Microbiology curriculum

Bacteria are one-celled organisms with no nucleus; archaea also lack one but form a separate domain of life. Fungi are eukaryotes that make no chlorophyll, algae are plant-like water dwellers, protozoa are microscopic single cells, and helminths are many-celled worms usually visible as adults. Viruses are nucleic acid in a protein coat, not cells. One discriminator: protozoa can multiply inside a human, but adult helminths cannot.

A virus packs its genes in a protein coat but cannot copy itself; it must infect a cell and use the host's machinery. A viroid is smaller still, a circular single strand of RNA that codes for no protein. A prion replicates without DNA or RNA intermediates: it is one of the body's own proteins, misfolded into a form that causes illness.

Hooke's Micrographia gave biology the word cell, for the boxy spaces in cork: plant structure, not microbes. Leeuwenhoek, probably spurred by that book, used single-lens microscopes to watch swimming “animalcules” in water. Hooke found such lenses hard on his eyes, yet admitted a single lens could show more than his two-lens instruments.

Redi covered meat with gauze; flies laid eggs on the gauze and the worms hatched there, not in the flesh. Needham's warmed, cork-stoppered infusions swarmed with life, but Spallanzani boiled hermetically sealed vessels for an hour and found none. Needham replied that heat had weakened a vital force. Pasteur's curved-neck flasks left boiled broth open to the air while germs settled in the bend; it changed only when tipped into that dust.

Miasma theory blamed disease on bad air. Semmelweis showed that childbed fever was contagious and pressed for hand hygiene, Snow traced a cholera outbreak to one water pump, and Lister, reading Pasteur, sprayed wounds with phenic acid to destroy microbes. Koch then tied one specific microbe, the anthrax bacillus, to one disease, and later identified the bacteria behind tuberculosis and cholera.

A species name is a two-part combination: a capitalized genus noun followed by a lowercase species epithet, and only the pair names a species. The genus can be shortened to its initial, as in C. difficile for Clostridioides difficile. Names are expressed in Latin and typically built from Latin and Ancient Greek roots.

Woese used 16S ribosomal RNA as a molecular clock and found the archaea, a third domain of life hidden among cells long lumped with bacteria because neither has a nucleus. So having no nucleus does not mark a single lineage. Mitochondria, which keep their own small genomes, appear to descend from free-living bacteria.

A nanometer is one billionth of a meter, the scale of light's wavelengths and of many virus particles, while bacteria are measured in micrometers. Viruses have long been screened as particles that pass “sterilizing” filters with pores under 0.3 micrometers, yet the giant mimivirus, 0.75 micrometers across, is easy to see in a light microscope, so size alone is a weak way to sort a microbe.

Light from the source passes an adjustable field diaphragm, which cuts stray light, and a condenser lens then focuses it onto the sample so the whole field is evenly lit. The objective lens gathers the light coming from the specimen and focuses it, and the eyepiece, or ocular, adds further magnification.

Total magnification is the objective's power times the ocular's, so a 40X objective under a 10X eyepiece gives 400X. Magnification is not resolution: resolution is the smallest distance at which two objects still look separate, set by the light's wavelength and the objective's numerical aperture. Immersion oil raises that aperture, since the aperture includes the refractive index of the medium.

Phase-contrast microscopy is valued for watching the shape and motion of live syphilis spirochetes, and darkfield is reported to be more sensitive for detecting them. A fluorescence microscope excites a dye that then emits light of a longer wavelength, and a confocal microscope uses a pinhole to throw away light from planes outside the focus.

Conventional scanning electron microscopy works in a vacuum, so samples must be dehydrated; wet ones would boil, and nothing alive survives that. Scanning instruments image whole bulk samples, while transmission work looks through ultrathin sections, commonly stained with uranium and lead compounds, to show internal structure. Drying and other preparation can strip loosely attached features and alter delicate structure.

A wet mount puts a drop of sample and saline on a slide under a coverslip so fresh material can be read directly, which is how Trichomonas vaginalis can be spotted by its motility. A smear for Gram staining is spread thin on a clean slide, air dried and heat fixed before the stain goes on.

The Gram stain is a differential stain: it separates bacteria by their cell envelope. Crystal violet and iodine form a complex that a thick peptidoglycan wall keeps through decolorizing, so Gram-positive cells stay purple. Gram-negative cells lose the complex, and a counterstain leaves them red or pink. The acid-fast stain uses carbol (phenol) fuchsin and an acid-alcohol decolorizer to pick out mycobacteria.

A prokaryotic cell, such as a bacterium, lacks a nucleus, while a eukaryotic cell has a membrane-bound nucleus and other organelles. Ribosomes differ too: bacteria assemble 70S ribosomes from 30S and 50S subunits, and eukaryotes assemble 80S ribosomes from 40S and 60S. Notice the subunit numbers do not add up to the whole, so never sum them.

Shape and grouping are the first clues on a Gram stain. Cocci are round cells and bacilli are rods; cocci in pairs and chains point toward streptococci, while clusters point toward staphylococci, a split the catalase test helps check. Spirochetes are flexible helices that move by internal axial filaments rather than outside flagella.

A Gram-positive cell has a single membrane under a thick peptidoglycan wall that also carries teichoic acids. Crystal violet enters every cell, so the color depends on what happens next: the thick wall traps the dye–iodine precipitate through decolorizing and the cell stays purple. One genomic study therefore proposes reading a Gram result as a proxy for wall thickness.

A Gram-negative cell has an outer membrane outside a thin peptidoglycan layer, with lipopolysaccharide in that membrane's outer leaflet and the periplasm between the layers. Decolorizer disrupts the outer membrane, and the thin wall cannot hold the dye complex. The membrane is not required for that result: one genomic study reports Bacillota with no such membrane, only other layers over a thin wall, that still stain Gram-negative.

Mycobacteria link long-chain mycolic acids to their peptidoglycan through arabinogalactan, building a lipid-rich envelope that keeps many drugs out. Mycoplasmas have no peptidoglycan wall, so drugs that kill by bursting a wall cannot lyse them. Some methanogenic archaea build pseudomurein from different sugars and bonds than bacterial peptidoglycan; one review argues it still counts as peptidoglycan, and calls “archaea lack it” a misconception.

A capsule is an outer polysaccharide layer that helps a cell resist drying, stick to surfaces and escape a host's immune system; it can even block phages by hiding their receptors. Cells that settle on a surface can build a biofilm, an organized community, and conjugation passes DNA only between cells in direct contact.

Flagella may be single and polar, tufted, or all over the cell. With flagella all over, reversing the motor makes the bundle fly apart and the cell tumble, while a polar cell briefly reverses; chemotaxis biases those changes toward attractants and away from repellents. Some bacteria form spores, an inactive state that needs no nutrients and resists harsh conditions. Conjugative plasmids are small DNA circles that can jump between cells.

Labs usually stack evidence to name a prokaryote. Gram reaction and colony shape, size, color and hemolysis give early clues, and bench tests such as catalase, oxidase and latex agglutination narrow the field. Gene sequences add another line: 16S ribosomal RNA sequencing can even detect microbes that cannot yet be grown in culture.

Catalase splits the Gram-positive cocci: staphylococci are positive and form clusters, streptococci are negative and form chains or pairs, and coagulase testing then helps pick out Staphylococcus aureus. Among the rods, Bacillus is large and spore-forming, Clostridium perfringens forms spores but is anaerobic, and Listeria is a small catalase-positive rod that tumbles at 26 degrees C and grows in the refrigerator.

Actinomycetes are Gram-positive soil bacteria that make medically important natural products, and Streptomyces species among them are studied for their antibiotics. Each strain carries more than 30 likely gene clusters for such compounds, yet few products appear in ordinary lab culture. Some actinomycetes carry long-chain mycolic acids in their walls, the same class of lipid that marks the mycobacterial envelope.

The Proteobacteria, now renamed Pseudomonadota, are the textbook Gram-negatives: an outer membrane with lipopolysaccharide over a thin wall. Enteric bacteria are Gram-negative rods that are facultative anaerobes, and Escherichia coli is a well-studied member of the gamma class. Pseudomonas aeruginosa differs in running a branched aerobic respiratory chain.

Chlamydia, Rickettsia, Ehrlichia and Anaplasma are restricted to life inside host cells, and their study long lagged for lack of genetic tools. Their lifestyles differ: Chlamydia, Ehrlichia and Anaplasma alternate infectious and replicative forms inside vacuoles, while Rickettsia escapes its vacuole and grows in the host cytosol. Spirochetes are flexible helical Gram-negatives moved by internal axial filaments rather than external flagella.

Phototrophs harvest energy from light, autotrophs fix carbon from carbon dioxide, and both are called primary producers because they pass energy and carbon on to consumers. Cyanobacteria are bacteria, despite the everyday name blue-green algae, and they are the most common cause of harmful algal blooms in fresh water; blooms are likelier when water is warm, slow-moving and full of nutrients.

Woese's first archaea were methanogens, heat-loving and acid-loving thermophiles, and salt-loving halophiles, though not all archaea come from extreme environments. Their membranes set them apart: isoprenoid chains ether-linked to glycerol-1-phosphate, versus the ester-linked fatty acids of bacteria and eukaryotes, and some archaeal lipids span the membrane as a single layer.

A eukaryotic cell keeps most of its DNA in a membrane-bound nucleus and has organelles such as mitochondria, endoplasmic reticulum and Golgi. Its ribosomes are the larger 80S type, and microtubules both support the cell and give structure to its flagella and cilia. A bacterial flagellum is a different machine, a protein assembly encoded by about 40 genes, so the shared name misleads.

Protozoa that infect humans are grouped by how they move: amebae, flagellates, ciliates, and sporozoa, whose adult stage is not motile. Stages differ too, as in the flagellate Giardia: the hardy cyst spreads the infection and can survive months in cold water, while trophozoites multiply in the small intestine. Both can appear in stool, so a lab may find either.

Algae are plant-like organisms that live in water, and their blooms can turn harmful by making toxins, growing too dense, using up the water's oxygen or releasing harmful gases. In salt water dinoflagellates or diatoms are the most common causes, and people can be sickened by eating contaminated shellfish or fish. Cyanobacteria, the main freshwater culprits, are bacteria rather than algae.

Fungi make no chlorophyll and range from single-celled yeasts to molds built of multicellular hyphae. Thermally dimorphic fungi such as Histoplasma switch form with temperature: they grow as hyphae in soil, shedding airborne spores called conidia, and as yeasts in the body. A potassium hydroxide preparation of nail scrapings can make hyphae visible.

Helminths fall into flatworms, which include the flukes (trematodes) and tapeworms (cestodes), the thorny-headed worms, and the roundworms (nematodes). Taenia tapeworms show how a life cycle can split across hosts: humans, the definitive hosts, carry the adult worm, while cattle or pigs carry larval cysts in muscle. Eggs or worm segments passed in stool are the stages a lab can find.

Ticks, fleas, lice and mites are ectoparasites that attach to or burrow into skin for weeks to months, and arthropods can cause disease in their own right. They matter even more as vectors that carry other pathogens: mosquitoes and sand flies, for example, pass blood and tissue protozoa from one person to the next.

A capsid is built from many copies of identical protein subunits; an icosahedral shell offers only 60 symmetrically identical positions, so larger capsids place copies in slightly different settings. Some viruses also carry a membrane envelope, while naked particles, such as hepatitis A shed in stool, can resist drying. Contacts between viral proteins and host receptors influence host range and tissue tropism.

The Baltimore scheme sorts viruses by genome type and by how they make messenger RNA: double-stranded DNA, single-stranded DNA, double-stranded RNA, positive-sense RNA, negative-sense RNA, and reverse-transcribing RNA, with a seventh class added later. The classes describe replication strategy, not ancestry; they do not track evolutionary relationships among viruses.

A lytic phage takes over its host, copies its genome, builds capsids and then bursts the cell to release progeny. A temperate phage can instead integrate its DNA into the bacterial chromosome as a prophage, replicating along with the host, protecting it from similar phages and perhaps giving it new traits; cues such as cell density can tip it between the two paths.

An animal virus moves through attachment, entry, genome replication, protein synthesis, assembly and release, using host machinery at each step. Attachment depends on viral proteins meeting specific host receptors, and many viruses also need co-receptors or host proteases: HIV must bind CD4 and then CCR5 or CXCR4, which limits it to particular immune cells.

Some viruses linger for years. A retrovirus uses reverse transcriptase to become part of the host cell's DNA, and HIV can be present for years before symptoms. Long-lasting infections also link viruses to cancer: chronic hepatitis B or C infection can cause liver cancer, and high-risk human papillomaviruses cause nearly all cervical cancers.

Viruses multiply only inside living cells, so labs grow them in cell lines and watch for cytopathic effects, visible damage to the infected cells. A plaque assay counts infectious virus as clear spots in a stained cell layer, whereas standard PCR generally cannot tell infectious from inactivated virus, so the two answer different questions. A poorly matched cell line can give inconsistent plaques.

Viroids are small circular RNAs that infect plants and code for no protein, so their diseases were long blamed on hidden viruses. A prion is misfolded protein that replicates without DNA or RNA intermediates, and it can pass through contaminated meat, surgical equipment or transplants. One major cattle outbreak was likely tied to feed made from infected cattle.

Carbohydrates are made only of carbon, hydrogen and oxygen, usually about 1:2:1, and run from simple sugars to long polymers. Bacteria build with them: peptidoglycan strands alternate N-acetylglucosamine and N-acetylmuramic acid joined by beta-1,4 bonds, and lipopolysaccharide carries a core sugar chain plus a repeating O-antigen polymer.

Membrane lipids differ by linkage: bacteria and eukaryotes ester-link fatty acids to glycerol-3-phosphate, while archaea ether-link isoprenoid chains to glycerol-1-phosphate. A Gram-negative outer membrane is lopsided, with phospholipids inside and lipopolysaccharide outside, whose lipid part, lipid A, is a fatty-acylated sugar pair. Mycobacteria add very long mycolic acids to their walls.

Proteins are folded chains of amino acids; the 20 standard amino acids share one basic structure and differ by side chain. Most enzymes are proteins that speed a specific reaction by lowering the energy it needs. Only a matching substrate binds the active site, and many enzymes also need a cofactor, a helper such as a metal ion or a vitamin, to work.

A nucleotide joins sugar, phosphate and a nitrogen-containing base. DNA uses deoxyribose and thymine; RNA uses ribose and uracil and is usually single-stranded, and some viruses carry RNA as their genome. ATP is a nucleotide-based energy carrier, and NAD and FAD derivatives carry electrons between reactions.

Biochemical tests turn metabolism into a visible result. Catalase splits staphylococci (positive) from streptococci (negative), and coagulase helps single out Staphylococcus aureus. On triple sugar iron agar, yellow means acid and red means alkaline: a red slant over a yellow butt means glucose fermentation only, red over red means no fermentation, and black means hydrogen sulfide.

Catabolism breaks molecules such as glucose down to release energy, and anabolism uses energy to build larger molecules from small building blocks, many of them catabolic intermediates. Carriers such as NAD and FAD link the two through redox: they take up electrons and protons in one reaction and hand them on in another, finally to the respiratory chain.

Classify a microbe's nutrition by two questions. Where does its energy come from: light for phototrophs, chemicals for chemotrophs, including inorganic ones such as iron or sulfur for lithotrophs? Where does its carbon come from: carbon dioxide for autotrophs, organic molecules for heterotrophs? Humans and E. coli are both chemoheterotrophs.

The Embden-Meyerhof pathway turns glucose into two pyruvates in ten reactions; it spends ATP early and makes more later, so the net gain is small, and it also loads NADH. The Entner-Doudoroff pathway reaches pyruvate in only five enzymatic steps, and the pentose phosphate pathway interconverts sugars of three to seven carbons while making NADPH for biosynthesis.

The citric acid, or Krebs, cycle finishes oxidizing the carbon from pyruvate to carbon dioxide. It makes little energy directly, two GTP per glucose, but loads NADH and FADH2 with the electrons that drive the respiratory chain. In bacteria it runs in the cytoplasm, not in mitochondria, and its intermediates double as building blocks.

NADH hands electrons to quinols in the membrane, which pass them to a terminal oxidase that reduces oxygen to water. Energy released along the way pumps protons out, and their flow back through ATP synthase makes ATP, many times what glycolysis alone nets. Bacterial chains vary; E. coli has two NADH dehydrogenases and several terminal oxidases matched to oxygen level.

Anaerobic respiration still runs an electron transport chain but ends at a molecule other than oxygen. E. coli can use nitrate, nitrite, fumarate, DMSO or trimethylamine N-oxide, through terminal reductases in the inner membrane. Fermentation is different: it skips the respiratory chain and puts the electrons onto intermediates of the cell's own carbon metabolism.

Fermentation regenerates NAD+ by dumping electrons onto organic intermediates, skipping the respiratory chain. End products differ by organism: yeast ferments sugar to ethanol, human cells make lactate, and E. coli runs mixed-acid fermentation, shifting the mix as it needs NAD+ recycling or energy. On triple sugar iron agar, acid from fermenting glucose turns the medium yellow.

Photosynthesis uses sunlight to make carbohydrate from carbon dioxide and water, and it is done by plants, algae and some bacteria. Lithotrophs instead draw energy from inorganic chemicals such as iron or sulfur. Central pathways serve both directions: breaking down glucose supplies building blocks for new cells, and the pentose phosphate pathway supplies NADPH for building reactions.

In binary fission one cell becomes two, two become four, and so on, so the count doubles each generation: after n generations it is the starting number times 2 to the n. Plotted on an ordinary scale the numbers curve upward, but during exponential growth the natural log of biomass against time gives a straight line whose slope is the specific growth rate.

A batch culture passes through four phases. In lag the cells adjust their physiology before dividing; in exponential growth division is rapid and steady, the most reproducible phase for comparing strains; in stationary phase growth plateaus as nutrients run short; and in the death phase cells lyse under severe nutrient limitation.

A plate count reports colony-forming units per milliliter from plates in a countable range, 15 to 300 colonies in FDA's current method. Most probable number estimates a concentration from which tubes in a serial dilution show growth and suits low counts, as in milk and water. Turbidity measures light scatter, which reads poorly at high cell density.

Obligate aerobes grow only with oxygen and obligate anaerobes only without it. Facultative anaerobes manage either way, respiring when oxygen is present and fermenting when it is absent. Microaerophiles such as Campylobacter need low oxygen, often with extra carbon dioxide, and Clostridium perfringens is an anaerobe that tolerates air.

Every microbe has a minimum, optimum and maximum temperature and pH. The optimum temperature gives the label psychrophile, mesophile or thermophile; a psychrotroph can grow slowly below 15 degrees C while preferring warmth, which is how Yersinia enterocolitica multiplies under refrigeration. Moving away from the pH optimum in either direction slows growth.

Water activity measures the water free for a cell to use: pure water is 1.00, and dissolved salt or sugar lowers it. Most bacteria compete poorly for that water, but Staphylococcus aureus can grow down to 0.83, and Vibrio vulnificus is halophilic, needing salt. Below its minimum a bacterium does not necessarily die: some of the population may stay dormant yet infectious.

Selective media carry components such as antimicrobial agents that hold back non-target bacteria. Differential media make groups look different: on MacConkey agar, lactose fermenters form pink colonies. Enrichment raises recovery of a target organism from a sample. Quadrant streaking spreads a specimen across a plate to yield single colonies.

A biofilm is a community embedded in a matrix of polysaccharides, proteins and DNA that its own cells produce, attached to a surface. The matrix protects residents, so they tolerate stresses better than free-living cells and resist antibiotics, a problem on implanted devices. Many bacteria time such group behaviors by quorum sensing, responding once their signal molecules build up.

Griffith injected mice with heat-killed virulent smooth pneumococci plus a little live harmless rough culture and recovered live smooth bacteria. Avery, MacLeod and McCarty showed in 1944 that this transforming principle was DNA. Textbooks often credit the later Hershey-Chase phage experiment as the proof, but one historical essay argues that contamination kept it from showing that DNA was the genetic material.

DNA is two antiparallel strands wound into a double helix, with sugar-phosphate backbones joined by base pairs, adenine with thymine and guanine with cytosine. Bacterial DNA is often circular and supercoiled, and gyrase adds negative supercoils by cutting both strands, passing duplex through and resealing. Eukaryotic DNA instead wraps around histone proteins to fit in the nucleus.

In E. coli or Bacillus subtilis the circular chromosome copies as one unit: replication starts at a single origin, oriC, and runs in both directions until the two forks meet in a terminus zone opposite it. A helicase unwinds the parent strands and primase lays down primers. The leading strand is made continuously, the lagging strand in pieces, and some polymerases proofread as they go.

Linear eukaryotic chromosomes end in telomeres, repeated sequences that protect the ends and shorten slightly with each division. Many plasmids and single-stranded DNA viruses use rolling-circle replication: an initiator nicks one strand at the origin and the freed end primes one-way copying. Retroviruses copy their RNA genome into DNA with reverse transcriptase and join the host's DNA.

Transcription makes an RNA copy of a gene. RNA polymerase starts at a promoter just upstream of the gene; in bacteria a sigma factor joins the polymerase to recognize promoters, with one housekeeping sigma for everyday genes and alternative sigmas that switch on special sets such as flagellar genes. In eukaryotes the messenger RNA leaves the nucleus for the cytoplasm.

In translation a ribosome uses messenger RNA to link amino acids into a protein. Each codon, three nucleotides long, can start the chain, add a specific amino acid or end it, and transfer RNA helps make sure the right amino acid goes in. In eukaryotes one messenger RNA can be read by two or more ribosomes at once, so a single transcript can yield several copies of its protein.

The lac operon shows inducible control. The LacI repressor binds operator sites near the promoter until a derivative of lactose releases it so transcription can proceed. Glucose adds a second brake by lowering cAMP, which leaves the cAMP-CRP activator scarce. The textbook rule, lactose present and glucose absent, is a simplification: experiments in one lab strain measured logic between AND and OR.

Some regulators control many operons at once. cAMP-CRP is a global regulator that ties sugar use to glucose availability. Under nutrient starvation, the stringent response is a surge of the alarmones ppGpp and pppGpp, signaling nucleotides made in E. coli by RelA and SpoT. Quorum sensing switches behaviors on once self-made signal molecules reach a threshold concentration.

A point mutation adds, deletes or changes a single base pair. Most are harmless, but a missense change puts a different amino acid in the protein, and a nonsense change stops the protein early, leaving a shorter one that may not function. An insertion or deletion whose size is not divisible by three shifts the reading frame, garbling every codon after it.

Mutagens are chemical or physical agents, such as x-rays, ultraviolet light and many chemicals, that change DNA. The Ames test screens for them with Salmonella strains that cannot make histidine: a mutagen raises the number that revert and grow without it. Liver extract is added for metabolic activation of compounds. The test rests on an assumption, that bacterial mutagenicity predicts human mutagenicity.

Cells hold mutation rates down with proofreading by DNA polymerases and with mismatch repair, and strains that lose either system mutate faster. Heavy DNA damage switches on the SOS response, about 40 genes in E. coli that include error-prone polymerases, so mutation rates climb, which is one way certain antibiotics can speed up resistance.

In transformation a bacterium takes up free DNA from its surroundings, often from lysed neighbors, and recombines it into its own genome. Only competent cells can do it, using dedicated uptake machinery; some species are competent all the time, others only under signals such as stress, and the incoming DNA must be similar enough to the host's to recombine.

Transduction uses phages as couriers: a packaging error can load host DNA into a phage capsid, and generalized transduction then moves chromosomal fragments to a new cell. Conjugation instead needs direct contact between donor and recipient to pass mobile elements across. Plasmids that cannot transfer themselves can still move by borrowing a co-resident conjugative element's machinery.

Mobile genetic elements, including plasmids, transposons, integrons and phages, carry genes between cells and even between distantly related microbes. They spread resistance and stress-tolerance genes, and pathogenicity islands carry virulence genes whose presence varies from strain to strain. In Listeria the accessory genome, unlike the conserved core, is rich in such elements.

Molecular cloning isolates a DNA segment and makes many copies of it. Restriction enzymes, borrowed from bacteria's defenses against phages, cut DNA at the sites they recognize, and a vector, often a plasmid or virus, carries the segment into a host cell. As the bacterial or yeast host copies its own DNA, it copies the inserted recombinant DNA too.

PCR makes many copies of one chosen stretch of DNA, even from tiny starting amounts, so it can be detected. A pair of short primers binds the sample DNA and defines the region copied. A standard PCR result generally cannot tell infectious virus from inactivated virus, so a positive test alone does not show the virus was infectious.

Hybridization is the base-pairing of two complementary single strands, and every probe method depends on it. A Southern blot cuts DNA with restriction enzymes, separates the fragments in a gel, transfers them to a membrane and finds the target with a labeled probe; a Northern blot studies RNA the same way. A microarray instead sets molecules in a pattern on a surface such as a glass slide to analyze many genes at once.

Electrophoresis uses an electric current to separate substances such as proteins or nucleic acids, and a molecule's size and charge decide how far it moves. Cutting DNA with a restriction enzyme yields fragments of different lengths that can tell samples apart, and outbreak investigators have compared pulsed-field gel electrophoresis patterns to link a patient's isolate to a food.

DNA sequencing reads out the order of the bases along a molecule, and Sanger sequencing gave early insight into the many kinds of mutation. Metagenomics sequences DNA from every organism in a bulk sample, such as soil, water or skin, so a whole community can be studied without growing each member, which matters because many microbes have never been cultured.

Genetic engineering introduces, removes or changes an organism's genes with molecular biology techniques. Gene therapy often adds working copies of a broken gene or replaces a faulty one, and has been used against inherited diseases such as hemophilia. CRISPR began as an immune system in bacteria that destroys invading DNA, and it has been adapted into a widely used gene-editing tool.

Sterilization is a validated process that leaves an item free of all viable microbes, spores included. Disinfection destroys most pathogens on objects but not necessarily bacterial spores, so a disinfected item may not be sterile, while antisepsis acts on skin or tissue. An antimicrobial may kill microbes or merely stop their growth, and a word ending in “-cide”, such as bactericide or sporicide, names what it destroys.

Killing is often measured in tenfold steps rather than as all or nothing, and a death-rate curve plots it. In one FDA example, heat at 60 degrees C cut Salmonella tenfold in 0.18 minutes in a water-rich medium but needed 4.3 minutes when water activity fell to 0.94. Endospores withstand heat, radiation, drying and many chemicals, which is why even high-level disinfection can spare large numbers of them.

Heat kills by irreversibly coagulating and denaturing microbial proteins. Some spores survive an hour of boiling, so an autoclave uses saturated steam under pressure, which runs hotter than boiling. Pasteurization is milder, killing milk pathogens with limited protein damage to the milk. Dry heat is another sterilization method.

Ionizing radiation, from gamma rays, X-rays or electron beams, can reduce or eliminate microbes in food and, at far higher doses, sterilize it, without making the food radioactive. Ultraviolet germicidal irradiation is used to disinfect surfaces. Drying works differently: below its minimum water activity a bacterium may stop growing yet survive, and spores resist both radiation and drying.

Filters remove cells by size, but viruses were long defined by slipping through “sterilizing” filters with pores under 0.3 micrometers, so a filter that holds back bacteria can still pass viruses. Cold does not reliably stop microbes: Listeria and Yersinia keep multiplying in the refrigerator, and Yersinia can survive in frozen food for long periods.

Chemical agents fit different jobs. Hand sanitizers are recommended at 60 percent alcohol or more; chlorine kills bacteria and other organisms in water; formaldehyde kills germs and preserves specimens. Ethylene oxide gas sterilizes about half of sterile US medical devices, especially those with certain plastics or hard-to-reach parts that other methods may damage or miss, and vaporized hydrogen peroxide is another gaseous option.

A disinfectant's claim has to be tested. For device germicides, FDA ties a sterilant claim to a sporicidal test, and the minimum effective concentration comes from dose-response testing. Real performance shifts with organic load, dilution, water quality, temperature and pH, and a chemical indicator shows concentration only, not contact time or temperature.

Aseptic technique is the set of lab habits meant to keep unwanted microbes out of your samples. In healthcare, reprocessing follows the device's risk: critical devices that enter sterile tissue or the bloodstream are sterilized, semicritical devices touching mucous membranes need at least high-level disinfection, and noncritical surfaces get intermediate or low-level disinfection.

Paul Ehrlich framed selective toxicity: a drug that harms the microbe and spares you. Penicillin, found in 1928, fit it because beta-lactams block enzymes that build a bacterial cell wall your cells lack. The idea is oversimplified, though: your mitochondria carry bacterial-like ribosomes, so some protein-synthesis inhibitors reach them too.

A broad-spectrum drug acts on many kinds of microbes, which helps when the cause is unknown, but it adds selective pressure and can deplete the gut flora that keep C. difficile in check. Bactericidal and bacteriostatic are lab thresholds, not absolutes: bacteriostatic drugs also kill some bacteria, and dose, organism and conditions can shift a drug's label.

Beta-lactams, including cephalosporins and carbapenems, bind penicillin-binding proteins and block the cross-linking step of wall synthesis, so the weakened wall lyses. Vancomycin works from another side: it binds the D-Ala-D-Ala end of the wall precursor, which is why resistant enterococci swap that end for D-Ala-D-Lac. It cannot cross the outer membrane of gram-negative bacteria.

Aminoglycosides and tetracyclines bind the 30S subunit, but differently: aminoglycosides cause codon misreading and are bactericidal, while tetracyclines block incoming tRNA and are bacteriostatic. Macrolides lodge in the exit tunnel that a new protein leaves through. Selectivity rests on bacterial 70S ribosomes, yet your mitochondrial ribosomes resemble them, which is how chloramphenicol and linezolid can harm human cells.

Fluoroquinolones block DNA gyrase and topoisomerase IV, and rifampin blocks bacterial RNA polymerase. A sulfonamide mimics PABA and blocks a step of folate synthesis that your cells lack, since they take folate from food, which is what makes that step a selective target. Trimethoprim blocks dihydrofolate reductase, a separate enzyme in folate synthesis.

Polymyxins such as colistin are membrane-active and bind the lipopolysaccharide of gram-negative outer membranes. Most antifungals target ergosterol, the fungal membrane sterol: polyenes such as amphotericin B bind it, while azoles block its synthesis. Echinocandins instead block the synthase that makes 1,3-beta-glucan for the fungal wall, a target your cells lack, so the wall lyses.

Viruses replicate inside your cells, so few targets belong to them alone; one early antiviral stayed topical because it could not tell viral from host functions. Acyclovir solved this as a virus-activated prodrug that blocks herpesvirus DNA polymerase. Neuraminidase inhibitors work at the last step: they stop new influenza virions from cutting themselves free of the cell.

Worm drugs are often narrow: praziquantel treats flukes and tapeworms but not roundworms, while benzimidazoles act mainly on roundworms. Resistance to benzimidazoles in livestock parasites tracks mutations in a beta-tubulin gene. Some antiprotozoal effects ride on antibiotics: tetracyclines act on certain parasites, an effect largely explained by blocked protein synthesis in parasite mitochondria.

Bacteria resist in four ways: an enzyme such as a beta-lactamase destroys the drug, an altered target no longer binds it, an efflux pump expels it, or lost porins keep it out. Porin loss alone usually gives only low-level resistance, but mechanisms stack, and porin loss plus efflux plus an enzyme can make a gram-negative strain highly resistant.

A resistance mutation passes only to a cell's own descendants, but horizontal gene transfer moves genes between neighbors, even across species. Conjugation is the commonest route, with transformation and transduction adding more. Integron cassettes can carry resistance to several different drugs, so a single transfer may hand a cell more than one drug class at once.

A drug does not create resistance; it removes the susceptible cells, and any survivors carrying resistance genes multiply and take over. That is why even appropriate use creates selective pressure. Overuse, guessing at a bacterial cause for a viral illness, and broad-spectrum choices speed the process, and heavy use among the critically ill makes hospitals a hotspot.

MRSA carries the mecA gene for PBP2a, a penicillin-binding protein that most beta-lactams cannot block. VRE swap the end of their wall precursor so vancomycin no longer binds. ESBL producers resist nearly all penicillins and cephalosporins, carbapenemase producers defeat even the last-resort carbapenems, and MDR-TB resists both isoniazid and rifampin.

In Kirby-Bauer disk diffusion, drug-soaked disks sit on a lawn of the isolate, and the clear zone around each disk is read against standard tables; it is cheap but qualitative and takes about a day. A gradient strip, the E-test, and broth dilution give an actual MIC. Automated systems read growth faster, though they can disagree with reference methods.

The MIC is the lowest drug concentration that stops visible growth; the MBC is the lowest that kills 99.9 percent. An MBC no more than four times the MIC marks a drug as bactericidal. Both are test-tube numbers, so a dose also depends on how the drug behaves in the body. Stewardship programs aim at prescribing that cures the patient while slowing resistance.

The ID50 is the median infective dose. An FDA risk assessment puts it at 100 million for Vibrio parahaemolyticus, though a 2004 outbreak suggested a dose over 1,000 times lower. Other figures are minimums: as few as 10 to 200 Shigella cells can cause disease. Treat all of them with caution. Many come from outbreaks or from feeding studies on healthy young adults, and age, stomach acidity and medications shift the dose that makes a person ill.

Infection begins with exposure of a susceptible host, but exposure is not disease. Epidemiologists split the path into steps: infectivity is the share of exposed people who become infected, pathogenicity the share of infected who get sick, and virulence the share of cases that turn severe. The cycle closes only when the pathogen leaves through a portal of exit and reaches a new host.

A pathogen usually leaves from the site where it is living: influenza and tuberculosis exit the airways, cholera in feces. Many reuse the same portal to enter a new host, as respiratory viruses do, but gastrointestinal pathogens switch routes, leaving in feces and entering by mouth. The entry portal must reach tissue where the microbe can grow or its toxin can act.

Adhesins let a microbe hold on against flushing; FimH, at the tip of type 1 fimbriae, is the adhesin many enteric bacteria use. Holding on is colonization, not infection: about 20 to 30 percent of people carry Staphylococcus aureus in the nose without illness. Microbes that settle on a surface as a biofilm are far harder to clear than free-floating ones, which is why those infections persist.

Pathogens survive the immune response by hiding or misdirecting it. A capsule masks the cell surface from complement and antibody, so phagocytes cannot grip it. Staphylococcal protein A grabs antibodies by their Fc stem, the end phagocytes would bind. Gonococci keep reshuffling the gene for their pilus protein, so antibodies made against yesterday's version miss today's.

Exotoxins are secreted proteins, and they come in three designs. A-B toxins use a B subunit to bind your cell and an A subunit to act enzymatically inside it. Membrane-damaging toxins punch holes. Superantigens bind MHC II and T-cell receptors nonspecifically, switching on huge numbers of T cells at once. Because they are proteins, many can be inactivated into toxoid vaccines.

Endotoxin is not secreted; it is part of the lipopolysaccharide in the outer membrane of gram-negative bacteria and is released mainly when the cells die. Its toxic part, lipid A, is not an enzyme but an alarm: the TLR4 and MD-2 receptor on your phagocytes detects it and triggers inflammatory cytokines. At high levels that response is thought to help drive septic shock, though how much each sensing route contributes in people is unsettled.

Viruses have their own adhesins: influenza's hemagglutinin binds sialic acid on your cells, the first step of infection. Fungi lean on other tools, and for Cryptococcus the polysaccharide capsule is the main virulence factor. African trypanosomes evade antibodies by antigenic variation, repeatedly swapping the surface coat protein the immune system has just learned to recognize.

Microbes living in your gut, mouth, skin and vagina mostly cause no harm, and some actively protect you: normal gut microbiota hold C. difficile in check until antibiotics deplete them. The same residents turn opportunist when conditions change. Candida, usually harmless in the mouth, gut and vagina, causes infection when immunity is weakened or antibiotics upset the balance.

Infection means an agent has invaded your tissues, whether or not it causes disease, so infection and disease are separate steps. A symptom is any sign of disease the patient notices or feels. Some infections linger after the illness ends: chronic carriers of hepatitis B virus or Salmonella Typhi can harbor the agent for months or years and still pass it on.

The incubation period runs from exposure to the first symptoms, and even for one disease it spans a range. Being infectious does not wait for feeling ill: people with measles or hepatitis A can spread infection a few days before symptoms begin, and convalescent carriers can still transmit after they recover. That is why people who look well often spread disease.

Koch's test asks that a microbe be found in every case of the disease, not occur as a harmless passenger in other people, be grown as a pure culture, and recreate the disease when given to a healthy host. Many real causes cannot meet every rule, so later versions relax it: one generalized form drops the isolation step, and an ecological form blames an unbalanced microbial community rather than one species.

A reservoir is where an agent normally lives and multiplies, which is not always the source of your exposure: Clostridium botulinum lives in soil, yet most botulism comes from improperly canned food. Droplets are direct transmission because the spray travels only a few feet. The finer dried residue, conventionally cut off at 5 microns, stays airborne for long periods and counts as indirect, like vehicles and vectors.

Incidence counts new cases; prevalence counts all cases, new and existing, at a given time. Because prevalence depends on both incidence and how long illness lasts, a long-lasting disease can be common even when new cases are rare. Endemic means the usual level in an area, an epidemic is a rise above what is expected, and a pandemic is an epidemic spread over several countries or continents.

Devices are the main way in: central venous and urinary catheters, breathing tubes and implants can all be colonized, and biofilms on them drive a large share of healthcare-associated infections. Biofilm tolerates antibiotics, so a device infection may mean removing the device. Germs also travel between patients on healthcare workers' hands and on poorly cleaned equipment.

A notifiable disease is one that law requires to be reported to public health authorities on diagnosis. In passive surveillance those reports arrive without prompting; in active surveillance the agency goes out and asks for them. Many human diseases recognized in recent decades, including HIV/AIDS, Ebola and SARS, are thought to have emerged from animal hosts.

Skin is usually your first line of defense, and its cells also secrete antimicrobial proteins. In the airways, mucus traps particles and cilia push it up to be coughed out. When a breathing tube bypasses this clearance and suppresses the cough reflex, bacteria from the throat can reach the lungs and cause pneumonia.

Lysozyme cuts the sugar backbone of peptidoglycan, so it works well on gram-positive walls but poorly on gram-negatives, whose outer membrane shields the layer. Defensins are antimicrobial peptides that also attract immune cells. Stomach acid matters too: in people with low gastric acidity, the dose of some foodborne pathogens needed to cause illness may be lower.

All immune cells start as bone marrow precursors: a myeloid line gives neutrophils, eosinophils, basophils, mast cells, monocytes and dendritic cells, and a lymphoid line gives B, T and natural killer cells. NK cells blur the innate-adaptive split. They kill virus-infected and tumor cells at once, like innate cells, yet in mice some persist as memory cells.

Neutrophils, the most numerous innate immune cells, and macrophages ingest bacteria and degrade them inside internal compartments. Chemokines made at the infection site draw them in. Coating a microbe with antibody or complement fragments, called opsonization, flags it for these cells, which is why a capsule that blocks coating lets bacteria escape being eaten.

The four classic signs are redness, swelling, heat and pain. Mediators released at the site drive them: histamine widens vessels and makes them leaky, and prostaglandins add redness, swelling, pain and fever. The leakage that causes swelling is also how fluid and white cells reach the tissue, so the signs are the response working, not just damage.

Fever is driven from inside: endogenous pyrogens such as IL-1 beta and TNF act in the brain, leading to release of prostaglandin E2, and injected dead bacteria can trigger it. Most microbes that infect you do well at normal body temperature, so a fever makes survival harder for them and activates the immune system. Fever is a sign of a fight, not a disease itself.

Complement is a set of blood proteins activated three ways: the classical pathway by antibody, the lectin pathway by microbial sugars, and the alternative pathway by spontaneous C3 activation. All converge on C3, whose fragments coat microbes, recruit cells and end in a membrane attack complex that punches holes. Type I interferons, in contrast, signal antiviral responses.

An antigen is any molecule a B-cell or T-cell receptor can bind, and one pathogen carries many binding sites, so different cells that respond to the same strain usually recognize different parts of it. Size matters: a hapten, a molecule under about 1,000 daltons, cannot start a response alone but can once it attaches to a larger carrier protein, as in some skin allergies.

B and T cells start as bone marrow precursors, and T cells finish maturing in the thymus. While they mature, their receptor genes are randomly rearranged, which lets the system recognize threats it has never met but also produces receptors against self. Strongly self-reactive cells are deleted; some that slip through stay in a nonreactive, anergic state.

MHC class I sits on nearly every cell except red blood cells, so any virus-infected cell can display viral pieces to CD8 cytotoxic T cells. MHC class II is mostly limited to antigen-presenting cells such as dendritic cells and macrophages, which show antigens to CD4 helper T cells. Antigen alone cannot activate a T cell; it must arrive on the matching MHC.

CD8 cytotoxic T cells kill infected and cancer cells by releasing granules that trigger apoptosis. CD4 helper T cells instead steer the response through cytokines: TH1 cells mobilize macrophages against intracellular microbes, TH2 cells coordinate defense against worms, TH17 cells recruit neutrophils, and regulatory T cells damp other T cells to keep tolerance.

A B cell activates when its receptor binds antigen and it also receives danger cues from innate cells; it then divides and secretes its receptor as antibody, leaving memory cells behind. Polysaccharide antigens alone respond poorly in infants. Linking the sugar to a protein carrier recruits T-cell help, which is why conjugate vaccines work in young children.

An antibody has antigen-binding Fab regions and an Fc region, and the class decides where it works. IgG is the most common and the most specialized, while IgM matters most for complement activation. IgA guards the airways and gut and appears in saliva, tears and breast milk, IgE activates mast cells, and IgD is involved in activating basophils.

Antibodies coating a pathogen act three main ways. Neutralization blocks it from binding and infecting your cells, opsonization flags it for neutrophils and macrophages to engulf, and complement activation leads to proteins that punch holes in bacteria. The classes split the work: IgA is the key neutralizer in the gut, and IgM is especially important for complement activation.

Memory cells left after a first response let a second exposure be cleared before the pathogen gains a foothold, and vaccines build that memory without infection. Live attenuated vaccines can give lifelong immunity in one or two doses but are hard to make for bacteria and parasites. Subunit vaccines are safer but often need adjuvants. Herd immunity protects the few susceptible people, yet clusters of unvaccinated people still allow outbreaks.

In a type I reaction, an allergen cross-links IgE already sitting on mast cells, and the mast cells degranulate, releasing histamine and other inflammatory chemicals. Because the IgE is in place before the exposure, the reaction can start fast. The same immune system that targets parasites this way can, with food allergy, produce a severe and life-threatening response.

In type II reactions, IgG or IgM binds antigens on cell surfaces, as when antibodies destroy transfused red cells that carry foreign markers. In type III, antibody and antigen form immune complexes in the blood that lodge in skin, joints, vessels or kidney filters, where they activate complement and draw in inflammatory cells. The damage happens where the complexes settle.

Type IV reactions are run by T cells, not antibodies, so they take time to build. Contact allergy is one example: a small chemical, too little to trigger immunity alone, binds skin proteins, and the complex primes T cells. The tuberculin skin test uses the same delay on purpose, since a firm bump is read two to three days after the injection.

Autoimmune disease follows a lapse in tolerance, the safeguard that stops the immune system attacking your own tissues. One proposed route is molecular mimicry: immune responses to a newly found gut bacterium may cause some cases of rheumatoid arthritis, because targets on the bacterium and on joint tissue look alike. Researchers count between 80 and 150 autoimmune diseases.

Your immune cells read MHC, also called HLA, proteins to tell self from foreign, so donors and recipients are matched to lower the risk of rejection. Matching is rarely complete, so recipients take immunosuppressive drugs for life, trading rejection for higher risk of infection and some cancers. In a bone marrow transplant the danger can run the other way: donor cells attack the recipient.

Primary immunodeficiencies are rare genetic disorders, while an infection such as HIV can also cripple immunity. Either way, the tell is infection by microbes that seldom trouble healthy people, along with repeated infections from the same germ. Newborn screening for severe combined immunodeficiency, followed by early treatment, has raised five-year survival.

In agglutination, antibodies link many particles, such as red cells or whole microbes, into visible clumps. Blood typing reads which A, B and Rh antigens your red cells carry. For infections, a rising titer is what counts: leptospirosis, for example, is confirmed on paired samples by an agglutination test showing a fourfold or greater increase.

Precipitation shows soluble antigen and antibody meeting: in radial immunodiffusion, antigen spreads through an antibody-laced gel, and a visible precipitin ring forms where the two reach equilibrium, wider rings meaning more antigen. A neutralization assay asks a different question, whether serum stops a virus from damaging cultured cells.

An ELISA uses an enzyme-labeled antibody, such as one carrying peroxidase, to report binding. The plate may be coated with purified antigen, or with an antibody that traps antigen from the sample, the sandwich format. A positive antibody result cannot, by itself, tell current infection from past infection or vaccination.

Lyme disease testing shows why a Western blot often comes second: a sensitive enzyme immunoassay screens the sample first, and positives go on to a Western blot looking for IgM and IgG bands. The blot has drawbacks, including poor sensitivity early in disease and subjective reading, so a modified protocol that uses a second immunoassay instead is more sensitive with similar specificity.

In flow cytometry, cells stained with antibodies carrying fluorescent dyes pass a laser one at a time, and sensors record each cell's emitted light, hundreds to thousands of cells per second. That is how a lab counts, say, CD4 helper and CD8 cytotoxic T cells in blood. The technique began as fluorescence-activated cell sorting, which can also separate the cells it measures.

Antibodies take a few weeks to appear, so a test done too early can be falsely negative. A single positive cannot separate current from past infection, which is why rising levels between paired acute and convalescent samples carry more weight. Sensitivity is how many true cases a test catches; specificity is how well it rules out people without the condition. Cross-reacting antibodies can also give false positives.

Skin is your largest organ and keeps most germs out, so skin infections usually start at a break such as a cut or wound, or where moist folds rub together. The eye is defended differently: tears carry IgA antibodies, and the eye is an immunologically privileged site, where suppressive signals keep immune responses mild.

Staphylococcus aureus causes most staph infections, and skin infections are the most common kind; impetigo, crusted sores that start at a cut or scratch, is usually staph. What sets S. aureus apart is coagulase: it activates your own prothrombin so fibrinogen turns into fibrin, wrapping the bacteria in a clot-like capsule. Many people carry it harmlessly until a wound lets it in.

Group A strep is the most common cause of cellulitis, an infection of the skin and the deeper tissue under it, entering through a burn, cut or wound. The same organism causes necrotizing fasciitis, which is rare but spreads quickly through skin and tissue. What separates the two is the depth reached and the speed of spread, not the organism.

Pseudomonas aeruginosa shows how one skin organism can be two problems. In healthy people it causes mild illness, such as ear infections and skin rashes after a poorly cleaned hot tub or pool. In hospitalized patients with surgical wounds, breathing machines or catheters it causes serious infections, and some strains resist most or all antibiotics.

Herpes viruses stay with you. After chickenpox, the varicella-zoster virus remains in the body for years and can reactivate as shingles, usually a one-sided stripe of rash; shingles itself is not caught from others, though contact with its blister fluid can give chickenpox. Herpes simplex likewise returns as repeated outbreaks. Warts instead come from human papillomavirus.

Ringworm is a fungal infection, not a worm: tinea fungi cause ringworm, athlete's foot and jock itch, and spread by touch, damp shower floors or pets. Scabies is a burrowing mite that spreads through close skin contact in crowded places. Head lice cannot hop or fly, so they pass by head-to-head contact, and catching them has nothing to do with hygiene.

Pink eye, or conjunctivitis, is inflammation of the eye's outer layer and the inside of the eyelid; infectious forms spread easily but usually spare vision, and most clear without care, while the bacterial form is treated with antibiotic drops. Babies born to mothers with chlamydia can get eye infections. Herpes simplex is a leading cause of infectious blindness worldwide.

Your airways are a prime entry point, so they carry their own defenses: mucus traps particles, cilia sweep it upward to be coughed out, and immune hubs sit in the respiratory lining. The upper airway also has residents; strep often lives in the nose and throat. Anything that disables clearance, from a breathing tube to toxins that damage ciliated cells, lets microbes reach the lungs.

Strep throat matters partly for what can follow it: scarlet fever, and later rheumatic fever, which can damage the heart and joints, or glomerulonephritis, a kidney disease. Diphtheria affects the nose and throat, and its harm comes from a toxin whose A subunit shuts down protein synthesis, which is why a toxoid vaccine protects. Acute sinusitis often begins as a cold and then becomes a bacterial infection.

Bacteria are the most common cause of pneumonia, an infection that fills the lung's air sacs with fluid or pus, and bacterial pneumonia often follows a cold or flu. Legionella breaks the usual pattern: it is breathed in as mist from man-made water systems such as hot tubs and building plumbing, does not spread person to person, and causes outbreaks when many people share one water source.

Many people infected with tuberculosis never become sick: in latent infection the bacteria live in the body but cause no illness and cannot spread, while active disease can. A skin or blood screening test cannot tell the two apart, so a positive screen leads to sputum tests, including an acid-fast smear and a culture that takes 6 to 8 weeks. Granulomas are thought to contain the bacilli, though their role is still debated.

Whooping cough starts with a catarrhal stage that looks like a cold, then moves to a paroxysmal stage of coughing fits ending in a whoop. Pertussis toxin uncouples a family of host G proteins, while a separate tracheal cytotoxin damages ciliated airway cells. Q fever, by contrast, is a zoonosis of livestock work, and its bacterium is thought to infect at fewer than 10 cells.

Influenza changes in two ways. Antigenic drift is gradual: its error-prone polymerase, which lacks proofreading, introduces mutations that let new variants escape existing immunity. Antigenic shift is abrupt: two strains infecting one cell swap genome segments, and a new virus few people are immune to can start a pandemic. Colds, by contrast, come from over 200 viruses.

The major respiratory fungi are not caught from people. Histoplasma lives in soil rich in bird or bat droppings and Coccidioides in dry southwestern soil; you inhale spores when soil is disturbed, and most infections cause few or no symptoms. Pneumocystis is different: many people carry it harmlessly, it can spread through the air, and it causes pneumonia mainly when immunity is weakened.

Stomach acid is a major barrier, and lowering it can let a smaller dose of some pathogens cause illness. Further down, IgA neutralizes microbes in the gut, and immune hubs such as Peyer's patches sample the intestinal contents. Your resident microbes help too: some E. coli strains block harmful pathogens from colonizing, and an intact gut microbiota holds C. difficile in check.

Tooth decay starts when mouth bacteria turn sugars and starches into acid that pulls minerals out of enamel. A white spot marks early loss, and at that stage decay can stop or even reverse as saliva and fluoride restore minerals; only when losses outrun repair does a cavity form. Gum disease comes from plaque, a sticky film of bacteria that can harden into tartar and inflame the tissues holding the teeth.

Onset time separates the two. Staphylococcal food poisoning is an intoxication from toxin already made in the food, so symptoms come fast, usually within 1 to 7 hours, and cooking does not help because the toxin is highly heat stable. Salmonella and Campylobacter must grow inside you first, so illness begins later, roughly 6 to 72 hours and 2 to 5 days.

Some enteric bacteria need very few cells: as few as 10 to 200 Shigella, and an estimated 10 to 100 for E. coli O157:H7. Both are linked to hemolytic uremic syndrome, a severe complication involving the kidneys. Clostridioides difficile works differently: it strikes mostly after antibiotics have depleted the gut microbiota, letting its spores germinate and release toxins.

Helicobacter pylori is the main cause of peptic ulcers. It infects about 30 to 40 percent of people in the United States, usually from childhood, and most never have symptoms; in some it breaks down the stomach's protective lining and causes inflammation. Its ability to split urea is what the urea breath test detects, by tracing labeled carbon released as carbon dioxide.

Norovirus is the leading cause of foodborne illness in the United States and spreads from person to person, through food and water, and from surfaces; alcohol hand sanitizers do not destroy it. Rotavirus is likely to infect almost every U.S. child before age 5, and two vaccines exist. Giardia is a parasite you swallow from water, food or soil, and many people carry it without symptoms.

Most urinary tract infections ascend: bacteria enter the bladder and multiply, and if the infection keeps climbing it reaches the kidneys as pyelonephritis, which adds fever and back or side pain to bladder symptoms. Women get about four times as many UTIs as men, and needing a tube to drain the bladder also raises the risk.

Many sexually transmitted infections spread because they are silent: chlamydia usually causes no symptoms, and gonorrhea often does not. Syphilis runs in stages, from a painless sore through a rash to a latent stage lasting years and, untreated, a severe late stage, and it is most often passed on early. High-risk HPV types can persist at the cervix for years and lead to cancer if cell changes go unchecked.

Lymph nodes act as communication hubs: immune cells there sample material carried in from the tissues, and if they recognize a microbe they multiply and leave to fight it, which is why swollen nodes can signal an active response. The spleen does the same job for the blood. Bacteremia, bacteria in the bloodstream, matters because it can tip into sepsis.

Sepsis is the body's overactive, extreme response to an infection it already has, a chain reaction rather than the infection itself, and it can lead to tissue damage, organ failure and death. Bacteria are the most common trigger. With gram-negative bacteria, TLR4 detects lipid A and sets off cytokine release; a second route through cytosolic caspases is proposed mainly from mouse work, and how much each contributes in human sepsis is unsettled.

Infective endocarditis begins when germs in the bloodstream lodge on the heart's lining or valves and grow; bacteria from the mouth or skin can enter through cuts or dental work, and damaged valves or heart devices trap them more easily. Rheumatic fever is different: it is not an infection of the heart but a complication that can follow untreated strep throat and damage the heart and joints.

Plague bacteria live mainly in rats and their fleas, and bites spread them; the bubonic form inflames lymph tissue, the septicemic form multiplies in the blood, and only pneumonic plague spreads person to person. Lyme disease comes from blacklegged ticks, which usually must stay attached for more than 24 hours to pass the bacterium. Tularemia, from rabbits, is another zoonosis.

Malaria parasites, injected by female Anopheles mosquitoes, first stay in the liver for days to months, then move to the blood, where they reproduce inside red blood cells and destroy them, causing illness. Because the parasite matures inside the mosquito before it can pass on, malaria is biological rather than mechanical vector transmission. Toxoplasma infects tens of millions of Americans, mostly without illness.

Infectious mononucleosis is usually caused by Epstein-Barr virus, which most people catch at some point, often in childhood without symptoms; it spreads mainly through saliva. Cytomegalovirus, a relative, stays in the body for life once acquired and is serious mainly for babies and people with weak immunity. Viral hemorrhagic fevers such as Ebola damage blood vessels and affect many organs.

HIV destroys CD4 helper T cells, so the damage is indirect: as the count falls, viruses, bacteria and fungi that rarely trouble healthy people cause opportunistic infections. AIDS is the final stage, not a separate disease, and most people with HIV do not have it. HIV spreads through sex, shared needles and from mother to child, and treatment that suppresses the virus can make it untransmittable sexually.

The meninges are the thin tissue around the brain and spinal cord, and the cerebrospinal fluid flowing there normally carries almost no cells. The blood-brain barrier limits how far immune cells can enter, which makes the brain an immunologically privileged site that mounts weaker responses. So a microbe that does cross, as West Nile virus sometimes does, can cause life-threatening inflammation.

Viral meningitis is the most common kind; the bacterial form is rare but can be deadly and can leave stroke, hearing loss or brain damage behind. Neisseria meningitidis often sits harmlessly in the back of the nose and throat, and it passes through close or lengthy contact with saliva rather than casual contact. Spinal fluid is tested for white cells and bacteria, but treatment may start before the diagnosis is final.

Both toxins block transmitter release, but at opposite controls. Botulinum toxin stops acetylcholine vesicles fusing at the neuromuscular junction, so muscles go slack. Tetanus toxin travels back up motor axons to the spinal cord, where it blocks release of the inhibitory signals GABA and glycine; the motor neurons lose their brakes and fire, giving rigidity and spasms rather than weakness.

Several bacterial infections reach nerves late rather than early. Syphilis can affect the brain, spinal cord and nerves at any stage, and its untreated late stage brings dementia and blindness. Hansen's disease, caused by Mycobacterium leprae, primarily attacks the peripheral nerves, skin and nasal lining. Untreated Lyme disease can spread from the skin to the joints, heart and nervous system.

Viruses reach the nervous system by different routes. The viruses behind viral meningitis enter through the nose or mouth and travel to the brain. Poliovirus spreads by the fecal-oral route and attacks the nervous system, and in serious cases causes paralysis that may be lifelong. West Nile virus arrives by mosquito bite, and most infected people have no symptoms; the danger comes if it reaches the brain.

Rabies virus binds receptors at the neuromuscular junction and spreads along nerves to the brain, rarely through the blood. Symptoms have historically taken 1 to 3 months to appear, and that window is the point of post-exposure treatment: shots given right away can prevent rabies, while once symptoms begin the disease is usually fatal. In a review of 122 fatal cases where those shots failed, the median was 20 days, with a range of 9 to 61.

These reach the brain three ways. Cryptococcus neoformans starts in the lung, enters the bloodstream and crosses the blood-brain barrier, though how it crosses is still not fully understood. Neurocysticercosis is pork tapeworm larval cysts lodged in brain tissue. Prion disease has no microbe at all: a normal host protein misfolds and assembles into aggregates, a process that can run for years before symptoms appear.