Microbiology Bootcamp.com

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TABLE OF CONTENTS

Microbiology

1.

Fundamentals of Bacteriology

2.

Bacterial Genetics

3.

Bacterial Toxins

4.

Staphylococcus

5.

Streptococcus

6.

Enterococcus and Bacillus

7.

Clostridium

8.

Mycobacteria

9.

Non-Spore Forming Gram Positive Bacilli

10.

Lactose Fermenting Gram Negative Bacilli

11.

Non-lactose Fermenting Gram Negative Bacilli

12.

Gram Negative Curved Rods

13.

Gram Negative Diplococci

14.

Gram Negative Coccobacilli

15.

Spirochetes

TABLE OF CONTENTS

Microbiology

16.

Atypical Bacteria

17.

Dimorphic Mycosis

18.

Opportunistic Mycosis

19.

Tinea

20.

Gastrointestinal Protozoa

21.

Systemic Protozoa

22.

Nematodes

23.

Cestodes

24.

Trematodes

25.

Ectoparasites

26.

Approach to Virology

27.

Basics of Virology

28.

Cardiorespiratory Infections

29.

Infectious Neuropathology

30.

Infectious Dermatologic Disease

31.

Opportunistic Infections

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TABLE OF CONTENTS

Microbiology

32.

Antibiotics

33.

Antifungals

OUTLINE 1.

Microbiology: Fundamentals of Bacteriology

2.

Structural Bacterial Envelope A. Cell Wall B. Outer Membrane C. Lipopolysaccharide D. Lipooligosaccharide E. Lipoteichoic Acid F. Periplasm G. Inner Membrane H. Capsule Bacterial Adherence and Motility A. Flagellum B. Pilus C. Endospore D. Glycocalyx E. Biofilm Bacterial Form and Function A. Bacterial Morphology B. Intracellular Bacteria C. Anaerobic Bacteria D. Aerobic Bacteria E. Respiratory Burst Gram Stain and Variant Staining A. Process B. Poor Staining on Gram Stain C. Variant Staining

AfraTafreeh.com 3.

4.

5.

Bacterial Cultures A. MacConkey Agar B. Eosin Methylene Blue Agar C. Chocolate Blood Agar D. Sheep Blood Agar E. Eaton Agar F. Regan-Lowe, Bordet-Gengou Agar G. Cystine-Tellurite Agar H. Lӧffler Medium I. Charcoal Yeast Extract Agar J. Lӧwenstein-Jensen Agar K. Middlebrook Agar L. Mannitol Salt Agar M. Thiosulfate Citrate Bile Salt Sucrose Agar N. Bile Esculin Agar O. Sabouraud Agar

Microbiology: Fundamentals of Bacteriology

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Cell Wall: • Peptidoglycan: Peptides crosslinked by transpeptidase • N-acetylmuramic Acid (NAM), N-acetylglucosamine (NAG): Carbohydrate • Lipoteichoic Acid: (Gram + only) • Mycolic Acid: (Acid fast only) • ↑ Structural integrity • Thick à Gram +, Thin à Gram Outer Membrane: • Outer layer: Lipooligosaccharide (LOS), Lipopolysaccharide (LPS) • Inner layer: Phospholipids • Gram - only Lipopolysaccharide (LPS): • O-antigen: Outer domain, target for host antibodies (TLR4, CD14) • Core domain: Linked between O-antigen and lipid A • Lipid A: Phosphorylated glucosamine disaccharide w/ fatty acids, toxicity to host à Septic shock Lipooligosaccharide (LOS): • Similar to LPS, absence of O-antigen • Neisseria and Haemophilus Lipoteichoic Acid: • Anchored to inner membrane, target for host antibodies (TLR2) Periplasm: • Space between outer and inner membrane • Peptidoglycan and β-lactamase Inner (Cytoplasmic) Membrane: • Phospholipid bilayer à Hydrophobic layer • Penicillin-binding proteins • Enzymes à Essential for bacterial cell function Capsule: • Polysaccharide layer à Hydrophilic layer • Protects against complement-mediated destruction and phagocytosis • S. pneumoniae, Staphylococcus aureus, Neisseria meningitidis, Haemophilus influenza type b, E. coli, Pseudomonas aeruginosa, Salmonella, Klebsiella • Poly-D-glutamate capsule in Bacillus anthracis

Microbiology: Fundamentals of Bacteriology

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Flagellum: • Motility Pilus: • Adhesion to host cells or other bacteria à Neisseria, E. coli • Sex Pilus à Connects 2 bacteria à F-factor transmission during conjugation Endospore: • Protective layer surrounding spore à Protects against desiccation, radiation, temperature, and chemical damage • Core à DNA, Dipicolinic acid • Formed during stress (↓ Nutrient availability) à Metabolically inactive • Bacillus, Clostridium Glycocalyx: • “Slime layer” • Adhesion to foreign surfaces or host cells Biofilm: • Aggregation of bacteria, “stuck” together and/or to a surface • Slimy extracellular matrix composed of extracellular polymeric substances • Grouped protection from clearing mechanisms • “Seeding” into systemic circulation • S. epidermidis à Catheters and prosthetics (foreign body) • Pseudomonas aeruginosa à Respiratory (VAP), contact lenses • Nontypeable H. influenzae à Middle ear (AOM) • Viridans streptococci à Native heart valves, dentition

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Microbiology: Fundamentals of Bacteriology

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Bacteria Morphology: • Bacilli: Rod-shaped • Cocci: Sphere-shaped • Coccobacilli: Combination of rod-sphere-shape • Spirochete: Spiral-shaped Intracellular Bacteria: • Obligate: Unable to generate ATP independent of host à Chlamydia, Rickettsia, Coxiella • Facultative: Able to generate ATP independent of host à Mycobacterium, Listeria, Legionella, Yersinia, Neisseria, Salmonella, Brucella, Francisella Anaerobic Bacteria: • Obligate: Unable to grow in presence of oxygen à Gut flora à Bacteroides, Clostridium, Actinomyces • Facultative: Able to grow in presence and absence of oxygen à Staphylococcus, Streptococcus, Bacillus cereus Aerobic Bacteria: • Only able to grow in the presence of oxygen à Pseudomonas, Mycobacterium, Bordetella, Nocardia Respiratory Burst: • Oxidative burst pathway à Generates reactive oxygen species (ROS) à Destroy pathogens w/in phagolysosomes • NADPH Oxidase: O2 + NADPH à O2-ᐧ + NADP+ • Superoxide Dismutase: 2ᐧO2- à H2O2 • Myeloperoxidase: H2O2 + Cl- à HOClᐧ • Chronic granulomatous disease à ↑ Risk for catalase + pathogen infection • Pseudomonas aeruginosa à Pyocyanin à Generates ROS à Destroy competing pathogens

Microbiology: Fundamentals of Bacteriology

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Process: • Preparation: Begin with heat-fixed smear of bacteria • Crystal dye stain: Peptidoglycan retains the violet-blue color • Iodine: “Fixes” the crystal violet dye (Prevents easy removal) • Acetone or ethanol: Decolorizer (Wash out of dye) • Safranin: Counterstain Poor Staining on Gram Stain: • No cell wall à Mycoplasma, Ureaplasma • ↓↓↓ Cell wall thickness à Leptospira • ↑ Lipid content/Mycolic acid à Mycobacteria • ↓ Peptidoglycan à Chlamydia • ↓ Lipopolysaccharide à Treponema • Intracellular à Poor staining à Legionella, Rickettsia, Bartonella, Anaplasma, Ehrlichia • Bipolar staining (“closed safety pin”), classic on Giemsa stainà Yersinia enterocolitica Variant Staining: • Carbol fuchsin (Ziehl-Neelsen stain): ↑ Affinity for mycolic acid, stains red à Mycobacteria, Nocardia, Cryptosporidium • Auramine-rhodamine stain: ↑ Affinity for mycolic acid, yellow-red fluorescence à Mycobacteria, Nocardia, Cryptosporidium • Giemsa stain: Chlamydia, Histoplasma, “Owl-eye” inclusions (CMV), Parasites (Trypanosoma, Plasmodium) • Periodic acid-Schiff (PAS): Stains glycogen red, Fungi, parasites, Whipple disease, Glycogen storage diseases, ⍺1AT def. • Silver stain: Legionella, Bartonella, H. pylori, Fungi • India ink: Stains capsule light on dark background (halo), Cryptococcus neoformans • Mucicarmine stain: Stains capsule bright red, Cryptococcus neoformans, Blastomyces, Coccidioides • Dark-field microscopy: Treponema

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Microbiology: Fundamentals of Bacteriology

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MacConkey Agar: • E.coli, Klebsiella, Enterobacter, Citrobacter, Serratia à Pink/red colonies • Non-lactose fermenters à Colorless • Sorbitol-MacConkey Agar à Selective: E. coli O157:H7 does not turn pink/red Eosin Methylene Blue Agar: • E. coli à Green sheen colonies • Klebsiella, Serratia à Purple/black colonies (Enterobacter and Citrobacter can be variable) • Non-lactose fermenters à Colorless Chocolate Blood Agar: • Contains lysed red blood cells (not the same as blood agar) • Contains Factor V (NAD+), X (hematin) • Haemophilus influenzae, Neisseria • Thayer Martin Media: Vancomycin, Trimethoprim, Colistin, Nystatin à Selective: Neisseria Sheep Blood Agar: • ⍺-hemolysis: Partial hemoglobin oxidation à Biliverdin/green hemolysis; Streptococcus pneumoniae, Viridans streptococci • β-hemolysis: Complete hemoglobin breakdown à Translucency peripheral to bacteria; Staph aureus, Strep pyogenes, Strep agalactiae, E. coli, Listeria • Ɣ-hemolysis: No hemolysis occurs à Agar unchanged peripheral to bacteria • Haemophilus influenzae does not grow à Satellite phenomenon with hemolytic bacteria cross-streaking (S. aureus) Eaton Agar: Mycoplasma pneumonia Regan-Lowe Medium, Bordet-Gengou Agar: Bordetella pertussis Cystine-Tellurite Agar: Corynebacterium diphtheriae à Black colonies with brown halo Lӧffler Medium: Corynebacterium diphtheriae à Add methylene blue à Dark-blue metachromatic granules Charcoal Yeast Extract Agar: Legionella pneumophila, Francisella, Nocardia Lӧwenstein-Jensen Agar: Mycobacterium tuberculosis Middlebrook Agar: Mycobacterium tuberculosis Mannitol Salt Agar: Staphylococcus, Enterococcus; Most species will remain the color of the medium, S. aureus à golden/yellow colonies Thiosulfate Citrate Bile Salts Sucrose Agar: Vibrio species; V. cholerae à yellow colonies, V. parahaemolyticus à green colonies Bile Esculin Agar: Enterococcus species, Streptococcus bovis Sabouraud Agar: Fungi

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Item 1 of 1 Question ID: 0072

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A researcher is attempting to identify an unknown bacterial organism that may be implicated in an outbreak of diarrheal illness in the Northeast region of the United States. Samples collected from affected patients reveal the bacteria is a gram-positive bacillus. The researcher then attempts to grow colonies of the unknown bacteria on sheep blood agar and perform a cross-streaking method with Haemophilus influenzae. Satellite growth was observed peripheral to the growth of the unknown bacteria. Further analysis reveals that the unknown bacteria was able to replicate within and outside of host cells and is not encapsulated. Which of the following most resembles the pathogen causing the diarrheal outbreak?

AfraTafreeh.com ⚪ A. Vibrio cholerae ⚪ B. Mycobacterium tuberculosis ⚪ C. Staphylococcus aureus ⚪ D. Bacillus anthracis ⚪ E. Listeria monocytogenes

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Microbiology: Bacterial Genetics

2.

3.

4.

5.

DNA Structures and Genetic Material Exchange A. Vertical Gene Transfer B. Horizontal Gene Transfer C. DNA Structures Transformation A. Mechanism B. Classic Bacteria Demonstrating Competence C. Considerations Conjugation A. Mechanism B. High Frequency Recombination C. Considerations D. Aerobic Bacteria E. Respiratory Burst Transduction A. Generalized Transduction B. Specialized Transduction C. Considerations Transposition A. Transposons B. Considerations

Microbiology: Bacterial Genetics

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Vertical Gene Transfer: • Exchange of genetic material from parent to offspring • Random Mutations à Slow, ↑ Virulence • Antigenic Variation à Fast, ↑ Virulence Horizontal Gene Transfer: • Exchange of genetic material not from parent to offspring • Transformation • Conjugation • Transduction • Transposition DNA Structures: • Chromosome: Contains chromosomal DNA • Plasmid: Nonchromosomal DNA, replicates independently, contains genes for antibiotic resistance and toxins • Bacteriophage: Viruses that infect bacteria (Lytic, Lysogenic) • Transposon: DNA sequence, cannot replicate independently, “jumps” between plasmid ßà chromosome ßà bacteriophage

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Microbiology: Bacterial Genetics

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Mechanism: • Donor bacteria releases free segments of DNA to environment • Free DNA (chromosomal or plasmid) segment from environment combines with recipient DNA • New gene expression in recipient bacteria Classic Bacteria Demonstrating Competence: • Neisseria • Haemophilus influenzae type b • Streptococcus pneumoniae Considerations: • Non-competent bacteria will generally not be able to uptake bacterial DNA • Deoxyribonuclease breaks down free DNA à Inhibits transformation

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Microbiology: Bacterial Genetics

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Mechanism: • F factor plasmid within donor • Donor (F+) bacteria contains genes for sex pilus • Donor (F+) completely transfers plasmid DNA fragment to recipient (F-) via sex pilus • Recipient plasmid is self-transmissible • Single plasmid strand transferred (No chromosomal DNA) à Plasmids create complementary strands • Results in both donor (F+) and recipient (F+) High Frequency Recombination (Hfr): • F factor integrated into donor (Hfr) chromosomal DNA • Hfr donor incompletely transfers plasmid DNA fragment to recipient (F-) via sex pilus • Recipient plasmid is not self-transmissible • Results in a Hfr donor and recipient (F-) Considerations: • Antibiotic resistance

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Microbiology: Bacterial Genetics

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Generalized Transduction (Lytic): • Bacteriophage infects donor bacterium à Injects bacteriophage DNA à Replication of bacteriophage DNA • Bacteriophage progeny form with phage capsids à Some progeny mistakenly carry donor DNA (“packaging error”) • Donor bacterium cell lysis and release of bacteriophage progeny • Bacteriophage with donor DNA infects recipient bacteria à Transfers donor bacterial DNA Specialized Transduction (Lysogenic): • Bacteriophage infects donor bacterium à Injects bacteriophage DNA à Bacteriophage DNA incorporates into donor DNA (at specific location) • Bacteriophage DNA remains in an inactive state à Eventually activated à Replication of bacteriophage DNA • Bacteriophage progeny form with phage capsids • Bacteriophage DNA is excised with flanking bacterial DNA regions to be carried by progeny • Donor bacterium cell lysis and release of bacteriophage progeny • Bacteriophage with donor DNA infects recipient bacteria à Transfers donor bacterial DNA Considerations: • Specialized à Encoding bacterial toxins à Botulinum, Cholera, Diphtheria, Erythrogenic, Shiga

Microbiology: Bacterial Genetics

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Transposons: • Genes that “jump” across plasmid, bacterial chromosome, bacteriophage DNA • Excised from one location à Re-inserted into new location à Genetic diversity and variable expression of genes Considerations: • Antibiotic resistance (genetic diversity among plasmids with antibiotic resistance genes) à vanA gene • Plasmids containing multiple antibiotic resistance genes

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Question ID: 0073

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A group of researchers identify unique changes in pathogenic virulence among two strains of Streptococcus pneumoniae. Strain 1 is referred to as cap08 and is known to be virulent. Strain 2 is referred to as uncap08 and is known to be nonvirulent. cap08 and uncap08 are injected into mice and survival is measured 72 hours after the injection. Data from the experiment is collected below. Which of the following would most likely increase the survival of mice in experiment E?

⚪ A. Adding the live cap08 strain in experiment D

Experiment

Injected Strain(s)

Total mice prior to injection

Surviving mice after injection

A

Live uncap08

36

36

B

Live cap08

36

1

C

Heat killed cap08

35

35

D

Heat killed cap08 Live uncap08

35

0

E

Unknown*

35

0

⚪ B. Removing the heat killed cap08 strain in experiment C ⚪ C. Adding the heat killed cap08 strain in experiment E ⚪ D. Adding DNase to experiment D ⚪ E. Adding DNase to experiment E

*The unknown species in this experiment was isolated from mice at the end of experiment D.

OUTLINE 1.

Microbiology: Bacterial Toxins

2.

3.

Endotoxin A. Properties B. Mechanism C. Pathogenic Associations D. Considerations Sepsis A. Bacteriemia B. Systemic Inflammatory Response Syndrome C. Sepsis D. Severe Sepsis E. Multiorgan Dysfunction Syndrome F. Septic Shock Exotoxin A. Properties B. Mechanism C. Pathogenic Associations D. Considerations

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Microbiology: Bacterial Toxins

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Properties: • Located in outer membrane (Gram negative) • Lipopolysaccharide (LPS): O-antigen, core, lipid A • Lipid A à Virulence factor • ↓ Antigenicity, ↓ Toxicity • Heat-stable Mechanism: • Endotoxin binds CD14/TLR4 receptor à Macrophage activation à IL-1, IL-6, TNF-⍺, NO à Fever, vasodilation, ↑ capillary permeability • Complement activation à ↑ C3a (Anaphylatoxin) à ↑ Histamine à Vasodilation, ↑ capillary permeability • Complement activation à ↑ C5a (Neutrophil chemotaxis) à Neutrophilic inflammatory infiltration • Endothelial damage à ↑ Bradykinin à Vasodilation à Septic shock • Endothelial damage à ↑ FIII (Tissue factor) à Binds FVIIa (Extrinsic)à Activation of FX à Common pathway à DIC Pathogenic Associations: • Septic shock • Waterhouse-Friderichsen Syndrome • Necrotizing enterocolitis Considerations: • No vaccination • Encoded by bacterial chromosome

Microbiology: Bacterial Toxins

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Bacteremia: • Presence of bacteria in bloodstream +/- signs of infection Systemic Inflammatory Response Syndrome (SIRS): • Inflammatory reactions from various causes (including noninfectious) • At least 2 of the 4 criteria below needed: 1. Temperature: >100.4℉ (38℃) or 90/min 3. Respiratory Rate: >20/min or PaCO2 12,000/mm3 or 10% band cells Sepsis: • Dysregulation of patient response to infection • Endotoxin-mediated in gram negative bacteria • SIRS + Suspected/confirmed underlying infection (i.e., SIRS + Viable bacteremia) Severe Sepsis: • Sepsis + Dysfunction of at least 1 organ or system Multiorgan Dysfunction Syndrome (MODS): • Dysfunction of at least 2 organs or systems • #1 cause à Sequela of severe sepsis or septic shock Septic Shock: • Persistent hypotension à Requiring vasopressors to maintain MAP • Persistent lactic acidosis à Refractory to fluid resuscitation • Presentation: Warm, dry skin (early) à Cold, clammy skin (late) • ↑ Mixed venous O2 saturation

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Microbiology: Bacterial Toxins

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Properties: • Gram positive and gram negative • Polypeptide • ↑ Antigenicity, ↑ Toxicity • Heat-labile (exceptions exist) Mechanism: • Type I: Superantigen à Modulate MHC II-CD4+ receptor activity • Type II: Cytotoxic • Type III (MC): AB Toxin à Component A: Active (ADP ribosyltransferases are common), Component B: Binding and uptake Pathogenic Associations: • Bacillus anthracis à Anthrax toxin (Edema factor, lethal factor, protective antigen) à Anthrax • Bordetella pertussis à Pertussis toxin à Pertussis (whooping cough) • Bacillus cereus à Heat labile toxin à Gastroenteritis • Clostridium botulinum à Botulinum toxin à Botulism • Clostridium tetani à Tetanospasmin à Tetanus • Clostridium perfringens à ⍺-toxin à Gas gangrene • Corynebacterium diphtheriae à Diphtheria toxin à Diphtheria, myocarditis • Enterotoxigenic E. coli à Heat labile toxin, Heat stable toxin à Gastroenteritis • Enterohemorrhagic E. coli à Shiga-like toxin à Gastroenteritis, Hemolytic uremic syndrome • Pseudomonas aeruginosa à Exotoxin A à Ecthyma gangrenosum • Shigella spp. à Shiga toxin à Hemolytic uremic syndrome • Staphylococcus aureus à Enterotoxin B, exfoliative toxin, TSST-1 à Gastroenteritis, SSSS, Bullous impetigo, Toxic shock syndrome • Streptococcus pyogenes à Erythrogenic Exotoxin A, Streptolysin O à Scarlet fever, Toxic shock syndrome • Vibrio cholera à Cholera toxin à Cholera Considerations: • Toxoid can be used for vaccination à Humoral IgG response • Transmitted directly via plasmid (conjugation) or via bacteriophage (specialized transduction)

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Item 1 of 1 Question ID: 0074

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A 34-year-old postpartum female is transferred to the intensive care unit for hypotension. Twenty-two hours earlier a cesarean section had been performed and the patient subsequently developed purulent postpartum endometritis evidenced by a fever, purulent uterine discharge and uterine tenderness. A blood culture was obtained just prior to initiation of empiric antibiotic therapy with vancomycin and gentamycin. Her vital signs abruptly deteriorated despite aggressive fluid resuscitation requiring immediate vasopressor infusion. Blood cultures would later grow colonies on eosin methylene blue agar displaying a green metallic sheen appearance. Given the limited information provided, which of the following is most likely contributing to this patient’s presentation?

AfraTafreeh.com ⚪ A. Active bacterial secretion of a heat-labile toxin ⚪ B. Active bacterial secretion of a heat-stable toxin ⚪ C. Active bacterial secretion of a Shiga-like toxin ⚪ D. Bacteriolysis causing release of a heat-labile toxin ⚪ E. Bacteriolysis causing release of a heat-stable toxin

AfraTafreeh.com OUTLINE 1.

Microbiology: Staphylococcus 2.

3.

4.

Staphylococcus Aureus A. General Principles B. Enzymes C. Polypeptides D. Polysaccharides E. Toxins F. Infectious Diseases G. Antibiotics Antibiotic Resistant Strains of Staphylococcus Aureus A. MRSA B. VRSA C. Risk Factors Staphylococcus Epidermidis A. General Principles B. Enzymes C. Toxins D. Foreign Body Infections E. Antibiotics Staphylococcus Saprophyticus A. General Principles B. Enzymes C. Urinary Tract Infection (Uncomplicated) D. Antibiotics

Microbiology: Staphylococcus

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General Principles: • Gram positive cocci à Clusters • Culture growth usually “golden” or yellow, can grow in NaCl up to 10% (Mannitol salt agar), β-hemolytic • Novobiocin sensitive, facultative anaerobe Enzymes: Catalase, coagulase, hemolysins, hyaluronidase, penicillinase Polypeptides: • Protein A à Bind Fc region on IgG à ↓ Complement activation à ↓ C3b • Modified penicillin-binding protein (MRSA) Polysaccharides: Capsule à ↓ Phagocytosis Toxins: • Enterotoxin B à Superantigen (Type I) à Gastroenteritis • Exfoliative toxin à Staphylococcal Scalded Skin Syndrome (SSSS) • Panton-Valentine leukocidin à Leukocyte destruction à Soft tissue necrosis • TSST-1 à Superantigen (Type I) à Toxic Shock Syndrome (TSS) Staphylococcal Toxic Shock Syndrome: TSST-1 super antigen, Prolonged use of tampons, shock and end organ dysfunction Staphylococcal Scalded Skin Syndrome: Exfoliative toxin cleaves desmoglein-1, Infants and young children, diffuse sloughing of skin Parotitis: Firm, erythematous, peri-auricular edema, trismus, fever, chills, ↑ serum amylase Gastroenteritis: Enterotoxin B (heat-stable), improper food handling, emesis, mild diarrhea, abdominal pain IVDU Endocarditis: Constitutional symptoms, tricuspid regurgitation, septic emboli à Splinter hemorrhages, Janeaway lesions, Osler nodes, Roth spots Osteomyelitis: Progressively worsening localized pain, worse with activity/palpation/percussion, +/- fever, +/- neurologic signs Additional Diseases: Necrotizing fasciitis, impetigo, pneumonia, meningitis Antibiotics: • MSSA penicillinase-sensitive à Penicillin • MSSA penicillinase-resistant à Oxacillin, nafcillin • Clindamycin (if PCN allergy) • MRSA à Vancomycin, linezolid, daptomycin

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Microbiology: Staphylococcus

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Methicillin-Resistant S. aureus (MRSA): • Acquire mec gene on bacterial chromosome à PBP-2A • PBP-2A has ↓ affinity for β-lactam antibiotics à ↑ Resistance to β-lactam antibiotics • Transduction à mec gene transfer among S. aureus • Typical resistance to methicillin, nafcillin, oxacillin, and cephalosporins • Rx: Vancomycin (usually) à Daptomycin, linezolid Vancomycin-Resistant S. aureus (VRSA): • Acquire vanA from Vancomycin-resistant Enterococcus (VRE) à D-ala, D-lactate • Transduction and/or conjugation à vanA gene transfer from VRE • Rx: Daptomycin, linezolid Risk Factors: • Prolonged hospitalization, ICU admission, recent antibiotic use, immunocompromised • Healthcare workers (exposure) à Contact precautions for MDR-bacteria

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Microbiology: Staphylococcus

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General Principles: • Gram positive cocci à Clusters • Does not ferment mannitol • Novobiocin sensitive • Facultative anaerobe • Ɣ-hemolytic Enzymes: • Catalase, urease • Coagulase negative Toxins: • PSM peptide toxin à Methicillin resistance Foreign Body Infections: • Fibrinogen + Fibronectin host protein coating à Binding site for S. epidermidis • Extracellular polysaccharide matrix forms à Biofilm à Seeding into systemic circulation • Frequently identified as contaminant on blood cultures • Catheter, central line, prosthetic valves, cardiac devices, VP shunt Antibiotics: • Methicillin sensitive: Oxacillin, nafcillin, clindamycin • Methicillin resistance: Vancomycin, daptomycin

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Microbiology: Staphylococcus

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General Principles: • Gram positive cocci à Clusters • Does not ferment mannitol • Novobiocin resistant • Facultative anaerobe Enzymes: • Catalase, urease à Does not reduce nitrate to nitrite • Coagulase negative Urinary Tract Infection (Uncomplicated): • Second most common cause in young females (1st E.coli) • ↑ Urinary frequency, urgency, dysuria, hematuria, suprapubic tenderness • Nitrite negative • Resistance to some E.coli UTI antibiotic regimens Antibiotics: • Nitrofurantoin • Trimethoprim-sulfamethoxazole • Local resistance patterns vary

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Item 1 of 1 Question ID: 0075

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A 34-day old male infant was brought to the emergency department with parents for multiple dermatologic lesions throughout the body that were first noticed 4 days earlier and had progressively worsened. Parents reported that the infant had a low-grade fever over the preceding several days with decreased oral feeding. There was no significant antenatal history reported. On physical examination there are multiple pustular lesions present over the face, trunk, and back with purulent discharge. Auscultation of the lungs revealed coarse breath sounds. Further microbial investigation including blood and wound cultures with antimicrobial sensitivities are performed revealing growth of methicillin-sensitive staphylococcus aureus. Targeted antibiotic treatment is completed, and the patient is subsequently discharged home with family in stable condition. Two weeks later the patient returns with a cough, fever, and respiratory distress. Chest X-ray reveals a left-sided pulmonary infiltrate. Blood cultures from this second admission would later grow methicillin-resistant staphylococcus aureus. Immunologic workup is performed, and a portion of the results are shown below. Which of the following is most likely the pathogenic mechanism leading to recurrent staphylococcal disease in this patient?

AfraTafreeh.com Diagnostic Test

⚪ A. Mutant bacterial DNA gyrase subunit (GyrB protein) ⚪ B. Bacterial-mediated extracellular polysaccharide matrix formation ⚪ C. Bacterial-mediated enzymatic inactivation of catalase ⚪ D. Bacterial-mediated enzymatic decomposition of hydrogen peroxide ⚪ E. Bacterial-mediated urea hydrolysis

Detail-Result

Serum Immunoglobulins

Normal for age.

CD18

Normal for age.

Dihydrorhodamine flow cytometry

Minimal green fluorescence of rhodamine at conclusion of this study.

Nitroblue tetrazolium test

Incubated leukocytes do not turn blue when exposed to nitroblue tetrazolium.

AfraTafreeh.com OUTLINE 1.

Microbiology: Streptococcus 2.

3.

4.

5.

Streptococcus Pneumoniae A. General Principles B. Pathogenesis C. Drug Resistant S. pneumonia D. Diseases E. Asplenia F. Antibiotics G. Vaccinations Viridans Group Streptococci A. General Principles B. Pathogenesis C. Diseases D. Antibiotics Streptococcus Pyogenes (Group A) A. General Principles B. Pathogenesis C. Diseases D. Diagnostics E. Antibiotics Streptococcus Agalactiae A. General Principles B. Pathogenesis C. Diseases D. Diagnostics E. Antibiotics Additional Streptococci A. Streptococcus Gallolyticus B. Streptococcus Anginosus

Microbiology: Streptococcus

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Microbiology: Streptococcus

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General Principles: • Gram positive “lancet”-shaped diplococci à Pairs or chains • Catalase negative • ⍺-hemolytic • Optochin sensitive, facultative anaerobe • Bile soluble • Neufeld-Quellung reaction positive à Used for capsular serotyping Pathogenesis: • Nasopharynx colonization • Polysaccharide capsule à ↓ Phagocytosis • IgA1 protease à Cleaves mucosal IgA • Pili à Adherence to cell surfaces, ↑ Inflammation Drug-Resistant S. pneumonia (DRSP): • Penicillin resistance à Alteration of penicillin-binding protein (PBP) Pneumonia: MCC in adults, classically lobar, rusty-color sputum, CXR Otitis Media: MCC in children Meningitis: MCC in adults Additional Diseases: Sinusitis, pharyngitis Asplenia: ↑ Risk of infection w/ encapsulated pathogens (Streptococcus pneumoniae) Antibiotics: • Pneumonia + Penicillinase sensitive à Penicillin, Amoxicillin, Azithromycin, Levofloxacin • Pneumonia + Penicillinase resistant à Vancomycin • Acute Otitis Media à Amoxicillin-clavulanate • Meningitis à Ceftriaxone and vancomycin (Covers Neisseria and H. influenzae) Vaccinations: • Pneumococcal conjugate (PCV13,15,20) à Infants, Elderly (Humoral IgG response) • Pneumococcal capsule (PPSV23) à (Humoral IgM response)

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Microbiology: Streptococcus

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General Principles: • S. mutans, S. mitis, and S. sanguinis • Gram positive in chains • Catalase negative • ⍺-hemolytic • Optochin resistant, facultative anaerobe • Bile resistant Pathogenesis: • Oropharynx colonization • Dextran à Adherence to surfaces, requires local fibrin deposition (damaged heart valves) (S. sanguinis) • Biofilm à Adhesion to oral surfaces (S. mutans, S. mitis) • Pili à Adherence to cell surfaces, ↑ Inflammation Disease of Dentition and Gingiva: Subgingival plaque à Penetrates gingival epithelium • Dental caries, gingivitis Subacute Bacterial Endocarditis: Dental procedure/trauma à S. sanguinis bacteremia à Heart valve/prosthetic device seeding • Antibiotic prophylaxis à High risk patients (Prosthetic heart valves, prior history of endocarditis) Antibiotics: • Endocarditis prophylaxis in high risk à Amoxicillin

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Microbiology: Streptococcus

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General Principles: • Gram positive in pairs and chains • Catalase negative • β-hemolytic • Bacitracin sensitive, facultative anaerobe • Pyrrolidinyl arylamidase (PYR) positive Pathogenesis: • Nasopharynx colonization • Erythrogenic exotoxin A, B, or C à Scarlett fever • Streptococcal pyrogenic exotoxins (SPE) à Toxic shock syndrome • Streptolysin, hyaluronidase à Damages host membranes and cells à Highly antigenic à Anti-streptolysin O Ab produced by host • Hemolysins • Hyaluronic acid capsule • M protein: ↓ Opsonization, phagocytosis à Molecular mimicry à Acute rheumatic fever • Protein F: Binds fibronectin à ↑ Adherence Tonsillopharyngitis: Pharyngeal erythema +/- gray-white tonsillar exudates, usually age 5-15 y/o • Additional: Otitis media, peritonsillar abscess Scarlett Fever: Mediated by erythrogenic exotoxins, “Scarlet sandpaper” maculopapular rash, “strawberry” tongue Soft Tissue Infections: • Erysipelas: Superficial dermis, sharply demarcated • Cellulitis: Deep dermis and subcutaneous tissue, poorly demarcated, induration • Impetigo: “Honey-crusted lesions” (Majority caused by S. aureus) • Necrotizing fasciitis: Pain out of proportion to degree of erythema, rapid progression, crepitus, skin necrosis, ↑ risk TSS Streptococcal Toxic Shock Syndrome: Associated with necrotizing fasciitis and myositis, ↑ mortality rate (vs Staphylococcal TSS) Acute Rheumatic Fever: Inflammatory sequela to GAS infection, cross reactivity of M protein Ab with host myocardial tissue Poststreptococcal Glomerulonephritis: Inflammatory sequela to GAS infection, S. pyogenes antigen-immune complex deposition in glomerular BM Diagnostics: • Throat culture, rapid antigen detection (Rapid Strep Test) • Serum antistreptolysin O (ASO), anti-deoxyribonuclease B (ADB) titer Antibiotics: • Penicillin, Ampicillin, Amoxicillin • 1st and 2nd generation cephalosporins

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Microbiology: Streptococcus

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General Principles: • Gram positive in pairs and chains • Catalase negative • β-hemolytic • Bacitracin resistant, facultative anaerobe • Pyrrolidinyl arylamidase (PYR) negative • Hippurate positive • CAMP factor à ↑ S. aureus hemolysis area on culture Pathogenesis: • Vaginal and GI colonization in mother à Ascend toward uterus à Chorioamnionitis, vertical transmission to newborn • Sialic acid polysaccharide capsule • Pilus à Adherence of mucosal surfaces • Hemolysins • C5a-ase Neonatal Meningitis: Bulging fontanelle, lethargy, muscle hypotonia, poor appetite, hyperthermia (or hypothermia) Neonatal Pneumonia: Respiratory distress, lethargy, pallor, hypotension, hyperthermia within the first 24 hours post-delivery Diagnostics: • Rectal and vaginal swabs in mother à Screen during pregnancy at 35-37 weeks à Positive culture à Intrapartum prophylaxis Antibiotics: • Ampicillin +/- Gentamycin • Penicillin • 1st and 2nd generation cephalosporins • Clindamycin

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Microbiology: Streptococcus

Streptococcus Gallolyticus (Group D): • Gram positive in pairs and chains • Catalase negative • Ɣ-hemolytic (usually) • Facultative anaerobe • Bile resistant • Does not grow in high salt concentrations (6.5% NaCl) • S. bovis biotype 1 = S. gallolyticus • GI colonization • Subacute bacterial endocarditis à ↑ Risk of colorectal carcinoma Streptococcus Anginosus (Group E): • Gram positive, non-motile, in pairs and chains • Catalase negative • Facultative anaerobe • Soft tissue infections, abscesses

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Item 1 of 1 Question ID: 0076

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A 9-year-old male presents to the emergency department with worsening swelling. His mother reports that he was treated with antibiotics 7 days ago for a sore throat and now believes that he may be having an allergic reaction. She reports that his urine has been a dark brown color for the past 12 hours. Vital signs reveal that the patient is afebrile with a blood pressure of 132/80 mmHg and a heart rate of 94/min. Physical examination reveals 2+ pretibial edema bilaterally with diffuse edema in the periorbital and scrotal regions. Serum laboratory evaluation is shown below. Renal biopsy is planned and reveals polymorphonuclear infiltration within the glomerular basement membrane and approaching the tubulointerstitial area along with mild thickening in the arterial walls. Granular staining of the renal biopsy with C3c was positive on immunofluorescent microscopy. Which of the following features most closely describes the bacteria responsible for this immune-mediated sequela in this patient? Hemoglobin: 11.3 g/dL Leukocyte count: 10,500/mm3 Platelet count: 155,000/mm3 Serum creatinine: 2.58 mg/dL Sodium 134 mEq/L Potassium 4.4 mEq/L Antistreptolysin-O antibody: Positive titer C3 22.5 mg/dL (ref: 84-175 mg/dL)

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Gram Stain

Catalase

Hemolysis capability

PYR* status

A.

+

+

β

-

B.

+

+

Ɣ

-

C.

+

-

β

+

D.

+

-

Ɣ

+

E.

+

-

⍺

-

⚪ A. ⚪ B. ⚪ C. ⚪ D. ⚪ E.

*Pyrrolidinyl arylamidase

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Microbiology: Enterococcus and Bacillus

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3.

Enterococcus (Group D) A. General Principles B. Pathogenesis C. Vancomycin-Resistant Enterococci D. Diseases E. Antibiotics Bacillus Anthracis A. General Principles B. Pathogenesis C. Diseases D. Prevention E. Medical Management Bacillus Cereus A. General Principles B. Pathogenesis C. Diseases D. Diagnostics E. Antibiotics

Microbiology: Enterococcus and Bacillus

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Microbiology: Enterococcus and Bacillus

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General Principles: • E. faecalis, E. faecium • Gram positive diplococci à Pairs or chains • Catalase negative • Urease negative • Ɣ-hemolytic • Facultative anaerobe • Pyrrolidinyl arylamidase (PYR) positive • Bile resistant, Bile esculin agar • Can grow in NaCl 6.5%, Mannitol salt agar Pathogenesis: • GI colonization à Recent GI or GU procedures • Polysaccharide capsule à ↓ Phagocytosis • Pili à Adherence to cell surfaces, ↑ Inflammation • Biofilm à Adhesion to foreign substances (urinary catheter) • Penicillin and early generation cephalosporin resistant Vancomycin-Resistant Enterococcus (VRE): Nosocomial infection Urinary Tract Infection: Hospitalized patient +/- catheterization, cannot convert nitrates to nitrites Cholecystitis: Bile-resistant properties Subacute Bacterial Endocarditis: Elderly patients, recent cystoscopy or colonoscopy Antibiotics: • Ampicillin +/- Gentamycin • Vancomycin • VRE à Linezolid, daptomycin

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Microbiology: Enterococcus and Bacillus

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General Principles: • Gram positive non-motile bacilli à ”Bamboo stick” shape, “box car” arrangement • Capsular halo (“Medusa head”) • Catalase positive • Spore forming • Ɣ-hemolytic • Can grow on blood agar Pathogenesis: • Transmission via spore inhalation, ingestion, or inoculation, generally from infected animals • ↑ Risk in areas with low animal vaccination rates and exposure to animal hides • Polypeptide D-glutamate capsule à ↓ Phagocytosis • Anthrax toxin consists of 3 components à Edema factor, lethal factor, protective antigen • Protective antigen: Binds cell surface à Permits entry of edema and lethal factor • Edema factor: Binds calmodulin à ↑ cAMP • Lethal factor: Cleaves amino terminus of MAPKK à Macrophage apoptosis Cutaneous Anthrax: • Most common form of disease, inoculation of spores • ↑ Risk w/ IVDU • Pruritic papule with central vesicle/bulla à Painless necrotic black eschar with surrounding non-pitting edema Pulmonary Anthrax: • “Woolsorter’s disease”, inhalation of spores • Prodromal phase: Constitutional symptoms, non-productive cough, nausea, vomiting, hemoptysis • Systemic phase: Lymphadenitis, mediastinitis, bacteremia à Respiratory failure, septic shock, hemorrhagic meningitis • Acute presentation with rapid deterioration • CXR: Widened mediastinum Gastrointestinal Anthrax: Ingestion of contaminated meat containing spores, mucosal ulcerations, hematemesis, melena Prevention: Post-exposure prophylaxis (Anthrax vaccination + prolonged antibiotics) Medical Management: Ciprofloxacin, doxycycline, clindamycin, linezolid +/- Anthrax immune globulin

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Microbiology: Enterococcus and Bacillus

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General Principles: • Gram positive motile bacilli • Catalase positive • Spore forming • β-hemolytic • Facultative anaerobe • Can grow on blood agar Pathogenesis: • Transmission via food (improperly refrigerated) à Reheated rice is classic • Enterotoxin I (Cereulide, pre-formed) à Emetic properties • Enterotoxin II à Diarrheal properties Gastroenteritis: Enterotoxin I and/or II (heat-stable), reheated rice, emesis, watery diarrhea, abdominal pain Medical Management: Supportive

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Item 1 of 1 Question ID: 0077

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A 73-year-old male with a past medical history of hypertension, hyperlipidemia, and type II diabetes mellitus who presents to his primary care physician with a chief complaint of painful urination over the past three days. He states he has sudden urges to urinate and has had one episode overnight when he was almost unable to get to the bathroom in time to void. He denies any recent surgical procedures, however states that he had a colonoscopy performed six days ago. Vital signs reveal a temperature of 37.9℃ (100.2 ℉), respiratory rate of 16 breaths/min, heart rate of 88 beats/min, and a blood pressure of 128/68 mmHg. Physical examination is relatively unrevealing. There is no evidence of suprapubic or costovertebral angle tenderness. Urinalysis results are shown below. Given the information provided, which of the following features are most consistent with the likely pathogen responsible for this patient’s presentation? Leukocyte esterase: 2+ Nitrite: Negative Protein: 1+ Glucose: 1+ Ketones: Negative Urobilinogen: Negative Urine pH: 6.30 Bacteria: Many

⚪ A. Lactose-fermenting gram-negative rod ⚪ B. Catalase-positive gram-positive cocci ⚪ C. Oxidase-positive gram-negative rod ⚪ D. Catalase-negative gram-positive cocci ⚪ E. Urease-positive gram-negative rod

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OUTLINE 1.

Microbiology: Mycobacteria

2.

3.

Mycobacterium Tuberculosis A. General Principles B. Pathogenesis Pulmonary Tuberculosis A. Pathophysiology B. Disease Variants C. Presentation D. Diagnostics E. Management F. Considerations Tuberculosis Screening A. Tuberculin Skin Test B. Interferon-Ɣ Release Assay C. Bacillus-Calmette Guérin Vaccine Mycobacterium Leprae and Leprosy A. General Principles B. Pathophysiology C. Presentation D. Diagnostics E. Management E. Considerations Additional Nontuberculous Mycobacterium A. General Principles B. Mycobacterium Marinum C. Mycobacterium Scrofulaceum D. Mycobacterium Avium-intracellular complex

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5.

Microbiology: Mycobacteria

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Microbiology: Mycobacteria

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General Principles: • Mycobacterium tuberculosis (MTB) • Acid-fast, non-motile, gram neutral bacilli • Ziehl-Neelsen stain, Auramine-rhodamine stain • Lӧwenstein-Jensen agar, Middlebrook agar • Catalase positive (negative in INH drug-resistance) • Facultative intracellular • Obligate aerobe Pathogenesis: • Transmitted via aerosol droplets • Mycolic acid à Does not absorb gram stain effectively • Cord factor (trehalose dimycolate) à “Serpentine” structure à ↑ TNF-⍺, ↑ Macrophage activation à Caseating granuloma • Additional glycolipids (sulfatides) à ↓ Phagolysosomal vesicle fusion • Catalase-peroxidase à ↓ ROS and H2O2 • KatG or inhA gene mutations à ↓ Catalase-peroxidase activity à ↓ Isoniazid activation à INH drug-resistance

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Microbiology: Mycobacteria

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Pathophysiology: • Transmitted via air droplet nuclei à Inhaled into lungs à MTB interaction w/ alveolar macrophages • MTB sulfatides à ↓ Phagolysosomal vesicle fusion à MTB replication within alveolar macrophages • Dendritic cells present MTB antigens à Naïve CD4+ T-cells à ↑ IL-12 à Th1-cell differentiation à ↑ IFN-Ɣ • Macrophage activation à Phagosome maturation, ↑ TNF-⍺, Langhan’s (multinucleated giant) cell formation • Cord factor à ↑↑↑ TNF-⍺ à Granuloma formation Disease Variants: • Active Tuberculosis • Latent Tuberculosis: MTB infection = Host immune response • Reactivation Tuberculosis: MTB infection >> Host immune response Active (Primary) Pulmonary Tuberculosis: Ghon complex, middle and lower lobes, symptomatic, contagious after initial exposure, TST positive, IGRA positive Latent Pulmonary Tuberculosis: Asymptomatic, generally not contagious, TST positive, IGRA positive Reactivation (Secondary) Pulmonary Tuberculosis: Upper lobe +/- cavitation, caseating granuloma, symptomatic, contagious, TST positive, IGRA positive Miliary Tuberculosis: ↑ Risk in immunocompromised, Pott disease (vertebrae), hepatosplenomegaly, scrofuloderma (skin) Gastrointestinal Tuberculosis: M. bovis, contaminated cow milk Presentation: • Non-productive cough à Hemoptysis, dyspnea • Fever (low-grade), lymphadenopathy, anorexia, night sweats • Variable pulmonary auscultation findings Diagnostics: • Sputum sample, NAAT, tuberculin skin test (TST), interferon-Ɣ release assay (IGRA) • CXR: Ghon complex (1°), hilar LAD (unilateral), consolidation, pleural effusion, cavitary lesions (2°, UL) Management: • Active and Reactivation: Rifampin + INH + Pyrazinamide + Ethambutol x 2m à Rifampin + INH x 4m • Latent: Isoniazid (INH), Rifampin, Rifapentine (multiple regimens exist) Considerations: • Immunocompromised may have negative diagnostic tests • Patients starting immunosuppressive therapy should be screened

Microbiology: Mycobacteria

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Tuberculin Skin Test (TST): • Purified protein derivative test (PPD), Mantoux test • Generates immune response intradermally via previously sensitized T-cells • Requires effective cell-mediated immunity (T-cell, type IV hypersensitivity reaction) • Does not distinguish between active and latent MTB infection • False positive: History of BCG vaccination, nontuberculous mycobacteria infection • False negative: Immunosuppression, sarcoidosis • Interpreter variability and varying induration diameters for positive result Interferon-Ɣ Release Assay (IGRA): • Measures IFN-Ɣ released by T-cells • Requires effective cell-mediated immunity (T-cell, type IV hypersensitivity reaction) • Does not distinguish between active and latent MTB infection • Preferred if prior BCG vaccination à Does not have false positives due to history of BCG vaccination • False negative: Immunosuppression, sarcoidosis Bacillus Calmette-Guérin (BCG) Vaccination • Live attenuated strain of Mycobacterium bovis • Not typically given in the U.S. • Avoid in immunosuppressed or pregnancy • May cause false positive TST

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Microbiology: Mycobacteria

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General Principles: • Mycobacterium leprae complex = M. leprae, M. lepromatosis • Reservoir of humans and armadillos • Acid-fast, non-motile, gram neutral bacilli • Ziehl-Neelsen stain • Cannot be cultured • Grows more readily in colder temperatures • Obligate intracellular • Obligate aerobe Pathophysiology: • M. leprae affinity for peripheral nerve tissue à Schwann cell destruction, demyelination • Tuberculoid Leprosy: Th1 response à T-cell mediated endoneurium non-caseating granuloma formation and epineurium fibrosis; Scarce bacilli on AFB • Lepromatous Leprosy: Th2 response à Hypergammaglobulinemia, M. leprae mediated, inadequate cell-mediated response; Numerous bacilli on AFB Presentation: • Tuberculoid Leprosy: Hypopigmented macules/plaques, hair loss, localized/asymmetric hyperesthesia à hypoesthesia • Lepromatous Leprosy: “Leonine facies”, nodular lesions, symmetrical length-dependent sensorimotor neuropathy (“glove-and-stocking distribution”) Diagnostics: • Tuberculoid Leprosy AFB: Noncaseating granulomas surrounded by epithelioid, Langhans, and lymphocytic cells, minimal bacilli • Lepromatous Leprosy AFB: Foamy histiocytes, minimal lymphocytes, numerous bacilli • Lepromin test: (-) test à Lepromatous Leprosy • PCR à Detects M. leprae DNA in tissue Management: • Dapsone + Rifampin +/- Clofazimine (for lepromatous) Considerations: • False positive VDRL or ANA

Microbiology: Mycobacteria

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General Principles: • Acid-fast, non-motile bacilli • Ziehl-Neelsen stain Mycobacterium Marinum: • Fish tank granuloma, classically a hand lesion Mycobacterium Scrofulaceum: • Cervical lymphadenitis (children) Mycobacterium Avium-intracellulare complex (MAC): • Disseminated disease à CD4+ count 1 lobe, usually) • Psittacosis CXR: Lower lobe consolidation Management: • C. pneumoniae: Azithromycin • C. psittaci: Doxycycline

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Microbiology: Atypical Bacteria

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General Principles: • Pleomorphic gram-variable rod • Facultative anaerobe • Normal vaginal flora Bacterial Vaginosis: • Vaginal irrigation, recent use of antibiotics, immunosuppression • Association with ↑ sexual activity (not sexually transmitted) • Dysbiosis: ↓ Lactobacilli, ↑ G. vaginalis and other anaerobes • Thin gray vaginal discharge, vaginal “fishy” odor • Nonpainful, many cases asymptomatic Diagnostics: • Clue cells (vaginal epithelial cells) covered with Gardnerella on wet mount microscopy • Vaginal pH > 4.5 • Amine (“Whiff”) test: Vaginal discharge + KOH à ↑ Characteristic amine (“fishy”) odor Management: • Metronidazole or clindamycin

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Microbiology: Atypical Bacteria

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General Principles: • Gram negative non-motile coccobacilli • Obligate intracellular Pathogenesis: • Tropism for vascular endothelial cells à Small vessel vasculitis Rocky Mountain Spotted Fever: • Rickettsia rickettsii • Transmitted via ticks (Dermacentor spp.), Eastern and midwestern U.S. (North Carolina) • Headache, fever • Centripetally spreading maculopapular rash, begins on wrists and ankles (includes palms and soles) • Thrombocytopenia • Complicated by systemic involvement à Multiorgan dysfunction, DIC, shock • Rx: Doxycycline Typhus: • Rickettsia typhi (Endemic), Rickettsia prowazekii (Epidemic) • Transmitted via rat and cat fleas (R. typhi) and human body louse (R. prowazekii) • Fever, myalgias, headache (more severe symptoms with R. prowazekii) • Centrifugal spreading rash (spares palms and soles) • Rx: Doxycycline

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Microbiology: Atypical Bacteria

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General Principles: • Gram negative • Obligate intracellular (Ehrlichia à monocytes/macrophages, Anaplasma à neutrophils) Ehrlichiosis: • Ehrlichia chaffeensis, Ehrlichia ewingii, Ehrlichia muris • Transmitted via ticks (Amblyomma americanum, Ixodes scapularis) • Fever, myalgias, headache +/- maculopapular/petechial rash • Hepatomegaly • Pancytopenia (lymphopenia), transaminitis • PBS: Morulae within monocytes (E. chaffeensis) • Rx: Doxycycline Anaplasmosis: • Anaplasma phagocytophilum • Transmitted via ticks (Ixodes scapularis, Ixodes pacificus) • Fever, myalgias, headache • No rash (usually) • Pancytopenia, transaminitis • PBS: Morulae within neutrophils (or other granulocytes) • Rx: Doxycycline

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Microbiology: Atypical Bacteria

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General Principles: • Incomplete cell wall (not visible on gram stain) • Cholesterol-stabilized membrane • Pleomorphic • I-antigen (binding site) • Eaton agar (Mycoplasma pneumoniae) Atypical Pneumonia, Tracheobronchitis: • Mycoplasma pneumoniae • Classically younger patients, close contact • Insidious onset of symptoms • Dry cough or minimal sputum, dyspnea • Myalgias, sore throat, headaches, +/- low grade fever • CXR: Diffuse patchy infiltrates in interstitial areas (>1 lobe, usually) • Rx: Macrolides or doxycycline or respiratory fluoroquinolones (levofloxacin, moxifloxacin) Autoimmune Hemolytic Anemia (Cold Agglutinin): • Mycoplasma pneumoniae • Other classic causes: EBV, Waldenstrom macroglobulinemia, CLL • General anemia features: Fatigue, conjunctival pallor, dyspnea • Painful acrocyanosis of distal extremities, livedo reticularis, Raynaud phenomena • Direct Coombs: Positive (Anti-C3b), ↓ Serum C3 and C4, ↑ LDH, ↓ Haptoglobin • Rx: Avoid cold exposure and triggers, maintenance w/ Rituximab Erythema Multiforme: • Mycoplasma pneumoniae • Other classic causes: HSV, β-lactam antibiotics, phenytoin • Symmetric and centripetally spreading maculopapular rash à Target lesions (can include palms and soles) • Nikolsky negative, no mucous membrane involvement unless major form • Rx: Symptomatic treatment in most cases Steven -Johnson Syndrome: • Mycoplasma pneumoniae • Other classic causes: Allopurinol, TMP/SMX, HIV, piroxicam, antiepileptics (phenytoin) • Painful erythematous/purpuric macules +/- targetoid appearance à Full-thickness epidermal necrosis, sloughing of tissue • Nikolsky positive, mucous membrane involvement • Rx: Fluid resuscitation, wound management +/- antibiotic therapy UTI: Ureaplasma urealyticum

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Microbiology: Atypical Bacteria

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General Principles: • Gram negative coccobacilli • Obligate intracellular • Reservoir: Farm animals, animal hides (cattle, goats, and sheep) • Endospore à Survival in harsh environments Q Fever: • Transmitted via inhalation of aerosol • ↓ ID50 • Fever, headache • Mild pneumonia • Transaminitis • Rx: Doxycycline Endocarditis: Culture negative • Other à HACEK organisms: Haemophilus, Actinobacillus, Cardiobacter, Eikenella, Kingella

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Item 1 of 1

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Question ID: 0087

Test Your Knowledge Difficulty Rating: ✪✪

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A 63-year-old previously healthy male presents to the emergency department for worsening chills and nausea over the past three days. He states that he believes this all started after a “bug bite” on a camping trip recently. Vital signs reveal a temperature of 101℉ (38.3℃), blood pressure of 94/54mmHg, heart rate of 108/bpm, and oxygen saturation of 97% on room air. Physical examination reveals conjunctival pallor and is otherwise relatively unremarkable. Serum laboratory studies are shown below including a peripheral blood smear sample. Which of the following vectors would be most consistent with the underlying disease process?

Laboratory Marker

Result

Leukocyte count

1,800/mm3

Hemoglobin

9.8 g/dL

⚪ B. Ixodes pacificus

Platelet count

84,000/mm3

⚪ C. Dermacentor andersoni

Glucose

122 mg/dL

Sodium

138 mEq/L

Potassium

3.7 mEq/L

Magnesium

1.8 mEq/L

Creatinine

1.4 mg/dL

Alanine aminotransferase

176 U/L

Aspartate aminotransferase

224 U/L

PCR Ehrlichia DNA

Undetectable

Reverse transcriptase PCR viral RNA

Undetectable

⚪ A. Amblyomma americanum

⚪ D. Musca sorbens ⚪ E. Dermacentor variabilis

OUTLINE 1.

Microbiology: Dimorphic Mycosis

2.

3.

Histoplasma A. General Principles B. Pathogenesis C. Histoplasmosis D. Diagnostics E. Management Blastomyces A. General Principles B. Pathogenesis C. Blastomycosis D. Diagnostics E. Management Coccidioides A. General Principles B. Pathogenesis C. Coccidioidomycosis D. Diagnostics E. Management Paracoccidioides A. General Principles B. Pathogenesis C. Paracoccidioidomycosis D. Diagnostics E. Management

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Sporothrix A. General Principles B. Pathogenesis C. Lymphocutaneous Sporotrichosis D. Diagnostics E. Management

Microbiology: Dimorphic Mycosis

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General Principles: • Histoplasma capsulatum • Dimorphic fungi à Temperature dependent (mold – cold, yeast – heat) Pathogenesis: • Mold form à Growth in environment (Sabouraud agar) • Yeast form à Growth in tissues (blood agar) • Inhalation of spores à Evasion of pulmonary defenses à Phagocytic infection à Dissemination (immunocompromised) • Not transmitted person to person Histoplasmosis: • Mississippi and Ohio river valley (Ohio, Indiana, Illinois, Iowa, Michigan, Nebraska) • Bat or bird droppings, immunosuppressed patient • Immunocompetent: Often asymptomatic or flu-like symptoms +/- pneumonia • Immunosuppressed: Disseminated disease à AIDS-defining illness • Fever, chills, headache, myalgias, chest pain, cough, and hemoptysis • Weight loss, hepatosplenomegaly, LAD, oral ulcerative lesions (palate, tongue) Diagnostics: • Positive polysaccharide antigen test (urine or serum) • Pancytopenia • CXR: Variable; diffuse patchy/nodular infiltrates vs focal consolidation, hilar/mediastinal lymphadenopathy • Silver stain, PAS stain, KOH wet prep: Yeast within macrophages (narrow-based budding, oval-shape) • Granulomas may be present • Sabouraud agar: Fungal culture • Yeast < RBC (size) Management: • Mild disease: Itraconazole, may be self limiting if immunocompetent • Severe disseminated disease: Amphotericin B

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Microbiology: Dimorphic Mycosis

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General Principles: • Blastomyces dermatitidis • Dimorphic fungi à Temperature dependent (mold – cold, yeast – heat) Pathogenesis: • Thick cell wall à ↓ Phagocytosis • Mold form à Growth in environment (Sabouraud agar) • Yeast form à Growth in tissues (blood agar) • Inhalation of spores à Evasion of pulmonary defenses à Phagocytic infection à Dissemination (immunocompromised) • Not transmitted person to person Blastomycosis: • Eastern and Midwestern U.S. • Immunocompetent: Often asymptomatic or flu-like symptoms +/- pneumonia • Immunosuppressed: Disseminated disease • Fever, chills, chest pain, myalgias, cough, and hemoptysis • Verrucous skin lesions with irregular borders • No LAD (usually) • Osteolytic bone lesions à Osteomyelitis Diagnostics: • CXR: Variable; diffuse patchy/nodular infiltrates vs focal consolidation • Silver stain, PAS stain, KOH wet prep: Yeast within macrophages (broad-based budding, thick walls) • Sabouraud agar: Fungal culture • Granulomas may be present • Yeast = RBC (size) Management: • Mild disease: Itraconazole, may be self limiting if immunocompetent • Severe disseminated disease: Amphotericin B

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Microbiology: Dimorphic Mycosis

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General Principles: • Coccidioides immitis, Coccidioides posadasii • Dimorphic fungi Pathogenesis: • Giant spherules containing endospores • Mold form à Growth in environment • Endospore/spherule form à Growth in tissues • Inhalation of arthroconidia à Endospores replicate in spherules in tissue à Rupture of endospore from spherule • Not transmitted person to person Coccidioidomycosis (“Valley Fever”): • Southwestern U.S., dust exposure • Immunocompetent: Often asymptomatic or flu-like symptoms +/- pneumonia • Immunosuppressed: Disseminated disease à AIDS-defining illness • Fever, chills, chest pain, myalgias, cough, and hemoptysis • "Desert Rheumatism”: Erythema nodosum (“desert bumps”), arthralgias, fever • Meningitis Diagnostics: • Eosinophilia • CXR: Variable; diffuse patchy/nodular infiltrates vs focal consolidation • Silver stain, PAS stain, KOH wet prep: Large spherules containing endospores • Sabouraud agar: Fungal culture • Spherules > RBC (size) Management: • Mild disease: Self-limited in many immunocompetent, fluconazole, itraconazole • Severe disseminated disease: Amphotericin B

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Microbiology: Dimorphic Mycosis

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General Principles: • Paracoccidioides brasiliensis, Paracoccidioides lutzii • Dimorphic fungi Pathogenesis: • Inhalation of spores à Evasion of pulmonary defenses à Phagocytic infection à Dissemination (immunocompromised) • Not transmitted person to person Paracoccidioidomycosis: • South America, Central America • ↑ Risk in men, soil exposure (agricultural occupational exposure) • Immunocompetent: Often asymptomatic or flu-like symptoms • Immunosuppressed: Disseminated disease • Fever, chills, weight loss • Oral and mucosal ulcerative lesions, LAD (cervical is classic) • Verrucous skin lesions with irregular borders Diagnostics: • Anemia, eosinophilia • CXR: Variable; diffuse patchy/nodular infiltrates vs focal consolidation • Silver stain, PAS stain, KOH wet prep: Budding yeast with “captain’s wheel” formation • Sabouraud agar: Fungal culture • Yeast > RBC (size) Management: • Mild disease: Self-limited in many immunocompetent, itraconazole • Severe disseminated disease: Amphotericin B

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Microbiology: Dimorphic Mycosis

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General Principles: • Sporothrix schenckii • Dimorphic fungi Pathogenesis: • Mold form à Growth in soil (Sabouraud agar) • Yeast form à Growth in tissues (blood agar) • Survives on vegetation à Traumatic inoculation (thorn prick) • Not transmitted person to person Lymphocutaneous Sporotrichosis (“Rose Gardener’s Disease”): • ↑ Risk in gardeners • Generally immunocompetent patient • Ulcerative, pustular lesions à Nodular ascending lymphangitis • Immunosuppressed: Disseminated disease Diagnostics: • Silver stain, PAS stain: Often negative, oval or “cigar-shaped” yeast • Sabouraud agar: Fungal culture Management: • Mild disease: Itraconazole or KI • Severe disseminated disease: Amphotericin B

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Microbiology: Dimorphic Mycosis

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*Not to scale

Disease

Location

Key Association/Feature

Histopathology

Histoplasmosis

Mississippi and Ohio river valley

Bat droppings, caves

Oval Narrow-based budding

Blastomycosis

Eastern and Midwestern U.S.

No lymphadenopathy Verrucous cutaneous lesions

Thick walls Broad-based budding

Coccidioidomycosis

Southwestern U.S.

Paracoccidioidomycosis

South and Central America

Agricultural/soil exposure Verrucous cutaneous lesions

Budding yeast “Captain’s wheel”

Sporotrichosis (Lymphocutaneous)

N/a

Gardening, landscaping Skin inoculation (vs inhalation)

“Cigar-shaped” yeast

Dust exposure AfraTafreeh.com “Desert Rheumatism”

Spherules w/ endospores

Size vs RBC*

≣

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Item 1 of 1 Question ID: 0088

Test Your Knowledge Difficulty Rating: ✪✪

A 27-year-old male presents to his primary care physician with a dry cough that “hasn’t gone away”. The patient reports that he recently went to an urgent care and received antibiotics for pneumonia. He also endorses significant unintentional weight loss over the past several weeks. He is afebrile and his vital signs are within normal limits. A painless skin lesion is identified on the dorsal right hand (figure 1). Similar skin lesions are identified on the left thigh and dorsum of the right foot. A chest x-ray reveals a large right-sided pleural effusion and poorly defined soft tissue nodules throughout both lung fields. No significant hilar or mediastinal lymphadenopathy was observed.

Figure 1

The patient is subsequently taken for pleurocentesis, and pleural fluid analysis is shown in the table below. A biopsy taken from the right hand is also performed and shown under high magnification (figure 2). Which of following would risk factors is most significantly correlated to the underlying pathology in this patient? Pleural Fluid

Result

Appearance

Straw color

pH

8 (ref: 7.6-7.64)

Glucose

110 mg/dL

⚪ A. History of Crohn’s disease

LDH

205 U/L

⚪ B. Archeological exploration

Gram stain

Negative

Acid fast stain

Negative

⚪ C. Rose gardening ⚪ D. Employment as a healthcare worker ⚪ E. Frequent cave exploration

Figure 2

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OUTLINE 1.

Microbiology: Opportunistic Mycosis

2.

Aspergillus A. General Principles B. Pathogenesis C. Aspergillosis D. ABPA E. Diagnostics F. Management G. Complications Candida A. General Principles B. Pathogenesis C. Oropharyngeal Candidiasis D. Esophageal Candidiasis E. Vulvovaginal Candidiasis F. Cutaneous Candidiasis G. Candidemia H. Diagnostics I. Management Cryptococcus A. General Principles B. Pathogenesis C. Cryptococcosis D. Diagnostics E. Management F. Complications

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3.

4.

5.

Mucor and Rhizopus A. General Principles B. Pathogenesis C. Mucormycosis D. Diagnostics E. Management F. Complications Pneumocystis A. General Principles B. Pathogenesis C. Pneumocystis Pneumonia D. Diagnostics E. Management F. Complications

Microbiology: Opportunistic Mycosis

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General Principles: • Aspergillus fumigatus, Aspergillus flavus • Monomorphic mold • Catalase positive Pathogenesis: • Inhalation of spores à Evasion of pulmonary defenses à Local invasion à Dissemination (immunocompromised) Aspergillosis: • ↑ Risk in immunocompromised à Chemotherapy, transplant recipient, chronic granulomatous disease (catalase +) • ↑ Risk in pulmonary disease à COPD, prior pulmonary infection (TB, PJP) • General symptoms: Fever, weight loss, night sweats, chills, dry cough • Pulmonary: Dyspnea, hemoptysis, pleuritic chest pain • Invasive disease: Hypotension, tachycardia, tachypnea à Septic shock • Aspergilloma: Pre-existing cavitary lesions (TB) à Mycetoma formation (mobile) Allergic Bronchopulmonary Aspergillosis (ABPA): • Hypersensitivity reaction to Aspergillus • ↑ Risk in bronchopulmonary disease à Asthma, cystic fibrosis • Dyspnea, wheezing, exacerbations of underlying pulmonary disease (asthma) • Bronchiectasis, productive cough (brown-black mucous casts) Diagnostics: • Invasive Disease: Positive galactomannan enzyme assay • Chest CT: Bronchiectasis (ABPA), Nodules +/- cavitation and consolidation (Invasive), mobile mycetoma (Aspergilloma) • Silver stain, PAS stain: Mold with septate hyphae branching dichotomously at 45° (acute) angles (Invasive) • ABPA: ↑ IgE, eosinophilia, Aspergillus IgG, Positive Aspergillus skin test • Serum 1,3-β-D-glucan (non-specific) Management: • Prophylaxis: Posaconazole • Invasive: Voriconazole or Posaconazole (1st line), Echinocandins (Caspofungin, anidulafungin, micafungin) (2nd line) • Aspergilloma: Surgical resection • ABPA: Prednisone Complications: • Invasive disease: Hemorrhagic dermatologic lesions, endocarditis, brain abscesses, meningitis, venous sinus thrombosis • Aflatoxin (A. flavus) à ↑ Risk of hepatocellular carcinoma

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Microbiology: Opportunistic Mycosis

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General Principles: • Candida albicans • Dimorphic fungi à Temperature dependent (pseudohyphae and budding yeast – cold, germ tubes – heat) • Catalase positive Pathogenesis: • Local Disease: Imbalance in flora à ↑ C. albicans à Local infection • Disseminated Disease: Local infection à Hematogenous spread à Multi-organ involvement (Immunocompromised) • ↑ Risk in immunocompromised à Chemotherapy, transplant recipient, HIV, chronic granulomatous disease (catalase +) • ↑ Risk in obesity, diabetes, neonates, pregnancy, recent antibiotics (vulvovaginitis) or steroid use (inhaled à oral) Oropharyngeal Candidiasis: Pseudomembrane candidiasis, “oral thrush”, can be scraped off Esophageal Candidiasis: AIDS-defining illness, odynophagia Vulvovaginal Candidiasis: • Thick white vaginal discharge, “cottage cheese” appearance, odorless • Local erythema, pruritis, dysuria, dyspareunia, burning sensation • Vaginal pH ~4-4.5, vaginal discharge + KOH à Pseudohyphae on wet mount Cutaneous Candidiasis: • Erythematous patches, satellite lesions • Intertriginous areas, skin folds (axilla, groin, beneath breasts) • Diaper dermatitis (infants) Candidemia: • Classically immunocompromised patient, IVDU, vascular catheters (parenteral nutrition) • Systemic symptoms (fever, chills, myalgias) à End organ damage • Endocarditis with IVDU Chronic Mucocutaneous Candidiasis: • ↓ T-cell response to Candida antigens: ↓ IL-17 response • AIRE protein deficiency • Refractory and recurring candida infections • No induration on Candida skin test Diagnostics: • KOH wet prep, silver stain: Yeasts, hyphae, and pseudohyphae • Endoscopy (esophagitis) • Blood culture (candidemia) à Germ tubes produced in serum • Serum 1,3-β-D-glucan (non-specific) Management: • Clotrimazole, miconazole, ketoconazole, nystatin (Local disease, usually topical) • Fluconazole (Esophageal) • Caspofungin or Amphotericin B (Systemic, intravenous)

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Microbiology: Opportunistic Mycosis

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General Principles: • Cryptococcus neoformans, Cryptococcus gatti • Monomorphic yeast • Urease positive Pathogenesis: • Thick polysaccharide capsule à ↓ Phagocytosis • Phenol oxidase • Inhalation of spores à Evasion of pulmonary defenses à Hematogenous dissemination (Immunocompromised) à Meninges • ↑ Risk in immunocompromised (Disseminated disease is AIDS-defining condition, CD4+