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MICROBIOLOGY

MICROBIOLOGY. Chris Keil – F2. You are not alone. Are there strong/powerful antibiotics? A lot of testing is with chromatography – the future will be genetic Apologies for pronunciation/mnemonics Cover gram positive/negatives and TB/quiz if time. REferences. For treatment – BNF guidelines

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MICROBIOLOGY

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  1. MICROBIOLOGY Chris Keil – F2

  2. You are not alone • Are there strong/powerful antibiotics? • A lot of testing is with chromatography – the future will be genetic • Apologies for pronunciation/mnemonics • Cover gram positive/negatives and TB/quiz if time

  3. REferences • For treatment – BNF guidelines • Microbiology and ID the basics – classification/treatment/everything you need to know • When you are an FY1 – microbiology guidelines • I won’t giving out the powerpoint – use the microbiology pdf – I will email this!

  4. Shapes – draw each one with your hand • COCCI • BACILLI • VIBRIO • SPIROCHAETE

  5. COCCI – ANY GENERALLY ROUND SHAPED BACETERIA

  6. Bacilli – rod shaped

  7. Vibrio – curved red/comma shaped – “VIBRONS” https://www.youtube.com/watch?v=4TWRFF79YsM

  8. SPIROCHAETE - spirals

  9. Why do I need to know about staining? • Is it clinically relevant for working as an FY1? • It comes up in exams • The future will be genetic testing – the culture will be important for growth but less so in identification and sensitivities • Help you navigate the branches of different bacteria

  10. Different tests • You should be aware of… • 2 types of staining • 4 different tests • 2 types of agar • 1 type of grouping

  11. Gram staining – 2 broad groups + poorly staining • Named after Hans Christian Gram • Why do Gram staining? How many ways are there to slice a cake? • POSITIVE – PURPLE • NEGATIVE - RED

  12. Another type of staining • ZiehlNeelsen Staining • USED FOR MYCOBACTERIA • THEY ARE ACID FAST – PINK/RED • What does acid fast mean? • THIS MEANS THAT THEY RESIST ACID DE-COLOURISATION PROCEDURES

  13. Gram Positive Specific tests

  14. Gram positive cocci CATALASE TESTS • TELLS YOU THE DIFFERENCE BETWEEN: • STAPHYLOCOCCI • STREPTOCOCCI/ENTEROCOCCI • staphylococci use catalase to protect against hydrogen peroxide – reaction you see bubbles – catalase positive • if not present there is no reaction – catalase negative • https://www.youtube.com/watch?v=K3-BMFHrsVg • 23 seconds

  15. Gram Positive Cocci Staphylococcus Strep/enterococcus

  16. Staphylococcus Coagulase positive • Used to differentiate between: • Staphylococcus aureus • Other Staphylococci COAGULASE is an enzyme that causes coagulation – fibrin to clot BACTERIA + PLASMA = CLOT - STAPH AUREUS – coagulase positive BACTERIA + PLASMA = NO CLOT – OTHER STAPH SPEICES – coagulase negative https://www.youtube.com/watch?v=IUIIDPCIvAE 1 minute 6 seconds

  17. Oxidase test • Identifies bacteria that are oxidase positive – produce cytochrome oxidase • Pseudomonas • Neisseria POSITIVE TEST RESULT – BLACK/PURPLE COLOUR NEGATIVE TEST RESULT – NO COLOUR CHANGE https://www.youtube.com/watch?v=d4PkuRtGfFo 25 seconds

  18. Optochin test • Differentiates: • Streptococcus pneumoniae – what type of cocci… • Diplococci in chains • From other alpha haemolytic streptococci • Clear zone of lysis – strep. pneumoniae Alpha haemolytic strep

  19. Agars

  20. Blood agar • Differentiates • Alpha haemolytic streptococci • Beta haemolytic streptococci Alpha – green pigment Beta – clear zones of lysis Non-haemolytic – no change Streptococci

  21. Macconkey agar – bile salts, lactose, ph indicator Enterobacteria/bacilli • Bile salts only permit the growth of enteric bacteria • Lactose fermentation causes an acidic environment – red/pink colour change with the indicator • Red/pink colony – E Coli, Klebsiella • Clear colony – Salmonella, Shigella, Pseudomonas

  22. Lancefield grouping • Differeniates beta haemolytic streptococci by detecting surface antigens: • Lots of groups • Group A Strep – pyogenes • Group B Strep - neonates

  23. Toxins • Exotoxin – secreted by bacteria (MAINLY GRAM POSITIVE) – specific actions – like paralysis with botulinum toxin • Endotoxin – released when bacteria is damaged, less specific action – septic shock

  24. Gram positive • Sexy Streptococcus spp • Students Staphylococcal spp • Can Corynebacterium spp ------- AEROBIC • Diphtheria • Look Listeria spp • Listeria monocytogenes – non-pasteurised/those with contact with animals – farmers/vets! • Bad Bacillus spp. – go to which type of restaurant • Anthracis • Cereus – reheated rice – in exams – Chinese restaurant • Come morning Clostridium spp. ------ANAEROBIC

  25. GRAM negative • Cocci • Neisseria • Meningitidis – what type of cocci? • Diplococci • Gonorrhoea • Moraxella catarrhalis – which condition? • COPD

  26. Gram negative bacilli • ANAEROBES • Bacteroidesfragilis – causes… • 90% of anaerobic peritoneal infections • All the others are aerobes

  27. Gram negative bacteria – aerobic bacilli • Division by growth requirements • MacConkey agar – lactose fermenters - ?properties • E coli – causes • gastroenteritis/UTI • Klebsiella – causes • Pneumonia/UTI Non lactose fermenters – MacConkey pale • Salmonella – causes • Typhoid, diarrhoea • Shigella – causes • diarrhoea in MSM (dysentery) • Proteus – causes • UTI

  28. Gram negative aerobic bacteria - other • Pseudomonas Aeroginosa – causes • COPD and cystic fibrosis • Nosocomial infections • Vibro cholerae – where? • 4 star rating on trip advisor

  29. Other gram negative aerobic bacilli • Fastidious growth requirements – complex • Haemophilus Influenza – Harry Potter • (IECOPD) Bordatella pertussis – Bought • (Whooping cough) Legionella pneumophilia – Lots of (Legionella – hotels/air conditioning) Brucella – Big (Brucellosis – unpasteurised milk) Campylobacter – Cookies for (diarrhoea/GBS) Helicobacter Pylori – Hagrid (ulcers)

  30. Other – poorly gram staining • • Chlamydia spp. - CRUNCHY • Psittaci – birds • Trachomatis - chlamydia • • Coxiellaspp. - CARROTS • Q fever • • Mycobacteria spp. - MAKE • TB, leprae • • Treponema spp. – THE • spirochaete - syphillis • • Borrelia spp. - BEST • Lyme disease • • Leptospiraspp. - LIGHT • leptospirosis (water and livestock –farmer) • • Mycoplasma spp. – MEAL FOR • mycoplasma pneumoniae • • Rickettsia spp. - RABBITS • typhus (not typhoid!) spread by ticks

  31. Tuberculosis • 1/3 of the world’s population is thought to be infected with TB!!! • Treatment – 4 antibiotics - RIPE • Rifampicin - RED urine, hepatotoxicity • Isoniazid – peripheral neuropathy – N for neuropathy • Pyrizinamide - hepatotoxicity • Ethambutol – ocular/EYE toxicity

  32. Urinary tract - UTI • Most common causative organism… • E Coli • Other causative organisms • Proteus • Klebsiella • First line • Trimethoprim/nitrofurantoin • Or amoxicillin

  33. Pyelonephritis • Most common causative organism: • E Coli • Other causative organism • Enterococcus faecalis • Treatment • Use cefuroxime or quinolone (floxacin – ciprofloxacin) • Gentamicin

  34. Prostatitis • Most common causative organism • E Coli • But also • Proteus Mirabilis • Klebsiella • Antibiotic • Quinolones (ciprofloxacin)

  35. SKIN - Impetigo • Most common organism • S Aureus • Treatment • Fusidic acid

  36. CEllulitis • Common organism • S Aureus • Management • Flucloxacillin

  37. RESPIRATORY - PNEUMONIA • Most common cause • Strep Pneumonia • Other causes • H Influenzae • Atypicals – • Coxiella, Chlamydophilia, Mycoplasma, Leigionella • Management – depends on severity calculated using the CURB65 • https://www.mdcalc.com/curb-65-score-pneumonia-severity

  38. CAP/HAP • CAP • Low severity • Amoxicillin Moderate • Amoxicillin High severity • Benzylpenicillin + clarithromycin (why clarithromycin?) HAP – broad spectrum Co-amoxiclav – if early onset (less than 5 days into admission) Tazoin – if late onset (more than 5 days)

  39. MSK - Osteomyelitis • Common organism • S Aureus • Other • Enterocbacter • Streptococcus • Bonus point – if sickle cell anaemia • Salmonella • Management • Flucloxacillin

  40. Septic arthritis • Common organism • S Aureus • Other • Streptococci • Neisseria – in sexually active young adults • Management • Flucloxacillin

  41. Eye • Common organism • S Aureus • Other causes • Streptococci • Haemophilus • Treatment • Chloramphenicol

  42. GASTRO infections – C Diff • Treatment • Metronidazole – use in situations where anaerobic bacteria are suspected

  43. CNS - meningitis • Treatment depends on causative organism • 2 most common • Neisseria Meningitidis • Streptococcus Pneumoniae • When unknown • 3 months -50 years • Cefotaxime • Over 50 years • Cefotaxime and amoxicillin

  44. Other typical exam characteristics • Listeria monocytogenes – causing listerosis (CNS infections and sepsis in immunocompromised) • - Grows in hot or cold temperatures • Cold – spread by PO route and growth not prevented by refrigeration Cholera causes what type of diarrhoea • Rice water • Which infection causes bovine cough • Croup • Which infection causes paroxysmal coughing • Whooping cough

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