Microbial Diseases 8/29/25

Vocabulary flashcards covering key terms, definitions, and concepts from the Microbial Diseases Part 1 lecture notes (fungi, parasites, and epidemiology).

Subclinical infection

Pathological changes are present in the body, but there are no noticeable signs or symptoms.

freqeuncy

Not only the number of health events such as the number of cases of meningitis in a population, but also to the relationship of that number to the size of the population

incidence

A measure of how often (new cases of) a disease occurs in a population over a specific time period

prevalence

A measure of the number of people in a population who have a disease or health condition at a specific time or during a specific period of time

attack rate

The proportion of people in a population who become ill or die from a disease during a specific time period

rates

compare disease occurrence across different populations

determinants

• Any factor, whether event, characteristic, or other definable entity, that brings about a change in a health condition or other defined characteristic

• “How” and/or “Why”

• Agent factors: infectivity, virulence, mode of transmission

• Host factors: age, immunity, comorbidities, behaviors

• Environmental factors: climate, population density, sanitation, healthcare access

non communicable diseases

• Group of conditions that are not spread person-to-person

• Result in long-term health consequences

• Often create a need for long-term treatment and care

• Cardiovascular diseases, diabetes, cancers, chronic respiratory diseases (COPD, asthma), mental health disorders

communicable diseases

Illness caused by infectious agents that can be transmitted from one human to another

• Bacteria, viruses, fungi, parasites

• Some infectious agents aren’t acquired from another human

• Blastomyces: acquired from inhaling spores from soil

Not all infectious diseases are communicable

Clinical infection

Presence of a pathogen in the body that produces signs and/or symptoms of disease.

Asymptomatic carrier

A person who carries a pathogen but may never develop disease.

Incubatory carrier

A carrier who has not yet developed disease symptoms but can transmit the agent.

Convalescent carrier

Infectious even after symptoms have resolved.

Chronic carrier

Infectious months to years after acquiring infection, often with lingering or intermittent symptoms.

portal of exit

how a microbe leaves it reservoir or host

mode of transmission

• Insect bite (vector)

• Ingestion of microbe in contaminated food, water

• Direct contact with infectious ulcer

• Sexual contact; body fluids

• Inhalation of infectious particles

• Contact/ingestion animal products (zoonotic)

portal of entry

the site at which a microbe enters a susceptible host

Endemic

Constant presence and/or usual prevalence of a disease within a geographic area.

blastomycosis in usa

Epidemic

A sudden increase or rise in cases above what is normally expected in a population.

zika virus 2015-16

Pandemic

An epidemic that has spread across multiple countries or continents.

covid

Outbreak

Epidemic confined to a more limited geographic area.

ebola 2014-16

Sporadic

Occurring infrequently and irregularly.

Sporotrichosis from plants

epicurves

• Magnitude of an outbreak (How many cases)

• Time trend or distribution of cases (Are cases still rising?How long since last case?)

• Incubation of agent important

• Index case?

common source outbreak/epidemic patterns

A group of persons are all exposed to an infectious agent or a toxin from the same source

point source outbreak/epidemic pattern

A single source, brief period of exposure

• Hepatitis A outbreak in a single restaurant where green

onions were the source of exposure

• Remove the source

• # of cases rises rapidly to a peak and falls gradually

• Majority cases within 1 incubation period

contiguous outbreak/epidemic pattern

Days, weeks, months of exposure

• Water contamination with fecal matter after an earthquake damaged a water treatment plant • Boil water order, chlorination

• Exposure is prolonged over a period of days, weeks, or longer

• Epi curve rises gradually and might plateau

propagated epidemic/outbreak pattern

• Transmission from one person to another

• Direct person-to-person (e.g. dermatophytes) • Classic epi curve shape of progressively taller peaks

• Each being one incubation period apart

vector borne outbreak

Continuous common-source but can resemble propagated (if vector not removed)

• Leishmania in endemic area - sandfly control

other outbreak/epidemic pattern

not common course and not spread between people

Incidence

Measure of new cases of a disease in a population over a specific time period.

Prevalence

Number of people with a disease in a population at a given time or over a period.

Attack rate

Proportion of people in a population who become ill during a defined period.

Dermatophytes

Keratinophilic molds (Microsporum, Trichophyton, Epidermophyton) that cause infections of the skin, hair, and nails. Eats keratin as food - only infects area w/ keratin

Reservoirs/transmission: some human only by direct contact or fomites. Some animals, soil, decomposition

Typically warm, humid climates

Microsporum

• Primarily infect skin and hair

• Zoonotic transmission (e.g., dogs)

• Ectothrix hair invasion (infection outside the hair shaft)

spindle shaped macroconidia

Trichophyton

• Infect skin, hair, and nails

• More common in chronic, persistent infections

• Some are zoonotic (dogs, cats, cattle, horses)

cigar shaped macroconidia

Epidermophyton

• Infects skin and nails but does not infect hair

• Causes common infections like jock itch and athlete’s foot

• Person-to-person; indirectly through contaminated surfaces/objects

Beaver tail macroconidia

dermatophyte infections

• Tinea capitis: capit = head, Common in children

• Tinea corporis: corpus = body

• Tinea cruris: cruris = groin (jock itch)

• Tinea pedis: ped = foot (athlete’s foot)

• Tinea unguium: unguis = nail

• Onychomycosis: nail infection

• Tinea barbae: beard

dermatophyte diagnosis

Skin or nail scraping, hair plucking

• KOH prep

• Look for branched, septate hyphae and macroconidia

• Wood lamp - especially for Tinea capitis

• Look for fluorescence … not always positive :(

dermatophyte treatment

• Keep skin dry

• Cutaneous mycoses can all be cured with topical therapy Exception: Tinea capitis (drug has to penetrate hair follicles)

• Topical: imidazoles (clotrimazole, ketoconazole)

• Oral: Terbinafine, azoles (fluconazole and itraconazole)

macroconidia

seen in dermatophyte pictures

Malassezia furfur

Lipophilic yeast that overgrows in oil-rich skin areas in the stratum corneum only, causing tinea versicolor.

Overgrowth of skin normal flora.

Risk factors: puberty, tropical climates

Diagnose: Wood lamp examination: yellowish-white fluorescence, Potassium hydroxide (KOH) prep with blue fungal stain of scale, “Spaghetti and meatballs” – pseudohyphae and yeast, Can culture

Tinea versicolor (pityriasis versicolor)

Hypo- or hyperpigmented patches on skin due to Malassezia furfur overgrowth.

TINEA BUT NOT A DERMATOPHYTE

Treat: topical selinium sulfide, zinc pyrithone shampoo, -azole cream, terbinafine cream, oral -azoles, avoid oily products

Wood’s lamp examination

Fluorescence examination used to help diagnose certain fungal infections (often yellowish-white for Malassezia in tinea versicolor).

KOH prep

Potassium hydroxide preparation used to visualize fungal elements by clearing human cells.

Spaghetti and meatballs

Microscopic appearance (KOH prep) of Malassezia furfur: yeast cells with short hyphae.

Septate hyphae

Hyphae with cross-walls (septa); typical of many molds including Aspergillus.

Non-septate hyphae

Hyphae lacking cross-walls; characteristic of Mucorales (e.g., Mucor, Rhizopus).

Angioinvasive

Invasion of blood vessels by hyphae leading to thrombosis and tissue necrosis, seen in mucoromycetes.

Aspergillus fumigatus

Common mold with septate hyphae (45 deg. angles); often causes invasive aspergillosis. Spores are usually cleared by lung macrophages.

Reservoir: spores inhaled from soil or compost. opportunisitc pathogen

Diagnose: Biopsy, histology – septate hyphae, acute (45o) branching, CT/MRI scans, X-ray, Cultures, silver stain, Galactomannan antigen testing – invasive, Allergic – IgE, eosinophilia

Treat: For Acute invasive sinusitis: Voriconazole (IV first, oral when stable), 6-12 weeks at least, Surgical debridement, Reduce immunosuppression, if possible.

aspergillus risk factors

•Neutropenia, Esp. profound

• Hematologic malignancies

• HIV, other immunosuppression

• COPD, CF, interstitial lung disease

• Long-term steroid use

chronic invasive sinusitis

• Immunocompetent or mildly immunocompromised

• Slowly progressive facial pain or swelling

• Orbit may be involved

• Chronic headache

• Possible bone erosion on imaging

acute invasive sinusitis

Immunocompromised, neutropenic

• Rapid onset of severe facial pain and swelling

• Fever

• Black necrotic tissue in the nasal cavity or palate (tissue invasion)

• Ophthalmic involvement (vision loss)

• Neurologic deficits if spread to CNS

dermatological aspergillosis

• Primary cutaneous = spore into skin

• IV catheter sites, burns, trauma, occlusive dressings, agricultural or outdoor trauma

• Usually immunocompromised

• Painful erythematous papules, nodules, or plaques

• May progress to necrotic ulcers with black eschar

• Often localized at catheter insertion sites or injured skin

aspergillus pathogenesis

• Hyphae are multi-cellular structures that disrupt normal tissue/organ function

• Immune response

• Hyphae are angioinvasive

• Vascular invasion = infarction and tissue necrosis, abscesses

blastomyces dermatiditis

Dimorphic fungus (mold/cold, heat/yeast). Broad based budding paired yeast (BB8!).

Reservoir: spore inhalation from decaying plant matter, soil, dust, decay. Mid-east USA, some africa/india

diagnose: Chest X-ray/CT (Lobar, alveolar infiltrates), Direct microscopy/biopsy (Broad-based budding yeast, Periodic acid-Schiff stain), Culture, Antigen detection – urine, sputum etc., PCR.

Treat: Itraconazole for 6-12 months, Severe/disseminated- Amphotericin B (IV 1-2 weeks) then itraconazole (6-12 months)

blastomyces risk factors

• Living in, or traveling to, endemic areas

• Outdoor activities/jobs that disturb soil and decaying vegetation: Construction or excavation work, Forestry, agriculture, landscaping, Hunting, camping, hiking, Clearing brush, cutting wood

• Immunosuppression (both HIV/AIDS and non-HIV)

• Pregnancy (severe/disseminated)

primary blastomycosis

pulmonary.

• Resembles bacterial pneumonia

• May have hemoptysis

dermatologic blastomycosis

• Verrucous (rough) lesions on skin

• Irregular borders

• Ulceration

• Can be extensive if disseminate

disseminated blastomycosis

bone, prostate, meninges, intracranial abscesses

Mucor/Rhizopus (Mucormycetes)

Mold with non-septate hyphae (90 deg. branches), broad branches, angioinvasion; causes mucormycosis. Opportunisitc pathogen by inhaled spores.

mucormycosis risk factors

•Diabetes mellitus, esp. ketoacidosis

• Iron overload

• Immunosuppression

—Solid organ, blood transplants

—Blood malignancies

—High-dose immunosuppressants

• Trauma or surgery

—Penetrating trauma with contaminated materials

• Prolonged broad-spectrum antibiotics

—Destroy protecting oro-flora

mucormycosis pathogenesis

Hyphae are multi-cellular structures that disrupt normal tissue/organ function

• Immune response

• Hyphae are angioinvasive

• Thrombosis, infarction, necrosis

mucormycosis HEENT

Rhinocerebral

• Necrotic lesions in paranasal sinuses

• Orbit, face, palate

• Most common in diabetic acidosis

• RAPID PROGRESSION, highly destructive

Cutaneous

• Traumatic introduction spores (burns, surgery)

• Necrotizing cellulitis

• Immunocompetent

mucormycosis diagnosis

• Clinical = rapidly progressing necrotic rhinosinus lesions

• CT/MRI scans

• Distinct hyphae in tissue samples

• Broad, irregular branching, no septations

mucormycosis treatment

Early and aggressive debridement is CRITICAL, May need multiple rounds

• Liposomal Amphotericin B - Careful with nephrotoxicity, Inserts into fungal cell membrane causing death

• Step-down – Isavuconazole (or if amphotericin B not tolerated)

Voriconazole, fluconazole, echinocandins are ineffective against Mucorales

mucormycosis prevention

• Glycemic control very important

• Minimize use and dosage of immunosuppressive medications

• Infection control in healthcare settings

• Limit contact with: Soil, compost, decaying leaves or wood, Unfiltered or contaminated air, Tap water (in sterile fields)

Broad-based budding

Yeast budding pattern seen with Blastomyces dermatitidis in tissue.

Sporothrix schenckii

Dimorphic fungus causing sporotrichosis, often via traumatic inoculation (“rose-handler’s disease”).

Reservoir/transmission: direct inoculation of spores (sometimes inhalation) from soil, decomposing plants into a cut, etc

Risk factors: lymphocutaneous(skin trauma while gardening,etc), outdoor hobbies/job, cat bite/scratch

Diagnose: • Culture – tissue biopsy, sputum, Sabouraud’s agar at room temp, Characteristic conidia (mold), Direct microscopy of lesion scraping, Oval/cigar shape (yeast)

Treat: cutaneous/lymph: itraconazole 3-6mo, or terbinafine 3-6 months

sporotrichosis

Lymphocutaneous – MOST COMMON

• Traumatic inoculation of conidia into subcutaneous tissue

• 1–4-week incubation

• Papule develops at site of inoculation, ulcerates

• Non-purulent, odorless drainage

• Similar lesions appear along the lymphatics

Joint infections

• Knee, wrist, elbow, ankle

• Chronic

Rose-handler’s disease

Common name for sporotrichosis caused by Sporothrix schenckii.

Leishmania species

Flagellated protozoan causing leishmaniasis; transmitted by sandflies that inject promastigotes while feeding; amastigotes in macrophages.

Endemic to india, bangdalesh, sudan, ethiopia, brazil (brazilienis can infect mucosa). some usa cases.

Cutaneous Leishmaniasis is endemic in americas, mediterranean, middle east, central asia

diagnose: Gold standard: Direct visualization of amastigotes

(Leishman-Donovan bodies) Giemsa-stained

• Bone marrow biopsy, Skin lesion biopsy - Amastigotes inside macrophages, Urine antigen test

treat: Mucosal: Liposomal amphotericin B - Binds to sterols in cell membrane, pores = death, Beware nephrotoxicity. Cutaneous: local therapy, cryotherapy, intralesional antimonials

cutaneous leishmaniasis

Weeks/months after sandfly bite

• Skin/mucosal papules

• Progress to nodule or ulcer

• Raised, well-demarcated border

• Painless ulcer with raised indurated borders and a central crater (“volcano ulcer”)

• May ooze or scab

• Often self-healing (months → years)

• Leaves disfiguring scars

mucosal leishmaniasis

• L. braziliensis (South America)

• Months, years after initial cutaneous lesion heals

• Chronic destructive lesions of mucous membranes

• Nose, mouth, pharynx, larynx

• Starts with nasal congestion, nosebleeds

• Progresses to ulceration and tissue destruction

• Can lead to severe facial disfigurement and functional impairment

leishmaniasis transmission

sandfly bite during blood meal inject flagellated promastigotes → they get phagocytosed by macrophages and transform into amastigotes (no flagella) → another sandfly bites and ingests the infected macrophages with amastigotes

Amastigotes

Intracellular form of Leishmania within macrophages used for diagnosis.

Acanthamoeba species

Amoeba protozoan Ocular infection, often in contact lens wearers; diagnosed by trophozoites/cysts in corneal scrapings.

diagnose: Visualization of trophozoites/cysts in corneal scrapings, PCR on samples

treat: Antiseptics kill trophozoite and cyst, Polyhexamethylene biguanide, chlorhexidine, Corneal transplant

acanthamoeba keratitis

• Immunocompetent contact lens wearers (long term)

• Poor lens hygiene, homemade or expired lens solution

• Infection of cornea: Severe pain out of proportion to clinical signs, Corneal ulceration, opacification, reduce vision, Blindness without treatment / delayed

• Trophozoites can be visualized via staining of cornea scrapings with fluorescent dye

trichinella spiralis

nematode (pork roundworm)

Definitive host: pig, rodents, boar, etc

Humans are accidental, dead end hosts.

Ingestion of larvae in undercooked meat, usually game. Curing, drying, smoking meat doesn’t kill it.

Diagnose: Serology, eosinophiloa, Muscle biopsy, (visualization of larvae), History of eating undercooked/raw pork or wild game meat

Treat: Mild cases are self-limiting, Albendazole or mebendazole Best if given early, before larvae encyst, Corticosteroids for severe inflammation

trichinella spiralis life cycle

Human infection - accidental, dead-end definitive host: Ingestion of larvae in undercooked or raw meats

Larvae develop into adults in small intestine →

New larvae made, enter circulation →

Encysted larvae in striated muscles throughout body (Diagnostic)

trichinellosis

2 weeks after ingestion, classic symptoms –larvae enter muscle

• Muscle pain, tenderness, swelling, and weakness, Swelling of the face, particularly the eyes (periorbital edema), High fever lasting weeks, Subungual splinter hemorrhages, conjunctival/retinal hemorrhaging,

Myalgia (muscle pain): Classically severe, migratory, and worsens with movement

Most symptoms due to severe immune response to the larvae/cysts

Tinea capitis

Dermatophyte infection of the scalp, common in children; hair shaft invasion.

Tinea corporis

Dermatophyte infection of the body (skin surface).

Tinea cruris

Dermatophyte infection of the groin (jock itch).

Tinea pedis

Dermatophyte infection of the feet (athlete’s foot).

Onychomycosis (Tinea unguium)

Dermatophyte infection of the nails.

Candida albicans

Most common Candida species; yeast; budding; pseudohyphae; opportunistic pathogen.

Reservoirs: normal flora of colon, oral, skin, vagina

Oropharyngeal candidiasis (thrush): white patches

Cutaneous candidiasis (diaper rash): red, itchy, scaly rash, maybe pustules

Diagnose: KOH prep and look for budding yeast w/ pseudohyphae

Treat: fluconazole to inhibit ergosterol synthesis

candidiasis prevention

ALL:

• Avoid unnecessary antibiotics, especially broad-spectrum • Optimize glucose control in patients with diabetes

• Minimize corticosteroid use, especially inhaled and systemic forms

• Promote skin hygiene and keep folds dry to prevent cutaneous overgrowth

• Hospital, infection control, and public health measures

Oropharyngeal:

• Rinse mouth after using inhaled corticosteroids

• In HIV/AIDS, maintain CD4+ count >200 cells/mm³ through ART

• Prophylaxis not warranted (risk of resistance > prophylaxis)

Candida auris

Multidrug-resistant (to azoles, polyenes, echinocandins), nosocomial Candida species; persists on surfaces and causes outbreaks. High mortality.

Itraconazole

Azole antifungal used for Blastomyces, Sporothrix; typical course long (months).

Albendazole/Mebendazole

Anthelmintics used to treat Trichinella spiralis infections; most effective early.

Liposomal amphotericin B

Antifungal with reduced nephrotoxicity used for invasive fungal infections (e.g., mucormycosis).