Microbiology

• Viruses (obligate intracellular parasites)
• Bacteria
• Fungi—Yeast and Molds
• Parasites—Protozoa (single cell) and Helminths (worms)

• Prokaryotes: all bacteria
• Eukaryotes: Fungi and Parasites

• Virion (nucleic acid of DNA or RNA)
• Capsid (protein coat)
• +/- Lipid Envelope
• Arrangement of capsomere (basic unit of capsid): Icosahedral (sphere), Helical (rod)

• 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

• 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

• 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

• 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

• 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).

• 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

• Protozoa: Unicellular
• Metazoa: Multicellular Nematodes (round worms), Platyhelminthes (flat worms; trematodes, cestodes), Arthropods (crustaceans, arachnids, Insecta)

• 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

• 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)

Any organism capable of causing disease

Any organism that always causes disease

The ability to cause disease

The degree to which an organism can cause disease.

Results from exposure to microbes from external environment

Results from introduction of normal flora into inappropriate sites.

• Microbe persists in host tissue without evidence of disease
• A change in the environment will cause disease.

Host’s immune system fails to completely eradicate microbe.

• 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.

• Acquisition
• Attachment
• Invasion (spread)
• Evasion of host’s defenses

• Structures: capsule, spores, endotoxin (LPS, LOS)
• Antigenic proteins: exotoxins, adhesins, superantigens
• Degradative enzymes
• Antibiotic resistance

• 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

• 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)

• 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.

• Ingest and destroy pathogenic bacteria.
• 1st responders to bacterial infection.
• Presence in high amounts indicate significant bacterial infection.

• Ingest and destroy all pathogenic microbes.
• Production of TNF.
• Antigen presentation.
• Activation of acute phase reactants.

Non-phagocytic cells that destroy and kill viruses.

Thick peptidoglycan layer; teichoic acid.

• Thin peptidoglycan layer.
• Complex outer membrane of lipopolysaccharide (LPS).

• 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.

• Dormant structure; forms inside cell.
• Extremely resistant to heat, radiation, and various chemical agents.
• Only 2 genera: Bacillus and Clostridium (both Gram pos rods)

• Mostly limited to Gram neg bacteria.
• Especially common among pathogens of mucosal surfaces.

• Lipopolysaccharides (LPS) located in the outer membrane of Gram neg bacteria.
• Poorly antigenic.
• Powerfully immunogenic.

• Polypeptides produced and secreted by both Gram pos and Gram neg bacteria.
• Antigenic.
• Many types with different mechanisms of action.
• Superantigens are powerful exotoxins.

• 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)

• 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.

• 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.

• 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.

• 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

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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).

• 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.

• 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.

• (Aerobic)
• Bacillus
• Corynebacterium
• Erysipelothrix
• Listeria
• Gardnerella

• Large Gram pos rods.
• Virulence factors: endospores, enterotoxins

• 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)

• 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.

• 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.

• 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.

• (Anaerobic. Colonize skin and mucosal surfaces.)
• Actinomyces
• Clostridium
• Lactobacillus
• Mobiluncus
• Propionibacterium

• 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.

• Anaerobic rods
• Spore formers.
• Ubiquitous in soil, water, human GI tract.
• 4 species medically important: C. perfringens, C. botulinum, C. tetani, C. difficile

• 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.

• 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)

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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)

• 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.

• 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.

• 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.

• 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

• 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

• 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.

• 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.

• 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.

• 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

• Saprophytic: Acinetobacter, Pseudomonas
• Zoonotic: Brucella, Francisella, Pasteurella
• Respiratory: Bordetella, Haemophilus, Moraxella, Legionella
• Less Common Pathogenic: Bartonella, Capnocytophaga, Prevotella, HACEK group

• 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.

• E. coli 5 subdivisions
• Enterotoxigenic
• Enteropathogenic
• Enteroadherent
• Enterohemorrhagic
• Enteroinvasive

• 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.

• 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.

• 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.

• 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.

• 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

• 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

• 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.

• 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.

• 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.

• 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

• Gram neg bacilli.
• Virulence factors: LPS, polysaccharide capsule

• Most commonly associated with otitis media and sinusitis (also consider strep pneumo and Moraxella catarrhalis)
• β-lactamase resistance can be problem

• Etiologic agent of chancroid (soft chancre) and ulcerative venereal dz.
• Most common in Africa/Asia

• 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.

• 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.

• 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

• 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.

• Thin, coiled bacteria with flagella
• Spirochetes: treponema and Borrelia
• Leptospira: Leptospira

• 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

• Spirochete with multiple flagella
• Weakly stains Gram neg.
• B. burgdorferi: etiologic agent of Lyme Dz
• B. recurrentis: etiologic agent of relapsing fever

• Animal reservoir for human infection; exposure to pet urine.
• Wide spectrum of dz from mild (subclinical) to fatal (Weil’s dz)

• Lack cell walls
• Cell membrane contains sterols
• 2 medically important genera: Mycoplasma, Ureaplasma

• 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

• 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.

• 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)

• 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.

• Important cause of upper and lower respiratory infection.
• Role in atherosclerosis.

• Etiologic agent of psittacosis (parrot fever)
• Any bird can be reservoir for infection
• Infection acquired via respiratory route and then hematogenous spread.

• 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.

• 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

• Infection by inhalation or traumatic implantation.
• Immunocompetent pts: cutaneous, chronic pulmonary dz
• Immunocompromised pts: bronchopulmonary, severe cutaneous, or CNS dz

• 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.

• Ubiquitous in soil, water, fowl.
• Multiple manifestations of pulmonary dz in immunocompetent pts.
• Disseminated dz in immunocompromised pts, especially those with AIDS.

• 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.

• 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)

• Causes upper and lower respiratory tract; clinical presentation similar to RSV.
• Exacerbates asthma.
• Tx must include bronchodilator

• Measles: like RSV causes giant cell formation, only one serotype
• Mumps: many infections asymptomatic, bilateral parotitis + fever, CNS complications not uncommon, only one serotype

• 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

5 genera (3 infect humans): enteroviruses (polio viruses, Coxsackie A & B viruses, ECHO viruses, enteroviruses), rhinoviruses, heparnavirus (Hepatitis A virus)

• 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.

• 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.

• 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

• 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

• 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.

• 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

• 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

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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

• 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.

• 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.

• Superficial: Malassezia furfur
• Cutaneous dermatophytes: Trichophyton spp, Epidermophyton floccosum, Microsporum spp.
• Cutaneous non-dermatophytes: Candida spp, multiple genera of fungi can cause onychomycosis

• Lipophilic yeast that causes superficial infection.
• Etiologic agent of tinea versicolor.

• 3 common genera: Epidermophyton, Trichophyton, Microsporum
• Geophilic, Zoophilic or Anthropophilic
• Clinical presentation: tinea (ringworm)
• Ringworm can be treated topically except for scalp.

• 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.

• 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.

• 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.

• Systemic fungi that are not dimorphic.
• Candida spp.
• Cryptococcus neoformans
• Aspergillus spp
• Zygomycetes
• Fusarium and other non-pigmented molds
• Pneumocystis jiroveci

• 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.

• 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.

• 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

• “Hyaline” molds
• Capable of causing opportunistic dz.
• Fusarium spp: cause eye infections, conjunctivitis, keratitis, especially in immunocompromised who wear contact lenses.

• Etiologic agent of Pneumocystis jiroveci pneumonia (PCP)
• Infection by inhalation.
• Most common AIDS infection.

• 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)

• 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).

• 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.

• 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.

• 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

• 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.

• 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.

• 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.

• 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

• 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

• 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)

• 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.

• Associated with undercooked pork.
• Etiologic agent of trichinosis.
• Found in most animals.
• Infections can be asymptomatic.
• Freezing reduces transmission.

• Tapeworms
• Infections usually acquired via ingestion of contaminated food (raw or undercooked meat)

• Rhinovirus
• Coronavirus

Influenza A and B

• Adenovirus
• EBV
• Herpes
• Coxsackie

• Adenovirus
• Rhinovirus
• Bacterial

• Some People Must Cough Helping Infect
• Strep pneumo
• Moraxella catarrhalis
• Haemophilus influenza

• Some People Must Cough Helping Infect
• Strep pneumo
• Moraxella catarrhalis
• Haemophilus influenza

• RSV
• Human metapneumovirus

• Parainfluenza
• Influenza C, RSV
• Human metapneumovirus
• Chlamydia pneumoniae
• Mycoplasma pneumoniae
• Bordetella pertussis

• Influenza
• Streptococcus pneumonia
• Chlamydia pneumonia = atypical
• Mycoplasma pneumoniae
• Legionella
• Pneumocystis jiroveci

• 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

• 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

• Bronchitis: Parainfluenza, Influenza C, RSV, Human metapneumovirus
• Bronchiolitis (children < 2): RSV, Human metapneumovirus
• Pneumonia: Influenza

• Bronchitis: Chlamydia pneumoniae, Mycoplasma pneumoniae, Bordetella pertussis
• Pneumonia (presence of rales): Streptococcus pneumoniae (typical, look very sick), Atypicals include; Chlamydia pneumoniae, Mycoplasma pneumoniae, Legionella

• Patients with chronic pulmonary dz, smokers
• Etiologies: S. pneumoniae, H. influenzae, M. catarrhalis
• Tx: antibiotics, vaccinate for influenza and pneumococcal pneumonia

• Group A, B or G Streptococci
• Staphylococcus aureus
• Pseudomonas spp
• Chlamydia trachomatis
• E. coli

• Children up to 5yo: usually viral, Strep pneumoniae, H. influenzae, Staph aureus (rare)
• Adolescents/Adults: Strep pneumoniae, Mycoplasma pneumoniae, Chlamydia pneumoniae, H. influenzae, Legionella

Aerobic Gram Neg Bacteria: Enterobacter, Klebsiella, Acinetobacter, Pseudomonas

• 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

• Enterovirus
• ECHO
• Coxsackie A and B
• HSV-2

• Group B Streptococci
• E. coli
• Listeria monocytogenes
• Misc gram pos and gram neg rods
• “Listless Babies Seldom Eat”

• 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

• No agents
• Blood is only transport mechanism.

• 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

• 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)

• Gram neg rods
• Obligate intracellular bacteria
• Animal and arthropod vectors
• Humans accidental hosts
• 3 groups: Spotted Fever Group (SFG), Typhus group, Scrub typhus group.

• Etiological agent: Rickettsia rickettsii
• American dog tick most common vector
• High mortality if tx delayed

• 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

• 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

• Staphylococci (especially coagulase neg)
• Corynebacteria
• Propionibacteria
• Streptococci (only transient inhabitants)
• Clostridium perfringens

• 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.

• Live in cells of sebaceous glands.
• Superficial infections: Acne (Propionibacterium acnes), Rosacea, 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

• 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

• 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)

• 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)

• 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

• 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.

• 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

• 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

• Stomatitis/HSV
• Herpangina, hand/foot/mouth dz: Coxsackie
• Aphthous ulcers/?
• Mucocutaneous ulcers/HSV; single ulcer in mouth almost always herpes

• 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)

• 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.

• 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.

• 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

• 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.

• Staphylococci
• Corynebacteria
• Propionibacteria
• Streptococci
• Clostridium perfringens

• Candida
• Malassezia furfur
• Torulopsis glabrata

• Streptococci; Viridans group
• Actinomyces israelii
• Neisseria
• Haemophilus

• Peptostreptococcus
• Lactobacilli
• Fusobacterium

Vesicles on an erythematous base

Vesicles on an erythematous base

• Varicella
• Showers of lesions
• Lesions present in all stages.
• Little papules

• Herpangina
• Hand/foot/mouth dz

• Skin rashes that follow viremias.
• Usually accompanied by fever.
• Measles, Rubella, Roseola, Fifth Disease

Pasteurella multocida

• Staphylococcus spp
• Streptococcus spp

• Capnocytophaga canimorsus (cats/dogs)
• Eikenella corrodens (humans)

• Haemophilus spp
• Pseudomonas spp

Secretes low molecular weight peptide that attracts neutrophils, creating acne.

• Common postpartum infection.
• Staphylococcus aureus (most common) MSSA and MRSA
• Group A and B Streptococci
• E. coli
• Bacteroides
• Coagulase neg Staphylococci

• Staph infection on top of the lesion.
• Can look like herpes or secondary herpes; difficult to separate out.
• Treat for both strep and staph.

Group A strep

Staphylococcus aureus

• Group A strep
• Staph aureus (rare)

• Nocardia
• Vibrio
• Vulnificus

No normal flora

• Usually long bones.
• Usually staph aureus but any organism possible.
• Infection by hematogenous spread from cutaneous site.
• Specific dx required for treatment.

• Kingella kingae (gram neg rod)
• Femur, talus or calcaneus

• Boils
• Furuncles
• Abscesses
• Need to know if MRSA or MSSA

• Yeast: Normal flora of skin, oropharynx, GI tract and female GU tract
• Usually opportunistic
• Intertrigo (skin opposing skin)

• Generally restricted to keratinized layers of integument.
• Geophilic, zoophilic, anthropophilic.
• Tinea (ringworm) classic presentation

• Caused by various dematiaceous fungi.
• Generally slow growers.
• Xylohypha is deadly.

• Mostly confined to feet
• Prevalent in tropical areas
• Treatment: dapsone, SMZ/TMP

• Enterotoxin
• TSS toxin
• Exfoliatin
• β-lactamases
• Proteolytic enzymes
• Coagulase (some)

Staphylococcus aureus

• Boils, furuncles
• MRSA or MSSA
• Scales on top, fluid filled

• 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

• 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.

• Colonized with microbes at birth.
• Diverse collection throughout life.

• Small numbers
• Lactobacilli
• Streptococci

• 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

• 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.

• Infants: Rotavirus A, Adenovirus (serotypes 40/41), Coxsackie virus, Sapovirus (Calicivirus)
• Children/Adults: Caliciviruses, Norovirus, Astrovirus, Reovirus

• 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.

• 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.

• 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.

• RNA virus
• Multiple serotypes.
• Asymptomatic shedding important role in transmission.
• Transmission: fecal/oral, person-person

• Enterobacteriaceae
• Enterococcus
• Bacteroides
• Clostridium spp

Helicobacter pylori

Escherichia coli (ETEC)

• Quick onset due to toxin.
• S. aureus
• C. botulinum
• B. cereus

• Caused by the bacteria growing in gut, delayed onset usually after at least 12 hrs.
• Campylobacter jejuni
• Salmonella spp
• Shigella spp

• C. difficile
• C. perfringens
• E. coli (EHEC)
• Vibrio cholerae
• Listeria monocytogenes
• Yersinia spp

• Usually ascites. Fluid becomes infected.
• Enterobacteriaceae (70%)
• S. pneumoniae
• Enterococcus
• Anaerobes

• Enterobacteriaceae
• Bacteroides
• Pseudomonas aeruginosa

• S. aureus (mostly)
• S. epidermidis
• Sterile (20%)

• Enterobacteriaceae
• Enterococcus
• Bacteroides

Mycobacterium avium-intracellulare (MAI)

• 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.

• 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.

• 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.

• 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.

• 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.

• 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

• Like EHEC, colon is site of activity
• Relatively rare
• Disease can be mild to severe hemorrhagic colitis

• 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.

• 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.

• (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.

• Gastroenteritis
• Enterotoxin A is preformed in food.
• Ingestion disrupts intestinal mucosa.
• Vomiting and watery diarrhea
• Onset within 2-4 hours after digestion

• 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.

• 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.

• 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

• Mycobacterium avium-intracellulare (MAI)
• Giardia lamblia
• Cryptosporidium parvum
• Isospora belli

• Giardia lamblia
• Clostridium parvum
• Bacillus hominis (controversial)

Entamoeba histolytica

• 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

• 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.

• Normal flora GI tract, small bowel/colon
• Cholecystitis / biliary disease
• Peritonitis; primary and secondary
• Diverticulitis

• Endotoxins (LPS)
• Antibiotic resistance
• Pili
• Surface antigens
• LPS (O antigens)
• Capsule (K antigens)
• Flagella (H antigens)
• Exotoxin (enterotoxin)

• Gastroenteritis
• Contaminated water, poor sanitation

• 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

Little colonization except uncircumcised males.

• 2 populations: indigenous, transient
• Indigenous: Lactobacillus, Corynebacterium, Staphylococcus (coagulase-neg)
• Transient: Enterobacteriaceae, Candida, Enterococcus

• 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

• 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)

• 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.

Neisseria gonorrhoeae

• 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)

• 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

Treponema palladium

Haemophilus ducreyi

Chlamydia trachomatis (serovars)

• Polymicrobic
• G. vaginalis
• Mobiluncus
• Non-fragilis bacteroides
• Actinomyces

• 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

• Primary: characteristic chancre develops at site of inoculation
• Secondary: flu-like symptoms followed by diffuse rash
• Tertiary: any organ, now rare, CNS manifestations, gummas

• 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

• 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

• 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.

• 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.

• 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

• Normal flora in female genital tract
• Bacterial vaginitis
• Results from disruption in normal flora
• Clue cells on saline wet prep

• 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.

• 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)

• Trichomoniasis: T. vaginalis
• Pubic lice: Phthirus pubis
• Scabies: Sarcoptes scabei

• 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.

• 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

• #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.

• 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)

• 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

• 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

• Especially gram neg, enterotoxins
• Bacterial sepsis/septic shock
• TSS (toxic shock syndrome), Staphylococcal (superantigen)
• TSS, Streptococcal (superantigen)

• Kawasaki Syndrome (limited to children)
• Rheumatic fever (sequelae of Group A strep)

• Pyelonephritis
• Hepatitis
• Typhoid fever

• 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

• HSV-1
• HIV
• Togavirus
• Rabies
• Flavivirus

• Enterovirus
• Enteric cytopathogenic human orphan (ECHO) virus
• Coxsackie A & B
• HSV-2

• Belongs to paramyxovirus group
• Usually causes parotitis
• 50% patients have CNS involvement with 10% symptomatic

• Group B streptococci
• Escherichia coli
• Listeria monocytogenes
• Misc gram pos and gram neg rods account for ≈ 20%

• S. pneumoniae (#1 cause)
• N. Meningitidis
• H. influenzae (rare)

• S. pneumoniae (#1 cause)
• L. monocytogenes
• Misc gram neg bacilli

• No agent
• Usually transient
• Blood is transport mechanism

• Age is significant factor in etiology.
• Bloodstream usually seeded from distant site.

• Group B streptococci
• E. coli
• Enterobacter spp
• Klebsiella
• H. influenzae (in infants > 1 wk old)
• Staph aureus (rare)

• H. influenzae
• S. pneumoniae
• N. meningitidis
• S. aureus (both MRSA and MSSA)

• S. aureus (#1 cause)
• Group A streptococci
• Legionella
• Salmonella
• Enterococcus spp
• Viridans streptococci
• E. coli

• Staphylococcal spp (coagulase-neg)
• L. monocytogenes (pregnant women; can cause spontaneous abortion)
• S. pneumoniae

• Gram neg bacteria (Enterobacteriaceae including Pseudomonas)
• Fungi; Candida, Aspergillus
• Staph aureus

• 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

• 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.

• 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.

• Gram neg rods
• 3 groups: Spotted Fever Group (SFG), Typhus group, Scrub typhus group

• 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.

• 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

• Dreaded sequelae of Group A streptococcal infection
• Follows only Group A streptococcal pharyngitis.
• ASO titers diagnostic.