Microorganisms and their groups

Once a bacterium has been grown from a patient’s sample, the first question is what its wall looks like, and the Gram stain answers it. A violet dye is applied and fixed with iodine; alcohol is then used to decolourise; a red counterstain follows. Bacteria with a thick peptidoglycan wall retain the violet and appear purple — Gram-positive, as many staphylococci and streptococci are. Bacteria with a thin peptidoglycan layer and an outer lipid membrane lose the violet, take up the counterstain and appear pink — Gram-negative, as Escherichia coli is. The wall is not only a laboratory label; it is a drug target. Penicillin and the related beta-lactams block the enzyme that cross-links peptidoglycan strands, so a growing bacterium cannot maintain its wall. Water then enters by osmosis, the cell swells and bursts. Human cells have no wall and no peptidoglycan, and that absence is exactly what makes the attack selective: the drug damages the bacterium far more than the patient. Fungi present a different wall — chitin, the material of an insect’s shell — which is why an antibacterial does nothing for ringworm and an antifungal must target chitin synthesis or the fungal membrane instead. Three nursing habits follow from this. Take the specimen before the first antibiotic dose, so the laboratory can still grow the organism. Never read a Gram stain as a species name: the colour narrows the group but not the identity. And complete an antifungal course, because a fading rash does not prove the fungus has gone.

Binary fission looks harmless in a diagram, but its arithmetic is the reason food safety matters. Each division doubles the population, so the count after n generations is two to the power n. In warm food, a bacterium such as Escherichia coli can divide roughly every 20 minutes: three divisions an hour, eighteen in six hours, which is 2^18, or about 262,000 cells — and millions if the dish is left overnight. Growth is not linear; it explodes at the end, which is why a dish that seemed safe at noon can be dangerous by evening. Generation time is not fixed. Cold, dryness, acid and competition from other organisms slow it down, and that is the whole logic of refrigeration and of the rule to refrigerate cooked food within about two hours at room temperature. Viruses follow a different arithmetic because they do not divide at all. A virus particle attaches to a host cell, injects its nucleic acid, and uses the cell’s ribosomes and enzymes to make hundreds of new copies, which are released and infect neighbouring cells — so viral numbers rise only where living cells are available. Bacteria have a third trick as well: some form endospores by sporulation, a dormant state that resists heat, drying and many disinfectants. A spore is not reproduction, it is survival, and it germinates when conditions improve. This explains why alcohol hand rub may not kill Clostridioides difficile spores, so soap and water or chlorine are used instead, and why reusable instruments are autoclaved at about 121 °C under pressure for at least 15 minutes rather than simply wiped.

Three useful microbial processes deserve their mechanisms. Fermentation is the breakdown of sugars without oxygen: yeast converts sugar into ethanol and carbon dioxide, which makes bread rise and gives beer and wine their alcohol, while lactic-acid bacteria turn lactose into lactic acid and thicken milk into yoghurt. The microbe is not trying to help us; it harvests energy without oxygen, and we borrow the by-product. Nitrogen fixation is the work of the enzyme nitrogenase, found in soil bacteria such as Rhizobium that live inside nodules on legume roots. Nitrogenase converts inert nitrogen gas into ammonia, a form plants can absorb, which is why farmers rotate cereals with beans or groundnuts: the legume feeds the bacterium sugar, and the bacterium fertilises the soil for the next crop. Antibiotics came out of the same microbial world: in 1928 Alexander Fleming noticed that a Penicillium mould killed the bacteria around it, and penicillin — a secondary metabolite the fungus makes for competition — became the first of many antibiotics, most of which originate in soil bacteria and fungi. Their overuse creates the counter-mechanism: bacteria carrying an enzyme such as beta-lactamase, or a resistance gene on a plasmid, survive treatment and pass the gene to neighbours by conjugation — one of three gene-sharing routes. Transformation is the uptake of free DNA from the surroundings, transduction is DNA carried from one bacterium to another by a bacteriophage, and conjugation is a bridge built to a neighbour to transfer a plasmid directly. Nursing practice follows directly: give antibiotics only when a bacterial infection is likely, take cultures first, complete the prescribed course, never use leftover antibiotics, and expect that broad-spectrum drugs disturb the normal flora, which is why oral thrush or antibiotic-associated diarrhoea can follow a course.

Treating an infection begins by placing the microbe in a group, because the group predicts both the drug and the diagnostic test. A bacterium has a peptidoglycan wall, so an antibacterial can attack the wall, the ribosome or a bacterial metabolic pathway. A fungus has a chitin wall and a eukaryotic membrane, so it needs an antifungal such as a topical azole or terbinafine. A protist is a eukaryote like our own cells, so an antiprotozoal drug must exploit some difference in its metabolism; this is why malaria, caused by a Plasmodium protist, is treated with artemisinin-based combination therapy and not with penicillin. A virus has none of these structures, so antibiotics are useless and treatment is supportive, with antivirals only for certain viruses. The group also decides what the laboratory can see. An ordinary light microscope resolves bacteria and fungi — a Gram stain of a wound swab, or a potassium hydroxide preparation of a skin scraping — but viruses at 20 to 250 nanometres lie below its limit, so viral diagnosis relies on antigen tests or nucleic acid amplification such as PCR, and viral culture needs living cells. Standard precautions, by contrast, do not change with the group: hand hygiene, gloves, safe sharps disposal and cleaning physically remove or destroy organisms whatever their cell type. The exception is the spore, which survives alcohol and drying and demands soap and water, chlorine or steam. So the nurse does not need a species name to give safe care; she needs the group to know whether a drug can ever work.