Microbiology

Parasitology

Parasitology: Intestinal Protozoa, Helminths, and Immunocompromised-Host Infections

Intestinal protozoa are small and must be separated from nonpathogens, inflammatory cells, epithelial cells, yeasts, and pollen. Identification depends on size measured with an ocular micrometer, motility pattern seen only on wet mount, and nuclear and cytoplasmic detail on a permanently stained preparation (trichrome or iron hematoxylin). Report two populations from one specimen only when both are distinctly identified.

Intestinal amebae

Three genera (Entamoeba, Endolimax, Iodamoeba) inhabit the human colon; only E. histolytica invades tissue.

SpeciesSizeMotilityNucleiPeripheral chromatinKaryosomeInclusions
E. histolytica/E. dispar10-60 μm (commensal 15-20 μm; invasive >20 μm)Progressive, hyaline fingerlike pseudopods1Fine, evenly distributedSmall, discrete, usually centralErythrocytes (supports E. histolytica but may rarely occur with E. dispar); bacteria (noninvasive)
E. hartmanni5-12 μm (usual 8-10)Usually nonprogressive1Similar to E. histolyticaSmall, discrete, often eccentricBacteria
E. coli15-50 μm (usual 20-25)Sluggish, blunt pseudopods1Coarse, irregularLarge, discrete, eccentricBacteria, yeasts, debris
Endolimax nana6-12 μm (usual 8-10)Sluggish, blunt pseudopods1NoneLarge, irregularBacteria
Iodamoeba buetschlii8-20 μm (usual 12-15)Sluggish1NoneLarge, central, ringed by refractile achromatic granulesBacteria, yeasts, debris
Dientamoeba fragilis (flagellate, ameboid appearance)5-15 μm (usual 9-12)Angular/serrated/broad-lobed pseudopods1-2 (binucleate predominates)NoneLarge cluster of 4-8 granulesBacteria, yeasts
SpeciesSizeNuclei (mature)Chromatoid bodiesGlycogen
E. histolytica/E. dispar10-20 μm (usual 12-15)4 (1-2 in immature cysts)Elongate, bluntly rounded endsDiffuse; concentrated mass in young cysts
E. hartmanni5-10 μm (usual 6-8)4Elongate, blunt endsSimilar to E. histolytica
E. coli10-35 μm (usual 15-25)8 (occasionally 16+)Splinterlike, pointed endsUsually diffuse
Endolimax nana5-10 μm (usual 6-8)4AbsentDiffuse; concentrated mass in young cysts
Iodamoeba buetschlii5-20 μm (usual 10-12)1AbsentCompact, well-defined mass

Dientamoeba fragilis and Pentatrichomonas hominis form no cyst. E. coli’s 8-nucleus mature cyst is the single most reliable feature separating it from the 4-nucleus E. histolytica/E. dispar/E. hartmanni group. E. hartmanni is a small-bodied look-alike separated by micrometer measurement (trophozoite 12 μm or smaller, cyst 10 μm or smaller); fixative-induced shrinkage of true E. histolytica/E. dispar can cause overcalling of E. hartmanni. Five trophozoites measuring 8, 9, 10, 11, and 9.5 μm (mean 9.5 μm) fall within the E. hartmanni range and below the usual 15-20 μm commensal E. histolytica/E. dispar range.

E. histolytica and E. dispar are morphologically identical. Only antigen or molecular testing separates them. A laboratory without such testing must report “E. histolytica/E. dispar”. Erythrophagocytosis supports E. histolytica but is not reliable enough to separate the species.

Clinical disease from E. histolytica ranges from asymptomatic carriage through amebic dysentery to amebic colitis, the more common U.S. presentation. Trophozoites that breach the mucosa can form an amebic liver abscess (ALA). Stool examination recovers organisms in fewer than half of ALA cases. Serology is positive in about 95% of ALA, 70% of active intestinal disease, and 10% of asymptomatic carriers.

Blastocystis is frequently found in asymptomatic stool; most laboratories report it only to genus. Stool forms are pleomorphic (5-40 μm), classically with a large central body; on trichrome the central body typically stains green against pink peripheral cytoplasm.

Flagellates and ciliates

SpeciesSizeShapeMotilityNucleiDistinguishing feature
Giardia duodenalis (trophozoite)10-20 μm (usual 12-15)Pear-shaped, tapered posteriorlyFalling leaf2Ventral sucking disk; curved median bodies give a smiling-face appearance
Giardia duodenalis (cyst)8-13 μm (usual 11-12)Oval/ellipsoidal-Usually 4Axonemes cross beneath nuclei; cytoplasm often retracted from wall
Chilomastix mesnili (trophozoite)6-24 μm (usual 10-15)Pear-shapedStiff, rotary1Prominent cytostome, spiral ventral groove
Chilomastix mesnili (cyst)6-10 μm (usual 8-9)Lemon-shaped with hyaline nipple-1Curved cytostomal fibrils, safety-pin appearance
Pentatrichomonas hominis8-20 μm (usual 11-12)Pear-shapedRapid, jerking1Undulating membrane the full body length; no cyst
Trichomonas vaginalisUp to 23 μmSimilar to P. hominisJerky1Undulating membrane only about half the body length; urogenital habitat; no cyst
Enteromonas hominis4-10 μm (usual 8-9)OvalJerking1One side flattened
Retortamonas intestinalis4-9 μm (usual 6-7)Pear/ovalJerking1Cytostome extends about half body length

Giardia duodenalis is the most widespread waterborne protozoan pathogen; chlorination alone does not reliably inactivate cysts. Trophozoites attach to duodenal mucosa. Disease ranges from asymptomatic to a malabsorptive, steatorrheic syndrome. Suspect giardiasis in diarrhea persisting beyond 10 days. Shedding is intermittent, so multiple specimens plus antigen/NAAT improve yield over a single O&P.

Trichomonas vaginalis is a common sexually transmitted infection. Direct wet mount of vaginal, prostatic, or fresh urine sediment is fast but insensitive. CDC 2021 reports wet-mount sensitivity of 44-68% versus culture, falling to about 20% within 1 hour if the slide is not examined immediately, and recommends a more sensitive molecular test, including NAAT, with a negative wet mount when possible. Most platforms are cleared for female specimens only.1

Chilomastix mesnili, Pentatrichomonas hominis, Enteromonas hominis, and Retortamonas intestinalis are nonpathogenic commensals whose main clinical relevance is being mistaken for pathogens. Dientamoeba fragilis has flagellate ultrastructure but an ameboid light-microscopic appearance; permanent staining improves detection.

Balantioides coli (formerly Balantidium coli) is the only ciliate, and the largest protozoan, to infect humans, usually via hog, rodent, or nonhuman-primate contact. Trophozoites are 40 to >200 μm (usually 50-100 μm), uniformly ciliated, with a prominent macronucleus. Cysts are 50-70 μm with a kidney-bean-shaped macronucleus.

Cryptosporidium and the coccidia

OrganismOocyst sizeSporulation state as passedMature oocyst contentsAcid-fast?Autofluoresces?
Cryptosporidium hominis/C. parvum4-6 μmSporulated (infectious) when passed4 sporozoites, no sporocystsYes (modified cold Kinyoun)No
Cyclospora cayetanensis8-10 μmUnsporulated; needs 1-2 weeks environmental maturation2 sporocysts, each with 2 sporozoitesVariably (many ghost unstained forms)Yes, bright green/blue under UV
Cystoisospora belli12 × 30 μm (ellipsoidal)Unsporulated/partially sporulated; sporulates in 24-48 h at room temperature2 sporocysts, each with 4 sporozoitesYesYes
Sarcocystis spp. (intestinal)25 × 33 μm sporulated oocyst; wall often rupturesSporulated when passed2 sporocysts, each with 4 sporozoitesTrichrome stains poorlyYes

Cryptosporidium infects the intestinal brush border and resists chlorination. Diagnosis uses acid-fast stain of concentrated sediment, immunofluorescence, or antigen/NAAT. Immunocompetent disease is self-limited (about 9-23 days after an 8-day incubation); AIDS patients can develop prolonged secretory diarrhea. Cyclospora cayetanensis infects only humans; unstained ghost oocysts are common and must be size-differentiated from Cryptosporidium. Cystoisospora belli can persist for months to years in AIDS. Intestinal Sarcocystis follows eating raw or undercooked beef or pork; wet-mount and autofluorescence are the practical detection methods.

Intestinal helminths

Adult helminth length spans 1 mm to more than 10 m, and egg size spans roughly 25-150 μm. Both dimensions are diagnostic. Transmission is direct person-to-person (Enterobius vermicularis, Hymenolepis nana); environmental maturation of an egg or larva (Trichuris, Ascaris, Trichostrongylus); ingestion of an intermediate host; or skin penetration by larvae (hookworms, Strongyloides, Schistosoma).

SpeciesEgg/larva sizeKey morphologyDiagnostic specimen
Enterobius vermicularisEgg 50-60 × 20-40 μmOvoid, one side flattened, colorless; infective within hoursPerianal cellulose-tape/paddle preparation, morning, before bathing, preferably 3 consecutive mornings; stool is not preferred (historically positive in about 5-15% of confirmed cases)
Trichuris trichiura50-55 × 22-24 μmBarrel-shaped, bipolar refractile plugsDirect smear/concentration
Ascaris lumbricoides (fertile)55-75 × 35-50 μmRound-oval, yellow-brown mamillated coat, thick shell, unembryonated when passedDirect smear/concentration
Ascaris lumbricoides (infertile)Up to 90 μm, elongateThinner, irregularly mamillated shell; disorganized internal globules-
Ascaris lumbricoides (decorticated)As fertile, minus mamillated coatResembles hookworm egg-
Hookworm (Necator americanus, Ancylostoma duodenale, A. ceylanicum)58-76 × 36-40 μmThin-shelled, partially embryonated when passed; species eggs indistinguishableConcentration; rhabditiform larvae have a longer buccal canal and inconspicuous genital primordium versus Strongyloides
Trichostrongylus spp.Larger, more pointed than hookwormLarvae develop and are ingested (no skin penetration)Concentration
Strongyloides stercoralis (rhabditiform L1)Larva, not egg, usually seenShort buccal cavity, prominent genital primordiumStool concentration/culture; up to 7 specimens
Strongyloides stercoralis (filariform L3)Infective larvaNotched tail, esophagus about half body lengthSputum/BAL in hyperinfection
Capillaria philippinensis36-45 × 21 μmResembles Trichuris egg; thick, radially striated shellStool

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Enterobiasis is the most common childhood helminthic infection in the United States, Canada, and Europe; nocturnal pruritus ani is classic. Trichuriasis produces symptoms roughly in proportion to worm burden; more than 300 worms can cause dysentery-like disease and, in children, rectal prolapse. Ascaris females produce about 200,000 eggs/day. Eggs need 4-6 weeks’ environmental maturation, then hatch after ingestion, penetrate the gut, migrate to the lungs, and cause Loeffler syndrome in previously sensitized individuals. Direct fecal smears (2 mg feces each) yielding 132, 145, and 128 Ascaris eggs average 135 eggs per slide; more than 100 eggs per 2-mg slide denotes heavy infection.

Hookworm disease reflects chronic blood loss at the site of mucosal attachment. For a burden estimated at 40 adult A. duodenale and 25 adult N. americanus, midpoint daily blood loss of 0.20 mL and 0.03 mL per worm gives (40 × 0.20) + (25 × 0.03) = 8.75 mL/day, enough to produce iron-deficiency anemia over weeks to months.

Strongyloidiasis is distinctive for autoinfection: rhabditiform larvae can mature to infective filariform larvae without leaving the host, sustaining decades-long infection. T-cell-immunocompromised hosts can develop a life-threatening hyperinfection syndrome. Larva currens is a cutaneous marker of autoinfection. Agar-plate culture or coproculture gives the best sensitivity; serology is useful when infection is suspected but not demonstrable directly.

Cestodes

SpeciesEgg sizeEgg featuresScolexProglottid clue
Taenia spp. (eggs indistinguishable)31-43 μmSpherical, thick radially striated shell, 6-hooked embryoT. saginata: 4 suckers, unarmed; T. solium: 4 suckers, armed rostellum (2 hook rows)T. saginata uterus: 15-20 lateral branches/side; T. solium: 7-13/side
Hymenolepis nana30-47 μmOval, thin, colorless; 6-hooked oncosphere with polar filamentsArmed rostellum, single hook rowAll genital pores same side
Hymenolepis diminuta70-85 × 60-80 μmYellow-brown, moderately thick; no polar filamentsUnarmedAll genital pores same side
Dibothriocephalus/Adenocephalus spp.58-76 × 40-51 μmOperculate, small abopercular knobElongate, bothria, no suckersWider than long, midventral genital pore, centrally rosette-like uterus
Dipylidium caninum24-40 μm, singly or in egg packetsSpherical, 6-hooked embryo4 suckers, small retractable rostellumBarrel-shaped, two lateral genital pores

T. saginata eggs are not infectious to humans, so T. saginata taeniasis cannot cause cysticercosis. Accidental ingestion of T. solium eggs causes human cysticercosis, making careful, gloved proglottid handling essential. Hymenolepis nana is the most common cestode recovered in the United States; humans can be both definitive and intermediate host via internal autoinfection. Dibothriocephalus latus can reach 10 m; a small subset of northern-European patients develop vitamin B12 deficiency because the worm competitively absorbs B12. Dipylidium caninum is a dog/cat tapeworm accidentally acquired by children who ingest an infected flea; motile proglottids likened to rice grains or cucumber seeds are usually the presenting finding.

Trematodes

Eggs are operculate except schistosome eggs, which lack an operculum and contain a mature miracidium when passed. Each species requires a specific freshwater snail as first intermediate host.

SpeciesEgg sizeEgg featuresRoute of human infection
Fasciolopsis buski / Fasciola hepatica130-150 × 63-90 μm (F. gigantica 160-190 × 70-90 μm)Large, yellow-brown, operculate, unembryonatedAquatic vegetation
Heterophyes heterophyes / Metagonimus yokogawai20-30 × 15-17 μmSmall, embryonatedRaw/undercooked freshwater fish
Clonorchis sinensis / Opisthorchis spp.25-35 × 12-20 μmSmall, yellow-brown, embryonated, shouldered operculum + small abopercular knobRaw/undercooked freshwater fish
Nanophyetus salmincola60-80 × 34-50 μmBroadly ovoid, operculate, yellowish-brownRaw/smoked salmon or trout
Paragonimus spp.80-120 × 45-70 μmYellow-brown, shouldered operculum, thickened abopercular endRaw/undercooked freshwater crab or crayfish
Schistosoma mansoni116-180 × 45-58 μmLarge lateral spineCercarial skin penetration
Schistosoma japonicum75-90 × 60-68 μmSmall, inconspicuous lateral spineCercarial skin penetration
Schistosoma mekongi60-70 × 52-61 μmAs S. japonicum, smallerCercarial skin penetration
Schistosoma haematobium112-180 × 40-70 μmTerminal spineCercarial skin penetration; eggs recovered from urine
S. intercalatum / S. guineensis140-240 × 50-85 μmTerminal spine; recovered from fecesCercarial skin penetration

Liver flukes reside in the biliary tree. Chronic Clonorchis/Opisthorchis infection is linked to cholangiocarcinoma. Spurious Fasciola egg passage from eating infected liver is ruled out with a liver-free-diet follow-up stool exam. Lung flukes encyst in a host fibrotic capsule communicating with a bronchus, so eggs reach sputum or, if swallowed, stool. Blood flukes are dioecious. Three symptom phases are cercarial dermatitis, Katayama fever, and chronic fibrosis (hepatic pipe-stem fibrosis for intestinal species; bladder fibrosis and squamous-cell bladder carcinoma association for S. haematobium). Flotation under-recovers heavy schistosome eggs; sedimentation is required.

Tissue helminths

SpeciesSheath (Giemsa)PeriodicityTailVector
Wuchereria bancroftiPresent, does not stainUsually nocturnalPointed, nuclei do not reach the tipCulex, Aedes, Anopheles
Brugia malayiPresent, stains bright pink with Giemsa (not universal)NocturnalSwollen tip with two discrete nucleiMosquitoes
Loa loaPresent, does not stain with GiemsaDiurnalNuclei extend to the rounded tipChrysops deer flies
Onchocerca volvulusAbsentNonperiodic (dermal, not blood)No nuclei in tail tipSimulium black flies
Mansonella perstansAbsentNonperiodicNuclei extend to tail tipCulicoides midges

Wuchereria bancrofti causes classic lymphatic filariasis progressing to lymphedema and, in severe disease, elephantiasis. Loa loa produces migratory Calabar swellings and may be seen crossing the conjunctiva. Onchocerca volvulus is a leading cause of blindness in remaining endemic areas; diagnosis is by skin snip placed in saline. Zoonotic Dirofilaria produces a pulmonary coin lesion or subcutaneous nodule and rarely, if ever, circulating microfilariae in the accidental human host.

Other tissue nematodes include Dracunculus medinensis (Guinea worm); Angiostrongylus cantonensis (eosinophilic meningoencephalitis after ingesting infective larvae from snails, slugs, or contaminated produce); Trichinella (undercooked wild boar, bear, walrus, or unregulated pork; diagnosis rests on epidemiologic history plus EIA; muscle biopsy has low sensitivity); cutaneous larva migrans from dog/cat hookworm; visceral larva migrans from Toxocara canis (serology, because the organism is rarely recovered); and Anisakis/Pseudoterranova (raw-fish anisakiasis, usually diagnosed by endoscopic recovery).

Calcareous corpuscles mark cestode tissue in histologic sections. Neurocysticercosis is a leading cause of adult-onset seizures in endemic areas; enzyme-linked immunotransfer blot serology is more sensitive than crude-antigen ELISA. Hydatid disease serology uses EIA or IHA screening followed by confirmatory immunoblot.

Larval formCausative speciesStructure
CysticercusTaenia soliumTranslucent fluid-filled sac ≥5 mm with a single inverted protoscolex
Unilocular hydatidEchinococcus granulosus complexSingle (± daughter) cyst containing brood capsules and thousands of protoscoleces; hydatid sand
Multilocular/alveolar hydatidE. multilocularisInvasive alveolar growth without an outer capsule; mimics hepatic carcinoma
Polycystic hydatidE. vogeli, E. oligarthrusInvasive but produces brood capsules and protoscoleces; Latin America
SparganumSpirometra spp.Migratory subcutaneous larva
CoenurusTaenia multiceps, T. serialisLarge transparent sac with numerous budding scoleces

Parasitic infection in the immunocompromised host

Cellular (T-cell) immune defects cause most parasitic predisposition. Two important exceptions are more severe giardiasis with humoral immunodeficiency and more severe babesiosis after splenectomy. HIV co-infection does not markedly worsen malaria, schistosomiasis, ascariasis, amebiasis, or filariasis. Cryptosporidiosis and toxoplasmosis are more severe or more frequent in immunocompromised hosts; reactivation CNS toxoplasmosis is classically associated with AIDS. Strongyloidiasis is a particular problem in transplant recipients, HTLV-1 infection, and chemotherapy rather than in AIDS per se.

OrganismTypical immunocompromised settingLaboratory diagnosis
Cryptosporidium spp.Prolonged watery diarrhea (AIDS, transplant)Modified acid-fast stain or DFA on concentrated stool; antigen or NAAT; oocysts 4-6 μm
Cyclospora cayetanensis / Cystoisospora belliProlonged diarrhea and malabsorptionModified acid-fast stain; size (8-10 μm Cyclospora; 12 × 30 μm Cystoisospora); Cyclospora autofluoresces under UV; NAAT for C. cayetanensis
Toxoplasma gondiiReactivation CNS disease (AIDS); disseminated disease after transplantIgG documents latent infection; IgM and IgG avidity help time infection; NAAT on CSF, blood, or tissue for active disease
Strongyloides stercoralisHyperinfection or dissemination (corticosteroids, HTLV-1, transplant)Multiple stool examinations or agar-plate culture; sputum or BAL for filariform larvae in hyperinfection; serology as a screen before immunosuppression
Giardia duodenalisPersistent diarrhea, more severe with humoral immunodeficiencyStool antigen, DFA, or NAAT; microscopy of cysts and trophozoites
Babesia spp.Severe hemolysis, especially after splenectomyThick and thin blood films (Maltese-cross tetrads); NAAT; IFA is not a test for acute disease
References
  1. Centers for Disease Control and Prevention. Trichomoniasis. In: Sexually Transmitted Infections Treatment Guidelines, 2021. Accessed August 31, 2026.
  2. Centers for Disease Control and Prevention. Diagnosing pinworms. Accessed August 31, 2026.