AMSS Teaching Series ID Alyssa Pradhan What are

  • Slides: 36
Download presentation
AMSS Teaching Series: ID Alyssa Pradhan

AMSS Teaching Series: ID Alyssa Pradhan

What are we talking about? • Bacteria • Basic approach to micro • Guide

What are we talking about? • Bacteria • Basic approach to micro • Guide for organism v infection • Antibiotics • How do they work? • How do you pick? • Other • Viruses (very brief) • Fungi • Not covering – TB, immunosuppression, paediatrics Traditio | Spiritus | Gaudium

Basic Microbiology Definitions Bacteria? • Single celled organism • Prokaryote – cell wall but

Basic Microbiology Definitions Bacteria? • Single celled organism • Prokaryote – cell wall but no defined organelles, nucleus Virus? • “Obligate intracellular parasite” – needs to hijack another cells organelles to reproduce, doesn’t survive without a host Fungus? • Eukaryotic organisms, take yeast and mold form Parasites? • Organism that lives in / on another organism, damaging the host in the process Traditio | Spiritus | Gaudium

Basic Microbiology Bacterial structure Bacterial cell wall • Gram positive • Inner cytoplasmic membrane

Basic Microbiology Bacterial structure Bacterial cell wall • Gram positive • Inner cytoplasmic membrane • Outer, thick peptidoglycan layer • Gram negative • Inner cytoplasmic membrane • Thin peptidoglycan layer (5 -10% peptidoglycan) • Outer membrane with lipopolysaccharide (contains endotoxin) • Cytoplasm – contains chromosomes, ribosomes etc • Extra goodies – pili / fimbriae, flagella, capsule Traditio | Spiritus | Gaudium

Basic Microbiology • How to classify bacteria? • Shape of the bacteria • Gram

Basic Microbiology • How to classify bacteria? • Shape of the bacteria • Gram positive / negative • Other tests – aerobic / anaerobic, haemolysis, coagulase Traditio | Spiritus | Gaudium

Basic Microbiology What are Gram Stains? • Test relies on the difference in the

Basic Microbiology What are Gram Stains? • Test relies on the difference in the cell wall between bacteria • Heat -> crystal violet -> wash -> iodine -> wash -> alcohol -> wash -> safranin -> wash • Gram positive – cell wall holds the crystal violet, appear dark • Gram negative – cell wall does not hold the violet, counter stained with safranin, appear red Clinical relevance? • Helps determine the shape and features of the bacteria • Also determines behaviour – gram positive think peptidoglycan layer doesn’t block diffusion, easier for antibiotics to penetrate Traditio | Spiritus | Gaudium

Basic Microbiology Gram Stains & Shapes Shape Gram Positive Gram Negative Cocci Streptococcus Staphylococcus

Basic Microbiology Gram Stains & Shapes Shape Gram Positive Gram Negative Cocci Streptococcus Staphylococcus Neisseria Rods Corynebacterium Listeria Bacillus Clostridium Mycobacteria Enterics – E. Coli, Shigella, Salmonella, Yersinia, Klebsiella, Proteus, Enterobacter, Serratia, Vibrio, Campylobacter, Helicobacter, Pseudomonas Bacteriodes Haemophilus Bordetella Legionella Other – Brucella, Pasteurella, Gardnerella Traditio | Spiritus | Gaudium

Basic Microbiology Gram Stains & Shapes Shape Gram Positive Gram Negative Spirochetes Filamentous branching

Basic Microbiology Gram Stains & Shapes Shape Gram Positive Gram Negative Spirochetes Filamentous branching Pleomorphic No cell wall Treponema, Borrelia, Leptospira Actinomyces, Nocardia Chlamydia, Rickettsiae Mycoplasma Traditio | Spiritus | Gaudium

Basic Microbiology Relationship with oxygen • Obligate aerobes – need oxygen to live •

Basic Microbiology Relationship with oxygen • Obligate aerobes – need oxygen to live • Facultative anaerobes – prefer oxygen but can live without • Microaerophilic – can tolerate low amounts of oxygen • Obligate anaerobes – cannot live in the presence of oxygen • Other tests • Lactase • Coagulase • Haemolysis Traditio | Spiritus | Gaudium

Basic Microbiology Relationship with oxygen Obligate aerobes Facultative anaerobes Microaerophilic Obligate anaerobes Gram positive

Basic Microbiology Relationship with oxygen Obligate aerobes Facultative anaerobes Microaerophilic Obligate anaerobes Gram positive Nocardia Bacillus cereus Staphylococcus, B. anthracis, Corynebacterium, Listeria, Actinomyces Streptococcus Clostridium Gram negative Neisseria Pseudomonas Bordetella, Legionella, Brucella Most other gram negative rods Spirochetes Campylobacter Bacteriodes Acid-fast Mycobacterium No cell wall Mycoplasma Traditio | Spiritus | Gaudium

Bacteria by system General rules • Aerobic bacteria – places with air! • Respiratory

Bacteria by system General rules • Aerobic bacteria – places with air! • Respiratory – lungs, ears, nose, throat, neuro • Skin, exposed wounds / bones • Anaerobic bacteria – places without air! • Gastrointestinal tract • Urogenital tract Traditio | Spiritus | Gaudium

Bacteria by system Site Normal flora Less common but relevant Blood, organs Hopefully none

Bacteria by system Site Normal flora Less common but relevant Blood, organs Hopefully none Skin, outer ear Staph. epidermis S. aureus, diptheroids, strep, anaerobes, yeasts Nose Staph. aureus S. epidermis, diptheroids, misc strep. Oropharynx Viridans streptococci Misc strep. , non-pathogenic Neisseria, H. influenzae, Candida Stomach None Rest of GIT Gram negative rods Enterococcus / other strep, Escheria, Prevotella, Lactobacillus Vagina Lactobacillus Misc strep. , gram negative rods, diptheroids, yeast, Veillonella Traditio | Spiritus | Gaudium

Bacteria by system How to approach an infection • Is it usually sterile? •

Bacteria by system How to approach an infection • Is it usually sterile? • Yes – urinary / kidneys / male genital tract, blood stream, neurological system, internal organs (lungs, pleura, peritoneum, deep tissue) • No – whole GIT, lower female genital tract, upper respiratory system, skin • What is normally there? • Where could the bacteria come from? • Other clinical factors for infection? • Anatomical predisposition • Immune compromise – cancer, diabetes, immunosuppression (long term steroids, HIV) • Age • Random behaviours Traditio | Spiritus | Gaudium

Fun interactive Qs! Where did this bacteria come from? • Cut on skin –

Fun interactive Qs! Where did this bacteria come from? • Cut on skin – gram positive cocci • UTI – gram negative rods • Meningitis – upper airways • Cholangitis –gram negative rods, anaerobes • Pneumonia – upper airways, blood stream Traditio | Spiritus | Gaudium

Bacteria by system Infections Common Pathogens Endocarditis • Viridans strep. , Co. NS, S.

Bacteria by system Infections Common Pathogens Endocarditis • Viridans strep. , Co. NS, S. aureus, Enterococcus Respiratory Otitis externa • P. aeruginosa Otitis media • S. pneumoniae, H. influenzae Tonsilitis • Group A strep Sinusitis • S. pneumoniae, M. catarrhalis, H. influenzae CAP • Strep. pneumoniae, M. catarrhalis, H. influenzae, S. aureus, GAS Atypical • Mycoplasma pneumoniae, Chlamydophila pneumoniae, Legionella Nosocomial • Enteric GNB, P. aeruginosa, S. aureus (MRSA) Traditio | Spiritus | Gaudium

Bacteria by system Infections Common Pathogens Urogenital Cystitis /Pyelonephritis • E. Coli, Pseudomonas aeruginosa,

Bacteria by system Infections Common Pathogens Urogenital Cystitis /Pyelonephritis • E. Coli, Pseudomonas aeruginosa, enterococcus species, Klebsiella, Proteus mirabilis (associated with kidney stones), Staph aureus = bacteraemia Cervicitis / urethritis • Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma Gastrointestinal Toxin • B. cereus (emetic / diarrhoeal), S. aureus Watery • V. cholerae, ETEC, Salmonella species Dysentry • EHEC (or STEC), EIEC, Salmonella species, Shigella, Yersinia Non-bacterial • Norovirus, rotavirus, Giardia, Cryptosporidium, Entamoeba Traditio | Spiritus | Gaudium

Bacteria by system Infections Common Pathogens Skin / soft tissue Cellulitis / impetigo •

Bacteria by system Infections Common Pathogens Skin / soft tissue Cellulitis / impetigo • Staph aureus, Streptococcus pyogenes Necrotising fasciitis • Polymicrobial – aerobes / anaerobes (S. aureus, Bacteriodes, Enterobacteriaceae) Septic arthritis • N. gonorrhoeae, S. aureus, strep, gram negative (sepsis), S. pneumoniae + K. kingae (children), Co. NS (prosthetic joints) Osteomyelitis • S. aureus Meningitis • S. pneumoniae, N. meningitidis, L. monocytogenes, in children (GBS, E. Coli, S. pneumoniae) Traditio | Spiritus | Gaudium

Fun interactive Qs • 54 year old patient with a history of alcohol abuse

Fun interactive Qs • 54 year old patient with a history of alcohol abuse presents with productive cough, fever, chest pain, what is the likely groups of causative organisms? Mixed anaerobes! Traditio | Spiritus | Gaudium

Fun interactive Qs • 22 year old woman with history of congenital heart disease

Fun interactive Qs • 22 year old woman with history of congenital heart disease presents with a new murmur, chest pain, shortness of breath, fever. Went to the dentist last week. Likely causative organism? Oral flora – Viridans strep Traditio | Spiritus | Gaudium

Fun interactive Qs • 68 year old patient recovering from pneumonia gets profuse, watery

Fun interactive Qs • 68 year old patient recovering from pneumonia gets profuse, watery diarrhoea on the 5 th day of her hospital admission. Likely causative organism? Clostridium difficile Traditio | Spiritus | Gaudium

Common associations (stereotypes) • • • Migrant – TB, HBV Cat scratch – Bartonella

Common associations (stereotypes) • • • Migrant – TB, HBV Cat scratch – Bartonella henslae Bird-keeping – Chlamydia pscitticosis Abattoir worker – Q fever Institutionalised / young person - Mycoplasma Old air conditioner / dodgy water storage - Legionella Alcoholic / aspiration – Mixed anaerobes Renal stones – Proteus mirabilus IVDU – Staph in the right heart / lungs, HIV, HCV Swimmers ear - Pseudomonas Sickle cell patient with bone pain - Salmonella Traditio | Spiritus | Gaudium

Antibiotics • General approach • TAKE CULTURES • Start with broad spectrum to cover

Antibiotics • General approach • TAKE CULTURES • Start with broad spectrum to cover likely organisms • Narrow antibiotic choice to cover cultured organisms • Main groups • Cell wall inhibitors – penicillins, cephalosporins, carbapenems, glycopeptides • Protein synthesis inhibitors (50 S ribosomes) – macrolides, lincosamides • Protein synthesis inhibitors (30 S ribosomes) – aminoglycosides, tetracyclines • Anti-metabolites – TMP/SMX, nitrofurantoin • Topoisomerase inhibitors – fluoroquinolones Traditio | Spiritus | Gaudium

Antibiotics Cell wall inhibitors • Examples: Penicillins, cephalosporins, carbapenems, glycopeptides • Mechanism: B-lactam inhibits

Antibiotics Cell wall inhibitors • Examples: Penicillins, cephalosporins, carbapenems, glycopeptides • Mechanism: B-lactam inhibits cell wall synthesis (+/- B-lactamase inhibitor) • Coverage: • Penicillins - good gram +, enterococcus, syphilis • Cephalosporins – broader coverage, 5 generations • Carbapenems – broad spectrum (less MRSA) • Vancomycin – MRSA • SEs: allergy (immediate and delayed), diarrhoea • Vancomycin – Red Man Syndrome, nephro- and otoxicity Traditio | Spiritus | Gaudium

Antibiotics Penicillins • Benzylpenecillin (penicillin G), procaine penicillin Narrow + antistaphylococcal • Dicloxacillin, flucloxacillin

Antibiotics Penicillins • Benzylpenecillin (penicillin G), procaine penicillin Narrow + antistaphylococcal • Dicloxacillin, flucloxacillin • Amoxycillin, ampicillin Moderate • Amoxicillin + clavulanate Broad • Pipericillin + tazobactam Broad + antipseduomonal Traditio | Spiritus | Gaudium

Antibiotics Cephalosporins • Cefaplexin, cephazolin Moderate • Cefuroxime, cefaclor Moderate + anti-Haemophilus • Cefoxitin

Antibiotics Cephalosporins • Cefaplexin, cephazolin Moderate • Cefuroxime, cefaclor Moderate + anti-Haemophilus • Cefoxitin Moderate + antianaerobic • Cefotaxime, ceftriaxone Broad • Ceftazidime, cefepime Broad + antipseduomonal • Ceftaroline Broad + anti-MRSA Traditio | Spiritus | Gaudium

Antibiotics Protein synthesis – 50 S • Examples: Macrolides (erythromycin, clarithromycin, azithromycin) lincosamides (clindamycin,

Antibiotics Protein synthesis – 50 S • Examples: Macrolides (erythromycin, clarithromycin, azithromycin) lincosamides (clindamycin, linezolid) • Mechanism: Bind to 50 S subunit -> impair ribosomal function • Coverage: Gram + (not enterococcus), Gram – and atypicals • Uses: • Atypicals – chest infections, Chlamydia, skin / soft tissue • Linezolid – MRSA, VRE • SEs: • Macrolides – GI upset, acute cholestatic hepatitis, QT • Clindamycin – pseudomembranous colitis, GI upset Traditio | Spiritus | Gaudium

Antibiotics Protein synthesis – 30 S • Examples: Aminoglycosides (gentamicin, tobramycin), tetracyclines (doxycycline, tigecycline)

Antibiotics Protein synthesis – 30 S • Examples: Aminoglycosides (gentamicin, tobramycin), tetracyclines (doxycycline, tigecycline) • Mechanism: Bind to 30 S subunit -> impair ribosomal function • Coverage: • Gentamicin - gram -, including pseudomonas • Tetracyclines – Gram +, anaerobes, atypicals • SEs: • Aminoglycosides – ototoxicity / vestibular toxicity (irreversible), nephrotoxicity (reversible) • Tetracyclines – GI upset, hepatotoxicity, photosensitivity, teratogenic, teeth discoloration Traditio | Spiritus | Gaudium

Antibiotics Anti-metabolites • Examples: Trimethoprim-sulfamethoxazole, nitrofurantoin • Mechanism: Inhibit folic acid pathway, inhibit ribosomal

Antibiotics Anti-metabolites • Examples: Trimethoprim-sulfamethoxazole, nitrofurantoin • Mechanism: Inhibit folic acid pathway, inhibit ribosomal synth • Coverage: Gram + (inc. MRSA), Enteric gram • Uses: UTI, RTI, GI infection, skin / soft tissue, PCP proph • SEs: Hepatitis, SJS, bone marrow suppression, drug toxicity Traditio | Spiritus | Gaudium

Antibiotics Topoisomerase Inhibitors • Examples: Fluoroquinolones • Mechanism: Inhibits DNA gyrase -> inhibits replication

Antibiotics Topoisomerase Inhibitors • Examples: Fluoroquinolones • Mechanism: Inhibits DNA gyrase -> inhibits replication • Coverage: Poor Gram + cover, good for gram – (including pseudomonas) • Uses: UTI, bone / joint / skin / soft tissue / sepsis • SEs: Seizures, QT, allergy Traditio | Spiritus | Gaudium

Antibiotics Common Infection Causative Organism? Antibiotic Choice? Sepsis Lots Flucloxacillin + gentamicin Meningitis Gram

Antibiotics Common Infection Causative Organism? Antibiotic Choice? Sepsis Lots Flucloxacillin + gentamicin Meningitis Gram positive cocci, Neisseria Benzylpenicillin + ceftriaxone +/vancomycin Sinusitis, OM Gram positive cocci Amoxycillin + clavulanate* Strep throat Streptococcus pyogenes Penicillin V Cellulitis Gram positive cocci Flucloxacillin MRSA Vancomycin Acute cystitis Gram negative bacilli Trimethoprim Perforated viscus Anaerobes, everything Gentamicin + amoxycillin + metronidazole Endocarditis (native) Broad spectrum +/- MRSA Gentamicin, benpen, fluclox / vanc Traditio | Spiritus | Gaudium

Virology • Obligate intracellular pathogens • Structural basics • Nucleic acid – RNA or

Virology • Obligate intracellular pathogens • Structural basics • Nucleic acid – RNA or DNA, single or double standard • Capsid • Extras • Envelope • Surface proteins Traditio | Spiritus | Gaudium

Virology Viruses to know Virus Clinical Syndrome RSV, rhino Common cold Adeno, noro, rota

Virology Viruses to know Virus Clinical Syndrome RSV, rhino Common cold Adeno, noro, rota Gastro Influenza Flu HSV-1 Genital and oral herpes HSV-2 VZV Chickenpox, shingles CMV Retinitis, colitis, general CMV HPV Genital warts, cervical dysplasia / cancer Traditio | Spiritus | Gaudium

Virology Viruses to know Virus Clinical Syndrome Hepatitis A Hepatitis – acute, chronic, cirrhosis

Virology Viruses to know Virus Clinical Syndrome Hepatitis A Hepatitis – acute, chronic, cirrhosis Hepatitis B Hepatitis C HIV / AIDS Measles Mumps Rubella Polio Traditio | Spiritus | Gaudium

Fungi • What are fungi? • Eukaryotic organisms – can exist in yeast or

Fungi • What are fungi? • Eukaryotic organisms – can exist in yeast or mold form • Main clinical picture • Usually occur in immunocompromised hosts – HIV / AIDS, cancer, long term steroid use, diabetic, prolonged hospitalisation (after +++ antibiotics) • Often present after local bacteria have been irradiated • Can be acutely unwell but often more chronic Traditio | Spiritus | Gaudium

Fungi • Common / medically relevant fungi • Candida • Aspergillosis • Other –

Fungi • Common / medically relevant fungi • Candida • Aspergillosis • Other – mucormycosis, cryptococcus, PCP • How to treat? • -azoles ie. Fluconazole, clotrimazole • Nystatin – topical as too toxic for systemic use • Amphotericin B Traditio | Spiritus | Gaudium

Sources • • Clinically Microbiology Made Ridiculously Easy Kaplan Immunology and Microbiology First Aid

Sources • • Clinically Microbiology Made Ridiculously Easy Kaplan Immunology and Microbiology First Aid for USMLE Step 1 Electronic Therapeutic Guidelines Traditio | Spiritus | Gaudium