Final Exam Study Guide

The final covers all 15 chapters. Taking them one at a time would mean 15 piles of notes, so this guide groups them into seven themes instead. Each theme pulls together the chapters that share a way of thinking. What microbes are and how we see them. How they are built and classified. How they grow and change. How we kill them and treat infection. How they cause disease and spread. How the body fights back. And what goes wrong with that defense. Work one theme a day and all 15 chapters fit into a week. Every theme carries its own tables, its sequences in order, how to reason through the question types, the traps, and a 10-item self-test. The cram sheet at the end holds the whole book on one page.

Theme 1 · Chapters 1 and 2What microbes are, and how we see them

What to know

A microbe is any living organism too small to see unaided. Six groups fill the field. Bacteria and archaea are prokaryotes, with no nucleus. Fungi and protozoa are eukaryotes, with one. Helminths, the parasitic worms, join the list by tradition, because their eggs and larvae are microscopic even when the adults are not. Viruses are acellular, so they are not on the tree of life at all.

No archaea are known to cause human disease. That is worth holding, because it shows up as a distractor.

The split between prokaryote and eukaryote is what makes drug therapy possible. Selective toxicity means hitting a target the microbe has and the host lacks. A bacterial cell wall. A 70S ribosome. Human cells have neither. That same logic explains why antibiotics do nothing against a virus.

Your body is already covered in microbes. The microbiome is the community that normally lives on and in you, together with their genes, and the resident microbes are the normal flora. Most are helpful. They make vitamin K and some B vitamins. They crowd out invaders by taking the space and the food, which is competitive exclusion. They train the immune system early. And they keep a surface harsh, as vaginal lactobacilli do by holding the pH low.

An opportunistic pathogen is often normal flora that turns harmful once it is moved, left unopposed, or facing a weakened host. Transient flora are the passing microbes on your hands, and removing them is the entire point of hand hygiene.

Three states get confused constantly. Colonization means the microbe is present and multiplying, with no host response and no symptoms. Infection means it is invading tissue and the host is responding, though symptoms are not guaranteed. Disease means clear signs and symptoms and lost function.

Germ theory says specific microbes cause specific diseases, and all infection control stands on it. Three names carry the story. Semmelweis gave us hand hygiene. Pasteur disproved spontaneous generation and gave us pasteurization. Koch gave us the postulates that link one microbe to one disease.

Life sorts into three domains. Bacteria and Archaea are the prokaryotic two. Eukarya holds protozoa, fungi, plants and animals. Microbes carry binomial names, written as italic Genus species, and shortened to G. species after the first use.

Seeing a microbe takes a ladder of units. One millimeter is 1000 micrometers, and one micrometer is 1000 nanometers, so each step is a thousand times smaller. Most bacteria run about 1 to 3 µm. Viruses run about 20 to 300 nm. A red blood cell at about 7 µm is a handy yardstick. The naked eye resolves only to about 0.1 mm, which is roughly a hundred times too coarse to see a bacterium. So the lab grows one invisible microbe into a visible colony before it can work with it.

The compound light microscope uses two lens systems in a row. Light travels illuminator, condenser, specimen, objective, ocular. Total magnification is the ocular power times the objective power, so a 10× ocular with the 100× oil lens gives 1000×.

But magnification is not the limit. Resolution is, and it is the smallest gap at which two points still look separate. For light microscopy that bottoms out near 0.2 µm. Immersion oil matches the refractive index of glass, so it catches more light rays and sharpens the 100× image.

Cells are nearly clear, so staining supplies the contrast. A smear is air-dried and heat-fixed, which kills most organisms, sticks them to the slide and holds their shape. It does not sterilize.

Four stain types matter. A simple stain uses one dye and shows size, shape and arrangement. A differential stain uses two or more reagents and sorts cells into groups, and the Gram stain is the classic one. A special stain reveals one structure, such as a capsule or an endospore. A negative stain colors the background with an acidic dye and skips the heat, which suits capsules and fragile cells.

The Gram stain sorts bacteria by cell wall, and it reads in under an hour. Four steps. Crystal violet stains everything purple. Gram's iodine is the mordant that traps the dye in the wall. Alcohol or acetone is the decolorizer, and this is the make-or-break step. Safranin is the counterstain. Gram-positive cells keep the crystal violet and stay purple. Gram-negative cells lose it and take the counterstain, turning pink.

Then a specimen becomes an answer. Good results start with good collection. The right site, drawn before antibiotics, in the correct container, labeled accurately. A streak plate spreads cells apart so the last ones land far enough from each other to grow separate colonies, and one isolated colony gives a pure culture.

Sensitivity testing finds which drugs work. The Kirby-Bauer test measures the zone of inhibition around a drug disk. An MIC is the lowest concentration that stops visible growth. Either way the report comes back as S, I or R, meaning susceptible, intermediate or resistant. That report is what lets a team drop a broad drug for one targeted one.

The names, tests and numbers worth memorizing

The sequences, in order

Koch's postulates. The logical test that one microbe causes one disease.

1. The microbe is found in every case of the disease, and absent in healthy hosts.
2. It can be isolated from a sick host and grown in pure culture.
3. The cultured microbe causes the same disease in a healthy host.
4. The same microbe can be re-isolated from that newly diseased host.

The Gram stain, four reagents.

1. Crystal violet. Everything goes purple.
2. Gram's iodine. The mordant traps the dye in the wall.
3. Alcohol or acetone. The decolorizer. Gram-negative cells give the dye up here.
4. Safranin. The counterstain turns the colorless cells pink.

From specimen to answer.

1. Collect well. Right site, before antibiotics, correct container, accurate label.
2. Gram stain. Under an hour, and it guides the first drug.
3. Streak plate and colony. One isolated colony gives a pure culture in 18 to 48 hours.
4. Identify and test sensitivity. 48 to 72 hours, reported as S, I or R.
5. Narrow the drug. Drop the broad agent for one targeted one.

How to reason through the question types

The traps

Theme 2 · Chapters 3, 4 and 5How microbes are built, and how we classify them

What to know

The deepest split among cells is prokaryote against eukaryote. A prokaryote has no membrane-bound nucleus and no organelles, runs 0.2 to 2 µm, usually carries one circular chromosome, uses a 70S ribosome, and divides by binary fission. A eukaryote keeps its DNA in a nucleus, runs 10 to 100 µm, holds organelles, carries multiple linear chromosomes, uses an 80S ribosome, and divides by mitosis or meiosis.

Inside a bacterial cell, five parts matter. The plasma membrane is a phospholipid bilayer that controls transport and generates energy, and it is the polymyxin target. The cytoplasm is the water-based gel where metabolism happens. The 70S ribosomes build protein, and they are the target of many antibiotics. The nucleoid is the membrane-free region holding the coiled circular chromosome. And a plasmid is a small extra loop of DNA that carries resistance and toxin genes.

The cell wall is peptidoglycan, a mesh of cross-linked sugars and amino acids that no human cell shares. Beta-lactam drugs act there. Gram-positive cells have thick surface peptidoglycan woven with teichoic acids, no outer membrane, and they stain purple. Gram-negative cells have thin peptidoglycan sandwiched between two membranes, an outer membrane carrying LPS, and they stain pink. That outer membrane blocks many drugs, and its lipid A is the endotoxin that drives septic shock.

Four external structures carry virulence. The capsule is a sticky outer coat that resists phagocytosis, and it is a vaccine target. Flagella are long whips that rotate to swim, giving directed movement called chemotaxis. Fimbriae are many and short, and they handle attachment, which starts infection and builds biofilms. Pili, including the sex pilus, are few and long, and they transfer DNA by conjugation, which is how resistance genes spread.

An endospore is a dormant armored survival form, and it is not a method of reproduction. It is made mainly by Gram-positive Bacillus and Clostridium or Clostridioides. Sporulation packages DNA in protective layers under stress, and germination revives it when conditions improve. The growing form is the vegetative cell. Spores resist heat, drying and disinfectants, which is why C. diff needs soap and water and why instruments need autoclaving.

Bacteria are sorted first by shape and arrangement, and those clues are usually built into the genus name. The three basic shapes are coccus, a sphere, bacillus, a rod, and spirillum, a spiral. Vibrios and coccobacilli are in-between forms. Arrangement prefixes add a second layer, mostly for cocci. Diplo- for pairs, strepto- for chains, staphylo- for clusters.

Among the Gram-positive pathogens, three genera dominate. Staphylococcus is cocci in clusters, and S. aureus with its resistant form MRSA causes skin, wound and bloodstream infection. Streptococcus is cocci in chains, where group A brings throat infection, necrotizing fasciitis and rheumatic fever, group B brings newborn sepsis, and S. pneumoniae brings pneumonia and meningitis. Clostridium and Clostridioides are anaerobic spore-forming rods behind C. diff colitis, tetanus, botulism and gas gangrene.

Two bench tests separate the Gram-positive cocci. Catalase breaks down hydrogen peroxide, and staphylococci have it and bubble while streptococci do not. Coagulase clots plasma, and it separates S. aureus, which is coagulase-positive, from the other staphylococci. Hemolysis on blood agar groups the streptococci, where beta is a clear zone, alpha is a green zone and gamma is none.

Among the Gram-negative pathogens, three matter most. Escherichia coli is a facultative anaerobe from the colon, the top cause of UTIs and a common cause of Gram-negative sepsis, with the O157:H7 strain causing bloody diarrhea and hemolytic uremic syndrome. Salmonella is a facultative anaerobe from eggs, poultry and reptiles, causing gastroenteritis and typhoid fever. Pseudomonas aeruginosa is an obligate aerobe that loves water and moist equipment, and it is behind ventilator pneumonia, burn and wound infection, and cystic fibrosis lung disease.

Three special groups each break one rule, and each break changes the stain, the isolation or the drug. Mycobacteria have a waxy mycolic acid wall, so they are acid-fast and grow slowly, and M. tuberculosis needs airborne isolation. Spirochetes are thin coils that resist staining and culture, so Treponema pallidum for syphilis and Borrelia burgdorferi for Lyme are found by blood antibody tests. Mycoplasma has no cell wall at all, so penicillins fail against M. pneumoniae and a macrolide or tetracycline is used instead.

Oxygen sorts bacteria five ways. An obligate aerobe requires oxygen, as Pseudomonas and M. tuberculosis do. An obligate anaerobe is killed by it, as Clostridium and Bacteroides are. A facultative anaerobe uses oxygen if present and ferments if not, as E. coli and Staphylococcus do. A microaerophile needs low oxygen, as Campylobacter and Helicobacter pylori do. An aerotolerant anaerobe never uses oxygen but is not harmed by it, as Streptococcus pyogenes and some lactobacilli are.

A virus is acellular and an obligate intracellular parasite, so it cannot copy itself without a host cell. Every virus has a genome, DNA or RNA, single or double stranded, inside a protein capsid built of repeating capsomeres. RNA viruses change fast. Some viruses add a stolen lipid envelope carrying spike proteins, the keys they use to attach.

That envelope is a hand-hygiene decision. Enveloped viruses usually die to soap and alcohol, because the lipid coat dissolves. Hepatitis B is the notable exception, lasting seven days or more in dried blood, so a blood spill still needs bleach or a hospital disinfectant. Naked viruses such as norovirus, rotavirus, poliovirus and hepatitis A resist alcohol and need bleach plus scrubbing.

Viral replication runs five steps. Attachment is receptor-specific, and that is what decides which cells and which hosts a virus can infect. Then entry, biosynthesis, assembly and release. DNA viruses mostly copy in the nucleus. RNA viruses mostly copy in the cytoplasm with their own polymerase. Retroviruses use reverse transcriptase and integrase to join the host DNA, leaving a provirus. Naked viruses tend to exit by bursting the cell, and enveloped ones often exit by budding. Latency lets herpesviruses and HIV park a genome and reactivate later, and antivirals hit active copying, not a sleeping genome.

Fungi are eukaryotes. A yeast is a single cell that buds. A mold grows as threads called hyphae, and a tangled mass of them is a mycelium. A dimorphic fungus grows as a mold in the environment and switches to a yeast at body temperature. The fungal wall holds chitin and the membrane holds ergosterol, which is the target of most antifungal drugs. Because fungi resemble our own cells, antifungals have narrower selective toxicity and more side effects.

Protozoa are single-celled eukaryotes, and many switch between an active trophozoite and a tough cyst that carries the infection onward. Helminths are parasitic worms, found under the microscope by their eggs and larvae, and they cause slow long-running harm. An unexplained eosinophilia is a classic clue to a worm, above all one that invades tissue. Nematodes are the roundworms, including pinworm, Ascaris and hookworm. Platyhelminths are the flatworms, meaning the cestode tapeworms and the trematode flukes such as Schistosoma.

The names, tests and numbers worth memorizing

The sequences, in order

Viral replication, five steps, with the drug that blocks each.

1. Attachment. A viral protein binds a specific host receptor. Blocked by attachment blockers such as maraviroc in HIV.
2. Entry. The virus or its genome crosses into the cell. Blocked by fusion inhibitors such as enfuvirtide.
3. Biosynthesis. Host machinery mass-produces viral genome and proteins. Blocked by most antivirals, including acyclovir and the HIV reverse-transcriptase and integrase inhibitors.
4. Assembly. New parts snap together into complete particles. Blocked by protease inhibitors, the HIV drugs ending in -navir.
5. Release. New particles bud off or burst the cell. Blocked by neuraminidase inhibitors such as oseltamivir for flu.

The endospore cycle.

1. Vegetative cell. The active growing form, the one drugs and disinfectants kill.
2. Sporulation. Stress triggers packaging of DNA in protective layers.
3. Dormant endospore. Resists heat, drying and disinfectants. Not reproduction.
4. Germination. Better conditions revive it into a vegetative cell again.

How to reason through the question types

The traps

Theme 3 · Chapters 6 and 7How microbes grow, and how they change

What to know

Microbes need macronutrients. Those are carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur. They also need micronutrients, which are trace metals. Some also need ready-made growth factors, which are finished vitamins or amino acids they cannot build for themselves.

Two questions sort every microbe. Where does its carbon come from, and where does its energy come from? An autotroph builds from carbon dioxide and a heterotroph takes in organic compounds. A phototroph uses light and a chemotroph uses chemicals. Cross the two and you get four types, but only one matters here. Every human pathogen is a chemoheterotroph. A fastidious organism has fussy needs and grows only on enriched media.

Oxygen yields the most energy, but it also makes toxic reactive oxygen species. Surviving them takes two enzymes, catalase and superoxide dismutase. That is exactly why the oxygen classes exist. Anaerobic infections sit in tissue with very little oxygen. Deep wounds, abscesses and dead tissue are the usual sites. Their samples must be protected from air on the way to the lab.

Every microbe has cardinal temperatures, meaning a minimum, an optimum and a maximum. Psychrophiles prefer about 0 to 15°C. Psychrotrophs prefer about 4 to 25°C, which is the refrigerator, and Listeria is the one to remember there. Mesophiles prefer about 20 to 40°C, and nearly all human pathogens are mesophiles tuned to roughly 37°C. Thermophiles prefer about 50 to 60°C and hyperthermophiles about 80°C and above.

Most pathogens are neutrophiles, growing best near pH 6.5 to 7.5. Stomach acid is therefore a defense, and H. pylori is the organism that beats it. Salt and sugar preserve food by pulling water out of microbes through osmosis. A halophile needs high salt, while an osmotolerant organism such as S. aureus simply puts up with it. The practical line is that chilling something is not the same as sterilizing it, because Listeria grows in the fridge.

Bacteria multiply by binary fission, one cell into two. The generation time, also called doubling time, is how long that takes. Doubling makes growth exponential. A few cells become millions within hours. The arithmetic is N = N₀ × 2ⁿ, where n is the number of generations.

A closed culture runs four phases in a fixed order. Lag, where cells adapt and barely divide, which explains the delay before symptoms or before a culture turns positive. Log, also called exponential, where cells double fast and are at their most active. Stationary, where growth equals death as nutrients run out. Slow-growing cells tolerate drugs better here, and toxins or spores may form. Death, or decline, where cells die faster than they divide.

One consequence runs straight into practice. Antibiotics work best on log-phase cells, the ones actively dividing. So cultures are drawn before antibiotics start.

Agar, a jelly from seaweed, sets a medium solid, and microbes cannot digest it. Media come in five kinds. General-purpose grows a wide variety. Enriched adds nutrients such as blood or serum for fastidious organisms, as blood agar and chocolate agar do. Selective holds unwanted microbes back so the target grows, as MacConkey does for Gram-negatives and MSA for staph. Differential makes organisms look visibly different, as blood agar does by hemolysis and MacConkey by lactose. Transport keeps a specimen alive on the way to the lab.

A colony is the visible clone of one original cell, and one isolated colony gives a pure culture. Counts are reported as colony-forming units, or CFU.

Now to change. DNA stores instructions as base pairs, A with T and G with C. A gene codes for one product, and the whole set is the genome. The central dogma runs DNA to mRNA to protein, through replication, transcription and translation. Each of those three steps is an antibiotic target. Fluoroquinolones block DNA gyrase. Rifampin blocks RNA polymerase. Aminoglycosides, tetracyclines and macrolides block the ribosome.

A mutation is any change in the DNA sequence, and most arise as rare replication errors. A point mutation swaps one base, and it comes in three flavors. Silent, where the codon still means the same amino acid, so nothing changes. Missense, where one amino acid changes, which may alter a drug target. Nonsense, where the codon becomes a stop, cutting the protein short. A frameshift inserts or deletes a base, which shifts the reading frame and usually wrecks the protein. Mutagens such as chemicals, UV light and X-rays raise the mutation rate.

Chance mutation is the raw material of resistance. It is also why TB is treated with several drugs at once. One mutation is unlikely to defeat all of them.

Vertical transfer is ordinary parent-to-daughter inheritance. Horizontal gene transfer, or HGT, moves genes sideways between separate cells. It even crosses species. That is far faster than mutation alone. There are three routes. Transformation is a cell taking up free DNA released by a dead microbe, and the state that allows it is competence. Transduction is a bacteriophage carrying bacterial DNA to a new cell. Conjugation is direct cell-to-cell transfer through a sex pilus. It usually moves a plasmid. It is the biggest driver of multidrug-resistance spread.

A plasmid is a small circular loop of DNA separate from the chromosome. The chromosome is large and essential and carries core metabolism and structure. A plasmid is small and optional and carries resistance, toxins and special nutrient genes. An R plasmid carries antibiotic-resistance genes, often against several drugs at once, which is multidrug resistance. R plasmids frequently carry the conjugation machinery too, so they copy themselves into neighboring cells. Transposons are jumping genes that move between locations. Integrons capture resistance cassettes and line them up. Together they build the multidrug package.

One idea underlies all of it. Selective pressure means antibiotics do not create resistance. They kill the susceptible cells and let the already-resistant few survive and multiply until they take over.

Resistance then spreads mainly by contact. Several things widen it. Overprescribing, incomplete courses, broad-spectrum overuse, farm use and travel. The levers that slow it are hand hygiene, contact precautions, stewardship and teaching.

The names, tests and numbers worth memorizing

The sequences, in order

The central dogma.

1. Replication. DNA is copied before division, semiconservatively, so each new helix keeps one old strand.
2. Transcription. RNA polymerase copies a gene into mRNA.
3. Translation. The ribosome builds the protein, one codon at a time.

The growth curve.

1. Lag. Adapting, barely dividing.
2. Log. Doubling fast. The drug window.
3. Stationary. Growth equals death. Spores and toxins may appear.
4. Death. Dying faster than dividing.

How resistance takes over a population.

1. A rare mutation, or a gene arriving by horizontal transfer, makes one cell resistant.
2. A drug is given. It kills the susceptible cells.
3. Selective pressure. The resistant few now have the space and the food to themselves.
4. They multiply until they are the population.
5. Contact spread carries them to the next person, on hands, equipment and surfaces.

How to reason through the question types

The traps

Theme 4 · Chapters 8 and 9How we kill microbes, and how we treat infection

What to know

Microbial control is a ladder, and the words are not interchangeable. Sterilization destroys or removes all microbial life, endospores included, and it is used on instruments, IV fluids and implants. Disinfection destroys most pathogens on an inanimate surface and does not reliably kill endospores. Antisepsis reduces microbes on living tissue. Degerming removes microbes mechanically, as a pre-injection swab does. Sanitization lowers counts to a level judged safe for public health, as on dishes and food surfaces.

Two suffixes separate what an agent does. -cidal kills. -static only halts multiplying, so it leans on host defenses to finish. That distinction returns with the drugs.

Among physical methods, moist heat beats dry heat, and ordinary boiling does not sterilize, because endospores survive it. The autoclave holds 121°C at about 15 psi for roughly 15 minutes. It works with pressurized saturated steam. A Geobacillus spore biological indicator proves the cycle worked. Dry heat and flame sterilize too, but they need longer or hotter.

Ionizing radiation breaks DNA and forms free radicals, and it sterilizes heat-sensitive disposables, sutures and some foods. UV light is nonionizing. It makes thymine dimers that block replication. But it does not penetrate, so it only disinfects surfaces and air. Filtration physically strains microbes out, with a 0.2 µm membrane for heat-labile fluids and a HEPA filter for air.

Chemical agents mostly denature proteins or disrupt membranes. The same molecule can be a disinfectant on surfaces and an antiseptic on skin. Alcohols at 60 to 90 percent are the workhorse, and 70 percent alcohol out-kills 100 percent, because alcohol needs water to work. Chlorhexidine disrupts membranes and persists on skin, which is why it is used for surgical scrub and line-site prep. Iodophors such as povidone-iodine prep skin and injection sites. Chlorine, meaning bleach, is a strong oxidizer that kills spores on surfaces. Hydrogen peroxide oxidizes and kills spores at high concentration. Quats are detergent-like and used for routine cleaning. Glutaraldehyde and ethylene oxide alkylate proteins and DNA, and with long contact they sterilize heat-sensitive equipment. Ortho-phthalaldehyde, or OPA, is a high-level disinfectant for endoscopes and a poor sporicide, so it does not sterilize.

Use-dilution matters, and more is not always better. The Spaulding classification sorts items as critical, semicritical or noncritical. It matches the level of killing to how an item is used.

Microbes die logarithmically, a constant fraction per unit time, so true zero is never guaranteed. Sterility is therefore a probability. The sterility assurance level is set at 10⁻⁶. That is one chance in a million of a survivor. The D-value, or decimal reduction time, is the time needed to kill 90 percent. That is one log. It sets how long a process must run.

A kill speeds up with more time, more heat and higher concentration. It slows down with a big microbial load, resistant organisms, biofilm, and above all organic matter. Blood and pus both shield microbes and inactivate the agent, which is why you always clean before you disinfect.

Resistance to killing ranks in a fixed order. Prions and endospores are the toughest. Then mycobacteria, with their waxy walls. Then non-enveloped viruses. Then fungi. Then vegetative bacteria and enveloped viruses at the easiest end.

In practice, control splits two ways. Medical asepsis, or clean technique, reduces and contains microbes. It works through hand hygiene, gloves, gowns and cleaning. It is used with every person. Surgical asepsis, or sterile technique, aims to eliminate all microbes, and it is used whenever a natural barrier is breached. A sterile field is contaminated by anything nonsterile. Its 1-inch border counts. So does anything below waist level or out of sight. So does moisture strike-through. The governing rule is blunt. When in doubt, it is contaminated, so discard and restart.

Now the drugs. Selective toxicity is the whole foundation, and it means hitting a target the microbe has and the host lacks. The beta-lactams, meaning penicillins and cephalosporins, are the safest, because human cells have no wall to injure. But vancomycin also aims at the wall, and it is still hard on the kidney. So the target alone does not promise safety.

The therapeutic index is the gap between the helpful dose and the harmful one. Penicillins and cephalosporins have a wide index. Routine levels are not needed, and the concern is allergy rather than toxicity. Vancomycin and the aminoglycosides have a narrow index. So blood levels are monitored, and the timing of the draw is everything. A trough level is drawn just before the next dose.

Antibacterials hit five targets. The cell wall, with penicillins, cephalosporins and vancomycin, and this is the most selective because human cells have no wall. The ribosome, with aminoglycosides, tetracyclines and macrolides, which works because the bacterial 70S differs from the human 80S. Nucleic acid synthesis, with the fluoroquinolones. Folate metabolism, with sulfonamides and trimethoprim, which works because humans get folate from the diet while bacteria make it. And the cell membrane, with polymyxins and daptomycin, which is the least selective and is held in reserve.

Bactericidal drugs kill. Bacteriostatic drugs stall growth and lean on the immune system to finish. So someone with weak defenses usually needs a bactericidal drug.

Spectrum is the range of bacteria a drug covers. A narrow-spectrum drug hits few organisms. It spares most of the flora. It carries a lower superinfection risk and less resistance pressure. So it is preferred once the pathogen is known. A broad-spectrum drug hits many, wipes out much of the flora, invites superinfection with C. diff or yeast, and raises resistance pressure, so it belongs to the empiric phase.

Empiric therapy is the first best guess, started before culture results are back. Definitive therapy follows the culture and de-escalates to one targeted drug. Susceptibility testing finds the MIC. That is the lowest concentration that stops visible growth. Kirby-Bauer disk diffusion, the Etest and broth microdilution all measure it. The report comes back as S, I or R.

Bacteria fight back four ways. Drug inactivation, where an enzyme destroys the drug, as a beta-lactamase does to penicillins. Target modification, where the binding site changes, as in MRSA. An efflux pump, which pushes the drug back out, as in tetracycline resistance. And reduced uptake, which keeps the drug from entering, as altered porins do in Gram-negatives.

Those genes then spread fast by horizontal gene transfer on plasmids, driven by selective pressure. MRSA is the headline example. It resists all beta-lactams through an altered binding protein. That forces a switch to vancomycin or another non-beta-lactam.

Stewardship is the shared effort to use these drugs only when needed and to use them well. The right diagnosis, which means cultures before the first dose. The right timing, so levels stay effective. The right duration, with review and de-escalation. The right route, switching IV to oral when someone is stable and eating. The right person, with the allergy history verified. And prevention, through hand hygiene, timely device removal and teaching. Adherence matters too. Take as prescribed, never share or save antibiotics, and expect nothing from them for a viral illness.

The names, tests and numbers worth memorizing

The sequences, in order

The control ladder, strongest first.

1. Sterilization. All life, spores included.
2. Disinfection. Most pathogens on an object. Not reliable against spores.
3. Antisepsis. Fewer microbes on living tissue.
4. Sanitization. Counts down to a level judged safe.
5. Degerming. Mechanical removal only.

Resistance to killing, toughest first.

1. Prions.
2. Endospores.
3. Mycobacteria.
4. Non-enveloped viruses.
5. Fungi.
6. Vegetative bacteria and enveloped viruses.

From empiric to definitive therapy.

1. Draw cultures before the first dose.
2. Start empiric therapy, guided by the Gram stain and the likely organisms.
3. Read the S, I or R report at 48 to 72 hours.
4. De-escalate to one narrow targeted drug.
5. Switch IV to oral when the person is stable and eating, and set the duration.

How to reason through the question types

The traps

Theme 5 · Chapters 10, 11 and 15How microbes cause disease, and how they spread

What to know

A pathogen follows a script. Get in. Hold on. Multiply. Do damage. Then dodge the immune system long enough to reach the next host. Every step runs on a specific molecule, and every one of those is a drug or vaccine target.

Pathogenicity is whether a microbe can cause disease. Virulence is how much harm it does. A primary pathogen sickens a healthy host, as influenza, Salmonella and M. tuberculosis do. An opportunistic pathogen needs an opening, meaning a broken barrier, flora wiped out by a drug, or a weakened host.

Virulence factors sort into four jobs. Attaching, with adhesins. Spreading, with invasins and tissue-cutting enzymes. Damaging, with toxins. Evading, with capsules and antigenic variation. The numbers are the ID₅₀, the dose that infects half an exposed group, and the LD₅₀, the dose that kills half. Lower means more dangerous. Shigella needs only 10 to 100 cells. Vibrio cholerae needs roughly a hundred million. Botulinum toxin kills at about a nanogram per kilogram.

A microbe enters through a portal of entry. The respiratory tract is the most common, then the GI tract, then the genitourinary tract, then the conjunctiva, then skin breaks, then the parenteral route straight into tissue or blood. The same organism can be harmless at one portal and deadly at another, and E. coli in the colon, the bladder and the blood is the clearest case. Every catheter, line and tube is a portal nature never built.

Attachment uses adhesins binding host receptors, which explains tropism. Clumped slime-wrapped communities are biofilms, and they resist drugs and immune cells, which is why device infections are so stubborn.

Damage comes from two toxin families. Exotoxins are secreted proteins from both Gram groups. They are strong and specific, usually heat-labile, and they can be made into protective toxoids. The three styles are A-B toxins, where B binds and A acts, membrane-disrupting hemolysins and leukocidins, and superantigens that trigger a cytokine flood and shock. Endotoxin is the lipid A of LPS from Gram-negative cells only. It is released on lysis, it is heat-stable, it has no toxoid and no vaccine, and at flood level it drives fever, low blood pressure, septic shock and DIC.

Evasion tools are worth naming one by one. A capsule blocks phagocytosis and hides antigens, as in S. pneumoniae, N. meningitidis, H. influenzae type b and K. pneumoniae, and the first three have licensed capsular vaccines. Antigenic variation changes surface molecules, by small drift or whole-segment shift in influenza, and by pilus reshuffling in N. gonorrhoeae. Intracellular hiding keeps M. tuberculosis, Listeria and Salmonella out of antibody reach. IgA proteases chop mucosal antibodies. Coagulase walls S. aureus in fibrin. Antigenic masking coats the microbe in host protein, while molecular mimicry turns the host's antibodies against the host, as streptococcal M protein does in rheumatic fever.

Then infection runs five stages. Incubation, prodromal, illness, decline, convalescence. Symptoms peak during illness, but shedding usually starts in the prodrome, so people pass infection on before they look sick. Measles is most contagious through its three to four day prodrome. A few people become long-term carriers.

Zoom out and every transmission event needs six links. The chain of infection runs agent, reservoir, portal of exit, mode of transmission, portal of entry, susceptible host. Break any one and the chain fails.

Reservoirs are human, including symptom-free carriers, animal, which gives zoonoses such as rabies, Lyme and salmonellosis, or environmental, such as soil holding Clostridium tetani and water holding Legionella.

There are five modes of transmission. Contact, direct skin to skin or indirect through a fomite. Droplet, with large droplets falling within about 1 to 2 meters. Airborne, with tiny nuclei that drift. Vehicle, through one shared food, water or fluid. Vector, through a living carrier, mechanically as a fly does or biologically as a mosquito does.

Epidemiology counts disease. Incidence is new cases over a period. Prevalence is all current cases at one moment, and it runs close to incidence times duration. Morbidity is illness and mortality is death. Patterns run sporadic, endemic, epidemic or outbreak, and pandemic.

R₀ is the average new cases one case causes with no immunity around. Above 1 and cases grow. Measles sits near 12 to 18 and seasonal flu near 1.3. The herd immunity threshold is 1 minus 1 divided by R₀, so measles needs about 93 percent and an R₀ of 2 needs 50 percent.

A healthcare-associated infection is one picked up during care, and about 1 in 31 inpatients has one on any given day. The big four are CAUTI, CLABSI, SSI and VAP, three of which ride on a device. Each is prevented by a bundle, with every step done every time, and rates are counted per 1,000 device-days.

Infection control has two tiers. Standard precautions treat every person's blood and body fluids as infectious, and they apply to everyone all the time. Transmission-based precautions add contact, meaning gown and gloves, droplet, meaning a surgical mask within about 2 meters, or airborne, meaning an N95 and a negative-pressure room. Varicella and disseminated zoster need airborne plus contact. C. difficile needs soap and water plus bleach, because alcohol does not kill spores.

Chapter 15 puts all of this on a real body. In skin, depth names the diagnosis. Impetigo in the epidermis with a honey crust. Erysipelas raised and sharply bordered in the upper dermis. Cellulitis with fuzzy edges through dermis and fat. An abscess as a walled pocket. Necrotizing fasciitis along the fascia, with pain far worse than the skin looks, needing surgery. S. aureus and group A strep cause most of them. MRSA carries mecA and PBP2a, which defeats every beta-lactam, so vancomycin, linezolid or daptomycin is used, and it travels by contact.

In the airway, upper-tract infections are mostly viral, with strep throat the bacterial exception worth treating because of rheumatic fever. Pneumonia is grouped by where it was caught, since that predicts the organism, and community pneumonia is usually Streptococcus pneumoniae. TB is airborne and needs an N95 and negative pressure, with months of several drugs. Influenza is droplet-spread and viral, so vaccination beats antibiotics entirely.

In the gut, everything travels the fecal-oral route, and illness comes either from a multiplying organism, taking a day or more, or from a ready-made toxin, taking hours. Fluids are the mainstay. Suspected Shiga-toxin E. coli gets no antibiotics and no antimotility drugs, because both raise the risk of hemolytic uremic syndrome. C. difficile and norovirus both resist alcohol gel.

In the urinary and sexual tract, most UTIs come from a person's own E. coli climbing the urethra. Cystitis burns, and pyelonephritis adds fever and flank pain. CAUTI risk climbs with catheter days, and a positive culture with no symptoms is usually left alone. Among STIs, chlamydia, gonorrhea and syphilis are bacterial and curable, herpes is lifelong, and HPV usually clears within about two years, with lasting high-risk types 16 and 18 driving cancer risk.

In blood and brain, bacteremia is bacteria in the blood, sepsis is the body's own answer running wild, and septic shock is pressure that fluids will not fix. New confusion is often the first and most telling sign, and the bundle is cultures, antibiotics and fluids. Bacterial meningitis brings fever, severe headache and a stiff neck, antibiotics do not wait for the lumbar puncture, and N. meningitidis needs droplet precautions.

The names, tests and numbers worth memorizing

The sequences, in order

The disease process. Enter, attach, multiply, damage, evade.

The five stages.

1. Incubation. No symptoms. Hours for staph food poisoning, years for HIV and TB.
2. Prodromal. Vague and mild. Shedding usually starts here.
3. Illness. Microbe and symptoms both peak.
4. Decline. Symptoms fade; the host stays worn down.
5. Convalescence. Repair. A few become carriers.

The chain of infection. Agent, reservoir, portal of exit, mode of transmission, portal of entry, susceptible host.

Skin infections by depth. Impetigo, erysipelas, cellulitis, abscess, necrotizing fasciitis.

Blood infection, escalating. Bacteremia, sepsis, septic shock, multiple organ failure.

How to reason through the question types

The traps

Theme 6 · Chapters 12 and 13How the body fights back

What to know

The immune system is taught as three lines of defense. Innate immunity supplies the first two and is there from birth, answering in seconds to minutes, the same broad way every time, with no memory. Adaptive immunity is the third line. It takes days on a first exposure, it is tuned to one antigen, and it remembers. Innate buys the days adaptive needs.

The first line keeps microbes out, with three kinds of barrier. Physical: the keratinized shedding epidermis, and mucous membranes whose mucus traps microbes while cilia sweep them out on the mucociliary escalator. Chemical: sebum and sweat holding a low pH, lysozyme in tears, saliva and mucus digesting peptidoglycan, stomach acid, and vaginal acidity from lactobacilli. Biological: the normal flora, protecting by competitive exclusion, which is why wiping them out invites Candida and C. difficile.

The second line acts inside. Neutrophils are the most abundant white cell and the first to arrive, fast and short-lived. Macrophages grow from monocytes and are the long-lived cleanup crew. Dendritic cells alert adaptive immunity. NK cells kill virus-infected and tumor cells without classic phagocytosis. Eosinophils attack parasites and have a role in allergy.

Phagocytes reach trouble by chemotaxis, leave the blood by margination and diapedesis, and recognize invaders when PRRs bind PAMPs, the classic one being LPS. Opsonization with antibody or C3b speeds engulfment enormously. The killing sequence runs chemotaxis, adherence, ingestion into a phagosome, fusion into a phagolysosome, digestion, and exocytosis, and the leftovers are pus.

Inflammation gives four cardinal signs, redness, heat, swelling and pain, plus loss of function. Mast cells and injured tissue release histamine and other mediators that cause vasodilation, giving redness and heat, and raise vascular permeability, giving the edema you see as swelling. Pressure on sensitized nerves gives pain. Inflammation in one spot heals. Body-wide, it is sepsis. A threat that cannot be cleared turns it chronic, with a granuloma walling it off, as in tuberculosis.

Fever is a raised hypothalamic set-point, not lost control. Exogenous pyrogens such as LPS and endogenous pyrogens such as IL-1, IL-6 and TNF both act through prostaglandin E₂. The phases run onset with chills, plateau with warm dry skin, and defervescence with sweating. Cooling during the chills fights the set-point. A moderate fever helps, and above roughly 40 to 41°C it begins to denature the body's own proteins.

Complement is about 30 blood proteins in a cascade. Three pathways, classical from bound antibody, alternative from microbial surfaces and lectin from microbial carbohydrates, all converge on C3. Three outcomes follow. C3b opsonizes. C3a and C5a are anaphylatoxins that inflame and recruit. C5b to C9 build the membrane attack complex and lyse the microbe. Tag, recruit, destroy.

Interferons handle the problem complement cannot reach. A virus-infected cell releases type I interferon, IFN-α and IFN-β, which does not save that cell but puts neighbors into an antiviral state. IFN-γ mainly activates macrophages. Much of the aching and tiredness of a viral illness is your own interferon at work.

Then adaptive immunity, with two branches. Humoral, run by B cells and antibodies against threats outside cells. Cell-mediated, run by T cells against threats inside cells. An antigen is read at a small patch called an epitope, and clonal selection picks the one matching lymphocyte out of millions built in advance. The three hallmarks are specificity, memory and self-tolerance.

T cells mature in the thymus and see antigen only on MHC. MHC class I sits on almost every nucleated cell. MHC class II sits only on antigen-presenting cells, which are dendritic cells, macrophages and B cells. CD4 helper T cells read MHC II and conduct with cytokines. CD8 cytotoxic T cells read MHC I and kill with perforin and granzymes, so the target dies by apoptosis. The rule of eight keeps the pairings straight.

B cells mature in bone marrow. An activated B cell gives antibody-pumping plasma cells and long-lived memory B cells. An antibody is a Y, with variable tips that recognize and a constant stem that recruits. Antibodies work by neutralization, opsonization, agglutination and complement activation. The five classes are IgG, most abundant and the only one crossing the placenta, IgM, first and a pentamer, IgA, in secretions and breast milk, IgE, on mast cells, and IgD, on naive B cell surfaces.

The primary response lags one to two weeks, is small, and leads with IgM. The secondary response starts in hours to days, runs ten to a hundred times larger, and is mostly high-affinity IgG. Memory cells are the reason, and boosters and titers both run on them.

Immunity is active or passive and natural or artificial, giving four boxes. Active means the body made it, so memory forms and it lasts. Passive means borrowed antibody, so protection is immediate and temporary with no memory. Vaccines come as live attenuated, inactivated, subunit, conjugate, toxoid, and mRNA or viral vector. Only the live types can grow in a host, so only those are held back in pregnancy and serious immune suppression.

The names, tests and numbers worth memorizing

The sequences, in order

Phagocytosis.

1. Chemotaxis toward the signal.
2. Adherence, helped by opsonins.
3. Ingestion into a phagosome.
4. Fusion with a lysosome, making a phagolysosome.
5. Killing and digestion by enzymes, reactive oxygen and low pH.
6. Exocytosis of the leftovers. What stays is pus.

A fever. Onset with chills, plateau with warm dry skin, defervescence with sweating.

Complement. Three pathways, converge on C3, then tag, recruit and destroy.

B cell to antibody. Antigen binds, helper T push, clonal selection, plasma cells, memory B cells.

Primary to secondary. One to two week lag with IgM, memory cells left behind, then hours to days with ten to a hundred times more high-affinity IgG.

How to reason through the question types

The traps

Theme 7 · Chapter 14What goes wrong with that defense

What to know

Theme 6 showed the defense working. Theme 7 shows it misfiring in four ways. It overreacts. It turns on the body. It gives out. Or it attacks help given on purpose.

A hypersensitivity reaction is an immune response that harms the host. It runs too strong, aims at the wrong thing, or is not needed at all. The damage comes from the immune system's own work. It does not come straight from the trigger.

Almost all of them need a first quiet exposure. That step is sensitization. It causes no symptoms. It just builds a stock of antibodies or primed T cells. So "no reaction last time" never means a drug is safe.

Gell and Coombs sorted them into four types. The memory aid is ACID. Type I is Anaphylactic. It uses IgE on mast cells, and it fires in seconds to minutes. Type II is Cytotoxic. It uses IgG or IgM against a cell-surface antigen, in minutes to hours. Type III is Immune-complex. It uses IgG in soluble complexes, in hours. Type IV is Delayed. It uses T cells and no antibody at all, and it takes one to three days.

The first three are fast for one reason. The antibody is already in place. Type IV has to call T cells to the site. That is why a tuberculin skin test is read at 48 to 72 hours.

A type I reaction runs in two acts. In sensitization, a harmless allergen prompts IgE. The allergen might be pollen, peanut, penicillin or bee venom. That IgE then coats mast cells in tissue and basophils in blood.

On the next exposure the allergen bridges two neighboring IgE molecules. That bridging is cross-linking, and it is the trigger. Within seconds the mast cell goes through degranulation. It dumps stored histamine and starts to build leukotrienes and prostaglandins.

Those mediators widen vessels, giving redness, warmth and falling blood pressure. They make vessels leak, giving swelling and hives. They squeeze smooth muscle, giving bronchospasm and cramping. And they drive glands, giving a runny nose and watery eyes.

A localized reaction stays near the contact site. That gives hay fever, a patch of hives, or asthma. A systemic reaction is anaphylaxis. It happens when the allergen reaches the bloodstream. Airway swelling and distributive shock can kill within minutes.

Epinephrine reverses it. It goes into the muscle of the outer thigh, at the first sign. Not after antihistamines, and not after a wait-and-see. It squeezes vessels to raise blood pressure. It relaxes airway muscle. And it calms mast cells. Antihistamines and steroids help, but they are too slow and too weak alone.

Then protect the airway and give oxygen. Lay the person flat with the legs raised, unless breathing is easier sitting up. Run IV fluids. And keep watching, because a biphasic reaction can return hours later.

Autoimmunity is lost self-tolerance. Self-reactive T cells, or antibodies called autoantibodies, slip past the early screening. They then attack the body's own tissue. The attack uses the same weapons as any hypersensitivity. Often type II, sometimes type III or IV.

Why tolerance fails is usually a mix. A genetic risk sets the stage, and it often links to certain HLA or MHC types. Then something in the world pulls the trigger, and that something is often an infection. Molecular mimicry is one route. Rheumatic fever is the classic case, where antibodies against Streptococcus pyogenes cross-react with heart tissue.

Autoimmune diseases are organ-specific or systemic. An organ-specific one aims at a single tissue. A systemic one aims at something found everywhere, such as the cell nucleus. Care rests on immunosuppression, which trades the attack for infection risk. Or it simply replaces what was lost, as insulin does in type 1 diabetes and thyroid hormone in Hashimoto disease.

Immunodeficiency is too little immune function. It opens the door to opportunistic infection. Primary immunodeficiency is present at birth and gene-based. It runs from selective IgA deficiency, which is often silent, up to SCID. In SCID both B cells and T cells are missing or do not work, so an infant has almost no defense.

Secondary immunodeficiency is picked up later, and it is far more common. Malnutrition leads worldwide. Leukemias and lymphomas do it too. So do chemotherapy, radiation, aging, steroids and viral infection. Much of it is created by treatment.

HIV is a retrovirus. It destroys the CD4 helper T cell, the conductor of the whole response. It spreads through blood and sexual contact. It also passes from mother to child in pregnancy, at birth or through breastfeeding. It does not spread through casual contact.

AIDS is defined two ways. Either the CD4 count drops below 200 cells/µL, where normal is roughly 500 to 1,500. Or an AIDS-defining illness appears. That list takes in Pneumocystis jirovecii pneumonia, Candida of the esophagus, widespread TB, cytomegalovirus and Kaposi sarcoma.

Antiretroviral therapy blocks several steps of the viral life cycle. It can push the virus down to undetectable levels. It protects the CD4 count. And it makes the virus untransmittable through sex.

Red cells carry ABO antigens, and one rule covers them. Each person makes antibodies against the antigen they lack. A type A person has anti-B. A type O person has both. The Rh system adds positive or negative by the D antigen. Anti-Rh antibodies are learned, not present from birth. O-negative is the universal red-cell donor, and AB-positive the universal recipient.

An acute hemolytic transfusion reaction is a type II reaction from an ABO mismatch. It nearly always starts with an identification error. Fever, chills, flank or back pain, dark urine and low blood pressure follow, and it can reach kidney failure and death. Stop the transfusion. Keep the line open with saline. Notify the provider and the blood bank. Hemolytic disease of the newborn is the placental version, and Rh immune globulin prevents it.

Grafts are read as foreign by their MHC or HLA molecules. An autograft and an isograft are not rejected. An allograft is, unless the immune response is held down for life. A xenograft faces the strongest rejection of all.

Rejection comes in three tempos. Hyperacute hits in minutes, from antibody that was already there. Acute takes days to weeks, and T cells run it. Chronic takes months to years. Graft-versus-host disease runs the other way, with the graft's own immune cells attacking the recipient.

The names, tests and numbers worth memorizing

The sequences, in order

A type I reaction.

1. Sensitization. First exposure, no symptoms.
2. IgE made against that one allergen.
3. Mast cells armed in tissue, basophils in blood.
4. Re-exposure cross-links two neighboring IgE molecules.
5. Degranulation. Histamine out within seconds.
6. Local or systemic. Hives and wheeze, or anaphylaxis.

Anaphylaxis. IM epinephrine, airway and oxygen, position, fluids, then watch for a biphasic return.

A hemolytic transfusion reaction. Stop the transfusion, saline to keep the line open, notify the provider and blood bank, trace the identity error.

Rejection tempos. Hyperacute in minutes, acute in days to weeks, chronic in months to years.

How to reason through the question types

The traps

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