Makindo Medical Notes

🦠 Comprehensive Clinical Microbiology Tutorial for Medical Students 🧬

• 1. INTRODUCTION TO MICROBIOLOGY 🏥

  • 🔬 Microbiology = Study of microorganisms: Bacteria 🦠, Viruses 🧬, Fungi 🍄, Parasites 🐛
  • 🏥 Clinical Microbiology = Diagnosis & treatment of infectious diseases
  • 📚 Key concepts:
    • 👥 Normal flora vs. 💀 Pathogens
    • 🚪 Opportunistic infections (immunocompromised)
    • 🏠 Colonization vs. 🔥 Infection
    • 🛡️ Virulence factors: Toxins, enzymes, capsules

• 2. BACTERIOLOGY 🦠

  • 2.1 Bacterial Structure 🔬

    • 🧱 Cell wall:
      • 💜 Gram +: Thick peptidoglycan → Retains crystal violet
      • 🩷 Gram -: Thin peptidoglycan + outer membrane → Pink
    • 🛡️ Capsule: Streptococcus pneumoniae, Haemophilus influenzae
    • 🏃‍♂️ Flagella: Motility (E. coli, Proteus)
    • 🔗 Pili: Adherence (Gonorrhea)
    • 💣 Spores: Clostridium, Bacillus (heat resistant)

  • 2.2 Gram Staining Procedure 🎨

    • 🔵 Crystal violet → 🟣 Iodine → 💧 Alcohol (decolorizes Gram -) → 🟣 Safranin
    • 💜 Gram +: Purple (thick peptidoglycan)
    • 🩷 Gram -: Pink (lipopolysaccharide outer membrane)

  • 2.3 Gram Positive Cocci 🔵

    • 🟡 Staphylococcus aureus "Golden Staph"
      • 🌟 Golden colonies, 🧪 Catalase +, 🩸 Coagulase +
      • 🏥 Diseases: Cellulitis, Abscesses, Pneumonia, Osteomyelitis, Endocarditis, TSS
      • ⚠️ MRSA: Methicillin-resistant (vancomycin)
      • 🧪 Mannitol salt agar: Yellow colonies
    • 🔴 Streptococcus pyogenes (Group A β-hemolytic)
      • 🩸 Beta-hemolytic, 💊 Bacitracin sensitive, 🧪 PYR +
      < Lancefield A, M protein, Erythrogenic toxin
      • 🏥 Pharyngitis, Impetigo, Scarlet fever, Necrotizing fasciitis, Rheumatic fever
    • 🟢 Streptococcus pneumoniae "Pneumococcus"
      • 🩸 Alpha-hemolytic, 💊 Optochin sensitive, 🧪 Bile soluble, Quellung reaction
      • 🏥 Lobar pneumonia, Meningitis, Otitis media, Sinusitis
      • 💉 PCV13, PPSV23 vaccines
    • ⚫ Enterococcus faecalis/vimcinus
      • 🧪 Gut flora, Bile esculin +, PYR +, Grows in 6.5% NaCl
      • 🏥 UTI, Endocarditis, Abdominal infections
      • ⚠️ VRE: Vancomycin-resistant

  • 2.4 Gram Positive Bacilli 🟣

    • 🟤 Clostridium difficile
      • 💩 Pseudomembranous colitis (abx-associated), 🧪 Toxin A/B EIA
      • 💊 Vancomycin PO, Fidaxomicin
    • ⚫ Bacillus anthracis "Anthrax"
      • 🐑 Spores, 🩸 Non-hemolytic, 🧪 Medusa head colonies
      • 🏥 Cutaneous, GI, Pulmonary (Woolsorter's disease)
    • 🟣 Corynebacterium diphtheriae
      • ⚫ Gray pseudomembrane, 🧪 Tellurite agar (black colonies)
      • 💀 Diphtheria toxin → Myocarditis
    • 🟢 Listeria monocytogenes
      • 🥪 Cold enrichment, Tumbling motility at 25°C, Beta-hemolytic
      • 🏥 Pregnant women, neonates, elderly → Meningitis

  • 2.5 Gram Negative Cocci 🩷

    • 🔴 Neisseria gonorrhoeae
      • 🍆 Gonorrhea, Chocolate agar, Oxidase +, Gram - diplococci
      • 💊 Ceftriaxone + Azithromycin (resistance rising)
    • 🟣 Neisseria meningitidis
      • 🧠 Meningitis, Waterhouse-Friderichsen syndrome, Petechial rash
      • 💉 MenACWY, MenB vaccines

  • 2.6 Gram Negative Bacilli 🩷

    • Enterobacteriaceae 👥 (E. coli, Klebsiella, Proteus, Salmonella)
      • 🧪 MacConkey agar:
        • 🟣 Lactose fermenters: E. coli, Klebsiella (pink)
        • ⚪ Non-lactose: Salmonella, Shigella (colorless)
      • 🟣 E. coli: #1 UTI, Traveler's diarrhea (ETEC), HUS (O157:H7)
      • 🟣 Klebsiella: Currant jelly sputum, Alcoholics
      • 🟣 Salmonella: Typhoid (S. typhi), Gastroenteritis (S. enteritidis)
      • 🟣 Shigella: Bacillary dysentery, Shiga toxin
    • 🟢 Pseudomonas aeruginosa
      • 💚 Green pus, Sweet grape smell, UTI (catheters), Burn patients
      • 🧪 Pigment: Pyocyanin (blue), Pyoverdin (fluorescent)
    • 🔴 Haemophilus influenzae
      • 🍫 Chocolate agar, X&V factors, 💉 Hib vaccine
      • 🏥 Epiglottitis, Meningitis (pre-vaccine era)
    • 🟠 Legionella pneumophila
      • 🚰 Legionnaires' disease, Pontiac fever, Urine antigen
      • 💊 Levofloxacin, Azithromycin

  • 2.7 Anaerobes 😷

    • 🟤 Bacteroides fragilis: Abdominal infections, Penicillin resistant
    • ⚫ Clostridium perfringens: Gas gangrene, Food poisoning
    • 🦠 Actinomyces israelii: Sulfur granules, Cervicofacial

  • 2.8 Spirochetes 🌀

    • 🟣 Treponema pallidum: Syphilis
      • 1° Chancre, 2° Rash, 3° Gummas/Tabes dorsalis/Neurosyphilis
      • 🧪 VDRL/RPR (screen), FTA-ABS (confirm)
    • 🟢 Borrelia burgdorferi: Lyme disease (bull's eye rash)
    • 🟠 Leptospira: Weil's disease (rat urine)

  • 2.9 Acid-Fast Bacilli 🔴

    • 🟣 Mycobacterium tuberculosis
      • 🔬 Ziehl-Neelsen stain, Caseating granulomas, Night sweats
      • 🧪 AFB culture (6-8 weeks), Nucleic acid amplification
      • 💉 BCG vaccine (limited efficacy)

• 3. VIROLOGY 🧬

  • 3.1 DNA Viruses 🧬

    • 🟣 Herpesviruses (Enveloped, Latency):
      • 👄 HSV-1: Oral herpes
      • 🍆 HSV-2: Genital herpes
      • 🤒 VZV: Chickenpox → Shingles
      • 👁️ CMV: Retinitis (AIDS), Mono-like
      • 💋 EBV: Mono, Burkitt lymphoma
    • 🟢 Adenovirus: Conjunctivitis, Pneumonia, Gastroenteritis
    • 🟠 Poxvirus: Smallpox, Molluscum contagiosum
    • 🟣 HPV: Warts, Cervical cancer (16,18)
    • 🟣 Hepatitis B: Dane particle, HBsAg, Anti-HBc IgM

  • 3.2 RNA Viruses 🧬

    • 🔴 Orthomyxovirus: Influenza A/B/C → Antigenic drift/shift
    • 🟣 Paramyxovirus: Measles (Koplik spots), Mumps, RSV
    • 🟢 Picornavirus: Polio, Hep A, Rhinovirus, Enterovirus
    • 🟠 Flavivirus: Hep C, Dengue, Zika, Yellow fever
    • 🟣 Coronaviruses: SARS-CoV-2, MERS, Common cold
    • 🔴 Retroviruses: HIV (RT, CD4), HTLV (Adult T-cell leukemia)
    • 🟢 Togavirus: Rubella (congenital defects)

• 4. MYCOLOGY 🍄

  • 🟣 Candida albicans: Thrush, Vaginitis, Esophageal (HIV), Catheter lines
    • 🧪 Germ tube test, KOH prep (pseudohyphae)
  • ⚫ Cryptococcus neoformans: Meningitis (AIDS), India ink (halo), Antigen test
  • 🟤 Histoplasma capsulatum: Ohio/Mississippi valley, Bat/bird guano, Lung granulomas
  • 🟠 Coccidioides immitis: San Joaquin Valley fever, Desert rheumatism
  • 🟣 Blastomyces dermatitidis: Broad-based budding, Skin/lung
  • 🟢 Aspergillus fumigatus: Allergic bronchopulmonary, Invasive (neutropenic)
  • ⚫ Mucor/Rhizopus: Diabetics, Rhinocerebral, Angioinvasive

• 5. PARASITOLOGY 🐛

  • 5.1 Protozoa 🦠

    • 🩸 Plasmodium falciparum: Malaria (cerebral, Blackwater fever)
    • 💧 Giardia lamblia: Waterborne diarrhea, Stool antigen
    • 🫁 Entamoeba histolytica: Flask-shaped ulcers, Liver abscess
    • 🐱 Toxoplasma gondii: Cats, Ring-enhancing lesions (AIDS)
    • 🦟 Trypanosoma: African sleeping sickness (T. gambiense), Chagas (T. cruzi)

  • 5.2 Helminths 🪱

    • 🐍 Ascaris lumbricoides: Largest roundworm, Lung migration
    • 🐷 Trichinella spiralis: Undercooked pork, Periorbital edema
    • 🏊 Schistosoma: Swimmer's itch, Portal hypertension, Eggs in urine/stool

• 6. LABORATORY DIAGNOSIS 🧪

  • 6.1 Culture Media 🧫

    • 🩸 Blood agar: Most bacteria
    • 🟣 MacConkey: Gram - enteric (lactose pink)
    • 🍫 Chocolate agar: Haemophilus, Neisseria
    • 🟢 Sabouraud agar: Fungi
    • 🟤 Lowenstein-Jensen: Mycobacteria (egg-based)

  • 6.2 Stains 🔬

    • 💜🩷 Gram stain: Bacteria
    • 🔴 Acid-fast (Ziehl-Neelsen): TB, Nocardia
    • ⚫ India ink: Cryptococcus capsule
    • 🩸 Giemsa/Wright: Malaria, Borrelia

• 7. ANTIBIOTICS 💊

  • 7.1 Beta-Lactams 🛡️

    • 💜 Penicillins: Strep, Meningococcus
    • 🟣 Cephalosporins: 1st gen (Gram+), 3rd/4th (Gram-)
    • 🟢 Carbapenems: Broadest (ESBL, anaerobes)

• 8. HIGH-YIELD EXAM FACTS 🎯

  • Never miss:
    • 🟡 S. aureus = Surgical wounds, Endocarditis
    • 🟢 S. pneumoniae = Lobar pneumonia, Otitis
    • 🟣 E. coli = #1 UTI pathogen
    • 🟤 C. difficile = Abx diarrhea

🩺 UK-SPECIFIC ORGAN-SPECIFIC INFECTIONS & TREATMENT GUIDELINES 🏥

Based on NICE (NG250 for pneumonia, NG109/113 for UTI, NG141 for SSTI, NG240 for meningitis, NG199 for C. diff), BASHH for STIs, BSAC for endocarditis, and other UK sources like PHE/UKHSA. Always consult local guidelines, BNF, and specialists. Dates reflect latest updates as of 2025.

• 1. RESPIRATORY TRACT INFECTIONS 🌬️

  • 1.1 Community-Acquired Pneumonia (CAP) 🫁

    • Most Common Pathogens:
      • 🟢 S. pneumoniae (mainstay)
      • 🟣 Mycoplasma pneumoniae, Legionella, C. pneumoniae (atypicals)
      • 🟠 H. influenzae (esp. in COPD)
    • Assessment: Use CRB-65 score (NICE NG250). Score 0-1: Outpatient; 2: Hospital; ≥3: Urgent hospital.
    • Treatment (NICE NG250):
      • 🚶‍♂️ Low severity (outpatient): Amoxicillin 500mg TDS x 5 days (first-line). If atypical suspected or penicillin allergy: Doxycycline 200mg day 1, then 100mg OD x 4 days OR Clarithromycin 500mg BD x 5 days.
      • 🏥 High severity (hospital, non-ICU): Co-amoxiclav 1g TDS IV/PO + Clarithromycin 500mg BD. Switch to oral when stable.
      • 💉 Severe/ICU: Co-amoxiclav + Clarithromycin + consider adding Levofloxacin if Legionella risk. Add Corticosteroids (e.g., hydrocortisone) for high-severity.
    • Duration: 5 days; extend if not improving.

  • 1.2 Hospital-Acquired Pneumonia (HAP) 🎗️

    • Pathogens: Gram-negatives (Pseudomonas), MRSA.
    • Treatment (NICE NG139): Pip/taz 4.5g TDS IV OR Cefuroxime 1.5g TDS + Metronidazole if anaerobic risk. Add MRSA cover if needed (Vancomycin). Start within 1-4 hours.

  • 1.3 Pharyngitis/Tonsillitis 🤒

    • Group A Strep (Centor score ≥3): Phenoxymethylpenicillin (Pen V) 500mg QDS x 10 days (NICE). Allergy: Clarithromycin 250mg BD x 5 days.

• 2. URINARY TRACT INFECTIONS (UTI) 🚽

  • 2.1 Uncomplicated Lower UTI (Cystitis) 💧

    • #1 Pathogen: 🟣 E. coli.
    • Treatment (NICE NG109): Non-pregnant women: Nitrofurantoin 100mg BD x 3 days (first-line). Alternatives: Trimethoprim 200mg BD x 3 days (if resistance <20%). Pregnant women: Nitrofurantoin x 7 days (avoid 3rd trimester). Men: x 7 days.
    • Delay if mild: Back-up prescription with self-care advice.

  • 2.2 Acute Pyelonephritis 🩸

    • Treatment (NICE NG109): Ciprofloxacin 500mg BD x 7 days (avoid if resistance high; MHRA warnings). Alternatives: Co-amoxiclav 500/125mg TDS x 7-10 days OR Cefalexin 500mg QDS x 7-10 days.

  • 2.3 Catheter-Associated UTI 🩹

    • Treatment (NICE NG113): Only treat symptomatic. Ciprofloxacin 500mg BD x 7 days OR Co-amoxiclav. Remove/replace catheter.

• 3. SKIN & SOFT TISSUE INFECTIONS 🩹

  • 3.1 Cellulitis/Erysipelas 🟡

    • Pathogens: 🟡 S. aureus, 🔴 S. pyogenes.
    • Treatment (NICE NG141): Flucloxacillin 500mg QDS x 5-7 days (PO). Severe: IV 1-2g QDS. Allergy: Clarithromycin 500mg BD OR Clindamycin 300mg QDS.
    • MRSA risk: Clindamycin or Doxycycline.

  • 3.2 Abscess/Boil 🩸

    • I&D primary. Antibiotics if systemic symptoms: Flucloxacillin + Clindamycin for MRSA cover.

  • 3.3 Necrotizing Fasciitis ⚠️

    • Treatment: Urgent surgery + Clindamycin 600-900mg IV TDS (toxin suppression) + broad-spectrum (e.g., Pip/taz 4.5g TDS).

• 4. CENTRAL NERVOUS SYSTEM 🧠

  • 4.1 Bacterial Meningitis (Age-Based) 💉

    • Empiric (NICE NG240/UK JSSG): Give IV antibiotics ASAP (within 1 hour if sepsis). Ceftriaxone 2g BD (adults) + Dexamethasone 10mg IV QDS (before/with first dose, if pneumococcal suspected).
    • Neonates: Cefotaxime + Ampicillin (Listeria cover).
    • Children/Young Adults: Ceftriaxone (meningococcus/pneumococcus).
    • Adults >50/Elderly: Add Ampicillin 2g QDS for Listeria.
    • Duration: 7-14 days depending on organism.

  • 4.2 Brain Abscess 🩸

    • Treatment: Ceftriaxone 2g BD + Metronidazole 400mg TDS + consider Flucloxacillin. Surgery if needed.

• 5. GASTROINTESTINAL INFECTIONS 🤢

  • 5.1 Bacterial Diarrhea 🦠

    • Pathogen	Treatment (NICE/PHE)
      🟣 Salmonella (non-typhi)	Supportive (avoid abx unless severe)
      🟣 Shigella	Ciprofloxacin 500mg BD x 3 days
      🟤 C. difficile	Vancomycin 125mg QDS PO x 10 days (first-line, NICE NG199). Severe/recurrent: Fidaxomicin 200mg BD x 10 days. Stop offending abx.
      🟣 Campylobacter	Supportive; Azithromycin if severe

  • 5.2 Intra-abdominal Infections 🫀

    • Treatment: Pip/taz 4.5g TDS IV OR Ceftriaxone 2g OD + Metronidazole 400mg TDS.

• 6. SEXUALLY TRANSMITTED INFECTIONS 🍆

  • Disease	Pathogen	Treatment (BASHH 2023/2024)
    🦠 Gonorrhea	N. gonorrhoeae	Ceftriaxone 1g IM single dose + Azithromycin 2g PO single dose (or Doxycycline 100mg BD x 7d if macrolide allergy)
    🔴 Chlamydia	C. trachomatis	Doxycycline 100mg BD x 7 days (first-line) OR Azithromycin 1g single dose
    🟣 Syphilis	T. pallidum	Benzathine penicillin 2.4g IM (early); 3 doses weekly (late). Alternative: Doxycycline 100mg BD x 14/28 days
    🦠 Trichomoniasis	T. vaginalis	Metronidazole 400mg BD x 5-7 days OR 2g single dose

• 7. BONE & JOINT INFECTIONS 🦴

  • 7.1 Osteomyelitis 🦴

    • Empiric: Flucloxacillin 1-2g QDS IV (S. aureus cover). Add Clindamycin if MRSA.
    • Duration: 4-6 weeks total (IV 1-2 weeks, then oral switch if stable, per BSAC/BOA).
    • Children: Early OPAT consideration (BOAST).

  • 7.2 Septic Arthritis 💧

    • Treatment: Urgent aspiration/drainage + Flucloxacillin IV. Gonococcal: Ceftriaxone.
    • Duration: 2-4 weeks IV/PO.

• 8. ENDOCARDITIS ❤️

  • Organism	Treatment (BSAC/BNF)	Duration
    🟢 Viridans Strep (sensitive)	Benzylpenicillin 1.8g QDS IV	4 weeks
    🔴 S. aureus (MSSA)	Flucloxacillin 2g QDS IV	4-6 weeks
    🟡 S. aureus (MRSA)	Vancomycin IV (trough 10-20mg/L)	4-6 weeks
    ⚫ Enterococcus	Ampicillin 2g QDS + Gentamicin 1mg/kg TDS	4-6 weeks
    🟣 HACEK	Ceftriaxone 2g BD IV	4 weeks

  • Empiric: Vancomycin + Gentamicin + Flucloxacillin or Piperacillin/tazobactam.

• 9. HIGH-YIELD EMERGENCY ANTIBIOTICS 🎯

  • Neutropenic Fever: Pip/taz 4.5g TDS IV (or Ceftazidime).
  • Meningitis (empiric): Ceftriaxone 2g BD IV + Dexamethasone.
  • Sepsis (empiric): Pip/taz + Gentamicin (NICE sepsis bundle).
  • Bite wounds: Co-amoxiclav 500/125mg TDS x 5 days (NICE NG184).
  • Catheters: Vancomycin + remove device.

• 10. RESISTANCE PATTERNS ⚠️

  • MRSA: Vancomycin, Daptomycin, Linezolid.
  • VRE: Linezolid, Daptomycin.
  • ESBL: Carbapenems (e.g., Ertapenem).
  • Pseudomonas: Dual therapy e.g., Ceftazidime + Ciprofloxacin.

**🩺 KEY TAKEAWAYS FOR UK EXAMS (PLAB/MRCP):** - **NICE emphasis: Antimicrobial stewardship, short courses, local resistance data. - **MRSA/Pseudomonas: Risk assess (hospitalisation, ICU). - **Sepsis: Within 1 hour antibiotics (NICE NG51). - **Prophylaxis: No routine for IE (NICE CG64); focus on hygiene. - **Always: Source control + de-escalate based on cultures. Consult BNF for doses.