Structure, Staining & Appearance
SporesDipicolinic acid + calcium
- Bacillus
- Clostridium
Acid-fastMycolic acid in wall
- Mycobacterium
- Nocardia (partial)
- Oocysts: Cryptosporidium, Cystoisospora, Cyclospora
Nonmotile gram-positive rods
- C. diphtheriae
- Nocardia
- C. perfringens (other clostridia move)
- B. anthracis (other bacilli move)
Capsules
| Organism | Capsule note |
|---|---|
| S. pneumoniae | Polysaccharide; main virulence factor |
| H. influenzae | Type b polyribitol phosphate |
| N. meningitidis | Polysaccharide; vaccine target |
| K. pneumoniae | Large, mucoid colonies |
| P. aeruginosa | Alginate slime; cystic fibrosis lungs |
| C. neoformans | Only encapsulated pathogenic fungus |
| E. coli (meningitis strains) | K1 antigen |
| B. anthracis | Poly-D-glutamate |
| S. Typhi | Vi antigen |
| S. pyogenes | Hyaluronic acid; poorly immunogenic |
| B. pertussis | Capsule present |
Biofilm formers
- S. epidermidis: catheters and prosthetics
- S. mutans: dental plaque
- S. aureus
- P. aeruginosa
Pigments
| Organism | Color |
|---|---|
| P. aeruginosa | Blue-green (pyocyanin, pyoverdin) |
| Serratia | Red |
| S. aureus | Golden-yellow |
| C. diphtheriae | Gray-black colonies on tellurite |
Distinctive microscopy
| Feature | Organism |
|---|---|
| Metachromatic granules | Corynebacterium |
| Lancet-shaped diplococci | S. pneumoniae |
| Kidney-bean diplococci | Neisseria |
| Safety-pin bipolar staining | Yersinia pestis, Pasteurella |
| Gull-wing curved rods | Campylobacter |
Viral cytopathic effects
| Finding | Virus |
|---|---|
| Cytoplasmic Negri bodies | Rabies |
| Cytoplasmic acidophilic (Guarnieri) | Poxviruses |
| Nuclear owl's-eye | CMV |
| Nuclear Cowdry type A | HSV, SSPE (measles) |
| Syncytia | Herpesviruses, VZV, measles, mumps, RSV, HIV |
Virulence Determinants
Where virulence genes sit
| Location | Typical products |
|---|---|
| Chromosome | Endotoxin (LPS) |
| Plasmid | Most exotoxins, multidrug resistance |
| Prophage (lysogenic conversion) | See list below |
Phage-encoded virulence
- Cholera toxin
- Diphtheria toxin
- Botulinum toxin (some types)
- Erythrogenic toxin of S. pyogenes
- Shiga toxin
- Salmonella O-antigen conversion
Pitfall
- Non-toxigenic C. diphtheriae lacks the prophage and is not toxin-mediated
Antigenic variation
- N. gonorrhoeae pili
- Borrelia recurrentis
- Trypanosoma brucei
- HIV
Anti-host-defense factors
| Factor | Effect | Organism |
|---|---|---|
| Capsule / slime | Blocks phagocytosis | Encapsulated species; Pseudomonas |
| M protein | Blocks phagocytosis | S. pyogenes |
| Protein A | Binds Fc of IgG; blocks opsonization | S. aureus |
| Lipoteichoic acid | Adherence to host cells | Gram-positives |
| Pili | Attachment; antiphagocytic | N. gonorrhoeae |
Extracellular enzymes
| Enzyme | Action | Organism |
|---|---|---|
| Hyaluronidase | Breaks down ground substance; spread | S. pyogenes |
| Collagenase | Degrades collagen | C. perfringens, Prevotella |
| Kinases | Dissolve fibrin | Streptococci, staphylococci |
| Lecithinase (alpha toxin) | Lyses membranes | C. perfringens |
| Heparinase | Possible role in thrombophlebitis | B. fragilis, Prevotella |
| IgA protease | Cleaves mucosal IgA; colonization | Neisseria, Haemophilus, S. pneumoniae |
Intracellular Lifestyle
Enters host cell→Escapes antibody→Needs cell-mediated immunity→Granulomas / reactivation
ObligateCannot grow on lifeless media
- Bacteria
- All rickettsiae
- All chlamydiae
- M. leprae
- All viruses
- Protozoa
- Plasmodium, Babesia
- Toxoplasma
- Leishmania
- T. cruzi (amastigotes in heart muscle)
- No fungi are obligate
FacultativeCan also grow outside cells
- Francisella, Listeria, Brucella
- M. tuberculosis, atypical mycobacteria
- S. Typhi, Legionella, Yersinia pestis, Nocardia
- Histoplasma (only fungus)
Obligate parasites living outside cells
- Treponema pallidum
- Pneumocystis jirovecii
Reservoirs, Vectors & Transmission
Human-only reservoir
- M. tuberculosis
- Shigella
- S. Typhi
- R. prowazekii
- Group A strep, pneumococcus
- N. meningitidis, N. gonorrhoeae
- C. diphtheriae, T. pallidum, C. trachomatis
- M. leprae also infects armadillos
Zoonoses
- Anthrax, brucellosis, tularemia
- Leptospira, Borrelia, Listeria
- Nontyphoidal Salmonella
- Yersinia (pestis, enterocolitica, pseudotuberculosis)
- Campylobacter
- Most rickettsiae; C. psittaci; rabies
- Bite or scratch: Pasteurella, Capnocytophaga, Bartonella, Streptobacillus
- Water or seafood: M. marinum, V. vulnificus, V. parahaemolyticus
Insect vectors
| Vector | Diseases |
|---|---|
| Body louse | Epidemic typhus, epidemic relapsing fever, trench fever |
| Kissing bug | Chagas disease |
| Anopheles | Malaria |
| Aedes | Dengue, yellow fever |
| Culex and others | Arboviral encephalitides, filariasis |
| Sandfly | Leishmaniasis, bartonellosis |
| Midge | Some filariasis |
| Blackfly | Onchocerciasis |
| Deerfly | Loiasis, tularemia |
| Tsetse fly | African sleeping sickness |
| Flea | Plague, endemic typhus |
Non-insect vectors
| Vector | Diseases |
|---|---|
| Dermacentor tick | Rocky Mountain spotted fever, Colorado tick fever, tularemia |
| Ixodes tick | Lyme disease, babesiosis, ehrlichiosis, anaplasmosis |
| Amblyomma tick | Ehrlichiosis |
| Soft tick (Ornithodoros) | Endemic relapsing fever |
| Mites | Scrub typhus (transovarial in vector), rickettsialpox |
Helminths: infective stage
- Eggs ingested: pinworm, Ascaris, Trichuris, Toxocara, Echinococcus, Taenia solium (cysticercosis)
- All other helminths: larval stage
Not contagious person-to-person
- Nontuberculous mycobacteria
- Non-spore-forming anaerobes
- Legionella
- Fungi, except dermatophytes
Respiratory route
Droplet
- S. pyogenes, pneumococcus, meningococcus
- M. tuberculosis, B. pertussis, H. influenzae
- C. diphtheriae, M. pneumoniae
- Influenza, rubella, measles, varicella, Pneumocystis
Environmental inhalation
- Histoplasma, Coccidioides, Blastomyces
- MAC, Legionella, C. psittaci
- Pseudomonas (also ingestion, contact)
Transplacental pathogens
- Protozoan: Toxoplasma
- Bacteria: T. pallidum, Listeria
- Viruses
- CMV, rubella, HIV, parvovirus B19
- HSV-2 (primary maternal infection)
- Coxsackie B, polio
- Hepatitis B: under 5% of perinatal cases are transplacental
Tissue Pathology Patterns
Granuloma-producing infections
| Group | Examples |
|---|---|
| Intracellular bacteria | Francisella, Listeria, Mycobacterium, Brucella, Chlamydia (LGV) |
| Persistent-antigen bacteria | T. pallidum, Actinomyces, Bartonella (cat-scratch) |
| Fungi | Histoplasma, Blastomyces, Coccidioides |
| Helminth | Schistosoma egg granulomas |
Intracranial calcification
- Toxoplasma
- CMV
- Cysticercosis
- Cryptococcus
- Tuberculous meningitis
High-yield
- Granulomas depend on T-cell and macrophage cooperation
Laboratory Diagnosis
Special stains
| Stain | Target |
|---|---|
| Dieterle silver | Legionella |
| Methenamine silver | Pneumocystis, fungi |
| Ziehl-Neelsen / Kinyoun | Mycobacteria, Nocardia (weak), coccidian oocysts, microsporidia |
| India ink | Cryptococcus capsule; a negative result does not exclude |
| Calcofluor white | Fungal walls |
| Giemsa | Blood protozoa; Histoplasma in macrophages |
Named tests
| Test | Use |
|---|---|
| Tuberculin (Mantoux) | Tuberculosis exposure |
| Lepromin | Leprosy form |
| CAMP | Group B strep |
| Elek | Diphtheria toxin production |
| Weil-Felix | Rickettsial antibodies via Proteus OX antigens |
| Fungal skin tests | Show exposure or anergy only |
Growth requirements
| Organism | Need |
|---|---|
| Haemophilus | Factor X (hemin) and factor V (NAD / NADP) |
| Mycoplasma | Cholesterol |
| S. aureus | Grows on high-salt agar |
| Enterococcus | Grows in 6.5% NaCl |
| Vibrio | Salt-requiring (halophilic) |
| Francisella, Legionella, Brucella, Pasteurella | Cysteine-enriched media |
Slow cultures
- M. tuberculosis and most nontuberculous mycobacteria
- M. pneumoniae
- Endemic dimorphic fungi
Prophylaxis & Vaccines
Chemoprophylaxis targets
- N. meningitidis: household and day-care contacts
- Vaccinate in outbreaks
- M. tuberculosis: recent test conversion or close exposure
- Also untreated young positives
- H. influenzae b: unvaccinated young household contacts
- Vaccinate also
- Sexual contacts of gonorrhea or syphilis
- Plague exposure
- Newborn eyes: gonococcus, chlamydia
Vaccine types
| Type | Examples |
|---|---|
| Inactivated | Rabies, injected influenza, injected polio, hepatitis A, Japanese encephalitis |
| Live attenuated | Measles, mumps, rubella, varicella, yellow fever, rotavirus, smallpox |
| Live, enteric-coated capsule | Adenovirus (military) |
| Toxoid | Tetanus, diphtheria, acellular pertussis |
| Capsular polysaccharide (conjugated in children) | H. influenzae b, meningococcus, pneumococcus |
| Recombinant protein | Hepatitis B surface antigen, HPV capsid protein |
Caution
- Live vaccines are avoided in severe immunocompromise