1. 4 Major Groups in Microbiology
    • Viruses (obligate intracellular parasites)
    • Bacteria
    • Fungi—Yeast and Molds
    • Parasites—Protozoa (single cell) and Helminths (worms)
  2. Cellular Classification
    • Prokaryotes: all bacteria
    • Eukaryotes: Fungi and Parasites
  3. Components of Viruses
    • Virion (nucleic acid of DNA or RNA)
    • Capsid (protein coat)
    • +/- Lipid Envelope
    • Arrangement of capsomere (basic unit of capsid): Icosahedral (sphere), Helical (rod)
  4. Medically Important RNA Viruses
    • Paramyxoviridae: Parainfluenza virus, Measles virus, Mumps virus, RSV
    • Orthomyxoviridae: Influenza virus A,B,C
    • Caliciviridae: Norovirus
    • Retroviridae: HIV
    • Picornaviridae: Rhinovirus, Poliovirus, Coxsackie virus
    • Others: Coronavirus, Rubella, Hanta virus, Rotavirus, Ebola virus
  5. Medically Important DNA Viruses
    • Herpesviridae: Herpes simplex virus (HSV) 1 & 2, Varicella zoster virus (VZV), Epstein Bar Virus (EBV), Cytomegalovirus (CMV)
    • Parvoviridae: Parvovirus B-19
    • Adenoviridae: Adenovirus
    • Hepadnaviridae: Hepatitis B Virus
    • Papovaviridae: Human papilloma virus (HPV)
    • Poxviridae: Smallpox virus
  6. Bacteria Classifications
    • Shape: Bacillus (rod), Coccus (circle), Spirochete (spiral), Diplococci (pairs), Streptococci (chains), Staphylococci (clusters)
    • Gram stain + or –
    • Nutritional reqs: Autotrophs (rely solely on inorganic sources of C), Heterotrophs (rely on organic sources)
    • Oxygen reqs: Obligate Aerobes (require O2 for growth), Microaerophiles (grow in low amounts of O2), Facultative Anaerobes (grow with or without O2), Obligate Anaerobes (require absence of O2)
    • Most bacteria are Autotrophs and Facultative anaerobes
  7. Fungi: Yeasts and Molds
    • Yeasts: non-filamentous, unicellular, reproduce by budding, colonies appear creamy on lab media
    • Molds: filamentous, multicellular, reproduce sexually and sexually, basic unit is hypha (septate hyphae have transverse cross-walls), colonies appear fuzzy on lab media
  8. Fungal Structure
    • All fungi are Gram Positive!
    • Cell walls do not contain peptidoglycan. They contain chitin and other complex polysaccharides.
    • Some fungi are encapsulated.
    • Most are obligate anaerobes; none are aerobes.
    • They are unable to synthesize more complex compounds from CO2 (must have a preformed organic carbon source).
    • Few are Dimorphic and can grow in different forms at different temperatures (body temp grow as yeasts, room temp grow as molds).
  9. Medically Important Fungi
    • Yeasts: Candida albicans, Candida spp, Torulopsis glabrata, Cryptococcus neoformans, Pneumocystis carinii
    • Molds: Zygomycetes (Mucor, Rhizopus), Dermatophytic agents (Trichophyton, Malassezia), Dematiaceous fungi (Alternaria, Cladosporium), Opportunistic fungi (Aspergillus, Penicillium), Dimorphic fungi
  10. Parasites Taxonomy
    • Protozoa: Unicellular
    • Metazoa: Multicellular Nematodes (round worms), Platyhelminthes (flat worms; trematodes, cestodes), Arthropods (crustaceans, arachnids, Insecta)
  11. Medically Important Parasites
    • Intestinal tract: Entamoeba histolytica, Giardia lamblia, Cryptosporidium spp, Isospora belli
    • Urogenital: trichomonas vaginalis
    • Blood and Tissue: Plasmodium spp, Leishmania spp, Naegleria and Acanthamoeba spp, Toxoplasma gondii, Trypanosoma spp
  12. Medically Important Parasites
    • Enterobius vermicularis (pinworm)
    • Ascaris lumbricoides (giant roundworm)
    • Strongyloides stercoralis (threadworm, roundworm)
    • Necator americanus (hookworm)
    • Trichinella spiralis (causes trichinosis, referred to as pork worm)
    • Fasciola hepatica (common liver fluke or sheep fluke)
    • Taenia spp (tapeworm)
    • Toxocara canis and Toxocara cati (dog and cat roundworms)
  13. Pathogen
    Any organism capable of causing disease
  14. Strict Pathogen
    Any organism that always causes disease
  15. Pathogenicity
    The ability to cause disease
  16. Virulence
    The degree to which an organism can cause disease.
  17. Exogenous Infection
    Results from exposure to microbes from external environment
  18. Endogenous Infection
    Results from introduction of normal flora into inappropriate sites.
  19. Latent Infection
    • Microbe persists in host tissue without evidence of disease
    • A change in the environment will cause disease.
  20. Chronic Infection
    Host’s immune system fails to completely eradicate microbe.
  21. Anaerobic Infections
    • Truly endogenous.
    • Conditions that predispose to anaerobic infections: preceding aerobic infections (esp w/ tissue necrosis), trauma, decreased vascular supply.
    • Sites where normal flora is anaerobic: GI tract, vagina, upper respiratory tract, skin
    • Clues that pt may have anaerobic infection: the infection is at or near a site where anaerobes are normal flora, there is a foul-smelling discharge, no bacterial growth on routine aerobic cultures, gas is present, fails to improve on antibiotics that cover aerobic infections.
  22. Infection is a Step-wise Process
    • Acquisition
    • Attachment
    • Invasion (spread)
    • Evasion of host’s defenses
  23. Virulence Factors
    • Structures: capsule, spores, endotoxin (LPS, LOS)
    • Antigenic proteins: exotoxins, adhesins, superantigens
    • Degradative enzymes
    • Antibiotic resistance
  24. Transmission of Infection
    • Ability of organism to survive outside host is important.
    • Portal of entry used by microbe also a factor.
    • Modes of transmission: inhalation, ingestion, trauma/traumatic implantation, bites/stings, sexual contact, vertical transmission, fomites
  25. Invasion
    • Proteolytic enzymes facilitate spread and damage host cells.
    • Exotoxins.
    • Spreading factors: Hyaluronidase (found in many gram + genera), Streptokinase, Staphylokinase, Collagenase
    • Enzymes that cause lysis of host cell membranes: phospholipases, lecithinases (hemolysins, leucocidin)
  26. Immune Evasion
    • Mechanisms microbes use to overcome host immune system.
    • Ability to resist phagocytosis: avoid contact with or engulfment by phagocytic cell, survive inside phagocyte, kill phagocyte.
    • Disguise themselves as host molecules.
    • Antigenic variation.
    • Antibody neutralization.
    • Hide in places inaccessible to immune system.
  27. Neutrophils (PMNs)
    • Ingest and destroy pathogenic bacteria.
    • 1st responders to bacterial infection.
    • Presence in high amounts indicate significant bacterial infection.
  28. Macrophages
    • Ingest and destroy all pathogenic microbes.
    • Production of TNF.
    • Antigen presentation.
    • Activation of acute phase reactants.
  29. Natural Killer (NK) Cells
    Non-phagocytic cells that destroy and kill viruses.
  30. Gram Positive Bacteria
    Thick peptidoglycan layer; teichoic acid.
  31. Gram Negative Bacteria
    • Thin peptidoglycan layer.
    • Complex outer membrane of lipopolysaccharide (LPS).
  32. Plasmids
    • Intracellular extrachromosomal DNA.
    • Can be transmissible or non-transmissible.
    • Found in both Gram pos and neg bacteria but more common in Gram neg.
    • Carry genes for many functions. Antibiotic resistance probably most important.
  33. Spores
    • Dormant structure; forms inside cell.
    • Extremely resistant to heat, radiation, and various chemical agents.
    • Only 2 genera: Bacillus and Clostridium (both Gram pos rods)
  34. Pili/Fimbriae
    • Mostly limited to Gram neg bacteria.
    • Especially common among pathogens of mucosal surfaces.
  35. Endotoxins
    • Lipopolysaccharides (LPS) located in the outer membrane of Gram neg bacteria.
    • Poorly antigenic.
    • Powerfully immunogenic.
  36. Exotoxins
    • Polypeptides produced and secreted by both Gram pos and Gram neg bacteria.
    • Antigenic.
    • Many types with different mechanisms of action.
    • Superantigens are powerful exotoxins.
  37. Sites of Antibiotic Activity
    • Cell wall inhibitors: Work by inhibiting cross-linking of peptidoglycan. Most are β-lactams (Penicillins, Cephalosporins, Carbapenems, Monobactams)
    • β-lactams = Antibiotics
    • β-lactamases = Enzymes bacteria produce to inactivate β-lactams.
    • β-lactamase inhibitors = Medication compounds to inactivate β-lactamases
    • Cell membrane: Agent disrupts either cytoplasmic membrane or Gram neg outer membrane (ex: Polymyxin)
    • Ribosome: Agent disrupts protein synthesis at both 30S and 50S ribosomes (ex: Erythromycin)
    • Antimetabolism: Agents mimic the structure of a required metabolite (ex: Septra)
    • Inhibition of DNA or RNA synthesis: (ex: Cipro)
  38. Bactericidal vs Bacteriostatic
    • Bactericidal: killing bacteria
    • Bacteriostatic: inhibiting growth
    • Those that inhibit cell wall synthesis, nucleic acid synthesis, and alter cell wall permeability are bactericidal.
    • Those that inhibit protein synthesis can be either or both.
    • Folic acid inhibitors are bacteriostatic.
  39. Streptococci
    • Gram pos cocci.
    • Facultative anaerobes with complex nutritional requirements.
    • Grown in vitro on blood or serum-enriched media.
    • Arranged in pairs or chains.
    • Lancefield classification: groups A, B, C, F, G
    • Hemolysis classification: α-hemolytic, β-hemolytic, or non-hemolytic.
    • α-hemolytic zone of hemolysis on blood agar appears green.
    • β-hemolytic zone of hemolysis is clear.
  40. α-hemolytic Streptococci
    • Also known as viridans streptococci.
    • Important viridans streptococci: S. sanguis, S. mutans, S. mitis, S. salivarius
    • Viridans streptococci are normal flora of human upper respiratory tract and GI tract. (involved in development of dental caries, common cause of bacterial endocarditis)
    • Few virulence factors.
  41. β-hemolytic Streptococci
    • Most carry Lancefield designations (group A, B, C, G)
    • Numerous virulence factors, especially group A.
    • Group A: colonize upper respiratory tract (oropharynx) of children and to a lesser extent in adults. Labs typically look for Group A only.
    • Group B: Normal flora of perineum in 1/3 of adults (can be transferred from mother to child during birth.
    • Group C: Similar to group A
    • Group G: Infections of skin
  42. Group A Streptococci
    • Gram pos cocci.
    • AKA S. pyogenes and often designated as GAS.
    • Exudative pharyngitis is most common clinical picture.
    • Disease primarily of 5-15 year olds.
    • Pharyngitis is treated to prevent rheumatic fever.
    • Antibiotic treatment does not appear to prevent acute glomerulonephritis which is self-limiting.
    • Very responsive to Penicillin.
  43. Group A Streptococci Virulence Factors
    • M-proteins: surface cell wall proteins that facilitate spread through host tissue.
    • Adhesins: facilitate adherence; lipoteichoic acid, F-protein
    • Capsule: resists phagocytosis
    • Exotoxins: Streptolysins (lyse RBCs, WBCs, platelets), Streptokinases (lyse blood clots), Pyrogenic exotoxins (facilitate release of cytokines, superantigens), Proteins (coagulase, catalase, hyaluronidase, many inactivate antibiotics)
    • Superantigens: Polypeptide exotoxins that bind directly to class III MHC proteins and are able to turn on large numbers of T cells. This results in a massive release of IL-2 from T cells and TNF and IL-1 from macrophages which results in clinical fever, endothelial dysfunction and shock. Superantigens are produced by Group A Strep and S. aureus and other bacteria, viruses and fungi.
  44. Group B Streptococci
    • AKA S. agalactiae
    • Normal flora of perineum in 1/3 of population.
    • Neonates at ↑ risk of perinatal infections.
    • Infrequent cause of GU infections in adults.
  45. Streptococcus pneumoniae
    • Gram pos cocci in short chains or pairs.
    • Hemolytic pattern depends upon medium.
    • Normal flora of respiratory tract.
    • 84 serotypes.
    • #1 cause of sinusitis, otitis media, pneumonia, meningitis, and suppurative conjunctivitis.
    • Transmission via endogenous spread from colonized naso/oropharynx to distal sites.
  46. Staphylococcus Spp
    • Gram pos cocci in clusters.
    • Non-motile
    • Facultative anaerobes
    • Opportunistic
    • Diseases range from superficial skin infections, food poisoning (toxin-mediated), septic arthritis and pneumonia to life threatening sepsis.
  47. Staphylococcus Aureus
    • Most important member of group.
    • Only member found in humans that produces enzyme coagulase.
    • Collectively all other Staphylococcus spp grouped as coagulase negative Staph.
    • Virulence factors: enterotoxin (superantigen), TSS toxin (superantigen), exfoliatin, β-lactamases (cannot treat with Penicillin), numerous proteolytic enzymes.
    • #1 cause of bacteremia and sepsis, endocarditis, osteomyelitis
    • ↑ risk for hospitalized patients after surgery/trauma, foreign body, pts on antibiotic Rx
    • Common to skin, nasopharynx, GI and GU tracts.
    • Frequently colonizes (transiently) moist skin folds.
    • Can survive on dry surfaces for long periods.
    • Transmission by direct contact or fomites.
    • Nosocomial infection common.
  48. Methicillin-Resistant Staphylococcus aureus (MRSA)
    • Sensitive (MSSA)
    • Most commonly presents as superficial skin infection (closed collection of pus on skin, large abscess), but sepsis, pneumonia, meningitis possible.
    • Tx = incise and drain
    • Consider MRSA if there are blistery scales with violaceous color. Should treat immunocompromised pts, children, and if there are a large number of lesions.
  49. Coagulase Negative Staphylococci
    • Common on skin, in oropharynx, GI and GU tracts.
    • ↑ risk in hospital pts with indwelling devices, joint or heart prosthesis.
    • Virulence factors: glycocalyx capsule (attachment factor), proteolytic enzymes, cell wall structures (teichoic acid).
  50. Enterococcus
    • Gram pos cocci in pairs/short chains.
    • Facultative anaerobes.
    • Most important: E. faecalis and E. Faecium.
    • Found in small intestine in small #s and in the large intestine in large #s.
    • Important nosocomial infection.
    • Antibiotic resistance huge problem.
  51. Peptostreptococcus
    • Only clinically significant anaerobic Gram pos cocci.
    • P. magnus most common.
    • Normal flora of human (and many animal) GI tract; also urethra, vagina and skin.
    • Most often recovered from abscesses, wounds, and other polymicrobial infections.
    • ↑ risk of infection with surgery, immunodeficiency, malignancy, trauma, diabetes, any site with decreased vascular supply, and presence of foreign body.
  52. Medically Important Gram Positive Rods
    • (Aerobic)
    • Bacillus
    • Corynebacterium
    • Erysipelothrix
    • Listeria
    • Gardnerella
  53. Bacillus
    • Large Gram pos rods.
    • Virulence factors: endospores, enterotoxins
  54. Medically Important Species of Bacillus
    • B. anthracis: etiologic agent of anthrax
    • Anthrax has three clinical presentations: cutaneous (common, human infection through animal contact), gastroenteritis, inhalation (fatal, not transmitted person to person)
    • B. cereus: two clinical presentations, gastroenteritis (mediated by enterotoxins), ocular (conjunctivitis, mediated by trauma, leads to rapid progressive destruction)
  55. Corynebacterium
    • Gram pos rods.
    • C. diphtheriae is etiological agent of diphtheria.
    • All other species are ubiquitous in plants and animals.
    • Colonize human skin, GI, GU and respiratory tracts.
    • Common skin contaminant that is usually not clinically significant.
    • Collectively known as diphtheroids.
  56. Erysipelothrix
    • Small thin rods that form long filaments.
    • 3 species in genus; E. rhusiopathiae associated with human disease.
    • Grows slowly in media.
    • Colonize many animals, especially turkey, swine, fish.
    • Infections in humans usually zoonotic (transmitted from animals to humans), cutaneous.
    • Systemic form is rare, usually endocarditis.
  57. Listeria monocytogenes
    • Widely found in animals.
    • Asymptomatic carrier state, 1-5% as normal flora.
    • Human disease transmitted by contaminated food (esp. unpasteurized milk, soft cheese, cold cuts); vertical, zoonotic.
    • Virulence factors: hemolysis, listeriolysin O, able to survive colt temperatures.
  58. Medically Important Gram Positive Rods
    • (Anaerobic. Colonize skin and mucosal surfaces.)
    • Actinomyces
    • Clostridium
    • Lactobacillus
    • Mobiluncus
    • Propionibacterium
  59. Actinomyces
    • Anaerobic rods
    • Filamentous
    • A. israelii most commonly involved in human infections
    • Colonize upper respiratory, GI and female genital tracts
    • Low virulence.
    • Cause infection (actinomycosis) when mucosal barriers are disrupted.
    • Infections often chronic.
  60. Clostridium
    • Anaerobic rods
    • Spore formers.
    • Ubiquitous in soil, water, human GI tract.
    • 4 species medically important: C. perfringens, C. botulinum, C. tetani, C. difficile
  61. Clostridium perfringens
    • Anaerobic rods. Forms spores.
    • Grows easily and rapidly in vitro.
    • Human disease ranges from mild gastroenteritis to severe myonecrosis (gas gangrene).
    • Disease develops in wound that becomes infected with spores from environment.
    • 5 serotypes (A-E). A responsible for most human disease.
    • Virulence factors: lethal toxins, α-toxin (α-lecithinase) produced in large quantities by type A strains. Lecithinase lyses RBC, WBC, and any type of cell.
  62. Clostridium botulinum
    • Anaerobic rods. Forms spores.
    • Etiologic agent of botulism.
    • Bacteria divided into 4 groups; I, II, III, IV
    • Commonly found in soil but disease is rare.
    • Disease mediated by neurotoxin.
    • 3 clinical presentations: food borne (improper canning), infant botulism (giving toddlers honey, their normal flora is not fully developed yet), wound botulism (contaminated wounds)
  63. Clostridium tetani
    • Anaerobic rods. Forms spores.
    • Difficult to grow in vitro.
    • Virulence factors: Hemolysin, Neurotoxin (tetanospasmin) responsible for clinical expression of tetanus by blocking neurotransmitter release.
    • Etiologic agent of tetanus.
  64. Clostridium difficile
    • Anaerobic rods. Forms spores.
    • Most common etiologic agent of antibiotic associated colitis (AAC).
    • Normal GI flora in some; disrupted by antibiotics.
    • Virulence factors: Toxin A (enterotoxin), Toxin B (cytotoxin)
    • Have double digit diarrhea.
    • Nosocomial and opportunistic.
  65. Lactobacillus
    • Normal flora of mouth, GI and GU tracts
    • Often recovered in large #s of specimens (esp. urine) as contaminants.
    • Common clinical presentations; transient bacteremia, endocarditis, opportunistic septicemia.
  66. Mobiluncus and Gardnerella
    • Gram stain appear neg or variable but are classified as pos.
    • Have Gram pos cell wall, have antibiotic susceptibility profile similar to Gram pos, lack endotoxin.
    • Both colonize female genital tract in large numbers.
    • Increases dramatically in bacterial vaginitis.
  67. Propionibacterium
    • Genus of small, Gram pos rods that on Gram stain appears in clumps or chains.
    • Anaerobes, some aerotolerant.
    • Normal flora of skin, oropharynx, and female genital tract.
    • P. acnes is most medically important species.
    • Acne and deep inflammatory problem with prosthetics.
  68. Neisseria
    • Gram neg cocci.
    • 3 important genera: Neisseria, Eikenella, Kingella
    • Neisseria: 10 spp found in humans
    • N. gonorrhoeae and N. meningitidis most important.
    • N. gonorrhoeae is a strict human pathogen; not a colonizer, not normal flora.
    • Other spp frequently colonize upper respiratory tract and less frequently colonize anogenital mucosa.
    • N. gonorrhoeae and N. meningitidis unique virulence factors: lipooligosaccharide (LOS) instead of LPS which also functions as endotoxin, pili (attachment, motility, transfer genetic info), outer membrane proteins
    • Outer membrane proteins: I (porin) ↑ intracellular survival, II (opacity) mediates attachment to host epithelial cells, III (reduction-modifiable) prevents cidal action of serum.
  69. Neisseria gonorrhoeae
    • N. gonorrhoeae is a strict human pathogen; not a colonizer, not normal flora.
    • Capable of intracellular survival.
    • Cause dz in upper respiratory tract and anogenital mucosa.
    • Asymptomatic women provide reservoir for infection.
    • Transmission can occur perinatally.
    • About 2% of infections disseminate; blood, skin, joints (females, unilateral knee)
    • N. gonorrhoeae unique virulence factors: lipooligosaccharide (LOS) instead of LPS which also functions as endotoxin, pili (attachment, motility, transfer genetic info), outer membrane proteins
    • Outer membrane proteins: I (porin) ↑ intracellular survival, II (opacity) mediates attachment to host epithelial cells, III (reduction-modifiable) prevents cidal action of serum.
  70. Neisseria meningitidis
    • Encapsulated
    • Can survive intracellularly.
    • Cause dz in upper respiratory tract and anogenital mucosa.
    • Receptors in nasopharynx allow colonization by meningococcal pili.
    • About 10% of pop colonized.
    • Dz spread by direct contact or respiratory droplet.
    • Meningitidis develops as result of hematogenous spread.
    • Endemic in 0-5yo and peaks again in late adolescence.
    • Very young children tend to have atypical presentation, GI sx.
    • Prophylaxis is Cipro.
    • N. meningitidis unique virulence factors: lipooligosaccharide (LOS) instead of LPS which also functions as endotoxin, pili (attachment, motility, transfer genetic info), outer membrane proteins
    • Outer membrane proteins: I (porin) ↑ intracellular survival, II (opacity) mediates attachment to host epithelial cells, III (reduction-modifiable) prevents cidal action of serum.
  71. Acinetobacter
    • Causes meningitis, pneumonia, UTI, sepsis.
    • Ubiquitous saprophyte (grows on and derives its nourishment from dead or decaying organic).
    • Similar in niche to Pseudomonas and Enterobacter.
    • Can survive on both moist and dry surfaces for long periods.
    • Important nosocomial pathogen.
    • Normal flora in oropharynx in small % of pop,
    • Multi drug resistance.
  72. Acinetobacter baumannii
    • Gram neg coccobacilli.
    • Most common Acinetobacter.
    • Frequently isolated from skin, mucous membranes, urine of hospital pts.
    • Causes UTIs, sepsis, pneumonia.
    • Associated with battlefield injuries.
    • Drug resistance by plasmid becoming problematic.
    • ↑ risk for pts on ventilators or other indwelling instruments.
  73. Bordatella
    • Gram neg coccobacilli.
    • Strictly aerobic.
    • 7 known spp.
    • Bordetella pertussis is strictly human pathogen.
    • Found in bronchopulmonary.
    • B. pertussis etiologic agent of whooping cough.
    • Virulence factors: protein adhesins (inhibit phagocytosis and promote intracellular survival), toxins (mediate respiratory and systemic dz)
  74. Brucella
    • Gram neg coccobacilli.
    • Can survive intracellularly.
    • Important zoonotic pathogen similar to Francisella.
    • Has multiple animal reservoirs.
    • Usually get from unpasteurized goat cheese.
    • Pasteurization ↓ risk of human infection.
    • Causes brucellosis.
  75. Eikenella corrodens
    • Gram neg bacillus.
    • Corrodes agar medium and smells like bleach.
    • Normal flora of upper respiratory tract of humans.
    • Implicated in bite infections and endocarditis in pts with preexisting heart dz.
    • Belongs to HACEK group: Haemophilus species (Haemophilus parainfluenzae, Haemophilus aphrophilus, Haemophilus paraphrophilus), Actinobacillus actinomycetemcomitans, Cardiobacterium hominis, Eikenella corrodens, and Kingella species.

    • Francisella
    • Gram neg coccobacillus.
    • Important zoonotic pathogen similar to Brucella.
    • Capable of intracellular survival.
    • Only 2 spp; F. tularensis more important in US.
    • Humans often accidental hosts (arthropod bites, eating infected rabbits).
    • Inhalation associated with high mortality.
    • Infects respiratory tract.
  76. Kingella kingae
    • Anaerobic
    • Gram neg coccobacillus.
    • Normal flora of oropharynx.
    • K. kingae most common spp.
    • Belongs to HACEK group: Haemophilus species (Haemophilus parainfluenzae, Haemophilus aphrophilus, Haemophilus paraphrophilus), Actinobacillus actinomycetemcomitans, Cardiobacterium hominis, Eikenella corrodens, and Kingella species.
  77. Moraxella spp
    • 7 spp; catarrhalis most important.
    • Normal flora of oropharynx.
    • Infects sinuses, ear, eye.
    • Virulence factors: LPS (endotoxin), polysaccharide capsule, pili, β-lactamase production
    • Causes sinusitis, otitis media, suppurative conjunctivitis, bronchitis
  78. Pasteurella multocida
    • Gram neg coccobacillus.
    • Cats and dogs are natural reservoirs, oral flora.
    • Zoonotic transmission; cat bite, scratch.
    • Wound infection can cause bacteremia, osteomyelitis, endocarditis and meningitis if it crosses blood brain barrier.
    • Hand infection is always a surgical emergency.
    • Virulence factors: polysaccharide capsule, endotoxin
  79. Veillonella spp
    • Gram neg anaerobic cocci.
    • Normal flora of mouth, GI and female genital tract.
    • Virulence factor: LPS endotoxin
    • Infections rare in immunocompetent.
    • Infections are serious and include osteomyelitis (most common), meningitis, endocarditis.
  80. Gram Negative Rods
    • Enteric gram negative rods: Some cause both GI and extra-intestinal dz, some only GI dz, some are part of normal intestinal flora but only cause extra-intestinal dz, can also be found in soil and water.
    • Saprophytic gram neg rods found in soil and water are not commonly part of GI normal flora.
    • Respiratory gram neg rods.
    • Zoonotic gram neg rods.
    • Less common opportunistic gram neg rods.
  81. Enterobacteriaceae
    • AKA coliforms or enteric bacteria.
    • Ubiquitous; soil, water, vegetation, normal flora of human GI tract.
    • Infection via animal reservoir, human carrier, or endogenous.
    • Virulence factors: exotoxin (including enterotoxin), surface structural antigens (including LPS (O antigens), capsule (K antigens) and flagella (H antigens)), Pili, antibiotic resistance
    • Endotoxin LPS effects: fever, changes in WBC count, ↓ platelets, ↓ peripheral circ and perfusion, shock and death
    • Many are opportunistic and/or nosocomial pathogens.
    • As a group, account for 1/3 of all septicemias and 2/3 of all UTIs.
  82. Enteric Gram Neg Bacteria Diseases
    • Dz Inside and Outside GI Tract: Escherichia, Salmonella, Vibrio*
    • Dz Mostly Inside GI Tract: Shigella, Campylobacter*, Helicobacter*, Yersinia*
    • Dz Mostly Outside GI Tract: Klebsiella, Enterobacter, Serratia, Proteus, Providencia, Morganella, Bacteroides*
    • *Not Enterobacteriaceae
  83. Gram Negative Rods
    • Saprophytic: Acinetobacter, Pseudomonas
    • Zoonotic: Brucella, Francisella, Pasteurella
    • Respiratory: Bordetella, Haemophilus, Moraxella, Legionella
    • Less Common Pathogenic: Bartonella, Capnocytophaga, Prevotella, HACEK group
  84. Escherichia coli (E. coli)
    • Gram neg rod.
    • #1 cause of UTIs (community & nosocomial)
    • Etiologic agent of bacteremia, sepsis, neonatal meningitis
    • (Neonatal meningitis also caused by Group B strep and Listeria.)
    • Women at ↑ risk due to short urethra.
    • Anterior portion of urethra usually colonized.
    • Transmission via fecal contamination or catheter use.
    • Infecting strains originate from GI tract.
    • Virulence factors: include adhesins and exotoxins
    • ↑ resistance to multiple antibiotics is problem.
  85. Etiologic Agents of Gastroenteritis
    • E. coli 5 subdivisions
    • Enterotoxigenic
    • Enteropathogenic
    • Enteroadherent
    • Enterohemorrhagic
    • Enteroinvasive
  86. Salmonella
    • Gram neg rod.
    • Can colonize nearly any animal (like campylobacter)
    • Animal reservoir mostly responsible for non-typhoid human dz.
    • Transmitted by ingestion of contaminated food; eggs, poultry, dairy
    • Large inoculum required for infection.
    • Salmonella typhi, S. choleraesuis, and S. paratyphi A and B are serotypes that only infect humans and are transmitted by fecal-oral route. Chronic carrier state common. Typhoid spp only need small inoculum for infection.
    • At risk: travelers to SE Asia, Africa, Latin America
    • Salmonella usually NOT treated.
  87. Vibrio
    • Gram neg rod.
    • Commonly found in water.
    • V. cholerae: causes GI dz via contaminated water.
    • V. vulnificus: causes skin and soft-tissue infections, cellulitis
    • V. parahaemolyticus: causes acute gastroenteritis (mostly self-limiting) associated with consumption of contaminated seafood.
  88. Shigella
    • Gram neg rod.
    • Strictly human pathogen.
    • 4 spp: dysenteriae (A), flexneri (B), boydii (C), sonnei (D) is most prevalent.
    • Reservoir human GI tract.
    • Infection common in children (daycare centers) and those in custodial facilities.
    • Transmitted person to person, fecal-oral route.
  89. Enterobacteriaceae Klebsiella, Enterobacter, Serratia
    • Gram neg rods.
    • Klebsiella spp: most important and most commonly isolated.
    • Virulence factors: endotoxin (LPS), capsule, β-lactamase, urease
    • Causes pneumonia
    • Important nosocomial pathogen.
    • Enterobacter & Serratia: both important causes of nosocomial infections, especially UTIs and pneumonia. Multidrug resistance increasing problem.
  90. Enterobacteriaceae Proteus, Providencia, Morganella
    • Gram neg rods.
    • Proteus spp: mirabilis and vulgaris are important spp, common pathogen in community acquired UTIs, plays role in renal calculi, produce large amounts of urease.
    • Providencia stuartii and Morganella spp: important causes of nosocomial UTIs
  91. Campylobacter spp
    • Gram neg bacillus.
    • Most commonly cause gastroenteritis, sepsis, spontaneous abortion.
    • Microaerophilic.
    • Animals are natural reservoirs.
    • Human infection from ingestion of contaminated food, milk or water; also fecal-oral route.
    • Virulence factors: adhesins, cytotoxic enzymes, enterotoxin
  92. Campylobacter jejuni
    • Most common cause of gastroenteritis in US.
    • At risk: ingestion of large #s of organisms or those lacking gastric acid (people taking proton pump inhibitos)
    • Usually self-limiting but sometimes treat for severe infections.
  93. Yersinia
    • Gram neg rod.
    • Y. pestis: etiologic agent of plague, capsule, resistance to serum killing
    • Y. enterocolitica: infrequent cause of gastroenteritis, can grow at cold temp
    • Y. pseudotuberculosis: common animal pathogen, humans infected by consuming contaminated food.
    • Virulence factors: all three spp have genes that code for adherence, phagocytic inhibition, and inhibition of platelet aggregation.
  94. Helicobacter pylori
    • Gram neg comma shaped bacillus.
    • Virulence factors: urease (byproduct is ammonia which buffers stomach acid so it can survive in stomach), motility, adhesin, flagella, LPS
    • Human GI tract is only reservoir.
    • Transmission via fecal-oral route.
    • Associated with gastritis, peptic ulcer dz, gastric malignancies and enteric dz.
    • Drug resistance becoming problem.
  95. Bacteroides & Prevotella
    • Anaerobic Gram neg rods.
    • Bacteroides: below waist
    • Prevotella: above waist
    • Normal flora of colon.
    • Frequent cause of infection by breaching mucosal barriers.
    • Bacteroides fragilis: most important, virulence factors include LPS, capsule & proteolytic enzymes.
    • Prevotella: normal flora of upper respiratory and female genital tracts
  96. Haemophilus
    • Gram neg bacilli.
    • Virulence factors: LPS, polysaccharide capsule
  97. Haemophilus influenzae
    • Most commonly associated with otitis media and sinusitis (also consider strep pneumo and Moraxella catarrhalis)
    • β-lactamase resistance can be problem
  98. Haemophilus ducreyi
    • Etiologic agent of chancroid (soft chancre) and ulcerative venereal dz.
    • Most common in Africa/Asia
  99. Legionella spp
    • Gram neg.
    • L. pneumophila: most important, 85% of all infections
    • Can parasitize amoebae and replicate.
    • Can survive for years on biofilms.
    • Community and nosocomial infections of pneumonia.
  100. Pseudomonas aeruginosa
    • Gram neg rod.
    • Ubiquitous: soil, water, vegetative matter, can live in tap water
    • Found on human skin and mucosa.
    • Upper respiratory infections limited to ear and eye
    • Virulence factors: exotoxins, endotoxins, pili, polysaccharide capsule.
    • Important nosocomial pathogen; antibiotic overuse drives this.
  101. Bartonella
    • Gram neg rod.
    • B. quintana: etiologic agent of trench fever, strictly human dz, transmitted by body louse.
    • B. henselae: etiologic agent of cat scratch fever and bacillary angiomatosis, found in oropharynx of cats
  102. Capnocytophaga canimorsus
    • Gram neg bacillus.
    • Dysgonic fermenter.
    • DF-1 found in respiratory tract and saliva of human.
    • DF-2 found in dogs/cats
    • Commonly caused by bite infections (also Pasteurella multocida and Eikenella corrodens)
    • Mild to deadly infection.
    • Asplenic pts can have severe sepsis.
  103. Spirochaetales
    • Thin, coiled bacteria with flagella
    • Spirochetes: treponema and Borrelia
    • Leptospira: Leptospira
  104. Treponema spp
    • 2 species, pallidum and carateum, cause dz.
    • Several species have subspecies.
    • Treponema palladium subspecies pallidum: etiologic agent of syphilis.
    • Virulence factors: endotoxin, fibronectin prevents phagocytosis
  105. Borrelia
    • Spirochete with multiple flagella
    • Weakly stains Gram neg.
    • B. burgdorferi: etiologic agent of Lyme Dz
    • B. recurrentis: etiologic agent of relapsing fever
  106. Leptospira
    • Animal reservoir for human infection; exposure to pet urine.
    • Wide spectrum of dz from mild (subclinical) to fatal (Weil’s dz)
  107. Mycoplasmataceae
    • Lack cell walls
    • Cell membrane contains sterols
    • 2 medically important genera: Mycoplasma, Ureaplasma
  108. Mycoplasma
    • Colonize human GU tract.
    • M. pneumoniae: most important, strict human pathogen, causes both upper and lower respiratory dz
    • Virulence factors: adhesin protein, superantigen
    • M. hominis, M. genitalium: colonize GU tract, possible role in spontaneous abortions
  109. Ureaplasma
    • Colonize human GU tract.
    • U. urealyticum: most common/most important, infants (esp. females) colonized with species of both Mycoplasma and Ureaplasma at birth but this disappears shortly afterward and then increases again in early adulthood.
    • Important cause of urethritis.
  110. Chlamydiaceae
    • Gram neg
    • Energy parasites, use host ATP for own energy requirements.
    • 2 genera: Chlamydia, Chlamydophila
    • Chlamydia: C. trachomatis
    • Chlamydophila: C. pneumoniae, C. psittaci
    • Developmental cycle includes elementary body (analogous to spore, resistant, infectious form) and reticulate body (metabolically active, replicating form)
  111. Chlamydia trachomatis
    • 3 biovars: murine infection, C. trachomatis, lymphogranuloma venereum (LGV)
    • C. trachomatis: capable of infecting only certain cells, small abrasions/lacerations facilitate infection, infants can be infected at birth (like N. gonorrhoeae)
    • Virulence factors: unique life cycle (EB and RB), LPS endotoxin, capable of recurrent or persistent infection
    • Etiologic agent of cervicitis, urethritis, and in 3rd world countries, trachoma.
  112. Chlamydiaceae pneumoniae
    • Important cause of upper and lower respiratory infection.
    • Role in atherosclerosis.
  113. Chlamydiaceae psittaci
    • Etiologic agent of psittacosis (parrot fever)
    • Any bird can be reservoir for infection
    • Infection acquired via respiratory route and then hematogenous spread.
  114. Rickettsia, Ehrlichia, Coxiella
    • Coccobacilli similar in structure to Gram neg bacteria LPS
    • Obligate intracellular parasites
    • Humans are accidental hosts via bite of infected arthropods
    • Rocky Mountain Spotted Fever (RMSF) prototypical rickettsial dz
    • Headache + Fever + Myalgia = RMSF until proven otherwise.
  115. Aerobic Actinomycetes
    • Gram pos bacteria that resemble fungi.
    • Commonly found in soil, decaying vegetation, ventilation systems.
    • Able to colonize humans.
    • Only cause dz in immunocompromised.
    • Medically important genera: Nocardia, Tropheryma, Gordonia, Tsukamurella
  116. Nocardia spp
    • Infection by inhalation or traumatic implantation.
    • Immunocompetent pts: cutaneous, chronic pulmonary dz
    • Immunocompromised pts: bronchopulmonary, severe cutaneous, or CNS dz
  117. Mycobacteria tuberculosis
    • Non-motile rods.
    • Unique cell walls: lipid rich, mycolic acid, cannot be Gram stained.
    • Strict human pathogen.
    • Etiologic agent of tuberculosis.
    • Intracellular pathogen capable of lifelong infection.
    • M. tuberculosis complex includes M. leprae and M. bovis.
  118. Mycobacterium avium complex
    • Ubiquitous in soil, water, fowl.
    • Multiple manifestations of pulmonary dz in immunocompetent pts.
    • Disseminated dz in immunocompromised pts, especially those with AIDS.
  119. Parainfluenza Viruses
    • Dz limited to respiratory tract, mostly upper respiratory dz.
    • 4 serotypes: 1-3 always associated with croup, mostly in children; 4 causes more common cold type picture.
    • Generally mild dz.
    • Transmitted by inhalation.
  120. Respiratory Syncytial Virus (RSV)
    • Causes localized infection of respiratory tract.
    • Seasonal incidence; peaks late fall, early winter.
    • Spectrum from colds to pneumonia.
    • Very contagious.
    • Bronchiolitis in children < 2 is most classic association, especially present in 4-8mo old children.
    • Difficulty breathing, retractions, accessory muscles.
    • Can cause lower and upper respiratory dz (also influenza and human metapneumovirus)
  121. Human metapneumovirus
    • Causes upper and lower respiratory tract; clinical presentation similar to RSV.
    • Exacerbates asthma.
    • Tx must include bronchodilator
  122. Paramyxoviruses
    • Measles: like RSV causes giant cell formation, only one serotype
    • Mumps: many infections asymptomatic, bilateral parotitis + fever, CNS complications not uncommon, only one serotype
  123. Orthomyxoviridae
    • Influenza virus A, B, C
    • Infects birds, humans, animals.
    • Genetic diversity (instability) creates pandemics and epidemics (antigenic drifts with small changes and shifts with big changes)
    • Upper and lower respiratory pathogen.
    • A and B typically infect humans.
    • C only causes mild upper respiratory illness.
    • One of few respiratory viruses that cause fever.
    • Classic presentation: dry cough, fever, myalgia, sometimes has GI component
  124. Picorna Viruses
    5 genera (3 infect humans): enteroviruses (polio viruses, Coxsackie A & B viruses, ECHO viruses, enteroviruses), rhinoviruses, heparnavirus (Hepatitis A virus)
  125. Rhinovirus
    • Most important cause of common cold, more than 100 serotypes.
    • Transmitted by direct contact, inhalation or fomites.
    • Cool replication temperature (nose).
    • Average child has 3-8 colds/year.
  126. Enterovirus
    • Transmitted via fecal-oral route.
    • Resistant to detergent, acid, drying, extremes of temperature
    • Strictly human pathogens.
    • Neonates at increased risk.
    • Infant with serious neonatal infection like meningitis; consider Group B strep, Listeria, E. coli, Enterovirus.
  127. Rotavirus
    • Double stranded RNA
    • Types A and B
    • Capsid helps survive acidic environment.
    • Usually infects toddlers.
    • Usually starts with 1-2 episodes of vomiting, vomiting goes away and they have diarrhea that doesn’t go away.
    • “Happy diarrhea”, afebrile, happy, eating ok
  128. Norovirus
    • Cruise ship diarrhea
    • Environmentally resistant RNA virus
    • Group includes Norwalk, Calicivirus, and Astroviruses.
    • Common cause of community outbreaks of gastroenteritis.
    • Transmission: fecal-oral, respiratory droplet, person to person.
    • Self-limiting dz; 48-72 hrs
  129. Coronavirus
    • Most cause upper respiratory illness, nasal symptoms, head colds.
    • Able to survive GI tract and spread via fecal-oral route.
    • Spread mostly by aerosols/droplets.
    • Exacerbates asthma.
    • Etiologic agent of SARS.
  130. Medically Important DNA Viruses
    • Herpesviridae: Herpes simples (HSV) 1&2, Varicella zoster virus (VZV), Epstein-Barr (EBV), Cytomegalovirus (CMV)
    • Parvoviridae: Parvovirus B19
    • Adenoviridae: Adenovirus
    • Hepadnaviridae: Hepatitis B virus
    • Papovaviridae: Human papilloma virus (HPV)
    • Poxviridae: smallpox virus
  131. Herpes Viruses
    • Enveloped
    • Ubiquitous virus, infections common
    • Latent, persistent infection and asymptomatic shedding are important dz factors.
    • Transmission: direct (including sexual), contact, vertical, respiratory droplet
    • Human Herpesvirus 1-8
    • HHV 1&2 = HSV 1&2
    • HHV 3 = VZV
    • HHV 4 = EBV
    • HHV 5 = CMV
    • HHV 6&7 appears associated with roseola
    • HHV 8 associated with Kaposi’s sarcoma
  132. Human Papilloma Virus (HPV)
    • Double stranded DNA virus
    • Capable of persistent and latent infection.
    • Infects and replicates in squamous epithelium of skin and mucous membranes to induce epithelial proliferation (warts).
    • Some strains capable of oncogenic transformation and are associated with dysplasia.
    • Cofactors play important role; such as smoking.
    • Clinical manifestations: cutaneous, mucosal, anogenital.
    • Transmission via direct contact (including sexual) and perianal.
    • Cervical dysplasia requires frequent monitoring.
  133. Adenovirus
    • DNA virus
    • Varied clinical syndromes
    • Tissue tropism important factor.
    • Major cause of conjunctivitis.
    • Transmitted via direct, respiratory, or fecal-oral route.
    • Capable of latent infection.
    • Some strains may be oncogenic.
    • Sometimes clinical presentation looks like Group A strep.
  134. Parvovirus
    • Fifth’s Disease
    • B19 only known pathogen.
    • Etiologic agent of erythema infectiosum in children and migratory polyarthritis in adults.
    • Transmission via respiratory droplet.
    • Virus has affinity for RBCs
    • Can cause aplastic crisis in pts with chronic anemia.
  135. Hepadnavirus Hepatitis B Virus (HBV)
    • Enveloped
    • Transmission via parenteral and sexual routes
    • Vaccination part of childhood schedule.
    • ↑ risk for IVDU, homosexual males, immigrants from areas of high endemicity
    • Dz in children usually mild; asymptomatic carriers.
    • Chronic dz; chronic carrier state associated with increased risk of liver cancer.
  136. Heparnavirus Hepatitis A Virus (HAV)
    • Picornavirus
    • Transmission via ingestion of contaminated food and water and fecal-oral route
    • In adults, abrupt onset with moderate/severe symptoms.
    • In children, generally mild disease, asymptomatic carriers. Daycare centers are major source of spread.
    • HAV vaccine part of childhood schedule.
    • Not associated with chronic liver dz as in HBV.
  137. Hepatitis C Virus
    • Flavivirus
    • Similar transmission to HBV.
    • Transmission via parenteral and sexual routes
    • #1 cause of hepatocellular carcinoma.
    • Must have liver biopsy to determine treatment.
    • Response to Rx with interferon.
  138. Hepatitis D Virus
    • AKA delta agent
    • Viral parasite; replicates only in HBV infected cells.
    • Transmission same as hepatitis B & C.
    • Co-infection, super-infection possible.
    • Increases severity of HBV infections.
    • Chronic infection.
  139. Hepatitis E Virus
    • Calicivirus
    • Similar to Norwalk agent.
    • Transmission via fecal-oral route.
    • Similar to HAV in transmission and pathogenicity.
    • Infection especially serious in pregnant women.
    • No chronic dz.
  140. Dimorphic Fungi
    • Found in soil, usually enriched with bird/bat droppings.
    • Grow as molds at 25°C and as yeasts at 37°C.
    • Dissemination to skin and CNS is deadly.
    • Except for sporothrix, primary infection is always pulmonary.
    • 6 dimorphic fungi (all infect humans): Histoplasma capsulatum (also duboisii), Blastomyces dermatitidis, Sporothrix schenckii, Coccidioides immitis (also C. posadasii), Paracoccidioides brasiliensis, Penicillium marneffei
    • Histoplasma capsulatum (also duboisii): Eastern US, Caribbean
    • Blastomyces dermatitidis: Mississippi River basin, SE US
    • Sporothrix schenckii: not geographically restricted, usually infected by break in skin/traumatic implantation, systemic infection is rare
    • Coccidioides immitis (also C. posadasii): SW US and N. Mexico, desert fever, San Joaquin fever
    • Paracoccidioides brasiliensis: Central/S. America
    • Penicillium marneffei: Thailand, SE Asia
  141. Mechanisms of Fungal Pathogenesis
    • Cause human dz by: metabolic toxicity (accidental/intentional ingestion of fungi); hypersensitivity (air-borne fungal elements act as antigenic stimulants producing rhinitis, asthma, pneumonitis; host colonization with subsequent disease (few fungi cause dz in healthy people)
    • Fungi are low virulence organisms.
    • Humans are innately immune to fungal infections; intact skin and mucous membranes are barriers.
    • Most fungal infections in immunocompetent hosts are chronic and self-limiting.
    • Opportunistic fungal infections occur in immunocompromised.
    • Classified by level of host tissue invaded.
  142. Fungal Classification by Level of Tissue Invasion
    • Superficial mycoses: limited to outermost layers of hair and skin.
    • Cutaneous mycoses: extend deeper into dermis; nail infections.
    • Subcutaneous mycoses: involve subcutaneous tissue, including muscle and fascia.
    • Systemic mycoses: originate mostly in lungs but can spread to many organs (disseminated mycoses)
    • Opportunistic mycoses: fungi traditionally thought to be non-pathogens but paying increasing role in immunocompromised pts.
  143. Superficial & Cutaneous Mycoses
    • Superficial: Malassezia furfur
    • Cutaneous dermatophytes: Trichophyton spp, Epidermophyton floccosum, Microsporum spp.
    • Cutaneous non-dermatophytes: Candida spp, multiple genera of fungi can cause onychomycosis
  144. Malassezia furfur
    • Lipophilic yeast that causes superficial infection.
    • Etiologic agent of tinea versicolor.
  145. Dermatophytes
    • 3 common genera: Epidermophyton, Trichophyton, Microsporum
    • Geophilic, Zoophilic or Anthropophilic
    • Clinical presentation: tinea (ringworm)
    • Ringworm can be treated topically except for scalp.
  146. Subcutaneous Mycoses
    • Sporotrichosis: Sporothrix schenckii
    • Chromoblastomycosis: Cladosporium, Exophiala, Fonsecaea,
    • Mycetoma: Acremonium, Madurella
    • Except for sporotrichosis, these infections are rarely seen in US.
    • Wide spectrum of infections.
    • Infection by traumatic implantation.
    • Extremely difficult to treat; surgical intervention often required.
    • More common in tropical climates.
  147. Sporothrix schenckii
    • Etiologic agent of sporotrichosis.
    • Dimorphic fungi.
    • Ubiquitous in soil and decaying vegetation.
    • Infection associated with thorny injury, esp. roses and wood splinters.
    • Infections usually chronic.
    • Lesions develop along lymphatic pathway.
    • Prevent by wearing gloves.
  148. Systemic Mycoses
    • Most are soil organisms that aid in pathogenicity.
    • Primary infection is respiratory via inhalation but is almost always asymptomatic and self-limiting.
    • Disseminated disease (secondary) is clinical presentation.
    • Skin is common site of disseminated disease and lesions are often pathognomonic.
    • Sporothrix can cause systemic dz.
  149. Opportunistic Mycoses
    • Systemic fungi that are not dimorphic.
    • Candida spp.
    • Cryptococcus neoformans
    • Aspergillus spp
    • Zygomycetes
    • Fusarium and other non-pigmented molds
    • Pneumocystis jiroveci
  150. Aspergillus spp
    • Common mold; soil, decaying vegetation, construction sites
    • Colonizes human airway.
    • Can cause direct tissue invasion in immunocompromised.
    • Virulence factors: conidia able to bind to human fibrinogen, host of metabolic proteins, invasive disease associated with neutropenia and impaired neutrophil function.
  151. Candida
    • Species of Candida are the most common opportunistic fungi.
    • Virulence factor: yeast-to-hyphal transformation
    • Capable of invading deep tissues of multiple organs
    • Colonize oropharynx, gut, GU
    • Usually true endogenous infection caused by break in mucosal lining.
  152. Cryptococcus neoformans
    • Encapsulated yeast protects from phagocytosis and suppresses humoral and cellular immune responses.
    • CNS is preferred site of infection with meningitis being most common clinical manifestation.
    • Able to grow at 37°C (but is not dimorphic)
    • Meningitis differential: Strep pneumo (#1), Neisseria meningitidis, Listeria monocytogenes, Cryptococcus neoformans
  153. Non-Pigmented Molds
    • “Hyaline” molds
    • Capable of causing opportunistic dz.
    • Fusarium spp: cause eye infections, conjunctivitis, keratitis, especially in immunocompromised who wear contact lenses.
  154. Pneumocystis jiroveci
    • Etiologic agent of Pneumocystis jiroveci pneumonia (PCP)
    • Infection by inhalation.
    • Most common AIDS infection.
  155. Parasitology
    • Protozoa: unicellular
    • Metazoa: multicellular
    • Almost always acquired via an exogenous source.
    • Most common routes of infection are oral ingestion and direct penetration of skin or other host tissue.
    • Contamination of environment by human/animal waste facilitates spread.
    • Many acquired by bites of arthropod vectors.
    • Grouped by location where they cause dz (protozoa) or by morphology (metazoa).
    • Intestinal protozoa
    • Urogenital protozoa
    • Blood and Tissue protozoa
    • Nematodes (round worms)
    • Cestodes (tape worms)
    • Trematodes (flukes)
  156. Entamoeba histolytica
    • Has cyst and trophozoite forms.
    • Flies and cockroaches are important vectors.
    • Infection can result in asymptomatic carriage, intestinal infection, or extra-intestinal infection (liver, lungs, brain and heart are common sites where they form abscesses).
  157. Coccidia
    • Have asexual and sexual cycles.
    • Most important members: Cryptosporidium parvum, Isospora belli.
    • Cryptosporidium parvum: in most water supplies, can evade chlorination and water purification, usually mild and self-limiting illness
    • Isospora belli: important AIDS pathogen, transmitted via contaminated food or water, fecal/oral, or oral/anal routes; infection results in asymptomatic carriage, mild to severe gastroenteritis.
  158. Giardia lamblia
    • Cyst and trophozoite stages.
    • Wilderness niche; streams, lakes, “beaver fever”
    • Many animals infected, including domestic pets.
    • Transmission via contaminated water or food or person to person by fecal/oral route.
    • Epidemics common in daycare or other institutional settings.
    • Infection results in asymptomatic carriage, mild acute or chronic diarrhea (diarrhea for a few days then better, then repeats) or severe malabsorption (greasy frothy stool).
    • Most common intestinal protozoa you’ll see in this area.
  159. Trichomonas vaginalis
    • Genitourinary
    • Trophozoite form only.
    • Inhabits only female urethra and vagina (5-20%) and male urethra and prostate (2-10%)
    • Transmission: direct sexual contact, some evidence of fomite involvement
    • Males mostly asymptomatic carriers.
    • Females can be asymptomatic but most have mild symptoms
    • Clinical presentations: strawberry cervix, watery cervical discharge, vaginitis, discharge, postcoital bleeding
  160. Toxoplasma gondii
    • Coccidia
    • Develops in intestinal cells of cats; cysts mature and are excreted in feces.
    • Infection results from ingestion of infected oocytes or contaminated meat.
    • Most infections are asymptomatic.
    • Human infection ubiquitous.
    • Clinical manifestations of symptomatic disease: flu-like symptoms (acute), congenital infection (usually results in severe problems, abortion, stillbirth), reactivated disease in immunocompromised may cause brain, eye and lung diseases.
  161. Naegleria fowleri
    • Thermophilic free-living amoeba found in water (fresh water lakes, polluted lakes, swimming pools)
    • Acute meningoencephalitis is most common disease presentation.
    • Invades CNS via cribriform plate.
    • Rapidly fatal in children and young adults.
    • Identified by motility in CSF.
  162. Plasmodium spp
    • Coccidia
    • Mosquito important alternate host.
    • Causes Malaria.
    • Organism initially develops in liver and then parasitizes RBCs.
    • 4 species of Plasmodium: vivax, malariae, ovale, falciparum
    • #1 cause of parasitic death worldwide.
  163. Enterobius vermicularis
    • Pinworms
    • Infection occurs after ingestion of eggs.
    • Transmission via person to person contact, fomites, aerosol.
    • May cause asymptomatic carriage state or symptomatic disease.
    • Children have rectal itching.
    • Prepubescent girls could have vaginal irritation and discharge
  164. Ascaris lumbricoides
    • Most common intestinal helminth
    • Risks: poor sanitation/hygiene, use of human feces for fertilizer.
    • Infection occurs by ingestion of eggs.
    • Intestinal dz: abdominal pain, distention, vomiting
    • Pulmonary dz: cough, dyspnea, wheezing
  165. Ancylostoma spp/ Necator americanus
    • Hookworms
    • Common in SE US
    • Infection begins when larval form penetrates intact skin.
    • Adult worms lay 20k eggs/day
    • Clinical dz can be dermatologic (cutaneous larva migrans snake-like migrating rash), intestinal (diarrhea, abdominal pain, anemia), or pulmonary (wheezing, dry cough)
  166. Strongyloides spp
    • S. stercoralis most important species
    • Infections in US mostly in immigrants from endemic areas.
    • Similar to hookworms in morphology and pathogenicity.
    • Infection begins with skin penetration.
    • Able to maintain life cycle outside human host.
    • Autoinfection plays important role. Some larvae not passed in feces but transform themselves into another larval form that is capable of reinfection, leading to overwhelming dissemination.
  167. Trichinella spiralis
    • Associated with undercooked pork.
    • Etiologic agent of trichinosis.
    • Found in most animals.
    • Infections can be asymptomatic.
    • Freezing reduces transmission.
  168. Taenia spp
    • Tapeworms
    • Infections usually acquired via ingestion of contaminated food (raw or undercooked meat)
  169. Common Cold
    • Rhinovirus
    • Coronavirus
  170. Influenza
    Influenza A and B
  171. Pharyngitis
    • Adenovirus
    • EBV
    • Herpes
    • Coxsackie
  172. Otitis Media
    • Adenovirus
    • Rhinovirus
    • Bacterial
  173. Otitis Externa
    • Some People Must Cough Helping Infect
    • Strep pneumo
    • Moraxella catarrhalis
    • Haemophilus influenza
  174. Sinusitis
    • Some People Must Cough Helping Infect
    • Strep pneumo
    • Moraxella catarrhalis
    • Haemophilus influenza
  175. Bronchiolitis
    • RSV
    • Human metapneumovirus
  176. Bronchitis
    • Parainfluenza
    • Influenza C, RSV
    • Human metapneumovirus
    • Chlamydia pneumoniae
    • Mycoplasma pneumoniae
    • Bordetella pertussis
  177. Pneumonia
    • Influenza
    • Streptococcus pneumonia
    • Chlamydia pneumonia = atypical
    • Mycoplasma pneumoniae
    • Legionella
    • Pneumocystis jiroveci
  178. Upper Respiratory Pathogens
    • Common Cold: Rhinovirus, Coronavirus
    • Conjunctivitis, Keratitis: Adenovirus, HSV
    • Influenza: Influenza A & B
    • Laryngitis: Parainfluenza virus, Influenza virus, EBV, Adenovirus
    • Croup: Parainfluenza virus
    • Otitis Media: Adenovirus, Rhinovirus
    • Pharyngitis: Adenovirus, EBV, Herpes, Coxsackie
  179. Bacterial Upper Respiratory Pathogens
    • Otitis media: Streptococcus pneumoniae (most common bacterial cause), Haemophilus influenzae , Moraxella (Less common Streptococcus pyogenes and Staphylococcus aureus.)
    • Otitis externa: Pseudomonas aeruginosa (#1 cause), Staphylococcus aureus (if no water exposure and came on suddenly), Proteus, Escherichia coli
    • Blepharitis: Staphylococcal blepharitis, Staphylococcus aureus
    • Conjunctivitis/Keratitis: Chlamydia trachomatis, Moraxella
    • Stye: Staphylococcus aureus
    • Pharyngitis/Tonsillitis: Group A streptococcus (also Corynebacterium diphtheriae, Neisseria gonorrhoeae, Chlamydophila pneumoniae, Mycoplasma pneumoniae)
    • Tracheobronchitis/Sinusitis: Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis
  180. Viral Lower Respiratory Pathogens
    • Bronchitis: Parainfluenza, Influenza C, RSV, Human metapneumovirus
    • Bronchiolitis (children < 2): RSV, Human metapneumovirus
    • Pneumonia: Influenza
  181. Bacterial Lower Respiratory Pathogens
    • Bronchitis: Chlamydia pneumoniae, Mycoplasma pneumoniae, Bordetella pertussis
    • Pneumonia (presence of rales): Streptococcus pneumoniae (typical, look very sick), Atypicals include; Chlamydia pneumoniae, Mycoplasma pneumoniae, Legionella
  182. Acute Bacterial Exacerbation of Chronic Bronchitis (ABECB)
    • Patients with chronic pulmonary dz, smokers
    • Etiologies: S. pneumoniae, H. influenzae, M. catarrhalis
    • Tx: antibiotics, vaccinate for influenza and pneumococcal pneumonia
  183. Neonatal Pneumonias
    • Group A, B or G Streptococci
    • Staphylococcus aureus
    • Pseudomonas spp
    • Chlamydia trachomatis
    • E. coli
  184. Bacterial Lower Respiratory Pathogens
    • Children up to 5yo: usually viral, Strep pneumoniae, H. influenzae, Staph aureus (rare)
    • Adolescents/Adults: Strep pneumoniae, Mycoplasma pneumoniae, Chlamydia pneumoniae, H. influenzae, Legionella
  185. Hospital Acquired Pneumonias
    Aerobic Gram Neg Bacteria: Enterobacter, Klebsiella, Acinetobacter, Pseudomonas
  186. Meningitis
    • Bacteria: age significant factor in unusual etiology
    • Aseptic: usually viral, negative bacterial culture, common but often not diagnosed
    • Fungal/parasitic: rare, suspect compromised immune function
    • Cryptococcal meningitis most common
  187. Viral Meningitis
    • Enterovirus
    • ECHO
    • Coxsackie A and B
    • HSV-2
  188. Bacterial Meningitis: Neonates
    • Group B Streptococci
    • E. coli
    • Listeria monocytogenes
    • Misc gram pos and gram neg rods
    • “Listless Babies Seldom Eat”
  189. Bacterial Meningitis: Young Children/Adults
    • 1 month to 50 years: Strep. pneumoniae (#1 cause), Neisseria meningitidis, Haemophilus influenzae (rare)
    • Age > 50 years: S. pneumoniae (#1 cause), Listeria monocytogenes, misc gram negative bacilli
  190. Viral Sepsis
    • No agents
    • Blood is only transport mechanism.
  191. Bacterial Sepsis
    • Age is significant factor in etiology.
    • Bloodstream usually seeded from distal site.
    • Neonates: Group B strep, E. coli, Enterobacter spp, Klebsiella, H influenzae (infants<1wk), Staph aureus (rare)
    • Children: H. influenzae, S. pneumoniae, N. meningitidis, S. aureaus (both MSSA and MRSA)
    • Non-immunocompromised adults: S. aureus (#1 cause), Group A strep, Legionella, Salmonella, Enterococcus spp, Viridans streptococci, E. coli
    • Immunocompromised adults: Staphylococcus spp (coagulase-negative), Listeria monocytogenes, S. pneumoniae
    • Neutropenic adults: Gram neg bacteria (Enterobacteriaceae including Pseudomonas), Fungi (Candida, Aspergillus), Staph aureus
  192. Ehrlichiosis
    • Vector-borne infection (mite, flea, louse, tick)
    • Human monocytic ehrlichiosis (HME)
    • Systemic febrile syndrome (fever, rash, headache)
    • Ehrlichia chaffeensis
    • Emerging pathogen
    • April-September 95% of cases
    • Dz to humans via lone star tick common in SE US.
    • Pancytopenia (clue to dx)
  193. Rickettsia rickettsii
    • Gram neg rods
    • Obligate intracellular bacteria
    • Animal and arthropod vectors
    • Humans accidental hosts
    • 3 groups: Spotted Fever Group (SFG), Typhus group, Scrub typhus group.
  194. Rocky Mountain Spotted Fever (RMSF)
    • Etiological agent: Rickettsia rickettsii
    • American dog tick most common vector
    • High mortality if tx delayed
  195. Lyme Disease
    • Etiological agent: Borrelia burgdorferi
    • Transmission in ≈10% tick bites
    • Ixodes tick is primary vector
    • Leading vector-borne illness in US
    • May-Sept incidence
    • Erythema migrans (EM): pathognomic rash
    • 3 clinical stages with myriad of symptoms
  196. Anaplasmosis: Human Granulocytic Anaplasmosis (HGA)
    • Formerly granulocytic ehrlichiosis
    • Etiological agent: Anaplasma phagocytophilum
    • Emerging pathogen
    • Most common in New England states, north central US, and sites in CA
    • Ixodes tick is vector
  197. Skin Normal Flora
    • Staphylococci (especially coagulase neg)
    • Corynebacteria
    • Propionibacteria
    • Streptococci (only transient inhabitants)
    • Clostridium perfringens
  198. Viral Skin Infections
    • Exanthems of viral illness: skin rashes that follow viremias; usually accompanied by fever; measles, rubella, roseola, fifth dz
    • Mucocutaneous Herpes Simplex: HSV, pharyngitis, whitlow, gladiatorum
    • Molluscum contagiosum: Pox virus, DNA virus, strictly human virus, lesions are pearl-like and umbilicated papules, spread by direct contact (including sexual), autoinoculation plays important role, sometimes itches, sometimes asymptomatic, goes away on own in 6mo, usually only few 6-12 lesions, responds to cryotherapy, adults can have this as an STD like genital warts
    • Chicken pox/shingles: VZV (lesions present in all stages at same time, showers of lesions every few hours)
    • Herpes: vesicular lesion on erythematous base, starts as papule → vesicle → erosion → crusted scab; HSV-1 above waist, HSV-2 below waist
    • Herpes gladiatorum: very susceptible to secondary infections, outbreaks among wrestlers
    • Herpetic whitlow: lesions on fingertips, ↑ risk in occupations where they put their fingers in mouths, genital areas, such as nurses and daycare workers.
  199. Bacterial Skin Syndromes
    • Live in cells of sebaceous glands.
    • Superficial infections: Acne (Propionibacterium acnes), Rosacea, Bites
  200. Bites
    • Etiology depends on biter, location of bite, and type of injury inflicted.
    • Cat bites > human bites > dog bites
    • Extremities > head and neck
    • Punctures > lacerations
    • Early infections: Pasteurella multocida
    • Late infections: Staphylococcus spp, Streptococcus spp
    • Implicated: Capnocytophaga canimorsus, Eikenella corrodens
  201. Bacterial Skin Syndromes
    • Cutaneous infections
    • Boils, furuncles: Staph aureus (MRSA looks purplish, blisters, bed is very erythematous, pts think it’s a spider bite)
    • Cellulitis: Group A Strep (rare Staph aureus)
    • Erysipelas: Group A Strep
    • Impetigo: Group A Strep (classic), Staph aureus (bullous)
    • Folliculitis: Staph Aureus
    • Hot tub folliculitis: Pseudomonas aeruginosa
    • Rare bacterial causes of cellulitis and abscesses: Nocardia, Vibrio vulnificus
  202. Fungal Skin Infections
    • Classified according to colonization in tissues.
    • Superficial: outermost layer of skin/hair
    • Cutaneous: deeper epidermis and integuments
    • Subcutaneous: Dermis and subcutaneous tissues, muscles, and fascia (relatively uncommon except for sporothrix)
  203. Superficial Fungal Syndromes
    • Candida superficial infections.
    • Yeast: normal flora of skin, oropharynx, GI tract and female GU tract, usually opportunistic, intertrigo (skin opposing skin, dark and dam areas, under breast, skin folds, babies necks, can get Group A strep in those areas and it smells bad), diaper rash, paronychia (infection of nail fold caused by staph), onychomycosis (fingernails and toenails)
    • Treatment topical except for onychomycosis)
  204. Candidiasis
    • Very inflammatory.
    • Itches, butns and stings.
    • Do well on steroids for a day or two.
    • Intertrigo: plaque is usually beefy red, note satellite lesions, in people of color they may be hyperpigmented
    • Thrush: coating is easily scraped off with tongue blade, on buccal mucosa or tongue
  205. Dermatophytes
    • Generally restricted to keratinized layers of integument.
    • Geophilic, zoophilic, anthropophilic
    • Clinical presentation: tinea (ringworm)
    • Seen frequently in primary care.
    • Tinea corporis: usually has scales and central clearing as it gets older. Tx with topical ointment, put ointment on areas beyond what appears infected.
  206. Subcutaneous Fungal Infections
    • Chromoblastomycosis and Phaeohyphomycosis: caused by various dematiaceous fungi, generally slow growers, Xylohypha (deadly)
    • Mycetoma: mostly confined to feet, prevalent in tropical areas, soil organisms, traumatic implantation, painless, treat with dapsone/SMZ/TMP
  207. Mouth & Mucous Membranes
    • Normal flora: many organisms (mostly bacteria); second only to GI tract
    • Streptococci (viridans group and Group D)
    • Many anaerobes including
    • Peptostroptococci
    • Lactobacilli
    • Fusobacterium
    • Actinomyces israelii
    • Neisseria spp
    • Haemophilus spp
  208. Viral Oral Syndromes
    • Stomatitis/HSV
    • Herpangina, hand/foot/mouth dz: Coxsackie
    • Aphthous ulcers/?
    • Mucocutaneous ulcers/HSV; single ulcer in mouth almost always herpes
  209. Bacterial Oral Syndromes
    • Gingivitis/bacterial plaque; gram pos cocci and bacilli
    • Parapharyngeal space infections and polymicrobial infection: Strep spp, Eikenella corrodens, anaerobes
    • Periodontitis /polymicrobic: mostly gram neg
    • Caries: Strep spp (especially Strep mutans)
  210. Muscle Infections
    • No normal flora.
    • Gas gangrene/tissue toxic Clostridium spp: majority caused by C. perfringens
    • Incidence limited to pts with severe traumatic injuries.
    • Rapid treatment is essential.
  211. Bone Infections/ Osteomyelitis
    • No normal flora.
    • Usually long bones.
    • Usually Staph aureus.
    • Infection by hematogenous spread from cutaneous site.
    • Specific dx needed for treatment.
    • New emerging pathogen associated with osteomyelitis is Kingella kingae. Infections mostly involve femur, talus, or calcaneus. Non-skeletal sites of infection include the lower respiratory tract, blood stream, and heart valves.
  212. Osteomyelitis Special Circumstances
    • Sickle Cell patients: likely to be Salmonella
    • IVDUs: sternoclavicular joint and ribs also site of infection, Pseudomonas aeruginosa common.
    • Prosthetic valves, joints: also Staph epidermidis
    • Chronic infection possible: implanted orthopedic hardware
  213. Breast Infection
    • Mastitis
    • Common postpartum infection.
    • Caused by Staph aureus; also Group A strep, E. coli, and Bacteroides.
    • If no abscess, can keep nursing.
    • If abscess, need to excise.
  214. Normal Bacterial Skin Flora
    • Staphylococci
    • Corynebacteria
    • Propionibacteria
    • Streptococci
    • Clostridium perfringens
  215. Normal Yeast Skin Flora
    • Candida
    • Malassezia furfur
    • Torulopsis glabrata
  216. Normal Aerobic Oral Flora
    • Streptococci; Viridans group
    • Actinomyces israelii
    • Neisseria
    • Haemophilus
  217. Normal Anaerobic Oral Flora
    • Peptostreptococcus
    • Lactobacilli
    • Fusobacterium
  218. Herpes Simplex
    Vesicles on an erythematous base
  219. Herpes Zoster
    Vesicles on an erythematous base
  220. Pox Virus
    • Varicella
    • Showers of lesions
    • Lesions present in all stages.
    • Little papules
  221. Coxsackie Virus
    • Herpangina
    • Hand/foot/mouth dz
  222. Viral Exanthema
    • Skin rashes that follow viremias.
    • Usually accompanied by fever.
    • Measles, Rubella, Roseola, Fifth Disease
  223. Early Bite Infections
    Pasteurella multocida
  224. Late Bite Infections
    • Staphylococcus spp
    • Streptococcus spp
  225. Implicated Bite Infections
    • Capnocytophaga canimorsus (cats/dogs)
    • Eikenella corrodens (humans)
  226. Rare Bite Infections
    • Haemophilus spp
    • Pseudomonas spp
  227. Propionibacterium
    Secretes low molecular weight peptide that attracts neutrophils, creating acne.
  228. Mastitis
    • Common postpartum infection.
    • Staphylococcus aureus (most common) MSSA and MRSA
    • Group A and B Streptococci
    • E. coli
    • Bacteroides
    • Coagulase neg Staphylococci
  229. Impetigo
    • Staph infection on top of the lesion.
    • Can look like herpes or secondary herpes; difficult to separate out.
    • Treat for both strep and staph.
  230. Classic Impetigo
    Group A strep
  231. Bullous Impetigo
    Staphylococcus aureus
  232. Cellulitis
    • Group A strep
    • Staph aureus (rare)
  233. Rare Causes of Cellulitis and Abscesses
    • Nocardia
    • Vibrio
    • Vulnificus
  234. Bones
    No normal flora
  235. Osteomyelitis
    • Usually long bones.
    • Usually staph aureus but any organism possible.
    • Infection by hematogenous spread from cutaneous site.
    • Specific dx required for treatment.
  236. Osteomyelitis in Children
    • Kingella kingae (gram neg rod)
    • Femur, talus or calcaneus
  237. Staph aureus Infection
    • Boils
    • Furuncles
    • Abscesses
    • Need to know if MRSA or MSSA
  238. Candida Superficial Infection
    • Yeast: Normal flora of skin, oropharynx, GI tract and female GU tract
    • Usually opportunistic
    • Intertrigo (skin opposing skin)
  239. Dermatophytes
    • Generally restricted to keratinized layers of integument.
    • Geophilic, zoophilic, anthropophilic.
    • Tinea (ringworm) classic presentation
  240. Chromoblastomycosis / Phaeohyphomycosis
    • Caused by various dematiaceous fungi.
    • Generally slow growers.
    • Xylohypha is deadly.
  241. Mycetoma
    • Mostly confined to feet
    • Prevalent in tropical areas
    • Treatment: dapsone, SMZ/TMP
  242. Virulence Factors of Staphylococcus aureus
    • Enterotoxin
    • TSS toxin
    • Exfoliatin
    • β-lactamases
    • Proteolytic enzymes
    • Coagulase (some)
  243. #1 Cause of Bacteremia, Sepsis, Endocarditis, Osteomyelitis
    Staphylococcus aureus
  244. Staphylococcus aureus Clinical Syndromes
    • Boils, furuncles
    • MRSA or MSSA
    • Scales on top, fluid filled
  245. Epidemiology of Staphylococcus aureus
    • Common to skin, oropharynx, GI and GU tracts
    • Transiently colonized moist skin folds.
    • Survives on dry surfaces for long time (nosocomial)
    • Transmission: direct contact, fomites, nosocomial
    • Nasopharynx colonization
  246. Coagulase Neg Staphylococcus aureus
    • Common on skin, oropharynx, GI and GU tracts
    • ↑ risk for pts in hospitals, with indwelling devices, joint or heart prosthesis
    • Virulence factors: glycocalyx capsule, proteolytic enzymes, cell wall structure.
  247. GI Tract Normal Flora
    • Colonized with microbes at birth.
    • Diverse collection throughout life.
  248. Stomach Normal Flora
    • Small numbers
    • Lactobacilli
    • Streptococci
  249. Small Bowel/Colon Normal Flora
    • Many organisms, bacteria, fungi, parasites
    • 10^11 bacteria/gram in feces, mostly Bacillus fragilis group
    • Mostly anaerobes: Peptostreptococci, Enterobacteriaceae
    • Viruses: Adenovirus, Enterovirus
    • Fungi: Candida
    • Parasites: mostly amoebae, Blastocystis hominis (possible pathogen), Entamoeba coli, Endolimax nana, Trichomonas hominis
  250. GI Viral Clinical Syndromes
    • Most infectious gastroenteritis is viral (80%)
    • Usually dz is mild & self-limiting
    • Requires only symptomatic treatment
    • Infants and younger children at ↑ risk for dehydration, fluid imbalances
    • 3-day window: if symptoms are improving within 3 days it is probably viral. If symptoms last longer than 3 days then consider parasite or other cause.
  251. Viral Gastroenteritis
    • Infants: Rotavirus A, Adenovirus (serotypes 40/41), Coxsackie virus, Sapovirus (Calicivirus)
    • Children/Adults: Caliciviruses, Norovirus, Astrovirus, Reovirus
  252. Rotavirus A
    • Children 0-2 at greatest risk
    • Causes 50% of hospitalized cases of dehydration due to diarrhea in US.
    • Treatment: fluid/electrolyte replacement
    • Not usually sick, “Happy diarrhea”
    • Diarrhea may persist for weeks.
    • Control by handwashing and isolation.
  253. Enteric Adenoviruses
    • Types 40 and 41 implicated in GI disease.
    • Transmission: fecal/oral, person-person, fomites
    • Increased incidence in winter.
    • Clinical syndrome similar to Rotavirus.
    • Asymptomatic shedding a factor in transmission.
    • Accounts for about 5% of diarrheal illness in children.
  254. Caliciviruses/Norwalk Virus
    • Single stranded RNA virus
    • Norovirus and Sapovirus are important members and are resistant to drying out.
    • Norovirus affects all ages.
    • Sapovirus affects more children.
    • Common cause of community outbreaks of gastroenteritis.
    • Transmission: fecal/oral, person-person
    • Disease self-limits in 48-72 hrs.
  255. Astrovirus
    • RNA virus
    • Multiple serotypes.
    • Asymptomatic shedding important role in transmission.
    • Transmission: fecal/oral, person-person
  256. Cholecystitis / Biliary Disease
    • Enterobacteriaceae
    • Enterococcus
    • Bacteroides
    • Clostridium spp
  257. Gastritis / Peptic Ulcer Disease (PUD)
    Helicobacter pylori
  258. Gastroenteritis Traveler’s Diarrhea
    Escherichia coli (ETEC)
  259. Gastroenteritis Food Intoxication
    • Quick onset due to toxin.
    • S. aureus
    • C. botulinum
    • B. cereus
  260. Gastroenteritis Food Infection (big 3)
    • Caused by the bacteria growing in gut, delayed onset usually after at least 12 hrs.
    • Campylobacter jejuni
    • Salmonella spp
    • Shigella spp
  261. Gastroenteritis Others
    • C. difficile
    • C. perfringens
    • E. coli (EHEC)
    • Vibrio cholerae
    • Listeria monocytogenes
    • Yersinia spp
  262. Primary (Spontaneous) Peritonitis
    • Usually ascites. Fluid becomes infected.
    • Enterobacteriaceae (70%)
    • S. pneumoniae
    • Enterococcus
    • Anaerobes
  263. Secondary Peritonitis
    • Enterobacteriaceae
    • Bacteroides
    • Pseudomonas aeruginosa
  264. Continuous Ambulatory Peritoneal Dialysis (CAPD)
    • S. aureus (mostly)
    • S. epidermidis
    • Sterile (20%)
  265. Diverticulitis
    • Enterobacteriaceae
    • Enterococcus
    • Bacteroides
  266. AIDS-Associated Diarrhea
    Mycobacterium avium-intracellulare (MAI)
  267. When to Suspect Bacterial Gastroenteritis
    • Severe abdominal pain that doesn’t subside after passing stool
    • Large #s of stools
    • Bloody stools (often considered hallmark of gastroenteritis; does not happen with viral infection)
    • Fever ≥ 101°F
    • Fecal leukocytes
    • Tenesmus (stool urgency)
    • Bloody diarrhea + fever ± tenesmus = dysentery (bacterial gastroenteritis)
    • Do not need to wait for 3 days before treating these symptoms.
    • Treat presumptively.
  268. E. coli Gastroenteritis
    • Strains of E. coli that cause gastroenteritis are acquired exogenously.
    • 5 major groups:
    • Enterotoxigenic (ETEC)
    • Enteropathogenic (EPEC)
    • Enteroaggregative (EAggEC)
    • Enterohemorrhagic (EHEC)
    • Enteroinvasive (EIEC)
    • First 3 groups present watery diarrhea and are mostly a small bowel problem.
    • Last 2 groups tend to be invasive and cause bleeding and present with bloody diarrhea and are mostly a colon problem.
  269. Enterotoxigenic E. coli (ETEC)
    • Etiologic agent of Traveler’s diarrhea.
    • Not endemic in US.
    • Mediated by 2 classes of enterotoxins.
    • Produce profuse, watery diarrhea.
    • Mild disease.
    • Supportive treatment only.
    • Severe cases can be treated with SMZ/TMP or quinolone.
    • Prophylaxis not recommended.
    • Prevention: cooked food, bottled water.
  270. Enteropathogenic E. coli (EPEC)
    • AKA enteroadherent E. coli
    • Can be part of normal flora in adults.
    • Childhood diarrhea associated with daycare outbreaks.
    • Infection rarely seen in older children or adults.
    • Mild, self-limiting.
    • Non invasive.
  271. Enteroaggregative E. coli (EAggEC)
    • Similar to EPEC in disease.
    • Self-limiting diarrhea in children.
    • Rarely seen in older children or adults except travelers to endemic areas.
    • Vigorous adherence to mucosal cells, facilitated by fimbriae.
    • May be part of normal flora in adults.
  272. Enterohemorrhagic E. coli (EHEC)
    • Most common strain seen in developed countries.
    • Mediated by Shiga toxins (Shigatoxin E. coli; STED)
    • Small inoculum can cause infection.
    • Conon is site of infection.
    • Mild to severe hemorrhagic colitis.
    • 50 serotypes; 0157 most common in US; prolonged bloody diarrhea.
    • Hemolytic uremic syndrome (HUS) is dreaded complication, especially in children; ARF, thrombocytopenia, hemolytic anemia
    • Sources of EHEC 0157: alfalfa sprouts, apple juice/cider, unpasteurized deer meat, undercooked goat’s milk, unpasteurized undercooked ground beef, leaf lettuce, meat, unpasteurized milk, radish sprouts, sausages (particularly beef), fecal-contaminated lakes, non-chlorinated municipal water supply, petting farm animals, unhygienic person-person contact
  273. Enteroinvasive E. coli (EIEC)
    • Like EHEC, colon is site of activity
    • Relatively rare
    • Disease can be mild to severe hemorrhagic colitis
  274. Campylobacter
    • C. jejuni: most common cause of bacterial gastroenteritis.
    • (Food infection Big 3 are C. jejuni, Salmonella spp, Shigella spp)
    • Risk factors; <5 and 20-30yo, male, handling and consuming raw or undercooked meats, consumption of unpasteurized milk and dairy products, consumption of untreated water, contact with pets and farm animals.
  275. Salmonella
    • Gastroenteritis is most common clinical presentation of non-typhoidal salmonella.
    • (Food infection Big 3 are C. jejuni, Salmonella spp, Shigella spp)
    • Don’t treat!
    • Transmission: poultry, beef, eggs, fish, dairy product, consumption of contaminated water, exposure to infected reptiles, person-person
    • Fecal shedding serves as reservoir for new infections. Children < 5 may shed for months.
    • Typhoid presentation usually has constipation.
  276. Shigella
    • (Food infection Big 3 are C. jejuni, Salmonella spp, Shigella spp)
    • Mostly pediatric disease.
    • Transmission almost exclusively fecal/oral.
    • Travelers at risk.
    • As few as 10 bacilli = infective dose.
    • Symptoms range from mild to severe.
    • Prolonged fecal carriage is rare.
    • Antimicrobial therapy, even for mild disease, helps with complete eradication.
  277. S. aureus Food Intoxication
    • Gastroenteritis
    • Enterotoxin A is preformed in food.
    • Ingestion disrupts intestinal mucosa.
    • Vomiting and watery diarrhea
    • Onset within 2-4 hours after digestion
  278. C. botulinum Food Intoxication
    • Neurotoxin; Types A, B, E
    • Spore formation enables survival in extreme conditions.
    • Home canning is risky.
    • Organism can colonize colon in neonates; avoid honey.
    • Wound botulism is rare in US.
  279. Bacillus cereus Food Intoxication
    • 2 Toxins; heat stabile and heat labile
    • Can cause upper or lower food infection
    • Upper: emetic symptoms; spores in fried rice, onset 2-6 hrs
    • Lower: diarrheal symptoms; spores in reheated eats and vegetables (microwave); onset 24 hrs
    • Both forms self-limiting.
  280. Clostridium difficile
    • Agent of Antibiotic Associated Colitis (AAC)
    • Enterotoxin mediated, A and B toxins, work synergistically
    • Antibiotic resistance
    • Explosive bloody diarrhea
    • Normal GI flora in some; disrupted by antibiotics
    • Tx with metronidazole, vancomycin
  281. AIDS Patients / Protracted Diarrhea (Parasites)
    • Mycobacterium avium-intracellulare (MAI)
    • Giardia lamblia
    • Cryptosporidium parvum
    • Isospora belli
  282. Diarrheal Disease (Parasites)
    • Giardia lamblia
    • Clostridium parvum
    • Bacillus hominis (controversial)
  283. Intestinal Amoebiasis
    Entamoeba histolytica
  284. Cryptosporidium
    • Implicated in chronic diarrhea in AIDS patients.
    • Common cause of acute self-limiting diarrhea in immunocompetent hosts.
    • Worldwide distribution.
    • More common in summer
    • Seroprevalence ≈ 30%
    • Sources: contaminated water (drinking and recreational), apple cider, raw produce, daycare settings
  285. Giardia
    • Most common cause of parasitic diarrhea in US
    • Most common in late summer, fall
    • ≈ 5% of patients with diarrhea > 1 wk
    • Low infective dose
    • Antigenic variation important in pathogenesis
    • Infection can result in asymptomatic carriage, acute self-limiting diarrhea, chronic diarrhea, chronic diarrhea + malabsorption (greasy frothy stools)
    • Always look for Giardia in someone with IBS.
  286. Clinical Syndromes of Enterobacteriaceae
    • Normal flora GI tract, small bowel/colon
    • Cholecystitis / biliary disease
    • Peritonitis; primary and secondary
    • Diverticulitis
  287. Enterobacteriaceae Virulence Factors
    • Endotoxins (LPS)
    • Antibiotic resistance
    • Pili
    • Surface antigens
    • LPS (O antigens)
    • Capsule (K antigens)
    • Flagella (H antigens)
    • Exotoxin (enterotoxin)
  288. Vibrio cholerae
    • Gastroenteritis
    • Contaminated water, poor sanitation
  289. Normal Flora Female Genital Tract
    • Microbial population under hormonal influence; shift depending on menstrual cycle
    • Lactobacilli most predominant
    • Staphylococcus spp (mostly coagulase-neg)
    • Streptococcus spp (mostly Group B)
    • Gardnerella vaginalis
    • Mycoplasma
    • Ureaplasma
    • Enterobacteriaceae
    • Many anaerobes: Bacteroides, Clostridium, Peptostreptococcus
    • Role in UTIs
  290. Normal Flora Male Genital Tract
    Little colonization except uncircumcised males.
  291. Normal Flora of Female Anterior Urethra
    • 2 populations: indigenous, transient
    • Indigenous: Lactobacillus, Corynebacterium, Staphylococcus (coagulase-neg)
    • Transient: Enterobacteriaceae, Candida, Enterococcus
  292. Viral Genital Syndromes
    • Genital Warts (Condyloma acuminatum) / cervical dysplasia: Human papilloma virus (HPV)
    • Genital Herpes: Herpes simplex virus Type 2 (HSV-2)
    • HIV: Human Immunodeficiency Virus
    • Hepatitis Viruses: Hepatitis B, C, D
  293. Human Papilloma Virus (HPV)
    • Cutaneous, mucosal and anogenital syndromes
    • More than 100 types
    • Types 6 & 11 associated with genital warts.
    • Types 16 & 18 associated with cervical dysplasia.
    • Virus capable of oncogenic transformation; role of cofactors (smoking)
    • Can be transmitted via fomites
    • Asymptomatic shedding important in disease transmission
    • Male: balanitis (tip of penis)
  294. Genital Herpes
    • Herpes Simplex Virus; predominantly HSV-2, but also HSV-1
    • Acquired by sexual contact.
    • Can be acquired at birth, passed from infected mother
    • “Mixing and matching of mucous membranes.”
    • Prior infection of HSV-1 blunts response to HSV-2.
    • Primary infection with HSV-2 is very painful with fever and many lesions.
    • Women often get flare-ups with each menstrual cycle.
    • Triggers: stress, infection, antibiotic use, UV light, etc
    • Asymptomatic shedding especially 1st year.
  295. Gonorrhea, Urethritis, Cervicitis
    Neisseria gonorrhoeae
  296. Non-Gonococcal Urethritis (NGU) and Cervicitis
    • Chlamydia trachomatis (50%)
    • Mycoplasma hominis
    • Ureaplasma
    • Mycoplasma genitalium
    • In males, particularly, this implies clinical evidence of urethritis in the absence of gonococcal infection.
    • NGU twice as common as gonococcal urethritis.
    • Mixed infections can occur.
    • C. trachomatis most common bacterial STD.
    • Near epidemic in sexually active teenagers.
    • Alters vaginal normal flora → complex, ascending polymicrobial genital infections (pelvic inflammatory disease)
  297. Neisseria gonorrhoeae
    • Strict human pathogen
    • Main reservoir: asymptomatic women
    • Infection in males usually limited to urethra. Present with dysuria ± penile discharge. Epididymitis & prostatitis are rare complications.
    • Primary site of infection in females: cervix
    • Untreated: can result in ascending genital infection
    • 1-3% untreated women can develop disseminated disease.
    • Other infections: pharyngitis, neonatal conjunctivitis
    • Disseminated Gonococcal Infection: arthritis
  298. Syphilis
    Treponema palladium
  299. Chancroid
    Haemophilus ducreyi
  300. Lymphogranuloma Inguinale
    Chlamydia trachomatis (serovars)
  301. Bacterial Vaginitis
    • Polymicrobic
    • G. vaginalis
    • Mobiluncus
    • Non-fragilis bacteroides
    • Actinomyces
  302. Treponema palladium
    • Syphilis
    • Extremely labile
    • Humans only host
    • Not highly contagious
    • Transmission: sexual contact, congenitally, transfusion
    • Diagnosis: confirmed by serological tests (RPR, VDRL)
    • Confirmatory FTA: always remains positive
  303. 3 Stages of Syphilis
    • Primary: characteristic chancre develops at site of inoculation
    • Secondary: flu-like symptoms followed by diffuse rash
    • Tertiary: any organ, now rare, CNS manifestations, gummas
  304. Chlamydia trachomatis
    • Lymphogranuloma inguinale
    • Serovars
    • Non-gonococcal urethritis (NGU) and cervicitis
    • Epididymitis, prostatitis = males < 35 yo, C. trachomatis ± N. gonorrhoeae
    • Proctitis: anal receptive intercourse, C. trachomatis, N. gonorrhoeae
  305. Haemophilus ducreyi
    • Chancroid
    • Rare in developed countries
    • STD: Painful, irregular ulcers
    • Superficial exudate: yellow or necrotic, foul smelling
    • Few hundred cases annually in US
    • Markedly swollen, painful inguinal nodes (buboes)
    • Transmission strictly by sexual contact
  306. Lymphogranuloma venereum
    • Ulcerative STD, very rare in US, caused by a serovar of C. trachomatis (CT)
    • Varies from other infections caused by CT in that it affects lymphatic, not mucosal, tissue.
    • 3 stages
    • Primary: ulcerative
    • Secondary: papular lesions, systemic symptoms
    • Tertiary: extensive scarring, chronic lymphatic obstruction, genital elephantiasis. Buboes may also be present.
  307. Granuloma inguinale (Donovanosis)
    • Extremely rare in US.
    • Genital ulcerative disease.
    • Endemic in warmer climates; South America, Caribbean, South Africa
    • Etiologic agent: Klebsiella granulomatis
    • Acquired by sexual contact or trauma to genital area.
    • Very long incubation period.
  308. Vaginitis
    • Can be bacterial, parasitic (urogenital protozoan), or fungal
    • Bacterial vaginitis (BV): results from disruption of normal vaginal flora; clue cells seen on saline wet prep; Gardnerella and Mobiluncus implicated
    • Yeast vaginitis; usually caused by Candida spp
    • Trichomonas vaginitis: etiologic agent it Trichomonas vaginalis, is considered STD
  309. Gardnerella / Mobiluncus
    • Normal flora in female genital tract
    • Bacterial vaginitis
    • Results from disruption in normal flora
    • Clue cells on saline wet prep
  310. Balanitis
    • Male equivalent of vaginitis
    • Non-specific inflammation of the penis.
    • Can be infectious in etiology: Candida spp, HPV, T. palladium, Gardnerella spp, Group A strep, Group B strep
    • Etiologic agent often age associated.
    • May require treatment of partners.
  311. Fungal Genital Syndromes
    • Vaginitis/Balanitis: Candida albicans
    • C. albicans is prototypical species
    • Others may cause infection; tropicalis, pseudotropicalis, krusei, glabrata
    • Opportunistic infections.
    • Treatment: azoles, nystatin, topical or PO (topical is better than oral)
  312. Parasitic Genital Tract Syndromes
    • Trichomoniasis: T. vaginalis
    • Pubic lice: Phthirus pubis
    • Scabies: Sarcoptes scabei
  313. Trichomoniasis
    • Flagellated protozoa that exists in trophozoite form only.
    • Infection in men and women often asymptomatic.
    • Asymptomatic men serve as reservoir.
    • Transmission mostly by sexual contact. Fomites rarely serve as means of transmission.
    • Common clinical presentation: bleeding after intercourse, foamy discharge.
  314. Bacterial Urinary Syndromes
    • Acute cystitis (UTI; lower):
    • E. coli (uropathic strains, ≈ 80%)
    • Staph saprophyticus
    • Enterococcus spp
    • Enterobacteriaceae: Klebsiella, Proteus, Serratia marcescens, Providencia stuartii
    • Pyelonephritis (upper): same as above
  315. E. coli (Uropathic Strains)
    • #1 cause of UTIs (community & nosocomial)
    • Infecting strains originate from GI tract.
    • Numerous virulence factors.
    • Transmission via fecal contamination of urethra or catheter use.
    • Women at increased risk due to short urethra.
  316. Staphylococcus saprophyticus GU Infection
    • Gram pos cocci in clusters
    • Common in healthy young sexually active women
    • Normal flora in skin of GUI tract.
    • Poor hygiene plays role in infection.
    • Virulence factors: multiple antibiotic resistance, hemagglutinin, urease? (makes urine alkaline)
  317. Pathogens of Sterile Sites
    • Meningitis: CNS
    • Bacteremia / Septicemia (blood): Intermittent (focus of infection is distal site), Continuous (mostly intravascular)
    • Other sterile body fluids: peritoneal/ascitic, pleural, pericardial, joint/synovial, catheter urines
  318. Systemic Febrile Syndromes
    • Vector-Borne (mite, flea, louse, tick):
    • Bartonella (cat scratch fever)
    • Ehrlichiosis
    • Anaplasmosis
    • Lyme Disease
    • Babesiosis (blood protozoa, intracellular, can survive transfusion, similar geographically to Lyme dz)
    • Plague
    • Relapsing fever
    • Rocky Mountain Spotted Fever
    • Tularemia
  319. Sepsis/Shock Syndromes
    • Especially gram neg, enterotoxins
    • Bacterial sepsis/septic shock
    • TSS (toxic shock syndrome), Staphylococcal (superantigen)
    • TSS, Streptococcal (superantigen)
  320. Miscellaneous Systemic Febrile Syndromes
    • Kawasaki Syndrome (limited to children)
    • Rheumatic fever (sequelae of Group A strep)
  321. Infections that May Present as Febrile Syndromes
    • Pyelonephritis
    • Hepatitis
    • Typhoid fever
  322. Meningitis
    • Aseptic (usually viral): negative bacterial culture, common but often not diagnosed.
    • Bacterial: age significant factor in usual etiologic agent
    • Fungal, parasitic: Rare, suspect compromised immune function; Cryptococcal meningitis most common
  323. Viral Encephalitis
    • HSV-1
    • HIV
    • Togavirus
    • Rabies
    • Flavivirus
  324. Viral Meningitis (Aseptic)
    • Enterovirus
    • Enteric cytopathogenic human orphan (ECHO) virus
    • Coxsackie A & B
    • HSV-2
  325. Mumps Virus
    • Belongs to paramyxovirus group
    • Usually causes parotitis
    • 50% patients have CNS involvement with 10% symptomatic
  326. Neonatal Bacterial Meningitis
    • Group B streptococci
    • Escherichia coli
    • Listeria monocytogenes
    • Misc gram pos and gram neg rods account for ≈ 20%
  327. 1mo-50 Bacterial Meningitis
    • S. pneumoniae (#1 cause)
    • N. Meningitidis
    • H. influenzae (rare)
  328. >50 Bacterial Meningitis
    • S. pneumoniae (#1 cause)
    • L. monocytogenes
    • Misc gram neg bacilli
  329. Viral Sepsis
    • No agent
    • Usually transient
    • Blood is transport mechanism
  330. Bacterial Sepsis
    • Age is significant factor in etiology.
    • Bloodstream usually seeded from distant site.
  331. Sepsis in Neonates
    • Group B streptococci
    • E. coli
    • Enterobacter spp
    • Klebsiella
    • H. influenzae (in infants > 1 wk old)
    • Staph aureus (rare)
  332. Sepsis in Children
    • H. influenzae
    • S. pneumoniae
    • N. meningitidis
    • S. aureus (both MRSA and MSSA)
  333. Sepsis in Adults (non-immunocompromised)
    • S. aureus (#1 cause)
    • Group A streptococci
    • Legionella
    • Salmonella
    • Enterococcus spp
    • Viridans streptococci
    • E. coli
  334. Sepsis in Adults (immunocompromised)
    • Staphylococcal spp (coagulase-neg)
    • L. monocytogenes (pregnant women; can cause spontaneous abortion)
    • S. pneumoniae
  335. Sepsis in Adults (neutropenic)
    • Gram neg bacteria (Enterobacteriaceae including Pseudomonas)
    • Fungi; Candida, Aspergillus
    • Staph aureus
  336. Lyme Disease
    • Borrelia burgdorferi
    • Transmission in ≈ 10% tick bites
    • Ixodes tick predominant vector
    • Human accidental host
    • Leading vector-borne disease in US
    • May-September indicence
    • Erythema migrans (EM): pathognomonic rash (bulls eye rash)
    • 3 clinical stages with myriad symptoms
  337. Human Monocytic Ehrlichiosis (HME)
    • Etiologic agent: Ehrlichia chaffeensis
    • 95% between April – September
    • Transmitted via lone star tick
    • Common in southeast US
    • Fever, rash and headache.
    • Pancytopenia is clue to diagnosis.
  338. Human Granulocytic Anaplasmosis (HGA)
    • Anaplasmosis
    • Etiologic agent: Anaplasma phagocytophilum
    • Most common in New England states, north central US, and specific sites in CA
    • Ixodes is vector
    • Fever, rash and headache.
  339. Rickettsia
    • Gram neg rods
    • 3 groups: Spotted Fever Group (SFG), Typhus group, Scrub typhus group
  340. Rocky Mountain Spotted Fever (RMSF)
    • Rickettsia rickettsii
    • Strict intracellular parasite with multiplication in host cell cytoplasm.
    • Most common rickettsial disease in US.
    • American dog tick is most common vector.
    • High mortality if treatment is delayed.
    • Petechial rash is late finding.
  341. Kawasaki’s Disease
    • Virus?
    • Acute onset of fever, rash, conjunctivitis, stomatitis, swollen erythematous hands and feet
    • 6 wks to 12 years; males more than females
    • Carpet cleaning association?
    • No specific treatment
    • Watch for later cardiac abnormalities; valvular problems
  342. Acute Rheumatic Fever (ARF)
    • Dreaded sequelae of Group A streptococcal infection
    • Follows only Group A streptococcal pharyngitis.
    • ASO titers diagnostic.
Card Set
Microbiology course