Learn Microbiology from scratch
1The world of microorganisms
Microbiology is the study of organisms too small to see without a microscope. Most of them are harmless or useful: the bacteria in your gut help digest food and keep harmful microbes out.
A microbe that causes disease is a pathogen. The main groups differ in structure, and the structure decides how you treat them:
- Bacteria are single cells without a nucleus (prokaryotes), about 1–5 micrometres long. They have their own ribosomes and usually a cell wall, so antibiotics can target them.
- Viruses are not cells. They are DNA or RNA inside a protein coat (capsid), about 20–300 nanometres, and they can only multiply inside a host cell. Antibiotics do not work on them.
- Fungi have a nucleus (eukaryotes). They include yeasts such as Candida, which causes thrush, and moulds.
- Parasites include protozoa, such as Plasmodium, which causes malaria, and helminths (worms), such as tapeworms and roundworms.
- Prions are misfolded proteins with no DNA or RNA at all. They cause rare brain diseases such as Creutzfeldt–Jakob disease.
Self-check Why does an antibiotic not cure influenza?
- Antibiotics only work on Gram-negative organisms
- Influenza bacteria are always resistant
- Influenza is a virus, which has no cell wall or ribosomes of its own
- Influenza is caused by a fungus
Answer: Influenza is a virus, which has no cell wall or ribosomes of its own. Antibiotics attack bacterial structures such as the cell wall and bacterial ribosomes. A virus has none of these and uses the host cell’s machinery. Calling influenza a bacterium is the core mistake.
2Bacteria: shape, stain and survival
Bacteria are first described by shape: cocci are round, bacilli are rods and spirilla are spirals. Cocci in clusters are typical of staphylococci; cocci in chains are typical of streptococci.
The Gram stain sorts bacteria by their cell wall:
- Gram-positive bacteria have a thick peptidoglycan wall that keeps the crystal violet dye. They stain purple.
- Gram-negative bacteria have a thin wall and an outer membrane. They lose the dye and take up the pink counterstain. The outer membrane contains endotoxin (lipopolysaccharide) and keeps many antibiotics out.
- Mycobacterium tuberculosis has a waxy wall and stains poorly with Gram. It is shown with an acid-fast stain (Ziehl–Neelsen).
Bacteria also differ in their need for oxygen. Obligate aerobes need it, obligate anaerobes are killed by it (for example Clostridium), and facultative anaerobes grow with or without it.
Bacteria reproduce by binary fission: one cell splits into two. Some, such as Clostridium and Bacillus, form endospores: tough resting forms that survive heat, drying and alcohol.
Many bacteria release exotoxins, proteins with a specific effect. Tetanus toxin causes muscle spasms; cholera toxin causes watery diarrhoea.
Bacteria can resist antibiotics, for example by making an enzyme that destroys the drug (beta-lactamase), pumping it out (efflux pumps) or changing its target. Resistance genes can pass between bacteria.
Self-check Which result do you expect for a Gram-positive bacterium?
- No colour, because it has no cell wall
- Pink, because it has an outer membrane
- Purple, because it has an outer membrane with endotoxin
- Purple, because its thick peptidoglycan wall keeps the crystal violet
Answer: Purple, because its thick peptidoglycan wall keeps the crystal violet. A thick peptidoglycan wall holds the purple dye. The outer membrane and endotoxin belong to Gram-negative bacteria, which end up pink.
3How infections spread and how we stop them
An infection needs a chain of infection. Breaking any link stops it:
- The agent: the pathogen itself.
- The reservoir: where it lives, such as a person, an animal, water or soil.
- The portal of exit, such as coughing, blood or faeces.
- The mode of transmission: contact (hands), droplets, airborne particles, food and water (faecal–oral) or a vector such as a mosquito.
- The portal of entry, such as the mouth, a wound or a urinary catheter.
- A susceptible host, for example a person without immunity.
The incubation period is the time from infection to the first symptoms. A disease that passes from animals to humans is a zoonosis. The basic reproduction number R0 is the average number of people one case infects in a fully susceptible population.
Hand hygiene is the most effective single measure against spread in hospitals. Alcohol rub does not kill spores, so after contact with Clostridioides difficile you wash with soap and water.
Sterilisation kills all microorganisms including spores, for example in an autoclave with steam under pressure at about 121 °C. Disinfection reduces microorganisms on objects but may leave spores. Antisepsis does the same on skin or tissue.
Vaccines train the adaptive immune system. They can contain live weakened microbes (MMR), killed microbes or parts of them, or mRNA that makes the cells produce one viral protein.
Self-check An instrument must be free of all microorganisms, including spores. Which process is needed?
- Antisepsis with chlorhexidine
- Disinfection with an alcohol wipe
- Pasteurisation
- Sterilisation, for example in an autoclave
Answer: Sterilisation, for example in an autoclave. Only sterilisation kills spores. Disinfection and antisepsis reduce the number of microbes but can leave spores; pasteurisation kills many pathogens in food but is not sterilisation.
4How to think through a microbiology question
Most questions describe an organism or a patient. Work from structure to consequence:
- Decide the group: bacterium, virus, fungus, parasite or prion.
- For bacteria, recall the key features: shape, Gram result, oxygen need, spores, toxins.
- Ask where the organism lives and how it spreads. This tells you how to prevent it.
- Ask how it causes harm: by invading tissue, by a toxin, or by an immune reaction.
- Let the structure guide treatment and control. No cell wall means penicillin cannot work; spores mean alcohol is not enough.
5A worked example
Follow the reasoning. Try to predict the next step before you open it.
Worked exampleA hospital patient has had broad-spectrum antibiotics for a week and now has profuse, foul-smelling diarrhoea. What is the likely cause, and how is spread to other patients prevented?
1Broad-spectrum antibiotics kill much of the normal gut flora. This gives room to a resistant organism that the normal flora usually keeps in check.
2The classic cause is Clostridioides difficile, a Gram-positive, spore-forming, obligately anaerobic bacillus.
3It releases toxins that damage the lining of the colon. This causes diarrhoea and, in severe cases, inflammation of the colon.
4Spores leave the body in faeces and survive for a long time on hands, toilets and bed rails. They enter the next person through the mouth: faecal–oral spread.
5Isolate the patient with contact precautions, wear gloves and an apron, and wash hands with soap and water because alcohol does not kill spores.
Clean the environment with a sporicidal agent, such as a chlorine product, and stop antibiotics that are not needed.
Answer C. difficile infection after loss of normal gut flora; prevent spread with isolation, gloves and apron, soap-and-water hand washing and sporicidal cleaning.
6Common mistakes
- Treating viral infections with antibiotics. Antibiotics act only on bacteria.
- Reversing the Gram colours. Gram-positive is purple; Gram-negative is pink.
- Mixing up endotoxin (part of the Gram-negative outer membrane) and exotoxins (proteins released by bacteria).
- Calling disinfection sterilisation. Only sterilisation reliably kills spores.
- Relying on alcohol hand rub for spore-forming organisms such as C. difficile.
- Thinking a person cannot spread an infection during the incubation period. For some infections they can.
Self-check A nurse cares for a patient with C. difficile diarrhoea. Which hand hygiene is needed afterwards?
- Alcohol hand rub only
- Alcohol hand rub twice
- Gloves, so no hand hygiene is needed
- Washing with soap and water
Answer: Washing with soap and water. Spores are not killed by alcohol, so they must be washed off mechanically with soap and water. Repeating the alcohol rub does not solve this, and gloves never replace hand hygiene.
7How exam questions look
- Easy (key terms and facts): definitions and classic organisms. What a pathogen or an incubation period is, which organism causes malaria, what colour Gram-positive bacteria stain.
- Medium (applying the concepts): mechanisms. How resistance works, why a vaccine or a sterilisation method works, how a toxin causes symptoms.
- Hard (cases and analysis): a patient or a classic study. You identify the organism from the history, explain why a test or treatment fails, or interpret experiments such as Griffith’s or John Snow’s.
For hard questions, start from the organism’s structure. Wall, envelope, spores and toxins explain most symptoms, test results and treatment choices.
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