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Pathogens and Their Morphology
A complete guide to the morphological characteristics of the major pathogen groups: bacteria, viruses, fungi, and parasites.
I. BACTERIA
A. General Characteristics
Bacteria are prokaryotes - they lack a membrane-bound nucleus and membrane-enclosed organelles. They are generally 0.5-5 µm in size. Their genome is a single, circular, double-stranded DNA chromosome located in the nucleoid region (not a true nucleus).
Key structures:
- Cell membrane (phospholipid bilayer)
- Cell wall (peptidoglycan - the basis for Gram staining)
- Ribosomes (70S = 50S + 30S subunits)
- No mitochondria - energy generated at cell membrane
B. Basic Bacterial Shapes
| Shape | Term | Examples |
|---|
| Spherical | Coccus (pl. cocci) | Staphylococcus, Streptococcus, Neisseria |
| Rod-shaped | Bacillus (pl. bacilli) | E. coli, Bacillus, Clostridium, Salmonella |
| Comma-shaped | Vibrio | Vibrio cholerae |
| Spiral, rigid | Spirillum | Helicobacter pylori |
| Spiral, flexible | Spirochete | Treponema pallidum, Borrelia, Leptospira |
| Curved rod | Campylobacter | Campylobacter jejuni |
| Club-shaped | Pleomorphic | Corynebacterium diphtheriae |
C. Arrangement of Cocci
| Arrangement | Description | Example |
|---|
| Diplococcus | Pairs | Neisseria gonorrhoeae, S. pneumoniae |
| Streptococcus | Chains | Streptococcus pyogenes |
| Tetrad | Groups of 4 | Micrococcus |
| Sarcina | Cuboidal packet of 8 | Sarcina |
| Staphylococcus | Irregular clusters (grapelike) | Staphylococcus aureus |
D. Gram Staining - The Fundamental Classification
The Gram stain divides bacteria based on cell wall composition:
| Feature | Gram-Positive | Gram-Negative |
|---|
| Color | Purple/violet | Pink/red |
| Cell wall | Thick peptidoglycan (20-80 nm) | Thin peptidoglycan (2-7 nm) + outer membrane |
| Outer membrane | Absent | Present (contains LPS/endotoxin) |
| Teichoic acids | Present | Absent |
| Periplasmic space | Narrow | Wide |
| Toxin type | Exotoxins (mainly) | Endotoxin (LPS) + exotoxins |
Important Gram-positive pathogens:
- Cocci: Staphylococcus aureus, Streptococcus pyogenes, S. pneumoniae, Enterococcus
- Rods/Bacilli: Bacillus anthracis, Clostridium tetani, C. perfringens, C. difficile, Listeria, Corynebacterium diphtheriae
Important Gram-negative pathogens:
- Cocci: Neisseria meningitidis, N. gonorrhoeae
- Rods: E. coli, Klebsiella, Salmonella, Shigella, Pseudomonas, Haemophilus influenzae, Campylobacter, Helicobacter pylori, Vibrio cholerae, Yersinia pestis
E. Special Morphological Features
1. Spore-forming bacteria (endospores - highly resistant structures):
- Bacillus anthracis - central spore
- Clostridium tetani - terminal spore ("drumstick")
- C. perfringens - subterminal spore
- C. botulinum - subterminal spore
2. Capsule-forming bacteria (polysaccharide coat; anti-phagocytic):
- Streptococcus pneumoniae (polysaccharide capsule - visualized by Quellung reaction)
- Klebsiella pneumoniae (mucoid colonies)
- Haemophilus influenzae type b
- Neisseria meningitidis
- Cryptococcus neoformans (fungal - detected by India ink)
3. Flagella (motility):
- Monotrichous - single polar flagellum: Vibrio cholerae, Pseudomonas
- Lophotrichous - tuft at one pole: Helicobacter pylori (multiple at one end)
- Amphitrichous - both poles: Campylobacter
- Peritrichous - all around: E. coli, Salmonella, Listeria
- Non-motile (no flagella): Shigella, Klebsiella, Yersinia pestis
4. Fimbriae/Pili:
- Hair-like protein appendages; shorter and more numerous than flagella
- Function in adhesion to host cells
- Sex pili (F-pili): mediate conjugation (DNA transfer)
- E. coli, Neisseria gonorrhoeae (type IV pili)
F. Acid-Fast Bacteria (Mycobacteria)
Do not Gram stain well due to high mycolic acid content in cell wall. Identified by Ziehl-Neelsen (ZN) stain - appear red against blue background.
| Organism | Disease |
|---|
| Mycobacterium tuberculosis | Tuberculosis |
| M. leprae | Leprosy |
| M. avium complex | Opportunistic infection |
Morphology: Slender, beaded rods (~2-4 µm); slow-growing; obligate aerobes; waxy hydrophobic cell wall.
G. Atypical Bacteria (No Cell Wall or Different Structure)
| Organism | Morphology | Key Feature |
|---|
| Mycoplasma | Pleomorphic (no fixed shape) | No cell wall; smallest free-living organism; resistant to beta-lactams |
| Chlamydia | Obligate intracellular; elementary body (infectious) + reticulate body (replicating) | No peptidoglycan; cannot make own ATP |
| Rickettsia | Small coccobacilli | Obligate intracellular; arthropod-borne |
| Spirochetes | Helical, flexible | 0.1-0.5 µm wide, 5-250 µm long; motility via endoflagella (axial filaments) |
Spirochete morphology details:
- Treponema pallidum (syphilis): very thin, tightly coiled (~8-14 coils), 6-15 µm; cannot be cultured
- Borrelia burgdorferi (Lyme disease): loosely coiled, 10-30 µm; visualized on Giemsa
- Leptospira (leptospirosis): hooked ends, 6-20 µm; "shepherd's crook" shape
II. VIRUSES
A. General Structure
Viruses are non-cellular obligate intracellular parasites. They consist of:
- Nucleic acid core - either DNA or RNA (never both), single- or double-stranded
- Capsid - protein coat surrounding the nucleic acid; made of capsomeres
- Envelope (some viruses) - lipid bilayer derived from host cell membrane; contains viral glycoproteins
Size: Generally 20-300 nm (smaller than bacteria)
B. Capsid Symmetry
| Type | Description | Examples |
|---|
| Icosahedral | 20 triangular faces; 12 vertices (spherical-appearing) | Adenovirus, Picornavirus, Herpesvirus (inner capsid), Hepatitis B |
| Helical | Capsomeres arranged in a helix around nucleic acid | Rabies, Influenza, RSV, Measles |
| Complex | Neither icosahedral nor helical | Poxviruses (brick-shaped), Bacteriophages |
C. Enveloped vs. Non-Enveloped
| Feature | Enveloped | Non-Enveloped (Naked) |
|---|
| Structure | Lipid bilayer + glycoproteins | Capsid only |
| Stability | Labile (destroyed by detergents, heat, drying) | More stable in environment |
| Transmission | Requires close contact; respiratory/sexual/blood | Can survive on surfaces; fecal-oral |
| Examples | Herpesvirus, HIV, Influenza, Hepatitis B/C, Rabies, CMV, EBV | Adenovirus, Poliovirus, Hepatitis A, Norovirus, Rotavirus, Parvovirus |
D. DNA vs. RNA Viruses
DNA Viruses (most replicate in nucleus):
| Family | Morphology | Examples |
|---|
| Herpesviridae | Enveloped icosahedral; 150-200 nm | HSV-1/2, VZV, CMV, EBV, HHV-6/8 |
| Adenoviridae | Non-enveloped icosahedral; 70-90 nm | Adenovirus (pharyngitis, conjunctivitis) |
| Poxviridae | Complex, brick-shaped; 200-400 nm (largest DNA virus) | Smallpox, Vaccinia, Molluscum |
| Hepadnaviridae | Enveloped; partially dsDNA; 42 nm (Dane particle) | Hepatitis B virus |
| Papillomaviridae | Non-enveloped icosahedral; 55 nm | HPV (warts, cervical cancer) |
| Parvoviridae | Non-enveloped icosahedral; 18-26 nm (smallest DNA virus) | Parvovirus B19 |
RNA Viruses:
| Family | Genome | Morphology | Examples |
|---|
| Picornaviridae | +ssRNA | Non-enveloped icosahedral; 28-30 nm | Poliovirus, Rhinovirus, HAV, Enterovirus |
| Flaviviridae | +ssRNA | Enveloped icosahedral; 40-60 nm | HCV, Dengue, Zika, Yellow fever, WNV |
| Togaviridae | +ssRNA | Enveloped icosahedral; 70 nm | Rubella, Chikungunya |
| Coronaviridae | +ssRNA | Enveloped helical; 80-220 nm; crown-like spikes | SARS-CoV-2, MERS-CoV |
| Orthomyxoviridae | -ssRNA (segmented, 8 segments) | Enveloped helical; 80-120 nm; HA + NA surface proteins | Influenza A, B |
| Paramyxoviridae | -ssRNA | Enveloped helical; 150-300 nm | Measles, Mumps, RSV, Parainfluenza |
| Rhabdoviridae | -ssRNA | Enveloped helical; bullet-shaped; 75x180 nm | Rabies virus |
| Retroviridae | +ssRNA (diploid); reverse transcriptase | Enveloped icosahedral; 80-120 nm | HIV-1/2, HTLV |
| Reoviridae | dsRNA (10-12 segments) | Non-enveloped; double-layered icosahedral; 70-80 nm | Rotavirus, Reovirus |
| Bunyaviridae | -ssRNA (3 segments) | Enveloped; 80-120 nm | Hantavirus, Rift Valley fever |
| Filoviridae | -ssRNA | Enveloped helical; long filamentous; up to 14,000 nm | Ebola, Marburg |
HIV (detailed morphology):
- Enveloped, ~120 nm spherical
- Outer envelope: gp120 (binding) + gp41 (fusion) glycoproteins
- Matrix: p17
- Conical capsid: p24 (truncated cone shape - diagnostic on EM)
- Genome: 2 copies of +ssRNA + reverse transcriptase (p66/p51), integrase, protease
III. FUNGI
A. General Morphology
Fungi are eukaryotes with a cell wall made of chitin (not peptidoglycan). They reproduce by spores.
Two basic morphological forms:
| Form | Description | Examples |
|---|
| Yeast | Unicellular, round/oval; reproduce by budding | Candida, Cryptococcus |
| Mold (Hyphae) | Multicellular; grow as filamentous branching hyphae; network = mycelium | Aspergillus, Rhizopus, dermatophytes |
| Dimorphic | "MOLD in the cold, YEAST in the heat" - mold at 25°C, yeast at 37°C (body temperature) | Histoplasma, Blastomyces, Coccidioides, Paracoccidioides, Sporothrix |
B. Key Fungal Pathogens and Morphology
| Organism | Morphology | Key Feature |
|---|
| Candida albicans | Oval budding yeast (3-6 µm) + pseudohyphae + germ tubes at 37°C | Germ tube test (+); most common opportunistic fungus |
| Cryptococcus neoformans | Round yeast (4-20 µm) with large polysaccharide capsule | India ink - clear "halo" around organism; urease (+) |
| Aspergillus fumigatus | Septate hyphae with acute angle (45°) branching | V-shaped branching; conidiophore with conidia |
| Mucor/Rhizopus | Broad, non-septate (aseptate) hyphae with wide-angle (90°) branching | "Ribbon-like" hyphae; causes mucormycosis |
| Histoplasma capsulatum | Yeast inside macrophages (2-4 µm); mold phase has tuberculate macroconidia | Bird/bat droppings; Ohio/Mississippi river valleys |
| Blastomyces dermatitidis | Broad-based budding yeast (8-15 µm); thick double-refractile cell wall | "Figure-8" appearance |
| Coccidioides immitis | Spherules (20-60 µm) containing endospores in tissue | Arthroconidia in mold phase; desert Southwest |
| Pneumocystis jirovecii | Cysts (5-8 µm) with 8 intracystic bodies; trophic forms | Stained by GMS (silver) stain; CD4 <200 |
| Sporothrix schenckii | Cigar-shaped yeast in tissue; mold has "rosette" conidia arrangement | "Rose gardener's disease"; lymphocutaneous |
| Dermatophytes | Septate hyphae + macroconidia/microconidia | Trichophyton, Microsporum, Epidermophyton; infect keratinized tissue only |
C. Special Stains for Fungi
- GMS (Gomori Methenamine Silver): Black fungi on green background
- PAS (Periodic Acid-Schiff): Magenta/pink fungi
- India ink: Cryptococcus capsule (negative stain)
- Calcofluor white: Fluorescent staining of chitin
IV. PARASITES
A. Protozoa (Unicellular Eukaryotes)
1. Intestinal Protozoa
| Organism | Morphology | Key Feature |
|---|
| Entamoeba histolytica | Trophozoite (15-60 µm): motile, pseudopods, ingested RBCs; Cyst (10-20 µm): 4 nuclei | "Flask-shaped" ulcers; amoebic dysentery |
| Giardia lamblia | Trophozoite: pear-shaped, 2 nuclei, 4 pairs of flagella ("falling leaf" motility); Cyst: oval, 4 nuclei | Ventral sucking disk; mountain stream water |
| Cryptosporidium | Oocysts (4-6 µm): very small, acid-fast; 4 sporozoites per oocyst | Acid-fast stain; immunocompromised |
| Balantidium coli | Largest protozoan (50-100 µm); ciliated trophozoite; bean-shaped macronucleus | Only ciliate infecting humans |
2. Blood/Tissue Protozoa
| Organism | Morphology | Key Feature |
|---|
| Plasmodium falciparum | Ring forms (appliqué/accole); multiple rings per RBC; banana-shaped gametocytes | RBC not enlarged; causes malaria |
| P. vivax/ovale | Ring forms + trophozoites; enlarged RBCs; Schüffner dots | Amoeboid trophozoite |
| P. malariae | Band-form trophozoite; "rosette" schizonts | Normal or small RBCs |
| Trypanosoma brucei | Spindle-shaped trypomastigote (~25 µm); undulating membrane; single flagellum | Sleeping sickness; tsetse fly |
| Trypanosoma cruzi | Trypomastigote with C- or U-shape; "sickle" form; amastigotes in tissue | Chagas disease; reduviid bug |
| Leishmania | Promastigote (flagellated, extracellular) in sandfly; amastigote (non-flagellated, intracellular) in macrophages | Sandfly transmission |
| Toxoplasma gondii | Tachyzoites: crescent/banana-shaped (3x6 µm); bradyzoites in tissue cysts | Definitive host = cat; congenital infection |
3. Vaginal Protozoa
| Trichomonas vaginalis | Pear-shaped, 5 flagella (4 anterior + 1 in undulating membrane); no cyst stage | Jerky "tumbling" motility; STI |
B. Helminths (Worms)
1. Nematodes (Roundworms) - Cylindrical, unsegmented
| Organism | Size/Morphology | Key Feature |
|---|
| Ascaris lumbricoides | Large (15-35 cm); 3 lips around mouth | Largest intestinal nematode |
| Enterobius vermicularis | Small (1 cm); pointed tail (pinworm) | Scotch tape test; perianal pruritus |
| Trichuris trichiura | Whip-shaped; narrow anterior, thick posterior (whipworm) | Barrel-shaped eggs |
| Hookworms (Ancylostoma/Necator) | Cutting plates (Ancylostoma) or cutting plates with semilunate plates (Necator) | Blood loss; hypochromic anemia |
| Strongyloides stercoralis | Rhabditiform (free-living) vs. filariform (infective) larvae | Autoinfection; filariform larvae in stool |
| Wuchereria bancrofti | Sheathed microfilariae; nocturnal periodicity | Lymphatic filariasis; elephantiasis |
| Loa loa | Sheathed microfilariae; diurnal periodicity | Calabar swellings; eye worm |
| Onchocerca volvulus | Unsheathed microfilariae in skin | River blindness; black fly |
2. Cestodes (Tapeworms) - Flat, segmented
| Organism | Morphology | Key Feature |
|---|
| Taenia saginata | Unarmed scolex (no hooks); up to 10 m long; >12 uterine branches per proglottid | Beef tapeworm |
| Taenia solium | Armed scolex (hooks + suckers); <7 m; <12 uterine branches per proglottid; cysticerci in tissue | Pork tapeworm; neurocysticercosis |
| Echinococcus granulosus | Small tapeworm (3-6 mm) in dog intestine; hydatid cysts in human liver/lung | Hydatid disease; brood capsules with scolices |
| Diphyllobothrium latum | Broadest tapeworm (up to 15 m); scolex has bothria (grooves, no suckers) | Fish tapeworm; B12 deficiency |
3. Trematodes (Flukes) - Flat, non-segmented, leaf-shaped
| Organism | Morphology | Key Feature |
|---|
| Schistosoma mansoni | Adult male has gynecophoral canal holding female; eggs with lateral spine | Intestinal schistosomiasis; Africa |
| S. haematobium | Eggs with terminal spine | Urinary schistosomiasis; bladder cancer |
| S. japonicum | Small eggs with rudimentary lateral spine | Most eggs per worm; cerebral disease |
| Clonorchis sinensis | Small (12-20 mm); Chinese liver fluke; flask-shaped eggs with operculum | Bile duct; cholangiocarcinoma |
| Fasciola hepatica | Large (30 mm); sheep liver fluke; large operculated eggs | Liver fluke; biliary obstruction |
| Paragonimus westermani | Lung fluke; reddish-brown, 8-16 mm; operculated eggs | Hemoptysis; raw crab |
C. Ectoparasites
| Organism | Morphology | Key Feature |
|---|
| Sarcoptes scabiei | Oval mite (0.3-0.4 mm); 4 pairs of legs; burrows in skin | Scabies; intense pruritus |
| Pediculus humanus | Louse with clinging claws; nits attached to hair | Head/body lice |
| Phthirus pubis | Crab louse - short, broad body with crab-like claws | Pubic lice |
Summary: Quick Identification Table
| Pathogen Type | Cell Type | Cell Wall | Size | Unique Feature |
|---|
| Gram + bacteria | Prokaryote | Thick peptidoglycan | 0.5-5 µm | Purple on Gram stain |
| Gram - bacteria | Prokaryote | Thin PG + outer membrane (LPS) | 0.5-5 µm | Pink on Gram stain; endotoxin |
| Mycobacteria | Prokaryote | Mycolic acid-rich | 2-4 µm | Acid-fast (ZN stain) |
| Mycoplasma | Prokaryote | None | 0.1-0.3 µm | Smallest free-living organism |
| Viruses | Non-cellular | None (has capsid ± envelope) | 20-400 nm | Obligate intracellular |
| Fungi | Eukaryote | Chitin | 3-30 µm | GMS/PAS staining |
| Protozoa | Eukaryote | None or minimal | 1-100+ µm | Often have cyst + trophozoite stages |
| Helminths | Eukaryote (multicellular) | Cuticle | mm-meters | Eggs/larvae used for identification |
Sources: Jawetz, Melnick & Adelberg's Medical Microbiology, 28th ed. (Fundamentals of Microbiology, pp. 6-140); Medical Microbiology, 9th ed.; Sherris & Ryan's Medical Microbiology, 8th ed.