd and 3rd generation)
Clindamycin
The Peer Teaching Society is not liable for false or misleading information…

30. Approach to antibiotics
Learn mechanism of antibiotics
Much better to learn the empirical antibiotics used for each condition than trying to learn specific antibiotics for certain bugs
Empirical antibiotics may differ from trust to trust when you start working
Some bugs have definite antibiotics, such as:
Vancomycin for MRSA
Metronidazole for entamoeba histolytica, giardia
Co-trimoxazole for PCP
The Peer Teaching Society is not liable for false or misleading information…

31. Approach to antibiotics
Learn mechanism of antibiotics
Much better to learn the empirical antibiotics used for each condition than trying to learn specific antibiotics for certain bugs
Empirical antibiotics may differ from trust to trust when you start working
Some bugs have definite antibiotics, such as:
Vancomycin for MRSA
Metronidazole for entamoeba histolytica, giardia
Co-trimoxazole for PCP
The Peer Teaching Society is not liable for false or misleading information…

32. Approach to antibiotics
Learn mechanism of antibiotics
Much better to learn the empirical antibiotics used for each condition than trying to learn specific antibiotics for certain bugs
Empirical antibiotics may differ from trust to trust when you start working
Some bugs have definite antibiotics, such as:
Vancomycin for MRSA
Metronidazole for entamoeba histolytica, giardia
Co-trimoxazole for PCP
The Peer Teaching Society is not liable for false or misleading information…

33. Approach to antibiotics
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34. Virus PCR normally if needed
Infectious mononucleosis/glandular fever-like sx: Epstein-barr, cytomegalovirus, toxoplasmosis gondii (parasite), deadly in immunocompromised individuals
HIV
Upper respiratory tract infections
Deadly bugs: smallpox etc (learn more in 3a, paediatric bugs)
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35. Fungi Normally in immunocompromised individuals
Candida albicans – treat with antifungal eg topical nystatin, oral fluconazole
Pneumocystis pneumonia – treat with co-trimoxazole
Aspergilliosis – CF, bronchiectasis patients
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36. Helminths Very rare, need to know these at most:
Wucheria bancroftii – filariasis causing lymphoedema
Enterobius vermicularis – common in uk, itchy bum, spreads in household
Schistosomiasis – causes squamous cell bladder cancer
Hookworm - Worldwide cause of iron-deficiency anaemia
Treatment: normally mebendazole
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37. Protozoa Entamoeba histolytica: bloody diarrhoea, liver abscess
Treat with metronidazole
Malaria: learn in haematology, 5 types, plasmodium falciparum most important
Giardia: diarrhoea due to alteration of intestinal villi, reducing absorption
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38. Quiz What is the role of catalase test? A: identifies staph aureus
B: identifies staph from non-staph
C: identifies mycobacterium
D: identifies fungi
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39. Quiz What is the role of catalase test? A: identifies staph aureus
B: identifies staph from non-staph
C: identifies mycobacterium
D: identifies fungi
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40. Quiz What is the role of coagulase test? A: identifies staph aureus
B: identifies staph from non-staph
C: identifies mycobacterium
D: identifies fungi
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41. Quiz What is the role of coagulase test? A: identifies staph aureus
B: identifies staph from non-staph
C: identifies mycobacterium
D: identifies fungi
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42. Quiz For which group of bacteria should you do an optochin test?
A: alpha-haemolytic staph
B: alpha-haemolytic strep
C: beta-haemolytic strep
D: enterococcus
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43. Quiz For which group of bacteria should you do an optochin test?
A: alpha-haemolytic staph
B: alpha-haemolytic strep
C: beta-haemolytic strep
D: enterococcus
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44. Quiz Optochin +ve test: what is the bug? A: strep pneumoniae
B: strep viridians
C: strep pyogenes
D: strep agalactiae
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45. Quiz Optochin +ve test: what is the bug? A: strep pneumoniae
B: strep viridians
C: strep pyogenes
D: strep agalactiae
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46. Quiz Example of group A strep? A: strep pneumoniae B: strep viridians
C: strep pyogenes
D: strep agalactiae
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47. Quiz Example of group A strep? A: strep pneumoniae B: strep viridians
C: strep pyogenes
D: strep agalactiae
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48. Quiz Example of group B strep? A: strep pneumoniae B: strep viridians
C: strep pyogenes
D: strep agalactiae
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49. Quiz Example of group B strep? A: strep pneumoniae B: strep viridians
C: strep pyogenes
D: strep agalactiae
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50. Quiz Which of the following describes C. difficile?
A: gram –ve bacilli
B: gram –ve cocci
C: gram +ve cocci
D: gram +ve bacilli
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51. Quiz Which of the following describes C. difficile?
A: gram –ve bacilli
B: gram –ve cocci
C: gram +ve cocci
D: gram +ve bacilli
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52. Quiz Antibiotic for C. difficile A: amoxicillin B: cefotaxime
C: carbapenem
D: metronidazole
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53. Quiz Antibiotic for C. difficile A: amoxicillin B: cefotaxime
C: carbapenem
D: metronidazole
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54. Quiz Which of the following is gram +ve diplococci on microscopy
A: Neisseria gonorrhoea
B: strep pneumoniae
C: Moraxella catarrhalis
D: mycobacterium tb
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55. Quiz Which of the following is gram +ve diplococci on microscopy
A: Neisseria gonorrhoea
B: strep pneumoniae
C: Moraxella catarrhalis
D: mycobacterium tb
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56. Quiz Which of the following is gram -ve diplococci on microscopy
A: Neisseria gonorrhoea
B: strep pneumoniae
C: Moraxella catarrhalis
D: mycobacterium tb
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57. Quiz Which of the following is gram -ve diplococci on microscopy
A: Neisseria gonorrhoea
B: strep pneumoniae
C: Moraxella catarrhalis
D: mycobacterium tb
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58. Quiz When is chocolate agar important? To culture: A: mycobacterium tb
B: haemophilus influenza
C: Treponema pallidum
D: Not important, blood agar can be substituted
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59. Quiz When is chocolate agar important? To culture: A: mycobacterium tb
B: haemophilus influenza
C: Treponema pallidum
D: Not important, blood agar can be substituted
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60. Quiz MacConkey test – shows yellow, what possible bug?
A: pseudomonas aeruginosa
B: e.coli
C: klebsiella pneumoniae
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61. Quiz MacConkey test – shows yellow, what possible bug?
A: pseudomonas aeruginosa
B: e.coli
C: klebsiella pneumoniae
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62. Quiz MacConkey test – shows pink, what bug? A: pseudomonas aeruginosa
B: staph aureus
C: strep pneumoniae
D: e.coli
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63. Quiz MacConkey test – shows pink, what bug? A: pseudomonas aeruginosa
B: staph aureus
C: strep pneumoniae
D: e.coli
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64. Quiz Which stain is needed for mycobacteria?
A: Lowenstein-Jensen stain
B: Methylene blue
C: Oxidase purple
D: Ziehl-Neelsen stain
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65. Quiz Which stain is needed for mycobacteria?
A: Lowenstein-Jensen stain
B: Methylene blue
C: Oxidase purple
D: Ziehl-Neelsen stain
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