Sterilization, Normal Flora & Vaccines
Who lives where, how to kill it, and how to prime immunity
Normal flora
Resident flora by site. Each body site has characteristic commensals. Neonates are born sterile and are colonized during and after birth. Most flora-derived infections happen when a commensal reaches a site where it does not belong or when the protective resident population is lost.
| Site | Dominant flora | Clinical link |
|---|---|---|
| Skin | Staphylococcus epidermidis | Prosthetic joint and IV catheter infection (biofilm) |
| Nose | S. epidermidis (S. aureus colonizes ~30%) | Nasal carriage is the main reservoir for S. aureus infection |
| Oropharynx | Viridans streptococci | S. sanguinis: subacute endocarditis on damaged valves |
| Dental plaque | S. mutans | Dental caries |
| Colon | Bacteroides > E. coli | Anaerobic abscess after perforation |
| Vagina | Lactobacillus | Loss allows bacterial vaginosis (Gardnerella) |
Commensals turned pathogens. S. epidermidis produces biofilm that lets it colonize prosthetic joints and IV catheters. Among viridans streptococci, S. mutans causes dental caries, and S. sanguinis makes dextrans that stick to fibrin-platelet deposits on previously damaged valves, causing subacute endocarditis. Vaginal Lactobacillus makes lactic acid that keeps the pH acidic; when it is lost, Gardnerella and anaerobes overgrow and cause bacterial vaginosis.
Sterilization, disinfection and antisepsis
Definitions. Sterilization destroys ALL microbes, including spores. Disinfection removes most pathogens from inanimate objects but usually not spores. Antisepsis reduces microbes on living tissue such as skin. Bacterial spores are the hardest microbes to kill; prions, which are not organisms, resist even standard autoclaving.
Physical methods. The autoclave (steam under pressure, 121 °C, ~15 psi, 15–20 min) is the gold standard for sterilization and reliably kills spores. Ethylene oxide gas sterilizes heat-sensitive equipment. Ionizing or UV radiation and 0.2-micron filtration, used for heat-labile liquids, are alternatives.
Chemical agents. 70% alcohol, chlorhexidine, iodophors and hydrogen peroxide disinfect but do NOT reliably kill spores at the concentrations used on skin and surfaces; only concentrated or vaporized hydrogen peroxide acts as a sporicidal sterilant. Chlorhexidine and iodine are the common skin antiseptics. Bleach (hypochlorite) and glutaraldehyde are stronger, sporicidal agents.
| Agent | How it acts | Kills spores? |
|---|---|---|
| Autoclave | Pressurized steam denatures proteins | Yes (gold standard) |
| Ethylene oxide | Alkylating gas; for heat-sensitive items | Yes |
| Bleach, glutaraldehyde | Oxidize or cross-link proteins | Yes |
| 70% alcohol | Disrupts membranes, denatures proteins | No |
| Chlorhexidine | Disrupts membranes | No |
| Iodophors, dilute hydrogen peroxide | Halogenate or oxidize | Not reliably |
Alcohol hand gel does not kill C. difficile spores; wash with soap and water instead, and clean rooms with a sporicidal agent such as bleach.
Active and passive immunity
Active immunity is earned. The host makes its own antibodies after infection or vaccination. Onset is slow, but protection lasts and memory cells allow a rapid secondary response.
Passive immunity is borrowed. Preformed antibodies are received. Onset is immediate, but protection lasts only as long as the antibody survives (IgG half-life ~3 weeks), and there is no memory. Natural passive immunity comes from maternal IgG crossing the placenta, which protects infants in their first months, and IgA in breast milk, which protects the infant gut. Therapeutic antitoxins or immunoglobulin are given after exposure to Tetanus, Botulinum, HBV and Rabies ("To Be Healed Rapidly").
Passive plus active. For HBV, rabies and tetanus, give immunoglobulin for immediate protection AND start the vaccine for lasting immunity. Examples are rabies post-exposure prophylaxis in an unvaccinated person and HBIG plus vaccine for the newborn of an HBsAg-positive mother.
Vaccine types
Live attenuated. A weakened organism replicates in the host and induces strong cellular AND humoral immunity, often lifelong. It can revert or cause disease in a weak host, so live vaccines are CONTRAINDICATED in pregnancy and immunocompromise. Examples: MMR, varicella, rotavirus, intranasal influenza, oral polio (Sabin), yellow fever and BCG. MMR and varicella may still be given to people with HIV whose CD4 count is ≥200. The live zoster vaccine (Zostavax) has been replaced by the recombinant subunit Shingrix, which is not live.
Inactivated. Killed pathogen produces a mainly humoral response that is weaker and needs boosters, but the vaccine is stable and safe in immunocompromised patients. The mnemonic is "RIP Always": Rabies, Influenza (injected), Polio (Salk), Hepatitis A. Oral Sabin polio vaccine induces gut IgA but can rarely revert and cause paralysis, which is why the injected Salk vaccine is used where polio has been eliminated.
Subunit, toxoid and conjugate. Subunit vaccines (HBsAg, HPV, acellular pertussis) contain only selected antigens, so they have fewer side effects but are weaker. Toxoids (tetanus, diphtheria) are inactivated toxins that induce antibodies neutralizing the toxin. Conjugate vaccines (Hib, PCV15/PCV20 pneumococcal, meningococcal) link a capsular polysaccharide to a protein carrier.
| Type | Examples | Response | Caveat |
|---|---|---|---|
| Live attenuated | MMR, varicella, rotavirus, intranasal flu, Sabin, yellow fever, BCG | Cellular + humoral, often lifelong | Avoid in pregnancy and immunocompromise |
| Inactivated | Rabies, injected influenza, Salk polio, hepatitis A | Mainly humoral | Needs boosters; safe if immunocompromised |
| Subunit | HBsAg, HPV, acellular pertussis, Shingrix | Humoral | Fewer side effects, weaker |
| Toxoid | Tetanus, diphtheria | Antitoxin antibodies | Neutralizes toxin, not the organism |
| Conjugate | Hib, PCV15/PCV20, meningococcal | T-cell-dependent, with memory | Protects infants |
A plain polysaccharide is a T-cell-independent antigen: it gives a short-lived, mostly IgM response without memory and works poorly before age 2. Linking it to protein recruits helper T cells, which convert it into a T-dependent antigen with class switching and memory that infants can respond to.
Cold chain and herd immunity
Cold chain. Vaccines, especially live attenuated and mRNA vaccines, must stay continuously refrigerated or frozen from manufacture to administration. A break in the cold chain degrades antigen and reduces efficacy, a major problem in low-resource settings.
Herd immunity. When a high enough fraction of a population is immune, transmission is interrupted, indirectly protecting people who cannot be vaccinated, such as young infants and those who are pregnant or immunocompromised and cannot receive live vaccines. The threshold is approximately 1 − 1/R0, so it rises with contagiousness.