MICROBIOLOGY

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 MICROBIOLOGY
Fungi
Mycobacteria
Parasites
STI Micro
UTI Micro
Diarrhea Micro
CNS Micro
CNS Viral Micro
TORCH
Cough Micro
Skin Micro
Joint Micro
 FUNGI
OPPORTUNISTIC FUNGAL INFECTIONS
General Pathogenesis & Morphology Clinical Presentation
Cryptococcus Neoformans • C. neoformans and C. gattii • Polysaccharide capsule → immune cell evasion • Immunocompromised
(gattii) • Causes systemic mycosis- cryptococcosis
• Melanin production → protects against oxidative stress 1. Pulmonary cryptococcosis:
• Most common cause of fungal • Nodular infiltrates on CXRAY (rare cavitation)
meningoencephalitis --------------------------------------------------------------------------------- • Latent infxn in healthy; reactivation in immunocompromised
• India ink stain → Spherical/oval encapsulated yeast → Fevers, chest pain, cough, dyspnea, hemoptysis, headache
• AIDs pts ↑ risk • Narrow Budding • Dissemination likely

• Transmission: inhalation of aerosolized cells; • Urease (+) 2. Skin:

transcutaneous rare • Capsular polysaccharide Ag detected • Resemble molluscum contagiosum umbilicated papules in
immunocompromised
• Found in tropical/subtropical soil w/ eucalyptus trees → Papules, cellulitis, abscess, ucler, vesicles, nodules
• a/w pigeon droppings
3. Meningoencephalitis:
• CSF ↑ pressure, ↓ glucose, ↑ protein, mononuclear cells
C.gattii → large lesions "cryptococcomas" (soap bubble lesions) and
neuro cx → papilledema, vision/hearing issues

• TXT: Amphotericin B + Flucytosine then Fluconazole

Aspergillus spp • A.fumigatus; A. flavus; A. niger; A. terreus • Aflatoxins: carcinogenic (HCC); liver damage w/ acute 1. Allergic Bronchopulmonary aspergillosis (ABPA)
• Causes aspergillosis intoxication • Hypersensitivity to Aspergillus growing in lung mucus
--------------------------------------------------------------------------------- • a/w asthma and CF
• Hyphae/mycelium form in host • Grows as hyaline mold in medium
• Infectious agent: Conidia • Multiple colors that are species specific 2. Aspergillomas:
• Branched, septate hyphae w/ "cotton ball" conidial head • Obstructive bronchial aspergillosis or true aspergillosis
• Transmission: respiratory tract • Hyphael branches at 45º → Acute Angle • Mycelial mass a/w underlying pulmonary disease (e.g. TB)
• Found in soil, air, decaying material • Pulmonary/ sinus hemorrhage

3. Invasive Aspergillosis: (immunocompromised)

• Bronchial aspergillosis: wheezing, dyspnea, hemoptysis
• Chronic necrotizing pulmonary aspergillosis: local tissue destruction
• Invasive pulmonary and disseminated aspergillosis: severe, life
threatening d/t immunodeficiency

• TXT: Voriconazole or Echinocandins

Pneumocystis jirovecii • P. carinii • Disc shaped yeast on methenamine silver stain 1. Pulmonary:
• Causes pneumocystosis (free trophic, uninucleate • Pneumonia = most common presentation
sporocyst, cyst) • DX: bronchoalveolar lavage or lung biopsy • CXRAY: diffuse b/l interstitial or alveolar infiltrates → ground glass
• f/c, tachypnea, cyanosis, nonprod. cough, fatigue, weight loss
• Most common opportunistic infection a/w AIDS
2. Extrapulmonary:
• Transmission: inhalation • Rare: eye, thyroid, spleen, bone marrow

TXT: SMX,TMP
Prophylaxis: Pentamidine, dapsone → CD4 < 200
Mucormycetes • Entomopthorales: Conidiobolus, Basidiobolus • Extremly angioinvasive • Rare disease but high mortality
• Mucorales: Rhizopus, Mucor, Lichthemia, • Mostly in diabetic ketoacidotic or neutropenic pts
Rhizomucor • Rhizopus spp encode ketone reductase → grows well in
• Causes mucormycosis (chronic granulomatous infxn) acidic conditions 1. Rhinoorbitocerebral mucormycosis: invasive infxn of nasal cavity,
--------------------------------------------------------------------------------- paranasl sinuses, CNS; linked to pts w/ metabolic acidosis → CX:
• Rhizopus arrhyizue - most common disease • For Mucorales: mold- broad hyaline coenocytic hyphae w/ bulb- Cavernous sinus thrombosus
causing species like sporangia and rhizoid structures
2. Pulmonary mucormycosis: pulmonary lesions, fungus-ball,
• Ubiquitous in soil and decaying material • In tissue, hyphae are ribbon-like structure w/ non-septate hemorrhage in neutropenic individuals
and wide angle (90º) branching
• Transmission: inhalation, ingestion, wound 3. Cutaneous mucormycosis: nodular skin lesions w/ ecchymotic center;
contamination of sporangiospores black necrotic eschar on face

• Risks: Immunocompromised and diabetics • TXT: Surgical debridement, amphotericin B or isavuconazole

Candida albicans • Dimorphic: Pseudohyphae in cold, germ tubes in • Virulence Factors: Phenotypic switching, Protease • Adults receiving TPN (e.g. vascular catheters)
heat • Oral and esophageal thrush → immunocompromised
• Pseudohyphae w/ blastoconidia • Vulvovaginitis
• Asexual: produce conidia by budding • Diaper rash
• Sexual: Conjugation between two cells • Endocarditis → IV drug users
• Disseminated candidiasis
• Chronic mucocutaneous candidiasis

• TXT: Clotrimazole (topical), Amphotericin B or Ketozonazole

(systemic), Nystatin, Echinocandins
SYSTEMIC FUNGAL INFECTIONS
Histoplasmosis • Most common cause for hospitalization d/t • Immunocompetent: disease based on intensity of exposure • Mostly asymptomatic/ subclinical
endemic mycoses • Targets reticuloendothelial system
• M⏀ filled with small oval yeast → smaller than RBC 1. Acute Pulmonary Histoplasmosis:
• Ohio & Mississippi river valley; central/midwest • Intracellular growth in phagocytes • Low intensity exposure: Flu like sxs; Self limited
• Conidia → yeast • High intensity exposure: can be fatal; severe respiratory distress
• Soil contamined w/ bat/bird droppings, caves • Intracellular yeast can remain in lung (pulm. infxn) or • Complication: mediastinal fibrosis
disseminate via M⏀
• At risk: Immunocompromised, kids, high burden 2. Chronic Pulmonary Histoplasmosis:
exposure • TNFα and IFNγ = important for resolution • pts w/ pulmonary disease; looks like Tb
--------------------------------------------------------------------------------- • Chest pain, productive cough, dyspnea, fatigue, fever
• Thermal dimorphism "mold in cold, yeast in heat" • Yeast cells: hyaline, spherical to oval, uninucleate, w/ single • Fibrotic apical infiltrates w/ cavitation on CXRAY
• Infectious agent: microconidia and hyphae bud attached by a narrow base; intracellular • Major inflammation disproportionate to fungal burden
(macrophages w/ oval bodies)
3. Disseminated Histoplasmosis:
• Culture: growth at room temp results in mold/hyphae formation • Acute/ fulminant (days-wks): septic shock, GI and orla bleeding,
w/ tuberculate macroconidia meningitis, endocarditis
• Histo size < RBC size • Subacute (wks- yrs): nonspecific sxs, oropharyngeal ulcers, HSmegaly
• Chronic: same as subacute
• Complement fixation: (+) if no RBCs lyse
• Immunodiffusion (M or H Ags): M alone is early or chronic Complications: reactivation in immunocompromised
disease; M+H - active infection • Pericarditis, arthritis, erythema nodosum

• DX: serum or urine antigen

Blastomycosis • Causes blastomycosis (B.dermatitidis; B. gilchristii) • Yeast resistant to phagocytosis and PMN killing 1. Acute Pulmonary Blastomycosis:
• Thermal dimorphism • Transition from mold to yeast (phase change) takes place in • Resembles bacterial/ viral pneumonia
• Can result in extrapulmonary dissemination tissues • Cough, initially nonproductive then purulent
• Fever, SOB, weight loss
• Mississippi River basin, Great Lakes, SE US • Adhesion BAD-1 • Alveolar infiltrates on radiography
• Moist soil w/ decaying matter • Thick cell wall resistant to phagocytosis • Fulminant respirator distress syndrome

• Transmission: inhalation of aerosolized conidia --------------------------------------------------------------------------------- 2. Chronic Pulmonary Blastomycosis:

• Yeast cells: non-encapsulated, hyaline, spherical, • Resembles TB → granulomatous nodules
multinucleated w/ thick, double-lined, refractile cell wall; • Low fever, prod. cough, hemoptysis, chest pain, weight loss
single bud attached by a broad base • Pulmonary mass lesions or fibronodular infiltrates on XRAY

• Culture growth slow on Sabouraud dextrose agar 3. Extrapulmonary Blastomycosis:

• Culture growth at room temp in mold/hyphae w/ oval, pyriform • Dissemination to bone/skin
conidia • Cutaneous blastomycosis (verrucous lesion)
• Osteomyelitis
• Blasto size = RBC size • Prostatitis/epididymo-orchitis
• "Blasto Buds Broadly" • Meningitis, abscess

Coccidioidomycosis • Causes coccidioidomycosis (pulmonary) • Arthroconidia, spherule, endospores resistant to phagocytosis • Asymptomatic in 50+%
• Dimorphism: mold v. SPHERULES and PMN killing
• Can result in extrapulmonary dissemination • Low infective dose 1. Primary coccidioidomycosis:
• Like community acquired pneumonia
• SW US, northern Mexico, Central and South • Phase change in tissues (extracellular) • Flu like sxs; systemic sxs
America, Arizona and Cali • Can disseminate hematogenously • Complication: allergic rxn d/t immune complex formation; erythema
• Host defense: Cellular immunity (TH1 mediated and TH17) multiforme; erythema nodosum
• Grows in desert soil w/ bat/rodent feces ---------------------------------------------------------------------------------
• Large round spherules w/ endospores 2. Secondary coccidioidomycosis:
• Transmission: inhalation of arthroconidia via dust • Growth at room temp: hyphae w/ • > 6 wks
alternating hyaline arthroconidia • Cavitary disease; progressive pulmonary disease
• Dissemination → meningitis
• Serology: complement fixation, immuno
diffusion, enzyme-linked immunoassays
• Ag detection: urine, serum, CSF
• ESR ↑ 2x

• Coccidiodomycosis size > RBC

Paracoccidioidomycosis • Causes paracoccidioidomycosis (pulmonary) • Granuloma formation at site of infection • Chronic disease = most common form
• P.brasiliensis; P.lutzii • Low Th1 response → active infxn; loss of immune control
• Estrogens may inhibit mold to yeast transition in F 1. Acute/Subacute (juvenile) paracoccidioidomycosis:
• Thermal dimorphism --------------------------------------------------------------------------------- • Disseminated
• Teleomorphic (no sexual stage) • Yeast cells: multiple buds (blastoconidia) connected by • Children and adults < 30 yo
isthymus (captain's wheel) • Lymph node enlargement, diffuse abd pain, skin abscesses
• South America • Fever, weight loss, LAD, HSmegaly, anemia
• High humidity, rich vegetation, acidic soil • Paracocci size >> RBC
2. Chronic paracoccidioidomycosis:
• Transmission: inhalation or traumatic inoculation • Growth at room temp: hyaline septate • Reactivation of 1º infxn yrs later
• a/w armadillos hyphae w/ intercalated chlamydoconidia • Pulmonary infiltrates and upper oral mucosal lesions
• Cough, painful oral ulcers, larynx involved
• Dissemination to any organ/tissue
• Complication: chronic resp. failure; Addison's disease

Talaromycosis • Causes talaromycosis marneffei • Yeast: single transverse septum • AIDS indicator disease
• Dimorphic • Culture: mold smooth conidiophores w/ multiple metulae
• Infectious agent: Conidia bearing phialides (red pigment in agar) • Disseminated disease: fever, cough, pulm. infiltrates, LAD, anemia,
leukopenia, thrombocytopenia
• SE asia → Mimics TB, histoplasmosis, cryptococcosis
• Isolated from bamboo rats
• Skin lesions: lesions like molluscum contagiosum on face/trunk
CUTANEOUS FUNGAL INFECTIONS
Malassezia furfur Asexual: produce conidia by budding 1. Spaghetti and Meatballs (round yeast like cells w/ short • Tinea Versicolor
Sexual: Form basidiospores hyphae branches) • Neonates on TPN
2. Collarette around budding point
---------------------------------------------------- • TXT: Topical Azoles (Ketoconazole or Itroconazole if widespread)
• Sabouraud w/ with olive oil grow cream colored colonies

Sporothrix schenckii • Causes sporotrichosis • Dimorphic • Rose Thorn disease

• Hyphae with spores (mold) on sabourauds agar • Pustule or ulcer w/ draining nodules
• Spores from thorn introduced into skin → rose • Cigar shaped yeast on blood agar • Ascending lymphangitis
gardener's disease
• TXT: Itraconazole or Potassium iodide

DERMATOPHYTES
Hortaea werneckii 1. Branched, dematiaceous (dark pigmented) septate hyphae • Tinea Nigra
2. Arthroconidia (fungal spores) produced by segmentation of
preexisting hyphae
-------------------------------------------
• Sabouraud agar grows black mold

Piedraia hortae 1. Spindle shaped ascospores (sexual means of reproduction • Black Piedraia
where spore is contained or produced in an ascus/asci)
2. Branched, pigmented hyphae
--------------------------------------------
• Sabouraud agar grows velvety appearance

Trichosporin beigelli Asexual: produce conidia by budding 1. Hyaline (clear/light colored) septate hyphae • White Piedraia
Sexual: Form basidiospores 2. Some arthroconidia and some blastoconidia
-----------------------------------------------------------
Sabouraud agar grows cream colored colonies

Microsporum spp. Macroconidia: numerous, large, thick and rough No dimorphism (but may show special structures in culture) • Tinea corporis, Tinea capitis
walled
• KOH preps, Long wavelength UV Wood's lamp

• TXT: Topical Azoles (Terbinafine, Griseofulvin), Detergents

Trichophyton spp. Asexual: produce conidia by budding • Macroconidia: rare, smooth, thin walled • Tinea infections
Sexual: Form basidiospores • Tinea capitis in children
• Tinea capitis in immunocompromised adults
• No dimorphism (but may show special structures in
culture) • DX: KOH preps
• TXT: Azoles (Terbinafine, Griseofulvin), Detergents

Epidermophyton • No dimorphism (but may show special structures in • Macroconidia: smooth walled, club shaped, borne in clusters of • Tinea pedis, Tinea cruris, Tinea ungium
fluccosum culture) two or three
• DX: KOH preps
• TXT: Azoles (Terbinafine, Griseofulvin), Detergents
 MYCOBACTERIA
MYCOBACTERIA TUBERCULOSIS
General Epidemiology Virulence Factors Laboratory Diagnostics
• Aerobic, acid fast, intracellular rods • Humans - natural reservoir • Prevention of phagosome lysosome fusion • Acid fast stain: Ziehl Neelsen, Kinyoun stain (carbolfuchsin stain); Auramine-
• Survive and replicate in phagosome rhodamine (fluorescent stain)
• Mycolic acids → lipid, waxy, clumpy • Transmission:
→ Aerosolized droplets • Mycobacterial lipids: • Nucleic Acid test
• Gram POS (not useful d/t mycolic acids) → Low infectious dose → Lipoarabinomannan (LAM): limits phagosome maturation
• Non-motile → Mannose-capped (ManLAM): attach to mannose receptor and DC-SIGN • Culture methods:
• Risk factors: → Sulfolipid: inhibits phagolysosome fusion → Slow growth (24 hr doubling time)
→ Foreign born → Cord factor: serpentine growth pattern in vitro; inhibits phagolysosome → Lowenstein-Jensen (malachite green, egg suspension) and Middlebrook media
→ HIV+ fusion; induces TNFα (granuloma formation) → Colony shape: colorless, raised w/ wrinkled surface and irreg. edges
→ Immunodeficient
→ Alcohol/drug abuse • Mycobacterial proteins: • PPD test
→ Close quarters → Protein tyrosine phosphatase (PtpA): interacts w/ host vacuolar H+ ATPase → Activates memory CD4+
and vacuolar sorting protein to prevent membrane fusion and phagosome → Type IV HSR
• Vaccine: acidification
→ Live attenuated BCG → BCG vx pts (+)
→ Most effective against disseminated TB in children • Type VII Secretion system (ESX-1): promotes membrane rupture, ↑ → > 5 mm: HIV (+), organ transplant, fibrotic changes in CXRAY, recent exposure
inflammatory response → > 10mm: immigrant, IVDU, child < 4, lab workers
→ > 15mm: all pts

• IFNγ release assay (Quantiferon Gold)

→ Measures IFNγ produced by sensitized T cells stimualted by M.tb Ag
→ BCG vx pts (-)

Pathogenesis Morphology Disease

• CD4 TH1 and CD8 Primary form (infection): • Leading cause of death in AIDS pts
• IFN γ, IL-12, TNFa • Begins in lungs (distal airspaces near pleura); drain to • All stages of HIV a/w ↑ risk fo TB
regional nodes
• Enters M⏀ by phagocytosis • Ghon complex: caseating lung lesion in Primary TB:
• Replicates in M⏀ → bacteremia and seeding of other sites middle/lower lobes w/ hilar LAD; 1-1.5 cm grey white • Previously unexposed → d/t exposure to exogenous organisms
• TH1 response → granuloma formation and caseous necrosis area of inflam. w/ consolidation and cetral necrosis • 5% develop sig. disease (miliary TB)
• Granulomatous inflammation w/ or w/o caseation
Innate Immunity: • Asymptomatic; Flu-like sxs; acute bacterial pneumonia
• Replicate in PMNs and use monocytes to disseminate Secondary form (reactivation): • Most infxn restricted to lungs in immunocompetent
• Neutralize ROS/NO, prevent phagolysosome fusion • Begins in upper lobes w/ foci of consolidation • Latent infxn most common (immune cells wall off infxn in granuloma)
• Promotes inflammation and immune cell recruitment • Central caseation
• NK cell activity ↓ in susceptible pts; IL-10 mediated suppression • Cavitary lesions (<10cm) Secondary TB:
• Granulomatous response w/ fibrosis and inflam. • Previosly exposed → reactivated infxn d/t immunosuppression
Antigen Presentation: • Bacilli elicit prompt tissue response
• Impair Ag presentation- preventing co-stimulation for T cell activation Progressive TB: • CXRAY → consolidation w/ hilar enlargement, cavities
• Results in anergic T cells and exhibit peripheral tolerance • Apical lesion expand into adj. lung and erode into
bronchi and vessels • Sxs vary from asymptomatic/localized to pulmonary or extrapulmonary
Adaptive Immunity: manifestations
• CD4 & TH1 cells control M.tuberculosis by (+) M⏀, CD40L receptors and Miliary TB: → Persistent productive cough, Dyspnea, chest pain, hemoptysis
TCR, and secreting IFNγ • Spread hematogenously and recirculates to lungs → Weight loss, fatigue, night sweats
• IFNγ and IL-12 further (+) M⏀to ↑ phagosome killing, proinflam. cytokines, • Multiple small (2mm) lesions ('millet seed')
and B7 co-stimulation to activate more T cells TXT:
• RIPE
Reactivation:
• d/t multiplication and escape from granuloma
• CD4 depletion and TNFα impairment
• CD8 cells involved in elimination
 MYCOBACTERIA LEPRAE
General Epidemiology Virulence Factors Laboratory Diagnostics
• Aerobic, acid fast, intracellular rods • Armadillos • Targets M⏀ and Schwann cells • Doesn't grow in cell-free medium
• Endemic in Mexico • Histopathology of biopsy specimens → main lab dx
• Non-motile • TLR1 and TLR2 on Schwann cells recognize M.leprae and apoptosis • Acid fast stains → paucibacillary v. multibacillary
• Non-spore forming • Transmission: close contact, aerosolize droplets • PGL-1 (phenolic glycolipid-1) a/w M⏀ and induces NO → peripheral
• Prefers lower temp neuropathy • Lepromin skin test determines type of leprosy
• Extremely slow growth (14 day doubling time) → Inactivated M.leprae injected → (+) edema/nodule = tuberculoid; (-) = lepromatous

Pathogenesis Morphology Disease

Leprosy: Lepromatous form: Leprosy (Hansen disease):
• Replicates in cool tissue → hands, face • Epidermis is stretched thin over skin nodules → • Slowly progressive infxn
• Most ppl have natural protective immunity uninvolved "clear zone" beneath • Involves skin and nerves

Lepromatous form: (TH2) • Large aggregates of lipid-laden M⏀ (lepra cells)

• Anergic w/ little or no resistsance; multiple lesions filled w/ bacteria Lepromatous form:
• Invades Schwann cells into endoneural and perineural macropahges and • "Leonine" faces
damages peripheral nerves • M⏀ act as incubators rather than destroying • Symmetric skin thickening and nodules
• Bacteria are NOT contained → No granulomas; Bacteria in blood and organisms • Can affect testes, eyes, upper airway, spleen, liver
sputum
• ↑ TH2, IL-4 • Multiple organisms present (multibacillary) Tuberculoid:
• Dry scaly skin lesions that lack sensation on extensor surfaces (cold)
Tuberculoid: (TH1) Tuberculoid form: • Begin as localized flat red skin lesions → indurated, elevated hyperpigmented
• Hyperergic w/ high resistance; single or few lesions • Granulomatous lesions like TB margins w/ depressed pale centers
• Granuloma formation • Can involve larger peripheral nerves
• ↑ TH1, IFNγ • Organisms are rare (paucibacillary) d/t strong host • Not typically fatal d/t slow growth
defense

MYCOBACTERIA AVIUM COMPLEX

General Epidemiology Virulence Factors Laboratory Diagnostics
• Opportunistic pathogen • Ubiquitous in environment • Biofilm • Colonies: smooth from clinical isolates; rough from environment
• Acid fast, intracellular rods • Resistant to abx and disinfectants • Nuclear acid tests
• Transmission: inhalation, ingestion, dermal contact • Translocation across epithelial layer to infect M⏀ • PCR restriction fragment analysis
• Non-motile • Risk Factors: pulmonary disease, smokers, AIDS
• Slow growth
• Mycolic acids in cell wall

• Includes M.avium and M.intracellulare

Pathogenesis Morphology Disease
• In immunosuppressed (AIDS, transplant, autoimmune disease):
→ Overt infection only in those w/ T-cell immunodeficiency
→ Involve lungs and GI tract particularly in widely disseminated infections
→ Nonspecific sxs: fever, night sweats, weight loss
→ Large numbers of organisms w/ minimal inflammation; no granulomas

• In immunocompetent: slowly progression granulomatous pulmonary disease (like

TB)

Mycobacteria marinum - hand infection in aquarium handlers

Mycobacteria scrofulaceum - cervical lymphadenitis in children
 PARASITES
• Albendazole: Inhibit synthesis of microtubules
• Praziquantel: ↑ Ca2+ influx, causing ↑ membrane permeability
• Diethylcarbamazine: Inhibit arachidonic acid metabolism → microfilaria more susceptible to immune attack
• Ivermectin: Activates glutamate Cl- channels

General Epidemiology Life Cycle Disease Lab DX

Roundworms (Nematodes)
Trichuris Trichiura • Whipworm • #3 roundworm in US • DX stage: unembryonated eggs in feces • Mostly asymptomatic • O&P: eggs in feces → barrel shaped, thick wall w/ plugs
• Causes trichuriasis • Tropical locations • IFX stage: ingestion of embryonated eggs • Sxs d/t worms burrowing in intestinal epithelium • Worms: in tissue
• Poor sanitation • Dehydration, anemia, eosinophilia
• Kids • Eggs hatch in small Intestine • DOC: Albendazole or Mebendazole
• Adults in colon • Heavy infxn: abd pain, diarrhea
• Complicxn: Rectal prolapse

Enterobius • Pinworm • #1 roundworm in US • DX & IFX stage: eggs in perianal folds • Asymptomatic • Eggs: scotch tape/paddle test
vermicularis • Causes • Kids (5-10 yo) • Transmission via autoinfection • Perianal pruritus • Wet mount → flat on one side, thick wall
enterobiasis • Abd pain, N/V, loss of appetite • Worms: colonoscopy → lfashlight test or fecal material
• Larvae hatch in small intestine • May cause vulvovaginitis in ♀
• Adults in colon • DOC: Mebendazole or Pyrantel Pamoate; Alt:
• Gravid females migrate nocturnally Albendazole
outside anus

Ascaris • Largest nematode • #1 human helminth • DX stage: eggs/worms in feces • All infxn require txt • Serology → eosinophilia, ↑ IgE
lumbricoides • Causes ascariasis • Kids • IFX stage: fertilized eggs • Early phase: Pulmonary • O&P: eggs → oval, lumpy, thick outer coat
• Tropical/subtropical (Asia) • Cough, SOB, hemoptysis, fever, wheeze • U/S, CT, XRAY → Visualize worms
• Rural SE US • Larvae invade intestinal mucosa • Loeffler syndrome (rare)
• Migrate to lungs and penetrate alveolar • TXT: surgery, anti-helminthic drugs
walls • Late phase: Intestinal
• Ascend bronchial tree to throat and • Abd pain, anorexia, N/V/D • DOC: Albendazole, Mebendazole or Pyrantel Pamoate
swallowed
• Adults in small intestine • Complicxn: intestinal obstruct. → volvulus, malnutrition,
biliary strictures, ectopic migration

Toxocara canis • Dog roundworm • Dog owners • Larvae invade intestinal wall • Tissue manifestation • O&P: no eggs develop
• Outdoor workers • Migrates through tissues • Mostly asymptomatic • Leukocytosis and ↑ IgE
• ELISA
• Lifecycle ends in humans → accidental • Visceral migrans: migration of worms to various • CT, MRI
host tissues (heart, liver, lungs, CNS)
• DOC: Albendazole or Mebendazole
• Ocular migrans: migration of worms to eye

Trichinella spiralis • Causes trichinosis • Worldwide • DX stage: encysted larvae in striated • Asymptomatic • Serology → eosinophilia, leukocytosis
muscle • Intestinal stage → N/V/D, abd pain • Muscle biopsy → ↑ CK
• IFX stage: ingest undercooked meat • Muscle stage → muscle pain, swelling, fever
(pork) w/ encysted larvae • TXT: steroids, anti-helminthics drugs
• Larval migration to striated muscles → edema, fever,
• Invade small intestine and develop into myalgias, eosinophilia, ocular sxs • DOC: Albendazole/Mebendazole + Corticosteroids
worms • Periorbital swelling
• Nurse cell involvement- larvae enter host • Severe → myocarditis, CNS involvement
muscle
• 2 hosts req. to perpetuate the life cycle

Strongyloides • Threadworm • Tropics/Subtropics • DX stage: rhabditiform larvae in stool • Asymptomatic • Rhabditiform larvae in stool
stercoralis • Causes • US applachia • IFX stage: filariform larvae invades skin • Immunosuppressed • Unusual tracks on agar plate
strongyloidiasis • Filariform enter through skin • Strongyloidiasis:
• Adults in small intestine (autoinfection) → • Ground itch, diarrhea, epigastric pain, duodenitis • DOC: Ivermectin; Alt: Albendazole
lungs → swallow • If pulm. → dry cough, throat irritation
• Can live free-living or stay w/n host to • Hyperinfection syndrome:
autoinfect • High worm burden → organ dysfxn or sepsis

Necator • Hookworm • #2 human helminth • DX: Eggs in stool • Cutting plates attach to SI → feed on blood • Wet mount → colorless, thin, smooth shell w/ 2-8 cells
americanus • Tropics/ Subtropics • IFX stage: filariform invades skin and • Iron deficiency anemia stage cleavage
• Dogs/cats = normal hosts migrates w/n epidermis • Ground itch: entry of filariform • Serology → mild eosinophilia
Ancylostoma • Transmission via burrowing through skin • Cutaneous larva migrans (creeping eruption)
→ lungs → trachea → swallow • Immune response to migrating worm • TXT: Albendazole/Mebendazole, iron replacement
• Travel to small intestine • TXT: Zoonotic form is self-limiting (weeks)
• Humans = dead end host • DOC: Albendazole/Mebendazole or Pyrantel Pamoate
Tapeworms (Cestodes)
Taenia spp • Causes taeniasis • Worldwide • DX stage: eggs or proglottids in feces • Taeniasis: usually asymptomatic → Mild GI sxs: • T. solium: scolex w/ 4 suckers & hooks, globular head
• ↑ in developing countries • IFX stage: eat cysticerci in uncooked epigastric pain, diarrhea, nausea • T. saginata: scolex w/ 4 suckers, NO hooks, pear head
• T. solium - pork meat
• T. saginata - beef • CX: Obstruction, appendicitis, cholangitis • O&P: eggs w/ radial striations
• Attach to small intestine
• DOC: Praziquantel (Taeniasis)

Taenia spp • Causes • Worldwide • DX stage: Cysticerci in striated muscle • Extraneural Cysticercosis: • Scolex w/ 4 suckers & hooks
neurocysticercosis • IFX stage: ingest eggs • Muscle/SQ most common
(T. solium) • Asymptomatic SQ and calcified intramuscular nodules • Biopsy → visualize cysts
• Hatch in small intestine • CT, MRI → visualize cysts
• Invade muscles, brain, liver, other tissues • Intraparenchymal neurocysticercosis: brain • Serology → detect Ab
→ form cysticerci
• Extraparenchymal neurocysticercosis: • DOC: Praziquantel or Albendazole + surgery
• Intraventricular lesions (Cysticercosis)
• Subarachnoid lesions
• Spinal lesions
• Ocular lesions

Echinococcus • Dog tapeworm • South America, Middle • Dog = definitive host • Cystic echinococcosis, hydatid disease: • Serology → ELISA for Ab
granulosis • Extremely small East, sub-Saharan Africa • Sheep = freq. intermediate host • Uncontrolled cyst growth • U/S, CT, MRI → visualize hydatid cysts
• Human = dead-end host • Asymptomatic initially
• Single organ involvement 85+% • TXT: Cyst > 5cm → surgery, PAIR (puncture, aspirate,
• Liver involvement: RUQ, N/V inject w/ EtOH to kill, re-aspirate)
• Lung involvement: Cough, SOB, hemoptysis • TXT: Cyst < 5cm → anti-helminthic rx

• CX: cyst rupture → Type 1 HSR • DOC: Albendazole

Diphyllobothrium • Fish tapeworm • Former soviet, northern • DX stage: unembryonated eggs in feces • Diphyllobothriasis: • Eggs and proglottids in stool
latum • Causes Europe, Japan • IFX stage: plerocercoid larva in • Mostly asymptomatic • Operculum and terminal knob
diphyllobothriasis undercooked/raw fish • Diarrhea, allergic, fatigue, weight loss
• DOC: Praziquantel, Niclosamide
• Adults in small intestine • Complicxn: megaloblastic anemia 2º B12 deficiency,
• Pass in stool obstruction
Flukes (Trematodes)
Fasciolopsis buski • Giant intestinal • Largest intestinal • DX stage: unembryonated eggs or adult • Usually asymptomatic • Wet mount → thin smooth wall, inconspicuous operculum
fluke trematode worms in feces • Bowel mucosal ulcers where worm attached • Worms → flattened leaf like body w/ uterus
• Causes • Hermaphroditic • IFX stage: ingestion of metacercariae
fasciolopsiasis • SE Asia (encysted larvae) • High worm burden: Anorexxia, vomiting, diarrhea, • DOC: Praziquantel
• Pig farmers malabsorption, ascites
• Adults in small intestine
• Transmission via contaminated water • Complicxn: Obstruction, perforation

Heterophyes • Intestinal fluke • Egypt, Sudan • DX stage: embryonated eggs in feces • Heterophyiasis and Metagonimiasis: • Wet mount → operculum w/ small terminal knob
heterophyes • IFX stage: metacercariae in fish tissue • Usually asymptomatic
• DOC: Praziquantel
• Adults in small intestine • High worm burden:
• Ulceration where worms attach
Metagonimus • Intestinal fluke • East Asia • Anorexia, abd pain, dyspepsia, diarrhea
yokogawai
• CS: Granulomatous lesions after ectopic distribution
of eggs

Schistosoma • Blood fluke • Africa, East Asia, South • Contaminated water w/ infected stool or • Schistosomiasis (snail fever) • Eggs with hook in feces or urine or ELISA and Indirect
species • Snails intermediate America urine. eggs hatch in water and infect snails • Swimmer's itch @ site of skin penetration hemagglutination
host and infect humans via skin penetration • Iron deficiency anemia (children) • Schistosoma mansoni → large lateral spine
• Swimmers at risk • Schistosoma japonicum → small terminal spine
• Migrate against portal blood flow → portal • Jaundice, cirrhosis (S. mansoni/ japonicum) • Shistosoma haematobium → large terminal spine
HTN (mansoni/japonium) • Hematuria, SCC of bladder (S. haematobium)
• Bladder (haemoatobium) • TXT: Praziquantel

Clonorchis • Liver fluke • Asia • Eating infected raw fish w/ chinese liver • Opisthorchiasis: mostly asymptomatic • Eggs in stool, duodenal aspirates and bile specimens
(Opisthorchis) • Snails intermediate fluke • Eggs have small knob and operculum
sinensis host • Acute: RUQ pain, diarrhea, fatigue, lymphadenopathy • Adult worms in endoscopy

• Chronic: biliary tract inflammation, obstruction, • TXT: Praziquantel

mechanical injury

• CX:pigmented gallstones, cholangitis,

cholangiocarcinoma

Paragonimus • Lung fluke • Asia, West Africa, Latin • Eating infected raw shellfish (crab meat) • Paragonimiasis: mostly asymptomatic • Eggs in sputum and stool
Westermani • Snails intermediate America • Eggs have operculum
host • Early infection (2 months): Fever, epigastric pain, • Adult worms in lung biopsy
urticarial, pleural effusions and pneumothorax
• TXT: Praziquantel
• Late infection: adult flukes living lungs → Chronic
cough w/ bloody sputum
Blood Protozoa
Plasmodium • Female mosquito • Africa, Southeast Asia, • Sporozoites → Schizonts → Merozoites • Malaria • P falciparum: ring form and Banana shaped gametocyte
species Anopheles South America, Central → Gametocytes • Febrile paroxysms • P. vivax: Schuffner dots and many randomly arranged
America, Caribbean • P. falciparum = severe, RBCs occlude capillaries of merozoites
• Hypnozoites = P.vivax/ovale brain, lungs, kidneys • P. ovale: Schuffner dots and fewer merozoites
• P. malariae: Rosette arranged merozoite
• P.vivax/ovale: 48 hours "Tertian" → only infects
reticulocytes (immature RBCs), Duffy Ag • TXT:
• P. malariae: 72 hours "Quartan" → only infects → Chloroquine: P.vivax/ovale, P.malariae
mature RBCs → Mefloquine: cholorquine resistant strains
• P. falciparum: irregular → infects all RBCs → Atovaquone/Proguanil: chloroquine resistant strains
→ Primaquine: hypnozoites
• CX: DIC → Quinidine, Artesunate (IV): severe (P. falciparum)

• Prophylaxis: Mefloquine

• -quines: prevents heme → hemozoin; ↑ toxic heme

• Artesimins: bind iron → generate free radicals

Babesia microti • Ixodes tick vector • NE US • Asplenic, adults over 50 yo • Flu like symptoms • Blood Smear: Maltese cross (merozoite tetrads)
• Hemolytic anemia, Jaundice, Hepatomegaly
• White footed • TXT: Atovaquone + azithromycin
mouse reservoir • CX: ARDS, DIC, heart or renal failure

Trypanosoma • Tsetse fly • T. brucei gambiense: • Painful bite • African Sleeping Sickness: recurring fever (d/t • Trypomastigotes in CSF
brucei West African antigenic variation of surface glycoproteins) • ↑ WBCs in CSF
• Morular cells of Mott: activated plasma cells with
• T. brucei rhodesiense: • Early → blood borne • Gambian/West Africa: Winterbottom's sign (cervical eosinophilic inclusions
East African • Late → CNS lymph nodes)
• Rhodesiense/East Africa: more CNS destruction, TXT:
• Gambiense: humans more virulent, *death within 12 months if untreated T. gambiense:
→ Pentamidine (early)
• Rhodesiense: Wild game → Eflornithine (late) - inhibits ODC

T. rhodesiense:
→ Suramin (early)
→ Melarsoprol (late) - blocks sulfhydryl groups

Trypanosoma • Reduviid bug • South America • Kissing bug feces scratched into bite • Chaga's disease: • Trypomastigotes in blood (Acute)
cruzi • Amastigotes in biopsies (Chronic)
• Dogs, cats, rats, 1) Acute phase: flu like sxs • Trypanosomes on cardiac biopsy
monkeys, possums, - Chagoma: indurated area @ bite site (eyelids/face)
bats, poor housing - Romanas sign: rash and edema around eyes and face • TXT:
conditions, → Nifurtimox (generates toxic nitroanion radical
deforestation 2) Chronic phase: Dilated cardiomyopathy, metabolite)
Megacolon, Megaesophagus, Achalasia → Benznidazole (inhibit protein and RNA synthesis)

Leishmania • Sandfly vector • Tropical or subtropical • Promastigotes = infective, motile form • Cutaneous Leishmaniasis: ulcer w/ scarring • Obligate intracellular protozoan
species areas • Amastigotes in macrophages w/ kinetoplast
• Vertebrates host • Amastigotes = mature, non-motile in • Mucocutaneous Leishmaniasis: nose/mouth lesion w/
• Cutaneous: most macrophages/RES mucous membrane destruction and severe facial • TXT: Amphotericin B, Sodium Stibogluconate
common disfuguration
• Visceral: most serious
• Visceral Leishmaniasis: HSmegaly, pancytopenia,
distended stomach and dermal leishmaniasis (pigmented
granulomas)
→ kala-azar (black fever) Leishmania donovani
Tissue Protozoa
Toxoplasma • Cats (definitive • Fecal oral • Undercooked infected meat contaminated • Acute disease: similar to mononucleosis • Tissue Bradyzoite
gondii host) acquire by with cat feces • Chronic: lymphadenitis rash, encephalomyelitis,
eating infected mice myocarditis • TXT: Sulfadiazine + Pyrimethamine
→ Sulfadiazine inhibits dihydropteroate synthase
• Disease in immunocompromised pts (involves brain, → Pyrimethamine inhibits dihydrofolate reductase
liver, lung, death) and can reactivate latent toxoplasma
→ major cause of encephalitis in AIDS • Prophylaxis: TMP/SMX
→ serious consequences for pregnancy (TORCHES)

Naegleria fowleri •Free living amoeba • Southern US (warm fresh • Contaminated water enters nasal mucosa • Primary amebic meningoencephalitis (brain eating): • Trophozoites and PMNs in CSF (Giemsa or wet mount)
in warm fresh water, water) and penetrates olfactory mucosa rapid onset of fever, headache, N/V, seizures, altered
soil mental status, taste and smell anormalities • TXT: Amphotericin B + rifampin

Tissue/Lymph Helminths (Nematodes)

Wucheria • Female mosquito • W. bancrofti: Africa, SE • Filarial larvae injected via bite • Lymphatic Filariasis (elephantiasis) 9mo - 1 yr • Sheathed microfilariae in peripheral blood (Giemsa)
Bancrofti Asia, India, Pac/Caribbean
• Develop in lymphatics • Acute: adenolymphangitis (painful episodes of fever w/ • TXT: Diethylcarbamazine, Ivermectin
• B.malayi: China, India, inflammation of inguinal lymph nodes) and filarial fever
Malaysia, Philippines, • Migrate in lymph and blood vessels • Chronic: lymphedema, chyluria, elephantiasis
Indonesia
• Cough when in lungs

Onchocerca "Black flies, Black • Africa (disease state • Filarial larvae injected via bite • Ocular onchocerciasis: river blindness microfilariae in • Microfilariae w/o sheaths on skin biopsy
volvulus skin, Black sight" differs by geography) eye
• Develop in SQ tissues • TXT: Ivermectin (single dose)
• SQ nodules: onchocercomata deep nodules over bony
prominences

• Skin disease: pruritic lesions w/ lymphadenopathy,

lichenified onchodermatitis

Dracunculus • Guinea Worm • Rural, isolated areas in • Contaminated water with water fleas that • Dracunculiasis (guinea worm disease): blister bursts to • Vesicle and thread like worm exiting vesicle
Medinensis Disease Chad, Ethiopia, Sudan contain larvae in copepods form ulcer with worm emergence
• Incapacitating pain and often secondary infection • Drink water through mesh straw
• Mature in abdomen and migrate to skin • Slowly extracted around pencil
• Niridazole

Loa Loa • Deerfly • Rainforest of West and • Filarial larvae injected via bite • Loiasis • Sheathed microfilariae in peripheral blood or visualization
(Chrysops), Horse Central Africa • Ocular sxs: worm in conjunctiva of worm in eye
fly, Mango fly • Calabar swellings: angioedema like swelling due to
hypersensitivity rxn • TXT: Diethylcarbamazine

• CX: encephalitis, cardiomyopathy and nephropathy

 STI MICRO
HSV 1 & 2 HPV Candida spp
General • Herpesviridae family • Papillomaviridae family • Opportunistic pathogen
• dsDNA • dsDNA • Normal commensal in GI, vagina, skin
• Enveloped • Non-enveloped • Nosocomial
• Icosadeltahedral • Icosahedral capsid
• Linear genome • Circular genome

Structure / • Lytic infection of epithelial cells & fibroblasts • Infects stratified squamous epithelium • Transmission endogenously
Life Cycle
• Latency in neurons: • L1 protein = viral attachment → binds to heparin • Risk factors: Diabetics, broad spec abx, high estrogen
→ HSV 1 → trigeminal ganglia proteoglycans & integrin α6 levels, immunosuppression, neutropenia < 500/mm3
→ HSV 2 → sacral ganglia
• Invades basal cells (stratum basale) → linked to life cycle
• CD8 cells & IFNγ maintain latency of keratinocyte
• Once reactivated, transient replication, depressed immunity →
lesions • Replicates via host cell DNA pol

• Tegument = viral proteins and enzymes for replication • As infected skin cell matures and works its way to surface,
→ Immediate early proteins (α): for gene transcription and virus matures and is shed w/ dead cells of upper layer
takeover cell
→ Early proteins (β): DNA pol and other enzymes
→ Late proteins (γ): structural proteins

Pathogenesis • HSV 1 → aquired by respiratory secretions and saliva • Acquired by direct contact through small breaks in • Phenotypic switching
/ Virulence • HSV 2 → acquired via sexual transmission or vertical skin/mucosa, sexual contact, vertical transmission • Catalase (+)
transmission
• HPV E6 protein: targets host cell p53 TS protein → • Hyphal wall protein- adherence
• HSV 1 binds quickly and efficiently unchekced cell proliferation • Proteinases
• HSV 2: greater potential to cause viremia • Phospholipases- lecithinase
• HPV E7 protein: targets Rb TS protein → unchecked cell
• Upper half v. lower half (below waist) proliferation

Lab • Cowdry bodies = eosinophlic intranuclear inclusions found in • Koilocytes → HPV infected cells from transition zone→ • 10% KOH
cells appear large & dense w/ wrinkled nucleus (often binucleated); • PAS, Grocott/Gomori methanemine silver stain, Gram
• Tzank smear → multinucleated giant cells infected w/ HSV Perinuclear halo, raisin like nuclei stain
• PCR = gold standard
• Definitive dx → viral Ag or DNA sample • PCR or DNA molecular probe for diagnosis • Budding yeast and pseudohyphae under
microscope
• pH < 4.5 (normal)
• Smooth white creamy domed colonies
• Oval yeast like cells that produce blastoconidia and
chlamydospores

• Germ tube test for C. albicans**

Clinical • "Dew drops on a rose" appearance to lesions • HPV 1-4: Verruca Vulgaris (common warts) • Most common cause of vaginitis (after bacterial
• Acyclovir, Valcyclovir → prevent outbreaks → Hands & feet of children vaginosis)
→ Transmission via physical contact
• Keratoconjunctivitis • Candida vulvovaginitis:
• Gingivostomatitis → initial outbreak of HSV1 • HPV 6 & 11: Laryngeal papillomatosis (true vocal cords) & → vaginal itching, burning, irritation, dysuria, dyspareunia
• Herpes labialis → cold sores condyloma acuminata (anogenital warts) • Vaginal mucosa and vulva erythema/edema
• Herpetic Whitlow → painful lesions on fingers **dentists • Cottage cheese like thick white discharge
• Eczema herpeticum • HPV 16, 18, 31 & 33: anogenital & squamous cell • Yeast-like odor
• Erythema multiforme → HSR 1-2 wks s/p HSV1 infxn w/ cancers; cervical carcinomas (**16, 18)
target lesions on hands and feet that move centrally • Cutaneous candidiasis:
• HIV infection may ↑ HPV E6 & E7 expression → develops in folds of skin (intertrigo); armpits, groin,
• HSV 1 → #1 cause of sporadic temporal lobe encephalitis • Immunosuppression can → ↑ risk of cancer d/t HPV fingers, under breasts / warm moist environments
in US
• HSV 2 → aseptic meningitis in teens/adults • Diaper dermatitis:
→ 2º infxn after bacterial infxn
→ Beefy red plaques, satellite papules, pustules

• Paronychia and Onychomycosis

• Perianal candidiasis

• Balanitis
→ pain, pruritus, erythema w/ curd-like exudate
→ small papules w/ eroded, dry glazed look

• Chronic Mucocutaneous candidiasis

→ a/w immunodeficiency
→ non-invasive infxns of skin, nails, mucous membranes

• Candida Endocarditis:
→ IV drug users → tricuspid valve

• Oral steroid use

 Chlamydia Trachomatis Neisseria Gonorrhea Treponema Pallidum
General • Common cause of Urethritis and cervicitis (D-K) • 2nd most common STD in US • 3rd most common STI in US
• Trachoma (A-C)- #1 cause of preventable blindness • Only infects humans • Exclusive to humans
• Transmission sexually or vertically • Transmission sexually or vertically
• Genital infections, Lymphogranuloma venereum • Microaerophile
• Conjunctivitis, Pharyngitis • NEVER a commensal • Lacks LPS
• Nonpathogenic species are part of upper respiratory tract

Structure / • Gram NEG but no muramic acid • Gram NEG diplococci • Gram NEG thin, corkscrew
Life Cycle • Obligate intracellular parasite → can't make ATP • Facultative anaerobe • Can't perform TCA cycle; lacks ETC and lacks AA/FA
• Oxidizes glucose only syn. pathways
• Elementary body is infectious, small, resist harsh conditions, • No capsule • Dependent on host for purines, pyrimiidnes, most AA
prevent phagolysosome fusion • Oxidase (+)
• Reticulate body is metabolically active, replicates, • Fastidious growth requirements (susceptible to drying & cold
intracellular temps)
• EB → RB and multiply in inclusion bodies
• Host cell ruptures and releases infectious EBs

Pathogenesis • Type III SS • Pili: major virulence factor; attachment and resistant to PMN • Hyaluronidase
/ Virulence • MOMP (outer membrane protein) → sero variants killing • Escapes immune recognition by camouflage w/ host
• Inhibit phagolysosome fusion • IgA protease ECM factors (fibronectin) and serum components
• LOS → tissue damage • Motility- Endoflagella → burrow through tissues
• Host tissue damage d/t direst destruction of cells during • Tissue damage a/w host immune response
replication and proinflammatory cytokine response • Complement evasion → host derived N-acetylneuraminic • Host immune response limits 1º infxn but
• Immunity is short lived after infection → Reinfection usually less acid (sialic acid) to LOS invasion/spread persists
aggressive → resistant to complement attack **C5b-C9 def.
• Resistance to phagocytosis
• Ag variation

Lab • NAAT- vaginal swabs, first-catch urine, rectal swab • Gram neg diplocci inside or around PMNs in males • Darkfield microscopy
• Cytoplasmic inclusions on Giemsa, iodine, fluorescent Ab • Thayer Martin Medium for isolation in females • VDRL and RPR screening: cardiolipin Ag to measure
stain IgM and IgG reaginic Abs (antimitochondrial Abs)
• NAAT • FTA and TPPA confirmation
• Oxidize glucose but not maltose → phenol red turns yellow • Can't culture
• Oxidase (+) → TMPD turns purple/dark blue

Clinical • Most common STI in US (D-K) • Cervicitis • 1º syphilis

• Cervicitis, Urethritis → asymptomatic in F → Contagious
• Dysuria, discharge • Complications: PID, Fitz Hugh Curtis syndrome, → 2-6 wks
• F more likely to be asymptomatic than M Bartholinitis → Painless chancre
• Abx are only effective against reticulate bodies
• Urethritis • 2º syphilis
• Untreated can lead to: scarring of fallopian tubes, PID, Fitz- → most have sxs in M → Contagious
Hugh Curtis syndrome (peritoneal cavity → liver capsule) • Complications: Epididymitis → 6-8 wks
→ Rash (palmar and plantar) - s/p untreated chancre
• LGV (L1-L3): • Proctitis → Condylomata lata (wart like lesions)
→ 1º painless ulcers that heal rapidly → mostly asymptomatic
→ 2º painful buboes (can form fistulas, strictures, obstruction, → more in MSM • Latent syphilis
elephantiasis) → Decades
→ proctitis and systemic spread • Cutaneous gonorrhea → No sxs (may relapse to 2º syphilis)
→ 1º pustule, ulcer, indurated abscess
• Keratoconjunctivitis (Trachoma- A-C): → 2º urogenital disease • 3º syphilis
→ Endemic in middle east, north africa, south asia, south → Gummas
america • Disseminated gonococcal infection: → Cardiovascular
→ 1º in children → Tenosynovitis + Dermatitis + Polyarthralgias → Neurosyphilis
→ Serovars ABC ("African blind children")
→ transmitted eye to eye by droplets, hands, clothing, flies, • Gonococcemia Congenital syphilis
aerosol → Late abortion/stillbirth
→ follicular conjunctivitis - corneal ulceraion and scarring - • Neonate conjunctivitis (earlier onset than Chlamydia → Infantile (5 wks- 3 mos)
inturned eyelashes = blindness neonatal conjunctivitis), Conjunctivitis, Pharyngitis • Snuffles
• Desquamating maculopapulr rash
• Adult conjunctivitis, Neonatal pneumonia, Neonatal • Barber's pole umbilical cord
conjunctivitis, Reactive arthritis • HSmegaly and LAD

→ Late Congenital (> 2 yo)

• Hutchinson teeth
• Mulberry molars
• Rhagades
• Interstitial keratitis
• Saddle nose
• Saber shins
• Sensorineural deafness
 Trichomonas Vaginalis Gardnerella vaginalis Haemophilus Ducreyi
General • Eukaryotic parasite • Major cause of bacterial vaginosis
• d/t disruption of normal vaginal microflora (Lactobacillus)

Structure / • Trophozoite in vagina/ urethra → feeding, motile, reproductive • Gram POS coccobacilli • Gram NEG small pleomorphic coccobacilli
Life Cycle • No cyst stage → poor survival outside of host • Facultative anaerobe • Non-motile
• Non-spore forming • Facultative anaerobe
• Resides in female lower genital tract and male urethra and • Non-motile • Fastidious
prostate
Pathogenesis • Pili • Small inoculum
/ Virulence • Vaginolysin → pore forming cytolysin
• Biofilm formation
Lab • Trophozoites → diagnostic and infective stage • Gram variable stain d/t low peptidoglycan • Requires factor X (hemin) and V (NAD)
• Flagellated
• Vaginal pH > 4.5 → Homogenous d/c • Gram stain of exudate → streptobacilli
• Undulating membrane → pH > 4.8
→ Clue cells → adherence to squamous epithelial cells • NAAT
• NAAT = gold standard → Positive amine whiff test

Clinical • Transmission sexually or vertically • 50-75% asymptomatic •M>F

• Linked to uncircumcised men and prostitution
• Asymptomatic infection common → scant, watery d/c • Bacterial vaginosis: Thin, off white gray discharge w/
fishy odor • Chancroid and soft chancres
• In symptomatic F: • Painful w/ bleeding base
→ purulent, foul, foamy d/c • Erythematous papules → eroded pustules that
→ vaginitis, dysuria, dyspareunia, abdominal pain ulcerate
→ "strawberry cervix"
• Unilateral inguinal LAD and bubo formation
• In M:
→ frequently asymptomatic
→ symptomatic: urethritis, epididymitis, prostatitis

Klebsiella Granulomatis Mycoplasma genitalium Phthirus pubis

General • Endemic in Papua New Guinea, South America, Caribbean, • Smallest free living organism • Phthiriasis pubis (crab/ pubic louse)
Southern Africa

Structure / • Gram NEG bacilli • Lacks cell wall • Infectious stage - adult
Life Cycle • Pleomorphic • Human to human transmission (sometimes fomites)

Pathogenesis • Capsule • Tip organelle - attachment • Clawed 2nd and 3rd legs for gripping
/ Virulence • Contributes to host tissue necrosis • Take blood meals

Lab • Donovan bodies in macrophage • Difficult to culture • Visualize louse and or nits (eggs) or feces
• Giemsa stain • NAAT

Clinical • Granuloma inguinale (Donovanosis) → chronic, progressive • Nongonococcal urethritis and cervicitis • a/w pubic hair; can infest other areas
ulcerative disease • Mostly asymptomatic or pruritus → allergic rxn to saliva

• Begin as painless papules → painless granulomatous ulcer • TXT: Permethrin, Malathion, Ivermectin
that bleeds on contact
"Pesty Mites and Lice NAG → inhibit Na+ channels,
• Spontaneous clearance → scars and deformation inhibit AChE, activate glutamate Cl- channels"
• LAD and pseudobubos (granuloma spread to inguinal region)
 UTI MICROBIO
Uropathogenic E. coli Proteus mirabilis Klebsiella pneumoniae Staphylococcus saprophyticus Enterococcus spp.
Etiology • Most frequent cause of UTI • A/w catheter infections • Opportunistic pathogen • Ubiquitous • E. faecalis and faecium = GI/GU
• GI commensal • Opportunistic pathogen • Upper respiratory tract and • Colonizes colon and GU tract of 5-10% F commensals
Large intestine commensal • Catheter associated UTIs
• Nosocomial infections
Microbe • Gram NEG rod • Gram NEG rod • Gram NEG rod • Gram POS cocci • Gram POS cocci (pairs or short chains)
• Facultative anaerobe • Enterobacteriaceae family • Facultative anaerobe • Facultative anaerobe • Lactic acid bacteria
• Enterobacteriaceae family • Non-motile • Coagulase NEG • Facultative anaerobe
• Enterobacteriaceae family

Virulence • Biofilm formation • Urease → urolithiasis • Capsule: antiphagocytic • Biofilm formation • Fewer virulence factors than Staph/Strep
Factors • P-pili and type 1 fimbriae: adhere to GU • Flagella → swarming • Ag variation of LPS O- • MSCRAMMs → bind ECM • Biofilm formation
tract epi • Capsule polysaccharide → tissue damage • UafA adhesion protein • Abx resistance
• Polysaccharide Ag K capsule: • Fimbriae • Type 1 and 3 pili • Urease → Oxacillin and cephalosporins
antiphagocytic • Biofilm • Siderophore • Ion transport systems → osmotolerance → Acquired aminoglycosides and
• α-hemolysin: destorys RBCs → • Urease vancomycin (VRE)
inflammation • Carbapenem resistance
• Cytotoxic necrotizing factor I: glutamine • FaecaLIS = LESS dangerous; more
deamination of small GTPases alters host cell common
cytoskeleton
• Type III SS
• Siderophore receptors

Labs • UA → pyuria and nitrites • Lactose fermentation (-) • Lactose fermentation (+) • NITRATES NEG (b/c urease +) • Catalase (-)
• Lactose fermentation (+) → pink colonies • Very high swarming • Urease (+) • Catalase (+) • γ hemolysis
on MacConkey agar motility • Oxidase (-) • Coagulase (-) • High salt growth (6.5%)
• Urease (-) • Urease highly active • String test (+) → mucoid • Novobiocin resistance • Optochin resistant
• Oxidase (-) • Oxidase (-) colonies • γ hemolytic • Bile resistant
• Hydrogen sulfide (+) • PYR (+)

Disease • Acute uncomplicated cystitis • Asymptomatic bacteriuria • Nosocomial UTIs • 2nd leading cause of UTI in sexually • Acute uncomplicated cystitis
• Complicated UTI in elderly and T2DM • Lobar pneumonia active females • Complicated UTI
• Urosepsis • Septicemia • Endocarditis → common s/p GI/GU
• Acute uncomplicated procedures
cystitis • Current jelly sputum
• Complicated UTI "3 A's: alcoholics, aspiration,
• Fishy odor abscess"

TXT • TMP-SMX • MDR

• Fluoroquinolone
• Gentamicin w/ ampicillin
or Ceftriaxone →
Pyelonephritis
 DIARRHEA MICRO
Organism Etiology Transmission/Incubation Disease / Complications Virulence Lab TXT
BACTERIA
H. Pylori • Gram NEG bacilli • Fecal oral • Gastritis (antrum of stomach) • Urease + • Stool Ag • Triple therapy = PPI +
• Curved/spiral shape • Posterior duodenal Ulcer • Polar flagella • Urea breath test Amoxicillin +
• Catalase + • Mucinase • Biopsy Urease test (CLOtest) Clarithromycin
• Oxidase + • Adenocarcinoma • pH sensitive adhesin (BabA) • Giemsa and Steiner silver stain
• T4SS → CagA
• VacA (cytotoxin A)

Enterotoxigenic E.coli • Gram NEG bacilli • Fecal oral • Traveler's diarrhea • Heat Labile toxin → ↑ cAMP • Lactose + (Pink on MacConkey agar) • Supportive care
• 10-72 hrs • Watery diarrhea (small intestine) • Heat Stabile toxin → ↑ cGMP • Metallic Green on EMB agar

• CX: Dehydration
Enteropathogenic E. • Gram NEG bacilli • Fecal oral • Pediatric diarrhea • Bundle forming pili • Lactose + (Pink on MacConkey agar) • Supportive care
coli • 9-12 hrs • Watery diarrhea (small intestine) • Pedestal formation (actin rearrange.) • Metallic Green on EMB agar
• T3SS: Tir, Map, EspF
• CX: Dehydration, malnutrition • Histology: loss of brush border

Enterohemorrhagic E. • Gram NEG bacilli • Fecal oral • Hemorrhagic colitis (large intestine) • Shiga Like Toxin (heat labile) • Lactose (+) MacConkey agar • Supportive care
coli • 4 days • Bloody diarrhea • T3SS: Tir, Map, EspF • Metallic Green on EMB agar
• O157:H7 is most • Sorbitol (-) MacConkey agar white
common serotype • Undercooked beef • Hemolytic Uremic Syndrome (Shiga colonies
• Low infectious dose toxin) = Renal failure, MAHA,
Thrombocytopenia

Enteroinvasive E.coli • Gram NEG bacilli • Fecal oral • Mild bacillary dysentery • Invades intestinal mucosa → necrosis and • Lactose + (Pink on MacConkey agar) • Supportive care
• Low infectious dose inflammation • Metallic Green on EMB agar
• CX: Dehydration

Shigella • Gram NEG bacilli • Fecal oral • Bacillary Dysentery/ Shigellosis • Shiga Toxin: inactivate 60s RNA • MacConkey agar Lactose NEG = white • Macrolides
• 8-48 hrs • T3SS: Ipa A,B,C colonies • Fluoroquinolones
• Hemolytic Uremic Syndrome • Invasion Plasmid Ag • H2S Hektoen colonies = green
• Very low infectious dose • Intracellular in macrophages • Oxidase NEG
(HIGHLY INFECTIOUS) • CX: Megacolon, obstruction, • Acid Resistant • ONPG neg (β galactosidase)
• Invade M cells using bacteremia
host actin filaments

Salmonella Enterica • Gram NEG bacilli • Fecal oral • Typhoid fever (extraintestinal • Similar to shigella • Motile • Fluoroquinolones
Typhi • 5-21 days invasion) • T3SS: SopB/SopE • Encapsulated
• Asymptomatic carriers • SCV (salmonella containing vacuole) for • MacConkey agar Lactose NEG • Live attenuated oral
• High infectious dose • Pea soup stools replication • Hektoen H2S POS: black colonies vaccine
• Rose spots on trunk • Facultative intracellular in macrophages

• CX: Septicemia, Ileal perforation

Salmonella Enterica • Gram NEG bacilli • Fecal oral • Inflammatory (blood in children) • Similar to shigella • Motile • Supportive care
Enteritidis • 8-72 hrs • Watery diarrhea • T3SS: SopB/SopE • Encapsulated
• Bloody diarrhea in children • SCV (salmonella containing vacuole) for • MacConkey agar Lactose NEG
• Contaminated foods replication • Hektoen H2S POS: black colonies
• Direct contact w/ animals • CX: Osteomyelitis in sickle cell, • Facultative intracellular in macrophages
Infective endocarditis

Vibrio Cholerae • Gram NEG • 2-3 days • Cholera • Bacteriophage CTX: lysogen encoding • Oxidase positive • Supportive care
• Comma shaped • Contaminated food/water • Diffuse watery diarrhea "rice water cholera toxin subunits (ctxA and ctxB) • Thiosulfate citrate bile salt sucrose agar
• Facultative anaerobe • Shellfish copepod stools" • Shooting star motility
reservoir • Cholera toxin AB5: ADP ribosylates Gαs → • Dipstick for O1 and O139 Ag
Vibrio parahaemolyticus ↑ cAMP/ PKA → Cl-, ions, H2O exit cell
and vulnificus → raw • High infectious dose
shellfish required • Serogroup O1 and O139 contain cholera toxin
• Asymptomatic carriers
Yersinia • Gram NEG bacilli • 4-6 days • Yersinosis • T3SS: YopE and Yop P/J • Bipolar "safety pin" staining • Aminoglycosides
Enterocolitica • Inflammatory diarrhea (terminal ileum) • Tetracyclines
• Fleas vector • Contaminated milk and
pork • CX: Pseudoappendicitis, DIC, shock
• Direct animal contact

Campylobacter • Gram NEG bacilli • 2-5 days • Campylobacteriosis/ Gastroenteritis • Cytolethal Distending Toxin • Oxidase POS • Erythromycin
• Curved (>10 BM/day) • Hypervariable sequences for immune escape • Microaerophilic • Ciprofloxacin
• Domestic animals • Invasive → bloody diarrhea • CadF adhesion
• #1 organism in invasive (puppies) and birds • Pseudoappendicitis in children
enterocolitis • Contaminated water/raw
milk and poultry • Reactive Arthritis
• Guillain Barre Syndrome (Ab to GM1
on myelin)

Listereria • Gram POS bacilli • 1 day • Listerioriosis/ Gastroenteritis • Facultative intracellular in macrophages • Tumbling at room temp • Ampicillin
Monocytogenes • Pregnant women • Inflammatory diarrhea • Listeriolysin O: pore forming toxin • Grows at 4C
• Contaminated meat, • Catalase +
dairy, vegetables • Dissemination: meningitis • Internalin (adhesion) binds E-cadherin • β hemolytic
• Transplacental • Neonatal disease: • ActA for propulsion
transmission 1) Early onset: stillbirth
2) Late onset: meningitis

Clostridioides difficile • Gram POS bacilli • Fecal oral • Pseudomembranous Colitis • Toxins A & B: disrupt cytoskeleton and • Lecithinase (-) • PO Vancomycin
• 3-7 days • C. diff associated diarrhea intercellular tight junctions → ↑ paracellular • Lipase (-) • IV Metronidazole
• Obligate anaerobe • Watery diarrhea permeability • Swarming (-) • Fidaxomicin
• Spore forming • Nosocomial s/p abx use
• Asymptomatic carriers • Fulminant disease: shock, ileus,
(normal flora) megacolon

Clostridium • Gram POS bacilli • 8-12 hrs • Clostridial food poisoning • α toxin (lecithinase) → damage cell • Lecithinase (+) • Supportive care
Perfringens • Watery diarrhea membranes (Myonecrosis and hemolysis) • Lipase (-)
• Obligate anaerobes • Contaminated meat • Myonecrosis (gas gangrene) • Swarming (-)
• Spore forming products after spore
germination • Necrotizing enteritis: bloody diarrhea
caused by pore forming β toxin

Bacillus Cereus • Gram POS bacilli • Emetic 1-6 hrs • Watery diarrhea • Heat stable emetic toxin: spores can survive • Catalase + • Supportive care b/c
• Diarrhea 18 hrs • Emetic disease cooking • β hemolytic preformed toxin
• Motile
• Ingestion of toxin in • Ocular infections • Heat labile toxin: activates AC and increases • Lecithinase positive
REHEATED rice or spores • Opportunistic infections cAMP like V. cholera **not for emetic disease b/c toxin mediated
in meats and vegetables

Staph aureus • Gram POS cocci • RAPID = 1-8 hrs • Watery diarrhea • Enterotoxins are heat stabile • PMN infiltration, mast cells activated • Supportive care b/c
• Emetic disease • Enterotoxin A, C, D = superantigens that • Brush border loss in jejunum preformed toxin
• Ingestion of toxin in meats stimulate cytokine release
• Enterotoxin A = food poisoning • PMN infiltration, Mast cell activation
• Enterotoxin C & D: associated w/
contaminated milk products
 VIRUSES
Yellow Fever • Flavivirus • Aedes mosquito • Bloody diarrhea • Councilman bodies (eosinophilic apoptotic • Live attenuated
• (+) RNA • Fever, black vomitus, jaundice globules) on liver biopsy vaccine
• Enveloped • Backache

Hepatitis A • Picornavirus • Contaminated water/ • Gastroenteritis • Self limiting • Acid stable • Supportive care
• (+) RNA shellfish • Hepatitis
• Naked • Jaundice • Inactivated/killed
vaccine

Norovirus • Calicivirus • Close quarters • Viral gastroenteritis • Seen more in vaccinated children than • Supportive care
• (+) RNA • Cruises • Watery diarrhea Rotavirus (rotavirus vaccinated by 3 mo in
• Naked • Daycare developed countries) → Rotavirus is MCC in
• Shellfish/buffets developing countries

Rotavirus • Reovirus • #1 cause of severe • Viral gastroenteritis • NSP4 enterotoxin • Supportive care
• dsRNA (+ & -) diarrhea in young • Watery diarrhea
• Naked children • Live attenuated PO
• CX: Intussusception vaccine
 PARASITES
Entamoeba "Entamoeba Eats • Anal-oral • Intestinal amebiasis • Trophozoites w/ endocytosed RBCs • Metronidazole (invasive
Histolytica Erythrocytes" • MSM • Flask shaped ulcerations • Stool O&P colitis) + Paromomycin/
• Bloody diarrhea • Stool Ag testing Iodoquinol (intraluminal
• Cysts in small intestine → • Amoebic liver abscesses w/ "anchovy • Serology (liver abscess) cysts)
Trophozoite in colon paste" consistency

• CX: Rupture to pleura/ peritoneum

Cryptosporidium • Cysts w/ 4 motile • Fecal oral • Severe diarrhea in AIDS (CD4 < 100) • Oocysts on acid fast stain • Filter water
sporozoites • Contaminated water • Mild watery diarrhea in • Ag detection • Nitazoxamide in
immunocompetent immunocompetent
• Isospora Belli → • MCC of diarrhea in AIDS • Spiramycin
Cryptosporidium like
symptoms; acid fast but
ELLIPOID shaped cysts

Giardia • Ingest cysts • Fecal oral • Steatorrhea • Multinucleated trophozoites • Purify water (boiling or
• Gastric acid secretion in • Foul-smelling diarrhea • Cysts in stool O&P w/ iodine)
duodenum → cysts • Non-invasive • ELISA stool Ag • Metronidazole
become trophozoites
• CX: Fat soluble vitamin deficiencies,
epithelial brush border enzyme
deficiencies (lactase)
 CNS INFECTIONS
Meningitis Bacterial Abscess
Neonates • Group B strep 6-60 yrs • S. pneumoniae • Streptococcus Risk Factors:
• E. Coli • N meningitidis • Staphylococcus • Immunocompromised
• Listeria • Enterovirus • Fusobacterium • Cyanotic heart disease
• HSV • Peptostreptococcus anaerobius • Dental abscess
6 mo - 6 yrs • S. pneumoniae 60+ yrs • S. pneumoniae • Assoc. w/ previous infxns (OM, sinusitis, mastoiditis) • Pneumonia
• N. meningitidis • N. meningitidis • Endocarditis
• H. influenza • H. influenzae • Head injury
• Group B strep • Group B strep
• Enterovirus • L monocytogenes
General Epidemiology Lab DX Transmission Pathogenesis Disease
Strep Agalactiae • Gram POS COCCI • Colonization of colon and GU • β- hemolytic • In neonate: high burden in mother, • Polysaccharide capsule: antiphagocytic and sialylated • #1 → Neonatal sepsis, Neonatal meningitis
• Vaginal carriage in pregnant • CAMP POS premature delivery, prolonged residues inhibit alternative complement pathway
• Catalase NEG • Bactracin resistant membrane rupture, intrapartum fever • Hypervirulent GBS adhesion protein (HvgA) in certain • Early onset: bacteremia, pneumonia, meningitis
• Non-motile • PYR NEG strains: adherence to BBB endothelium and choroid plexus • Neuro sequela: blindness, deafness, MR
• Facultative anaerobe • In adults: DM, chronic liver/renal epithelium • Serotypes Ia, III, V
disease, cancer
Immune response: • Late onset: acquired from exogenous source causes
• Abs develop against polysaccharide capsule for protection bacteremia w/ meningitis
• Complement (alternative and classical) are necessary for • Infxn in infants 1 wk to 3 mo.
elimination • Mostly serotype III (may have HvgA)
• Neonates have limited humoral adaptive immune • ↑ Neuro sequela
response and premature infants have low complement ------------------------------------------------------------------
proteins = more affected by GBS • Pregnancy: UTI, amnionitis, endometritis
• Older adults: Skin and ST infxn, pneumonia,
bacteremia, bone/joint infxn (Serotyves Ia, V)
Neisseria • Gram NEG DIPLOCCI • Colonizes nasopharynx • High amounts of PMNs in CSF • Respiratory droplets • Capsule: antiphagocytic Meningitis: abrupt onset of headache w/ Brudzinski
Meningitidis • 13 serotypes • Agglutination test detects capsule • IgA protease: escapes mucosal immunity (neck rigidity), Kernig (knee extension limited) signs
• Oxidase POS • Only infects humans polysaccharides • Risk: infants, toddlers, YA, close • LOS (toxic to cells) or nuchal rigidity, myalgias
• Catalase POS • Oxidizes maltose, glucose quarters, immunocompromised, • Outer membrane proteins and pili • 14 hours after 1st sxs, 50% untreated mortality
• Aerobic but can reduce • Phenol red test → turns yellow unvaccinated, complement
nitrite under low O2 deficiencies • Entrance into tissue mediated by transcytosis, phagocyte Meningococcemia (septicemia)
• Modified Thayer-Martin chocolate delivery or direct damage to epithelium • Small petechial/purpuric rashes on trunk and lower
agar: appendages (Purpura fulminans)
→ Vanco (kills GM POS) • Multiorgan failure
→ Colistin & Trimethoprim (kills • Can lead to Waterhouse Friderichsen (DIC)
GM NEG except Neisseria)
→ Nystatin (anti-fungal) • Pneumonia, Arthritis, Urethritis

Vaccines:
• MPSV4: polysaccharide vaccine
• MenACWY: conjugate vaccine
• Serogroup B meningococcal vaccines (10-25 yo)

Nocardia • Gram POS ROD • Found in soil, decaying matter, • Buffered charcoal yeast extract • Exogenously by inhalation, • Avoid phagolysosomal killing Nocardiosis
water • Slower growing on most medium traumatic introduction, ingestion • Survival and replication in macrophage mediated by Bronchopulmonary disease
• Weak acid fast staining • Aerial hyphae cord factor (trehalose dimycolate glycolipid) and prevent • Immunocompromised pts, pneumonia dyspnea, fever,
(d/t tuberculostearic acid • Risk: immunocompromised acidification of lysosome cough
and short mycolic acids) • Cavitation w/ spread to pleura
• Catalase POS • Dissemination to CNS or skin
• Aerobic
Brain Abscess
(Actinomyces is • Single or multiple abscess formation, may present as
ANAEROBE and NOT acid chronic meningitis initially
fast)
Cutaneous infxn, Lymphocutaneous infxn

Strep Pneumoniae • Gram POS DIPLOCOCCI • Colonizes nasopharynx and • Optochin sensitive • Carriage and disease in cool mo. • Adhesion: Pneumococcal surface proteins • Pneumococcal pneumonia: abrupt onset, f/c, chest
oropharynx of kids • α - hemolytic • Polysaccharide Capsule pain
• Catalase NEG • Bile soluble • Endogenous → aspiration to lower • Pneumolysin: lyses epithelial cells, phagocytes • Lobar pneumonia: Blood tinged sputum, crackles on
• Optochin sensitive • Most common cause of • Quellung reaction positive respiratory tract • Autolysin: lyses peptidoglycan auscultation
• Lancet shaped community acquired • Latex agglutination of capsular • Exogenous → respiratory droplets • IgA protease • Sinusitis, meningitis, bacteremia
• Facultative anaerobe pneumonia polysaccharide • C polysaccharide → inflammation via CRP
• C-polysaccharide in CSF • Hydrogen Peroxide → ROS Vaccines:
= Activates classical complement • PCV13: conjugate vaccine (2+ mo yo)
• PPSV23: polysaccharide vaccine (2+ yr yo)
Haemophilus • Gram NEG • GM NEG pleomorphic rods in CSF • Aerosol • Polyribosyl ribitol phosphate (PRP) capsule • Invasive Hib → bacteremia, meningitis, cellulitis,
Influenza COCCIBACILLI or sputum • Adhesins: pili, fimbriae, HiA adhesion, HMW1/2 (NTHi) epiglottitis, tracheitis, pneumonia, bronchitis, arthritis
• IgA protease • NTHi (commensal) → OM, sinusitis, tracheitis,
• Facultative anaerobe • Chocolate agar + Factor X (hemin) • LPS/LOS damages tissue pneumonia, bronchitis
• Oxidase POS and Factor V (NAD/NADP)
• Agglutination for serotyping Vaccines:
• Conjugate vaccine for HiB

Listeria • Gram POS RODS • Most common in pregnant • Cultures from blood, CSF • Dairy products, cold cut meats, • Listeriolysin O (pore forming cytolysin) lyses vacuolar • Meningitis in newborns
monocytogenes women, neonates and • β hemolytic on blood agar poultry membranes w/n host cells → selectively activated w/n • Food poisoning and gastroenteritis
• Facultative intracellular immunocompromised • Catalase (+) acidified phagosomes
• Growth at 4º C • Maternal: mild GI infxn
• Tumbling motility • Umbrella like growth in motility agar • In utero: abortion, stillbirth, death days after birth
extracellular • Neonatal: meningitis and sepsis
• Actin rockets → infxn through birth canal
intracellular/transcellular

Actinomyces • Gram POS ROD • Actinomyces israelii most • Grows very slowly • Endogenous infxns • Break in mucosal barrier • Cervicofacial actinomycosis
clinically relevant • Molar tooth colony • URT, GI, GU • Resists ROS • Pelvic, CNS actinomycosis
• Facultative anaerobe • Sulfur granules (yellow) • Abscess formation = abscesses!
• Filamentous branching • Commensal of mouth, GI, GU
• TXT: PCN G vs Sulfonamids (Nocardia)

"SNAP: Sulfonamids Nocardia, Actinomyces PCN"

Fusobacterium • Gram NEG ROD • Commensal of oral cavity • Long spindle shaped rod • Endogenously from oral cavity • FadA adhesion/invasion: binds cell jxn cadherin proteins • Cerebral aneurysm
Nucleatum • Anaerobic • Loosen jxns & ↑ endothelial permeability • Abscesses
• Induces proinflam. cytokines (IL-6, IL-8, TNF α) • Periodontitis
• GI disorders: Colorectal cancer, IBD
• Lemierre's: septic thrombophlebitis of internal jugular
vein
• Pregnancy: stillbirth, preterm, neonatal sepsis

Peptostreptococcus • Gram POS COCCI • Commensal of mouth, GI, • Inhibited by Sodium Polyanethol • Endogenous, break in mucosal • CNS: abscess
Anaerobius • Anaerobic vagina, skin Sulfonate (SPS) → other Gram POS barrier • Skin: Nec Fasc, decubitus ulcers, human/animal bites
cocci will grow • URI/ dental
• Risk: DM and • Female pelvic infxn
immunodeficient • Joint infxn: prosthetic joints and septic arthritis

Toxopasma gondii • Obligate intracellular • Worldwide • Serology: IgM = new infxn, IgG = old • Ingesting oocytes, raw or • Tachyzoite: infective trophozoite form of oocyst • Acute disease: similar to mononucleosis
protozoa • 1/2 adults have been infected infxn undercooked meats w/ tissue cysts • Bradyzoite: slowly multiplying encysted form • Chronic disease: lymphadenitis, rash,
• NAAT • Vertical transmission encephalomyelitis, myocarditis
• Histo: View cysts in tissues (retina, • Cats = definitive host
brain, muscle) Immunocompromised:
• Reactivation of latent toxoplasma in
immunocompromised and elderly

Congenital:
• Chorioretinitis
• Hydrocephalus
• Intracranial calcifications

Nagleria fowleri • Free living amoeba • Southern US • Microscopy or NAAT • Enter olfactory neuroepithelium and enters the brain • Primary amebic meningoencephalitis (brain
• Warm fresh water, soil, • Trophozoites in CSF w/ PMNs eating): rapid onset of fever, headache, N/V, seizures,
3 lifecycle stages: swimming pools • Low glucose, high protein and altered mental status, taste and smell anormalities
• Cyst pressure
• Trophozoites: infxn & dx • High mortality rate >90%
• Flagellated: dx
 VIRAL ENCEPHALITIS, MENINGITIS, POLIOMYELITIS
General Presentation: Aseptic Meningitis: Encephalitis: Myelitis:
• Fever • Non-bacterial inflammation of tisuses lining brain • Viruses that infect neurons w/n CNS and induce intense inflammation of parenchyma • Inflammation of spinal cord
• Headache Neck stiffness • Enteroviruses, HSV2, Arboviruses • Herpesviruses, Arboviruses • Polio
• Altered mental status
• Seizures
• Focal neuro signs
• Behavioral changes
• Language disturbance
General Transmission Clinical Presentation Pathogenesis
Flavivirus: West Nile Virus Vector: Culnex mosquito NON SPECIFIC • 1º replication in regional lymph nodes
• (+) RNA Reservoir: Bird • Mostly asymptomatic • Disseminates via blood to mononuclear phagocytic system
• Icosahedral • <1% → neuro disease • Second viremia required for neuroinvasion
Location: Africa, Tropical Asia, Mediterranean • Directly infects and LYSIS of neurons and glial cells
• Enveloped
• Symptomatic: nonspecific, self-limiting febrile (2-14 days)
• ID by serology of
Dengue Fever Vector: Aedes mosquito NON SPECIFIC 1. Virus replicates at injection site
CSF/ PCR Reservoir: Humans and monkeys 2. Disseminates to lymph nodes and spreads through blood to RES
• Mostly asymptomatic
• 4-7 day incubation 3. Cytokine production and (+) classical complement pathway
Location: Tropical Africa • SXS: fever, arthralgias/myalgias, rash 4. Immune complexes deposit = vascular leakage
• Breakbone fever: deep bone pain
• Conformational change to mature virus to be • Dengue shock syndrome
infectious depends on glycoproteins
Yellow Fever NON SPECIFIC 1. Virus replicates at injection site
• Mostly asymptomatic 2. Spread to lymph nodes and disseminates to liver targeting monocytes-macrophages
• 3-6 incubation 3. Cytokine production and decline in lymph counts
• SXS: Fever, hemorrhage, jaundice 4. Disseminates to other organs
• Period of infection → Period of remission → Period of intoxication → death
• Yellow fever vaccine (live attenuated)

Togavirus: WEEV, EEEV, VEEV EEE Vector: Culiseta, Coquillettide, Aedes mosquito ENCEPHALITIS • Envelop fuses w/ endosome not cellular membrane
• α virus ginus WEE Vector: Culnex mosquito EEE:
• (+) RNA VEE Vector: Culnex, Aedes, Mansonia mosquito • 4-10 day incubation • 1º replication in vascular endothelium and regional lymph nodes
• SXS: fever, drowsiness, neck rigidity → Confusion, paralysis, convulsions, coma • Disseminates via blood to distant lymph nodes, BM, spleen, liver
• Icosahedral Reservoir: • Fatality 50-75% → permanent neuro sequelae (deaf, blind, paralysis)
• Enveloped • Birds (EEE and WEE) • Second viremia and invasion of CNS by:
• Horses (VEE) WEE: 1. Passive transfer of virus through endothelium of CNS capillaries
• 2-7 day incubation 2. Viral rep. in vascular endothelial cells and release progeny into parenchyma
Location: • SXS: fever and myalgias only 3. Invasion of CSF w/ infection of choroid plexus and ependyma
• N/S America, Caribbean (EEE) • Fatality 3-10% 4. Carriage of virus in lymphocytes and monocytes → migrate into CNS parenchyma
• N/S America, west of Mississippi river (WEE)
• Venezuela, Columbia, Peru, Equador (VEE) VEE:
• 1-5 day incubation
• Systemic febrile illness → 1% develop clinical encephalitis

Chikungunya Virus Vector: Aedes mosquito NONSPECIFIC

Reservoir: Monkeys and humans • 3-12 day incubation
• SXS: headache, anorexia, constipation, fever
Location: Africa, S Asia, Caribbean, N/S America • Severe joint pain

Outer and intermediate capsid • Shorter febrile period and longer arthralgias than Dengue

Reovirus: Colorado Tick Fever Vector: Dermacentor andersoni tick MENINGOENCEPHALITIS • Primary viremia and infection of erythrocyte precursors
• dsRNA Reservoir: squirrels, rodents • 3-6 day incubation • Virus remains in mature RBCs, evading immune system. Can't replicate in mature RBCs
• 12 segments • SXS: "saddle-back" fever, HA, retroorbital pain, severe myalgias in back and legs, leukopenia • Viremia persists wks to months (even after no sxs)
Location: Western US and Canada • Can → meningoencephalitis and hemorrhagic fever • Promotion of transmission of the virus to the vector
• Icosahedral
• NON- Enveloped

Bunyavirus: La Crosse Virus Vector: Aedes mosquito ENCEPHALITIS:

• (-) RNA Reservoir: human, chipmunks, small animals • 6-15 day incubation
• 3 segments • SXS: mild febrile illness to encephalitis/ meningoencephalitis
Location: Mid-west, Mid- Atlantic, SE US • CNS: stiff neck, lethargy, nausea, HA, v omiting, seizures, coma, paralysis, brain damage
• Helical
• Enveloped

Lyssavirus: Rabies virus • Reservoir: wild animals ENCEPHALITIS • Long incubation up to 365 days then fast pathogenesis
• (-) ssRNA • Vector: wild animals, unvax dogs/cats • Encephalitis w/ hydrophobia
• Helical • Behavioral changes 1. Viral replication in muscle
• Target cell: neuron • Delirium w/ rapid progression to coma 2. Virion enters PNS
• Enveloped • Host receptor: ACh receptor 3. Passive ascent via sensory fibers
• Myelitis w/ ascending flaccid weakness
• "bullet shaped" • High mortality 4. Replication in DRG
Source of virus: • TXT: Post-exposure prophlaxis w/ rabies IgG vaccine 5. Rapid ascent in spinal cord
• Major: saliva in bite of rabid animal 6. Infection of spinal cord, brainstem, cerebellum
• Minor: aerosols in bat caves containing rapid bats 7. Descending infection to eye, salivary glands, skin, organs
Herpesvirus Herpesvirus α Herpesviruses: ENCEPHALITIS:
• dsDNA • Neurotropic • Acute focal neurological findings (< 1 wk)
• Linear • Fast life cycle (establish latent infection in • Altered consciousness, ataxis, focal seizures, speech problems, hemiparesis, amnesia, fever
neurons)
• Icosahedral • HSV 1/2, VZV
• Enveloped ASEPTIC MENINGITIS:
• Sudden onset headache, fever, N/V, malaise, photophobia
β Herpesviruses: • Rash, diarrhea, URI sxs
• Lympho-, neuro-tropic
• Slow life cycle (latent infxn in kidney, glands,
lymphoreticular cells)
• HCMV (HSV-5), HSV-6 (Roseola)

γ Herpesviruses:
• Assoc. w/ infxn, transformation of B & T lymphs.
• Slow life cycle (latent infxn in lymphoid tissue)
• EBV (HSV-4), Kaposi Sarcoma (HSV-8)

Enteroviruses Poliovirus • 3 serotypes (P1,2,3) • Mostly asymptomatic • Primary viral replication in oropharynx/ GI and shed through feces
• (+) RNA • Fecal-oral transmission • 7-14 day incubation • Second viremia
• NON-enveloped • Highly infectious • Invades motor neurons → poliomyelitis • Subsequent viremia:
• Muscle atrophy 1. 4-8% abortive poliomyelitis (flu like, URI, GI)
2. 1-2% non-parelytic aseptic meningitis (stiff neck, back, legs)
• SALK vaccine- inactivated/killed vs. SABIN vaccine- live attenuated (risk of reversion) 3. < 1% flaccid paralysis (selective lysis of motor neurons)

Paramyxovirus Measles: • Respiratory droplets • Prodrome: fever, cough, conjunctivitis, rash on head and spreads down 1. Growth in lymphoid tissue
• Encephalitis/ Meningitis 2. Virus seeded to mucous membranes
• Utilizes glycoprotein and fusion protein for • Complications: OM, croup, bronchitis, bronchopneumonia 3. Respiratiory sxs, conjunctivitis
attachment and entry 4. Koplik spots (inside mouth, specific for measles)
• (-)ssRNA • Post-infxn encephalitis → permanent neuro sequelae 5. Rash
• Enveloped • Subacute sclerosing encephalitis

• MMR vaccine (live attenuated)

Mumps: • MENINGITIS can present w/o parotid invovlement 1. Replication in respiratory tract
• ENCEPHALITIS unilateral nerve deafness 2. Viremia to systemic infection
3. Parotid gland: virus multiples in ductal epithelial cells (local inflam. and swelling)
• Painful edematous enlargement of parotic and other salivary glands 4. Disseminates to other glands
• Unable to talk or eat w/o discomfort 5. Pancreas: assoc. w/ juvenile diabetes
• Other glands: pancreas, ovary, thyroid, testicle
• Benign meningeal signs detectable in 10%

JC Polyoma virus JC Polyoma virus: • Fecal-oral • Primary infection: tonsils or GI • 1º infxn → latent infxn in kidney, BM and tonsils
• dsDNA • Reactivation in immunocompromised pts → oligodendrocytes
• Circular • Early and late genes expressed by transcription in • Develops into Progressive Multifocal Leukencaphalopathy
different directions (ciruclar genome)
• Non-enveloped
 TORCH INFECTIONS
Presentation: Common characteristics:
• Growth retardation • Mild maternal illness
• Hepatosplenomegaly • Vertical transmission
• Hemolytic anemia • Cause severe fetal anomalies
• Microcephaly • TXT of maternal infxn usually doesn't affect fetal prognosis sig.
• Rash
• Maternal history
Distinguishing features MOA/ Placental barrier breach Clinical presentation Diagnosis TXT
Congenital • Toxoplasma gondii Transmission: • Acute infxn in infants usually asymptomatic or mono-like sxs • ↑ fetal infection in 3rd trimester • Spiramycin (1st/2nd trimester)
Toxoplasmosis • Obligate intracellular • Ingesting oocytes, raw or undercooked • Microcephaly • ↑ fetal mortality in 1st trimester • Pyrimethamine/Sulfadiazine & Leucovorin
protozoa meats w/ tissue cysts
• Vertical transmission Triad: • PCR of blood, CSF, bronchoalveolar fluids • TMP-SMZ prophylaxis
• Cats = definitive host • Chorioretinitis • Isolated in cx from placenta, umbilical cord, serum
• Hydrocephalus • Serology: IgM = new infxn, IgG = old infxn
• Reactivation of latent toxoplasma in • Intracranial calcifications
immunocompromised and elderly • Blueberry muffin rash • Histo: View cysts in tissues (retina, brain, muscle)
• ↑ CSF protein

• Skin: Petechiae, Ecchymoses, Large hemorrhages

• Risk for severe neurodevelopmental sequelae

Congenital • Treponema pallidum Transmission: • Majority are asymptomatic at birth • Dark-field microscopy • Benzthine penicillin G for mom
Syphilis • Obligate intracellular parasite • Horizontal → sexual contact • IV/IM PCN for baby
• Gram NEG spirochete • Vertical → mother w/ 1º or 2º syphilis • Fetal effects: stillbirth, neonatal death, hydrops fetalis Non-treponemal and treponemal tests:
transmits in 2nd half of pregnancy • Serology: VDRL or RPR → detect anti-cardiolipin Abs • Jarisch-Herxheimer reaction (s/p PCN txt)
• Endoflagella → rotary • Early effects: • Confirmatory: FTA (treponemal test)
motility • Tissue damage mediated by host immune • Maculopapular or papulosquamous lesions anywhere, including
• Hyaluronidase response palms and soles
• No TCA cycle • Perioral fissures and scarring (rhagades)
• Lacks LPS • Rhinitis (snuffles)
• Lymphadenopathy, HSmegaly
• Anemia and jaundice
• Osteochondritis

• Late effects:
• Hutchinson teeth, Mulberry molars
• Saddle nose deformity
• Sabre shin
• Interstitial keratitis, Retinitis pigmentosa
• CN VIII deafness

Congenital • Togaviridae → Rubivirus Transmission: • Blueberry muffin rash • 1º site: nasopharynx/ lung/ lymph • MMR vaccine
Rubella • + ssRNA • Horizontal → respiratory droplets • Sensorineural deafness • 2º site: other tissues/skin • Supportive txt
• Icosahedral • Vertical → immune deficient mothers • Cataracts
• Enveloped • Cardiac defects → PDA, pulmonic stenosis • All pregnant mothers screened at 1st prenatal visit
Subgenomic gene expression: • IUGR, Microcephaly, HSmegaly • Serology/ PCR/ virus isolation
• Viral glycoprotein E1 → 1ª attachment to
phospholipid cellular receptors on cell surface " I ♥ little blue ears"
• Viral glycoprotein E2 → promotes entry by
binding cellular
Congenital CMV • Herpesviridae • Most common congenital infection • 90% asymptomatic at birth; sxs develop later during infection • Isolate virus from urine or saliva in first 3 wks after birth • Ganciclovir for 6 wks in symptomatic infants
→ Tegument (stores proteins for • Mild, subclinical self limiting illness • Hearing loss • PCR can track viral load
replication *latency) • Vertical → more severe congenital defects • IUGR • Presence of maternal IgG only shows past infection • Not recommended in asympotmatic infants
→ Envelope proteins for w/ earlier transmission (1st trimester) • Periventricular calcifications
attachment • Chorioretinitis and optic nerve atrophy
→ Encodes own viral DNA pol • Blueberry muffin rash
• Microcephaly
• dsDNA • Thrombocytopenia
• Icosahedral
• Linear "CMV circumnavigates ventricles (periventricular); Toxo
• Enveloped throughout (intracerebral)"

Gene Expression: Permanent effects of congenital CMV:

• Immediate early → TFs to • MRDICS: microcephaly, mental retardation, deafness, intracranial
activate early genes calcifications, seizures
• Early → for replication
Neonatal Herpes • DNA replication • Vertical → congenital infections in utero are • Typically asymptomatic at birth • CSF, blood PCR to detect genomes • Acyclovir (high dose)
• Late → for packaging rare but cause fetal death or severe systemic • Skin lesions: vesicles w/ erythematous halo around base and • Virus culture of maternal or infant lesions • 21 days in disseminated or CNS
disease involving CNS ulcerations anywhere on body • 14 days for lesions
• CMV (β-herpesvirus) → • Ocular involvement requires topical txt
Lymphotropic & neurotropic • Highest risk of transmission w/ primary • Cutaneous:
outbreak → shedding virus w/o active lesions • 5-21 days
• HSV (α-herpesvirus) → • Localized mucocutaneous lesions
Neurotropic • Latent in trigeminal and sacral ganglion • May progress to systemic involvement if untreated
(HSV 1/ HSV 2)
• Encephalitic:
• 2-4 wk of life
• Focal seizures
• Bloody lumbar puncture

• Disseminated:
• 4-8th day of life w/ fever
• Herpetic lesions on skin or mucus membranes
• Respiratory distress
• Hepatitis, DIC, shock
• CNS involvement (focal seizures)
OTHERS:
Distinguishing features MOA/ Placental barrier breach Clinical presentation Diagnosis TXT
VZV • Herpesviridae • 1º: Chickenpox Maternal infection < 20 wks → Congenital Varicella: • Live attenuated vaccine (VZV)
• α-herpesvirus • Reactivation: zoster • Congenital abnormalities • Acyclovir if sxs
• Neutropic • Latency in Dorsal root ganglia • Limb hypoplasia, dermatomal scarring, blindness
• Lytic once activated
Maternal infection in last few weeks of pregnancy to after birth:
• VZV IgG indicated in exposed infants
• Infant → skin lesions, pneumonitis, dissemination

Parvovirus B19 • Parvoviridae Transmission: Congenital presentation: • Infected mother → 33% transmission to fetus • Exchange transfusion in utero b/c RBC
• ssDNA • Horizontal → respiratory droplets • Slapped cheek rash (lacy look) • Serology/ PCR progenitors are preferentially infected
• Icosahedral • Vertical → transplacental • Anemia
• Linear • 1st and 2nd trimester • Cardiomyopathy
• Non-enveloped • Hepatic dysfxn
• Tropism: precursor RBC in bone marrow • Hydrops fetalis
(Erythrocyte P Ag = 1º receptor)

Hepatitis B • Hepadnaviridae Vertical transmission: • Rarely see sxs in newborns • Core Ag and surface Ag for serology • Purified HBsAg vaccine
• dsDNA w/ ssDNA regions • < 2% • Develop chronic antigenemia w/ mild and persistent ↑ liver enzymes
• Circular • Blood exposure during labor and delivery at 2-6 months old
• Icosahedral • Found in all bodily fluids
• Enveloped • Small % develop acute hepatitis by 2 months
• Can progress into cirrhosis and hepatocellular carcinoma
HIV • (+) ssRNA (2 copies) • gp120 envelope protein: attachment • Occurs in all age groups as stage 1, 2, 3 (based on CD4 counts) • p24 capsid for serology • ART for all infants, children, teens w/ HIV
• Enveloped • gp41 envelope protein: fusion and entry regardless of stage or CD4 count
• Icosahedral
Replication: Highest priority:
• Only RNA virus whose • Viral genome RT → cDNA • Stage 3/4
genome is produced by • cDNA integrates into host • Age < 2 yo
cellular enzyme (RNA pol II) • Gene expression, protein production, virus • Age 2 - 5 yo w/ CD4 count < 750 or < 25%
budding • Age > 5 yo w/ CD4 count < 250
• Only (+) RNA virus whose • Protease maturation of virus particle
genome is not directly
translated (integrates into host
genome)

Listeria • Slender, short RODS • Listeriolysin O (pore forming cytolysin) • Meningitis in newborns • Cultures from blood, CSF • Ampicillin and Bactrim
monocytogenes • Gram POS allows bacterium to escape phagocytic • Food poisoning and gastroenteritis • β hemolytic on blood agar
• Intracellular parasite of vacuole • Catalase (+)
macrophages • Growth at 4º C • Maternal: mild GI infxn
• Tumbling motility extracellular
• Actin rockets • Most common in pregnant women, • In utero: abortion, stillbirth, death days after birth
intracellular/transcellular neonates and immunocompromised
• Umbrella like growth in • Neonatal: meningitis and sepsis
motility agar Causes: → infxn through birth canal
• Dairy products, cold cut meats, poultry

Zika • Arbovirus (Flavivirus) • Aedes mosquito = vector Congenital Zika → Microcephalic: • PCR/ Serology
• Neurotropic • Zika in CSF
• (+) ssRNA Transmission: • Seizures
• linear • Milk • Delayed neuropsychomotor development
• Icosahedral • Semen • Dysphagia
• Placenta • Visual impairment
• Other body fluids
Congenital Zika → Normocephalic:
• Breastfeeding → perinatal Zika infxn • Locomotor and cognitive deficits
• Intrauterine → congenital Zika invxn • Postnatal growth impediments
• Adaptive and fine motor delay
• Language delay

Postnasal Zika:
• Fever, chills
• Rash
• Conjunctivitis
• Arthralgia, fatigue
• Headache
• Guillain-Barre
 COUGH MICRO
Bacteria Morphology Virulence Factors Transmission/ CX Disease TXT
Bordatella Pertussis • Gram NEG Coccobacilli • Filamentous Hemagglutinin - mediates interaction with • Direct contact • Pertussis "100 day cough" • Macrolides
epithelial cells • Respiratory droplets • Bronchitis
• Obligate Aerobe • Fomites for a short period of
• Cytotoxin paralyzes ciliary escalator & inhibits DNA time • Catarral
• Encapsulated synthesis in epi. cells • Paroxysmal
• Convalescent
• Adenylate Cyclase Toxin (ACT) & Pertussis Toxin
(PTX) evade innate immunity by altering intracellular
signaling

Haemophilus • Gram negative COCCOBACILLI • Polyribosylribitol Phosphate capsule = antiphagocytic • Person to Person • Epiglottitis • Augmentin (Amox +
Influenzae type B • Non motile and resists complement • Commensal in nasopharynx • Tracheitis (NTHi) Clavulinic acid)
• Oxidase POS • IgA protease • Meningitis
• Adherence: Pili, Fimbriae, HiA adhesin, HMW1/2 • Chocolate agar + Factors X • Pneumonia, Bronchitis (NTHi)
• BLNAR ( β lactamase negative, ampicillin resistant) (hemin) and V (NAD) • Sinusitis, Otitis Media
• Cellulitis, Bacteremia

Moraxella Catarrhalis • Gram NEG DIPLOCOCCI • Adhesion • Commensal of respiratory tract • Otitis Media in children • Augmentin (Amox +
• Respiratory mucosa invasion • Respiratory droplets • Acute bacterial Rhinosinusitis Clavulinic acid)
• Obligate Aerobe • Triggers proinflammatory immune response • COPD exacerbations
• β lactamase • Thayer Martin Agar • Tracheitis
• Oxidase POS • Hockey Puck Sign • Bacteremia, Pneumonia

Streptococcus • Gram POS DIPLOCOCCI • Polysaccharide capsule • Commensal in nasopharynx • Community acquired bacterial • Macrolides
pneumoniae • Lancet shaped • Pneumolysin and oropharynx in children pneumonia (Azithromycin)
• Autolysin (LytA) • Aspiration to lower respiratory • 3rd gen cephalosporin
• Catalase negative • Pneumococcal surface proteins (pspA and pspB) tract (Ceftriaxone)
• α hemolytic • Respiratory droplets
• Optochin sensitive
• Bile soluble
• Quellung reaction positive

Klebsiella • Gram NEG bacilli • Biofilm formation: resistance to host immune response • Ubiquitous in environment • Lobar pneumonia • Carbapenems
pneumoniae • Encapsulated and abx • Colonizes the colon • Abcess • Clindamycin if
• Non motile • Polysaccharide capsule: antiphagocytic (K1 serotype = • Opportunistic pathogen • UTI Carbapenem resistant
• Facultative anaerobic disseminated infection) • Nosocomial
• Urease positive • LPS: most inflammation and tissue damage • Polymixin B and
• Siderophore for iron acquisition (bacteria requires iron) • Lactose Positive MacConkey Colistin reserved for MDR
• Urease: hydrolyzes urea to carbamate agar
• Carbapenem resistance (carried on plasmid)
increasing

Staphylococcus • Gram POS COCCI • Capsule, Protein A • Commensal in nasopharynx • Bacterial pneumonia • Anti-staph PCN
Aureaus • Catalase POS • Cytotoxins: α, γ & β, δ: form pores & disrupt and skin (Nafcillin)
• Coagulase POS membranes
• Exfoliative toxin A & B: disrupts desmoglein-1 • Mannitol agar → Yellow
• Superantigens: TSST & enterotoxins • β-hemolytic

Mycoplasma • Pleiomorphic • P1 Adhesion- cilia arrest • Respiratory droplets • Atypical community acquired • Macrolides
Pneumoniae • No cell wall/peptidoglycan • CARDS toxin - pore forming pneumonia (walking • Doxycycline
• Very small • Eaton's agar: Fried egg pneumonia) • Fluoroquinolones
• Trilayered membrane w/ colonies
cholesterol • Cold serum agglutination
test
Legionella • Gram NEG bacilli • OMP binds C3 which causes opsonization and induce • Opportunistic • Legionnaire's disease → fever, • Macrolides
Pneumophila • Motile phagocytosis in alveolar macrophages • Transmission via inhalation of pneumonia, watery diarrhea, (Azithromycin)
• Facultative intracellular • DOT = Type 4 secretion system (prevents aerosolized contaminated water hyponatremia • Fluoroquinolones
• Aerobic phagolysosomal fusion and modifies Legionella (Levofloxacin/Moxifloxaci
Containing Vacuole) • Needs silver stain • Pontiac Fever → fever w/o n)
• Toxic enzymes (phospholipase, metalloproteases) • Bufferred charcoal yeast pneumonia
• Pili attaches to invade alveolar macrophage agar

Chlamydophila • Gram NEG • Elementary Body and Reticulate Body= 2 morphology • Respiratory secretions • Atypical community acquired • Macrolides
Pneumoniae • Pleiomorphic forms • Cytoplasmic inclusions seen pneumonia (Azithromycin)
• Obligate intracellular on Giemsa • Pharyngitis and sinusitis more • Tetracyclines
• Type 3 secretion system common

Acinetobacter • Gram NEG Coccobacilli • Resistent hospital acquired • Tigecycline

baumannii • Strict Aerobe infxns • Polymixin B and
• Oxidase NEG Colistin reserved for MDR
• Ventilator associated
pneumonia and septicemia in
immunocompromised pts

Burkholderia Cepacia • Gram NEG bacilli • Pneumonia in Cystic Fibrosis

• Catalase POS
 SKIN INFECTIONS
General Epidemiology Lab DX Transmission Pathogenesis Disease
Staph Aureus • Gram POS COCCI • Colonized in nasopharynx • Mannitol agar → Yellow • Community acquired or nosocomial • Capsule, Protein A • Deep skin infections: Cellulitis, Non-bullous
• Clusters • Nucleic amplification test • Cytotoxins: α, γ & β, δ: form pores & disrupt impetigo
• Catalase POS • β-hemolytic membranes
• Coagulase POS • Exfoliative toxin A & B: disrupts desmoglein- • TXT: MSSA: Nafcillin, MRSA: Vancomycin
1
• Superantigens: TSST & enterotoxins

Strep Pyogenes • Gram POS COCCI • Normal flora of skin and • Lancefield = GAS • Direct contact or respiratory • Capsule Hyaluronic acid • Superficial skin infections (erysipelas,
• Chains mucous membrane • ↑ Acute phase reactants droplets • M protein impetigo)
• Catalase NEG • β-hemolysis • Streptokinase, DNase • Non-bullous impetigo → (-) Nikolsky sign
• Streptolysin O and S
• TXT: PCN, β lactams or Azithromycin,
Clarithromycin, Clindamycin

Pseudomonas • Gram NEG ROD • Nosocomial • Blue/green miucoid colonies • Predisposing factors: • OmpF, pili, flagella: Adhesion • Skin: Folliculitis, Burns, Nec Fasc, Ecthyma
Aeruginosa (immunocompromised) • Grape like odor Burns, Cystic fibrosis, • Alginate: Biofilm formation gangrenosum
• Aerobic • Opportunistic infection • Grow at 42ºC neutropenia • Pyocyanin→ROS/ Pyoverdin→siderophore • Pulmonary infections
• Non-fermentative • Ubiquitous in nature • Multi drug efflux pumps for abx resistance • UTI, Ear/ Eye infections
• Oxidase POS • Exotoxin A (T2SS) • Bacteremia/ endocarditis
• Green/blue pigment • Elastase and Phospholipase C (T2SS)
• Abx resistent • T3SS → ExoS, ExoU • TXT: Fluoroquinolone, Carbapenems,
• Capsule Aminoglycosides

Bacteroides fragilis • Gram NEG ROD • Commensal in intestine, • Bile-esculin blood agar → • Endogenously: abd surgery, • Polysaccharide capsule: anti-phagocytic • Abscess formation
• Short pleomorphic mouth, female GU hydrolyzes esculin to produce black appendicitis, diverticulitis • Peritonitis
• Most common anaerobe precipitate • Collagenase, Hyaluronidase, Chondroitin • Contamination of skin wounds
• Bile resistant sulfatase → tissue destruction • Diarrheal disease

• Heat labile zinc metalloprotease toxin → • TXT: Clindamycin

Diarrhea
"Clindamycin for anaerobic infections above
diaphragm, Metronidazole for below
diaphragm"

Pasteurella Multocida • Gram NEG n/a • Bipolar staining • Animal bites • LPS: endotoxin is major virulence factor • Cellulitis (localized) → Osteomyelitis (deeper
COCCOBACILLI • Grows on 5% sheep's blood agar • Capsule: antiphagocytic soft tissue)
• Spreads rapidly • Respiratory tract infxn
• Facultative anaerobe • Toxigenic strain- PMT toxin that deamidates α • Systemic infxn (Bacteremia, meningitis) in
• Non-motile subunits of G proteins → cytoskeletal signaling immunodeficient
• Oxidase POS pathways
• TXT: PCN

Clostridium Perfringens • Gram POS ROD • Ubiquitous in soil • Anaerobic growth (9min to 2x) • Traumatic gas gangrene: wound • CPE enterotoxin → food poisoning • Food poisoning: watery diarrhea
• Non-motile • Spontaneous gas gangrene: • β toxin → Necrotizing enteritis (bloody • Clostridial myonecrosis: Traumatic (systemic
• Obligate anaerobe • Lipase NEG hematogenously diarrhea) spread) or Spontaneous (Immunodeficient)
• Spore former • Lecithinase POS • Reheated contaminated foods • α toxin → RBC lysis (Myonecrosis) • TXT: Clindamycin, PCN G
• Double zone of hemolysis • Perfringolysin O theta-toxin → pore forming
cholesterol dependent cytolysin

Actinomyces • Gram POS ROD • Actinomyces israelii most • Grows very slowly • Endogenous infxns • Break in mucosal barrier • Cervicofacial actinomycosis
• (Facultative) anaerobe clinically relevant • Molar tooth colony • URT, GI, GU • Resists ROS • Pelvic, CNS actinomycosis
• Filamentous branching • Commensal of mouth, GI, GU • Sulfur granules (yellow) → stain • Abscess formation = abscesses!
basophilic on H&E
• TXT: PCN G
Clostridium Tetani • Gram POS rod • Tetanus toxoid Ag vaccine • Swarming motility • Endospores enter wound Tetanospasmin: AB toxin Tetanus: toxin mediated disease of nervous
• Strict anaerobe (inactive protein) • Incubation period depends on • Zinc-dependent metalloproteinase (cleaves system
• Spore forming • Part of dTAP vaccine inoculation site ~ 8 days (lower SNARE) 1) Generalized: Trismus → Risus sardonicus
incubation time closer to head) • Opisthotonus: spasm of muscles arching torso,
Risks: • Targets glycinergic interneurons and arms flexed/legs extended (decorticate posturing)
• puncture wounds, lacs, descending GABAergic neurons & asphyxiation
abrasions • Spasms (spastic paralysis)
• IVDU, Diabetics • Ganglioside receptors • Recovery takes months b/c toxin binding is
• elderly due to lack of • Enters inhibitory neuron & catalytic A subunit irreversible
boosters enters cytosol
• Retrograde trafficking through motor neuron 2) Localized: spasms @ location of inoculation

= no inhibitory neurotransmitter release →

no muscle relaxation
Vibrio Vulnificus • Gram NEG • Risk: pts w/ liver disease • NaCl required in medium • Shellfish (oysters) • Polysaccharide capsule: anti-phagocytic • Skin: Cellulitis, Nec Fasc
• Comma shaped (iron overload) and pts w/ • Green on TCBS (no sucrose • Contaminated water to wound • VvhA: pore forming toxin • Primary septicemia
chronic illnesses (DM, renal fermentation) • MARTX toxin: cell lysis
failure) • Lactose fermentation • Metalloproteinase: extracellular digestive
enzyme

Aeromonas Hydrophila • Gram NEG ROD • Global distribution- fish • β hemolysis • Water • Aerolysin: cytotoxic pore forming toxic • Skin: Cellulitis, Nec Fasc, Myonecrosis
• Anaerobic pathogen • Grows at wide range of temps • Cytotoxic enterotoxin • Medical leech transmission
• Glucose fermentation POS - • T3SS, T6SS: apoptosis • Bacteremia/Septicemia
yellow • Flagella (immunocompromised)
• Indole test POS (tryptophanase) • Shiga toxin • Gastroenteritis (self limiting): HUS complication
→ Pseudomonas = red

Fusobacterium • Gram NEG ROD • Endogenous from oral cavity • Long spindle shape • Endogenously from oral cavity • FadA adhesion/invasion: binds cell jxn • Periodontitis
Nucleatum • Anaerobic cadherin proteins → loosen jxns & ↑ endothelial • GI disorders: Colorectal cancer, IBD
permeability • Cerebral aneurysm
• Lemierre's: septic thrombophlebitis of internal
• Induces proinflam. cytokines (IL-6, IL-8, TNF α) jugular vein
• Abscesses

Porphyromonas • Gram NEG ROD • Commensal of oral cavity • Can't metabolize carbohydrates • Endogenously from oral cavity • Gingipains → degrade antimicro. peptides • Periodontitis
Gingivalis • Anaerobic • Black colonies on blood agar and C3 • Linked to RA: peptidylarginine deiminase
• Glucose fermentation NEG • Fimbriae → attach to DC-SIGN on DCs (ACPA)
• Collagenase • Linked to Alzheimers

Prevotella • Gram NEG ROD • Commensal in oral cavity • Black colonies on blood agar • Endogenously from oral cavity n/a • Periodontitis
Melaninogenica • Anaerobic • Glucose fermentation POS • Abscess
• Anaerobic pneumonia
• Necrotizing fasciitis

Peptostreptococcus • Gram POS COCCI • Commensal of mouth, GI, • Inhibited by Sodium Polyanethol • Endogenous, break in mucosal • CNS: abscess
Anaerobius • Anaerobic vagina, skin Sulfonate (SPS) → other Gram barrier • Skin: Nec Fasc, decubitus ulcers, human/animal
POS cocci will grow bites
• Risk: DM and • URI/ dental
immunodeficient • Female pelvic infxn
• Joint infxn: prosthetic joints and septic arthritis

Clostridium Botulinum • Gram POS rod Risks: • Swarming motility • Foodborne Botulinum toxin: AB toxin Acute, bilateral cranial neuropathic w/
• Strict anaerobe • Improperly canned foods • Lipase POS • Wound • Zinc-dependent metalloproteinase (cleaves symmetrical DESCENDING weakness
• Spore forming • Infants < 1 yo "Floppy Baby" • Demonstration of toxin in serum, • Iatrogenic and Inhalational (rare) SNARE) • NO fever
• IVDU stool, food • Symmetrical neuro sxs
• Targets Ach excitatory neurons • HR normal/slow w/o hypotension
• Can't cross BBB • Blurred vision
• Ganglioside receptor • Responsive pt
Types of Botulism: • Synaptic vesicle membrane protein receptor
• Foodborne botulism: from 5 D's:
ingesting botulinum toxin in = no excitatory neurotransmitter release → • Diplopia (anti-cholinergic)
improperly canned foods no muscle contraction • Dysphonia (anti-cholinergic)
• Dysphagia (anti-cholinergic)
• Infant botulism: Floppy baby • Dry mouth (anti-muscarinic)
syndrome from ingesting spores • myDriasis (anti-muscarinic)
(e.g. in raw honey)
 JOINT INFECTIONS
General Epidemiology Lab DX Transmission Pathogenesis Disease
Borrelia Burgdorferi • Spirochete • #1 vector borne illness in US • Serology Antibody titer • Risk groups: young and elderly; • Tissue damage due to host inflam. response • Lyme disease
• Lacks LPS and toxins → IgM or IgG Abs by ELISA outdoors
• Single linear c'some • NE, upper midwest US • Confirm w/ western blot • Adhesins: • Stage I: Early localized (3-30 days)
• 21 plasmids • Spring/early summer • NAAT • Vector = Ixodes scapularis (deer tick) - Decorin binding proteins (DbpA/ DbpB) • Erythema migrans, flu like sxs
• No TCA cycle and ETC • Culture BSK - Fibronectin binding proteins • Stage II: Early disseminated (wks-months s/p 1º infxn)
→ Barbour Stoenner Kelly • Reservoir for Borrelia • MSK: migratory arthralgias
= white-footed mice • Motility: Endoflagella to burrow through tissues • Neuro: lymphocytic meningitis, cranial & peripheral
neuropathy
• Reservoir for tick • Immune evasion: • Carditis
= white tailed deer - Ag variation of outer membrane lipoproteins: causes • Stage III: Late disseminated (mo.- decades)
recurrent fever • MSK: chronic arthritis of knee
- Coats surface w/ host proteins as camouflage • Neuro: lyme encephalopathy, distal paresthesias,
cognitive issues
• Acrodermatitis chronica atrophicans: red/blue lesions

• TXT: Doxy (**Jarisch-Herxheimer: shock like rxn)

Chlamydia • Obligate intracellular • Major ID • Giemsa Stain • Mainly sexual • T3SS • Reactive arthritis
Trachomatis parasite • NAAT- vaginal swabs, first • Major Outer Membrane Protein (variants) • STD: PID, Fitz-Hugh-Curtis
• 3 serovars catch urine, rectal swab • Inhibits phago/lysosome fusion • Lymphogranuloma venereum:
→ 1º: painless papule or ulcer on genitals; heals rapidly
• Elementary body = infectious → 2º regional LAD w/ buboes; can form fistulas/strictures
• Extracellular, small, can't replicate, resistant → lymphatic obstruction; can lead to genital elephantiasis
• Reticulate body = metabolically active
• Intracellular, large, binary fission • Trachoma keratoconjunctivitis: blindness
• β Lactam abx NOT suitable txt

Strep Pyogenes • Gram POS COCCI • Normal flora of skin and • Lancefield = GAS • Direct contact or respiratory droplets • Molecular Mimicry: M protein and N-acetyl-β-D- • Acute Rheumatic Fever: JONES s/p prior GAS infxn
• Chains mucous membrane • ↑ Acute phase reactants glucosamine
• Catalase NEG • β-hemolysis • Enzymes: C5a peptidase, Streptokinase A & B, • TXT: PCN, β lactams or Azithromycin,
DNase A-D Clarithromycin, Clindamycin
• Cytotoxins: Streptolysin S, Streptolysin O
• Superantigens: Spe A-C

• Adhesion: VCAM-1 ↑ on valve surface for CD4+ cells

• Structural: Hyaluronic acid capsule, Fibronectin
binding proteins, Lipoteichoic acid

Staph Aureus • Gram POS COCCI • Colonized in nasopharynx • Mannitol agar → Yellow • Community acquired or nosocomial • Capsule, Protein A • Deep skin infections: Cellulitis, Non-bullous impetigo
• Clusters • Nucleic amplification test • Cytotoxins: α, γ & β, δ: form pores & disrupt
• Catalase POS • β-hemolytic membranes • TXT: MSSA: Nafcillin, MRSA: Vancomycin
• Coagulase POS • Exfoliative toxin A & B: disrupts desmoglein-1
• Superantigens: TSST & enterotoxins

Strep Pneumoniae • Gram POS • Colonizes nasopharynx and • Optochin sensitive • Carriage and disease in cool months • Adhesion: Pneumococcal surface proteins • Lobar pneumonia: Blood tinged sputum, crackles on
DIPLOCOCCI oropharynx of kids • α - hemolytic • Endogenous → aspiration to lower • Polysaccharide Capsule auscultation
• Bile soluble respiratory tract • Pneumolysin: lyses epithelial cells, phagocytes • Sinusitis, meningitis, bacteremia
• Catalase NEG • Most common cause of • Quellung reaction positive • Exogenous → respiratory droplets • Autolysin: lyses peptidoglycan • TXT: Vaccine, PCN G, Vancomycin
• Optochin sensitive community acquired • Latex agglutination of capsular • IgA protease
• Lancet shaped pneumonia polysaccharide • C polysaccharide → inflammation via CRP
• Facultative anaerobe • C-polysaccharide in CSF • Hydrogen Peroxide → ROS
= Activates classical complement

Coag- NEG Staph: • Gram POS COCCI • Nosocomial (S. epidermidis) • Grow in high salt (S. • Ubiquitous commensal on skin (S. • Biofilm formation • Implanted device infections → prosthetic joints
• Epidermidis • Clumps • Colonization of perineum (S. epidermidis) epidermidis) • Adhesion molecule that binds VWF (S. lugdunensis) (S. epidermidis, haemolyticus)
• Haemolyticus • Facultative anaerobe lugdunensis) • Sensitive to novobiocin • Highest abx resistance (S. haemolyticus) • Subacute endocarditis (S. epidermidis, lugdunensis)
• Lugdunensis • Coagulase NEG
• Catalase POS • TXT: Nafcillin, Cephalexin, Vancomycin

Neisseria • Gram NEG DIPLOCOCCI • 2nd most common STD • #1 NAAT • Sexual transmission • Pili • Septic arthritis
Gonorrheae • No capsule • Thayer-Martin medium • Por proteins: resist phagocytosis • GU: Cervicitis, Proctitis, PID, bartholinitis or urethritis,
• Oxidase positive • Glucose fermentation • IgA protease epididymitis
"MeninGococci: Maltose & • LOS: TNF α release • Cutaneous gonorrhea, Disseminated gonococcal
Glucose • Polysaccharide capsule infection
Gonococci: Glucose" • Antigenic variation • Conjunctivitis, Pharyngitis

• Facultative Intracellular • TXT: Cephalosporins, fluoroquinolones

Kingella Kingae • Gram NEG • Common in kids • Blood culture & PCR • Close contact • RTX: pore forming toxin • Septic arthritis in KIDS
COCCIBACILLI • Colonizes oropharynx • Chocolate agar • Fimbriae • Leading agent in osteomyelitis and septic arthritis
• NO MacConkey or Krigler • Polysaccharide capsule • Rhinorrhea, pharyngitis, stomatitis, diarrhea
• Pairs or short chains
• Facultative anaerobe • TXT: Cephalosporin, β-lactams