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Why Do Antibiotics Stop Working?

Topic 28 · Grades 9–12 · Natural selection in action

What this builds on from class
In this unit 9 sections
  1. What an antibiotic does
  2. Four ways to survive
  3. Resistant before the drug arrives
  4. Counting the change
  5. The drug in the environment
  6. Why two drugs at once
  7. Slowing it down
  8. Questions
  9. Where to go next

In September 2011, doctors at Patan Hospital and the Civil Service Hospital in the Kathmandu valley began a careful test of two medicines for typhoid, a fever caused by bacteria in dirty water and food. One was gatifloxacin, a tablet related to the ciprofloxacin that had cured typhoid in Nepal for years. In July 2014 the test was stopped early. Typhoid bacteria had appeared that the tablets could no longer kill, and in patients whose blood held typhoid bacteria, the tablets now failed one time in four.

Nobody had made a new disease. The bacteria were still typhoid bacteria. But something about them had changed, in a few years, in the bodies of people being treated in Nepal and India. That change is evolution by natural selection, the same process that shaped giraffes and tigers over millions of years, happening fast enough to measure. This topic shows how, with the numbers.

What an antibiotic does

An antibiotic is a medicine that kills bacteria, or stops them multiplying, without harming your own cells much. You met the first one, penicillin, in Grade 9 Grade 9: Kingdom Fungi, and in Grade 8 that antibiotics do nothing against viruses Grade 8: Negative effects.

How can a medicine tell a bacterium from your cells? Bacteria are prokaryotes, built differently from you Grade 9: Kingdom Monera. Each antibiotic attacks one part that bacteria have and your cells don’t, or that is shaped differently in them. That part is the drug’s target.

  • Penicillin and its relatives (amoxicillin, ceftriaxone) stop a bacterium building its cell wall. Your cells have no cell wall. A bacterium that grows without a proper wall bursts.
  • Azithromycin and tetracycline jam the bacterium’s ribosomes, the machines that make proteins (How does a gene make a protein?). Bacterial ribosomes are a different shape from yours.
  • Ciprofloxacin stops an enzyme the bacterium needs to copy its DNA.

The drug fits its target the way a key fits a lock. If the lock changes shape, the key no longer works.

A colorized electron microscope picture of a heap of golden-brown, rod-shaped bacteria on a rough surface, against a black background, with a 1 µm scale bar
Figure 28.1 E. coli bacteria, photographed through an electron microscope at 10,000 times. Each rod is about 2 µm long: 500 of them end to end would span a millimeter. A few kinds of E. coli cause diarrhea and urine infections; most live harmlessly in your gut. Photo: Photo by Eric Erbe, digital colorization by Christopher Pooley, both of USDA, ARS, EMU., Public domain

Your friend has a cold and asks for an antibiotic “to be safe”. What is the best reply?

Pick an answer to see why.

Four ways to survive

A bacterium that survives a drug that kills others of its kind is resistant to it; one that is killed is susceptible. A hospital laboratory finds out which by spreading bacteria from a patient on a dish of jelly and laying small paper discs on it, each soaked in a different antibiotic. Where a drug kills the bacteria, a clear ring forms around its disc.

A square dish covered in a pale streaky film of bacteria, with sixteen small white paper discs in rows; around most discs is a dark clear circle with no bacteria, of different sizes, but around one the bacteria grow right up to the paper
Figure 28.2 A test of which antibiotics work on Staphylococcus aureus bacteria. Each paper disc holds a different antibiotic. A clear circle means the drug stopped the bacteria. Where the bacteria grow right up to a disc (bottom row, second from left), they resist that drug. Photo: Dr Graham Beards, CC BY-SA 4.0

Resistance comes down to a few tricks, each made by a gene.

1 An enzyme breaks the drug2 A pump throws it out3 The target changes shape:the drug no longer fits4 Fewer openings:less drug gets incell wallcell membraneDNAplasmidribosomedrug moleculeA copy of the plasmidpasses to anotherbacterium
Figure 28.3 Four ways a bacterium survives an antibiotic, and how the gene for one can pass to another bacterium. Not to scale: the drug molecules and proteins are thousands of times smaller than drawn.
  1. Break the drug. An enzyme cuts the drug molecule before it can act. Penicillinase (one of the β-lactamases) breaks open the ring in penicillin that does the damage.
  2. Pump it out. Proteins in the cell’s membrane pump the drug out as fast as it gets in.
  3. Change the target. A small change in the gene for the target changes its shape a little. The cell still works, but the drug no longer fits.
  4. Keep it out. Fewer openings in the cell’s outer layer let less of the drug in.

The genes for these tricks come in two ways. A mutation, a copying error in the bacterium’s own DNA, can change a target (trick 3) or turn up a pump. And many bacteria carry small extra rings of DNA called plasmids, which they can copy and pass to a neighbor through a thin tube, even to a different kind of bacterium. A plasmid can carry the genes for several tricks at once. This is why one bacterium can become resistant to five or six drugs in a single step.

A plasmid carrying a gene for penicillinase passes from a resistant bacterium to a susceptible one. What happens?

Pick an answer to see why.

Resistant before the drug arrives

Does an antibiotic make some bacteria resistant, the way exercise makes muscles strong? Or were the resistant ones already there, by chance, before the drug arrived? In Grade 9 you saw that Darwin’s natural selection needs variation first: the giraffes’ necks already differed before the drought Grade 9: Natural selection. For bacteria, nobody knew until 1943.

A black-and-white photograph of a man in glasses, a white shirt and a striped tie, talking at his desk in an office with bookshelves, a telephone and diagrams pinned to the wall
Figure 28.4 Salvador Luria at his desk at the Massachusetts Institute of Technology, around 1969, the year of his Nobel Prize. Photo: U.S. National Library of Medicine, Public domain

The fluctuation test

Twenty cultures of the same bacteria are grown, then each is spread on a dish with the drug. Each dot is a colony grown from one resistant bacterium. Compare the two explanations, then grow new sets of cultures and see if the pattern holds.

1202211012801211414031128
Explanation:
A new set of 20:
Average per dish
10.1
Fewest to most
0 to 128
Dishes with none
3

If mutations happen by chance while the cultures grow, most cultures get a late mutant or none, and a few get an early one that doubles and doubles: a jackpot. This is what Luria and Delbrück saw.

A model: each culture grows from one bacterium to about 134 million; with chance mutations, each division has a 1 in 100 million chance of making a resistant mutant. The other explanation is set to give about 8 per dish.

Look at the spread, not just the average. If the drug caused resistance, the dishes would differ only a little, the way coin tosses do. With chance mutations, they differ enormously. In 1952 Joshua and Esther Lederberg went further: by copying dishes of bacteria onto fresh dishes with a pad of velvet, they picked out bacteria resistant to streptomycin from a population that had never touched the drug.

So the drug doesn’t create resistance. It finds the rare bacteria that already have it.

Counting the change

How fast does a rare resistant bacterium take over? Count it, generation by generation.

Bacteria multiply fast. In a warm flask with plenty of food, E. coli divides about every 20 minutes; in the body usually more slowly, but still far faster than any animal breeds. You and your parents are one human generation apart, about 25 years. In 25 years, E. coli in a flask could pass through over 600,000 generations. That is why we can watch bacteria evolve.

Here is a simple model of an infection being treated, with numbers made up to be easy to follow, but in the right range:

  • At the start there are 1,000,000 susceptible bacteria and 1 resistant one.
  • Each generation, the drug kills 9 out of every 10 susceptible bacteria; the survivors divide in two. So the susceptible ones are multiplied by 0.1 × 2 = 0.2 each generation.
  • The resistant ones are not harmed. But resistance costs a little: making an extra pump or enzyme uses food and energy. Say they leave 5% fewer offspring, so they are multiplied by 2 × 0.95 = 1.9 each generation.

Watch the share change

Here is the same model, with a sample of 50 of the bacteria shown above the graph. Give the drug for a few generations, then stop it, and watch how the share of resistant bacteria changes.

susceptibleresistantantibiotic given02550751000102030405060% resistantgeneration
Antibiotic:
Time:
Generation
0
Resistant
1 in 1,000,001
Resistant in the sample of 50
0

One bacterium in a million is resistant. Press Next generation and watch the share.

A model with made-up numbers: the drug kills 9 in 10 susceptible bacteria each generation; resistant ones leave 5% fewer offspring; only the shares are shown, as if there were always room for the survivors to multiply; no chance, no immune system.

The graph has the shape of a stretched letter S. For generations nothing seems to happen: one in a million, one in a hundred thousand, still too few to find in a sample. Then, within two or three generations, resistant bacteria become most of the population. Doctors often notice resistance only at this point, when a drug that worked last year suddenly fails.

Stop the drug, and the cost of resistance shows: the susceptible ones now leave a few more offspring, and the resistant share slowly falls. But far more slowly than it rose: the drug gave the resistant ones a huge advantage; without it, their disadvantage is small.

In a model like the one above, the drug kills more of the susceptible bacteria each generation (the drug is stronger). What happens to the time it takes for resistant bacteria to become most of the population?

Pick an answer to see why.

The drug in the environment

Natural selection always works the same way: where something in the surroundings, a predator, the cold, a drought, or a drug, kills some variants more than others, the share of the survivors’ genes rises. Change the surroundings, and the share changes. Antibiotics give us unusually clear evidence of this, because we know exactly where the drug is and how much.

The giant dish

A model of the MEGA-plate. Bacteria start at both ends. They can only move into a stronger band after a new mutation lets them live there. Watch where the mutations happen, then run it again: the steps are the same, but where and when they happen changes each time.

Drug: × the dose that stops the original bacteria03×30×300×3,000×300×30×3×0Resistance mutations:01234
Strongest drug reached
0
Mutations that broke into stronger drug
0

Bacteria are at both ends, where there is no drug. Press Start.

A model of the real experiment, with made-up chances: bacteria spread into a patch they can live in, and a new mutation lets a few into a band one step stronger. Colors show how many resistance mutations a patch’s bacteria have.

The same thing happens outside the laboratory, with real numbers.

  • When a drug is used less, resistance to it falls. In Finland in the early 1990s, doctors were asked to give fewer macrolide antibiotics (erythromycin and its relatives) for throat and skin infections. Macrolide use fell from 2.40 to 1.38 doses per 1,000 people a day between 1991 and 1992, and then stayed low. The share of throat and skin streptococci resistant to erythromycin fell from 16.5% in 1992 to 8.6% in 1996.
  • When the drug changes, the bacteria change. In Nepal and India in the late 1980s and the 1990s, many typhoid bacteria became resistant to the old drugs chloramphenicol, ampicillin and co-trimoxazole. Doctors moved to ciprofloxacin. In the years after, typhoid resistant to the old drugs became uncommon, while resistance to ciprofloxacin rose, until the 2014 trial in Kathmandu found it failing.
  • Where antibiotics are used more, resistance is commoner. Hospitals, where many patients take antibiotics, have more resistant bacteria than homes do. Farms where chickens are fed antibiotics to make them grow faster have more resistant bacteria in the chickens and in the soil around them. This is why many countries, Nepal among them, have banned colistin, one of the last drugs that still work on some resistant bacteria, for farm animals.

In Finland, resistance to erythromycin fell after doctors used it less. Which explanation fits natural selection best?

Pick an answer to see why.

Why two drugs at once

Tuberculosis (TB), caused by the bacterium Mycobacterium tuberculosis, is still one of the commonest serious infections in Nepal. It is never treated with one drug. Patients take a combination, usually four drugs for the first two months. The reason is a calculation of chances.

The lung of a person with advanced TB can hold a cavity containing roughly 100 million (10⁸) TB bacteria. Spontaneous mutants resistant to the main TB drugs turn up at about these rates:

Drug Resistant mutants in an untreated population (roughly)
isoniazid 1 in 1,000,000 (10⁶)
rifampicin 1 in 100,000,000 (10⁸)
ethambutol 1 in 100,000 (10⁵)

The mutations for different drugs are in different genes, and happen independently. The chance that one bacterium has both is the product of the two chances: just as the chance of two sixes with two dice is 1/6 × 1/6 = 1/36.

some already therealmost certainly none10⁻¹²10⁻⁹10⁻⁶10⁻³110³bacteria expected to resist, out of 100 million (each step is 10 times the last)ethambutol alone1,000isoniazid alone100rifampicin alone1isoniazid + rifampicin1 chance in a millionall three together1 chance in 100 billion
Figure 28.5 How many bacteria in a TB cavity of 100 million are expected to be resistant already, before treatment starts, to each drug alone, and to two or three drugs together. Each step on the scale is ten times the one before.

When TB treatment goes wrong, with doses missed or drugs taken alone, multidrug-resistant TB (MDR-TB) can evolve: TB that isoniazid and rifampicin no longer kill. The WHO estimated that in Nepal in 2018 about 2 in every 100 new TB patients, and about 15 in 100 patients who had been treated before, had TB resistant to rifampicin. It can still be cured, but with longer treatment and harder drugs. The same reasoning about chances is why HIV is treated with three drugs at once.

Slowing it down

You can’t stop bacteria mutating. But resistance spreads only where antibiotics are used, so how we use them decides how fast it happens. The public-health messages from the WHO and Nepal’s health services:

  • Take antibiotics only when a qualified doctor or health worker prescribes them, and never for colds or flu, which are caused by viruses.
  • Take them exactly as prescribed: the right dose, at the right times, for as long as the doctor says.
  • Don’t share them, and don’t use leftovers. The drug for someone else’s illness may be the wrong one for yours.
  • Don’t buy them without a prescription. Studies in Nepal have found that between two-thirds and nearly all of the pharmacies visited would sell antibiotics without one (as of 2022).
  • Prevent infections, so that fewer antibiotics are needed: wash hands with soap, drink safe water, and get vaccinated. In April 2022 Nepal gave a typhoid vaccine to more than 7 million children aged 15 months to 15 years, and it is now part of every child’s routine vaccinations at 15 months.

In 2024 Nepal’s government adopted a National Action Plan on Antimicrobial Resistance (2024–2028), covering hospitals, pharmacies, farms and food together, because resistant bacteria move between all of them.

Questions

A patient with a bacterial infection is given an antibiotic. Which statement about the resistant bacteria in her body is correct?

Pick an answer to see why.

In a population, resistant bacteria are 1 in 1,000. Under a drug, the ratio of resistant to susceptible bacteria is multiplied by 10 each generation. About what share is resistant after 3 generations?

Pick an answer to see why.

a.

Explain, using the ideas of variation, inheritance and selection, how a population of bacteria becomes resistant to an antibiotic.

Answer
  1. Variation: the bacteria in a population are not all the same. By chance mutation, or by receiving a plasmid, a few carry a gene that lets them survive the drug.
  2. Inheritance: when a bacterium divides, both daughters get a copy of its DNA, so the offspring of a resistant bacterium are resistant too.
  3. Selection: the antibiotic kills the susceptible bacteria, or stops them multiplying, while the resistant ones survive and multiply.
  4. Generation after generation, the share of resistant bacteria rises until most of the population is resistant, and the drug no longer cures the infection. Because bacteria divide so fast, this can happen within days in one patient, and over a few years in a whole country.
b.

A student grows 10 cultures of the same bacteria, each from a few cells, then spreads each on a dish with an antibiotic and counts the resistant colonies. These are made-up numbers, in the pattern of real experiments.
Set A: 12, 9, 14, 11, 10, 13, 8, 12, 11, 10
Set B: 0, 1, 0, 3, 0, 107, 2, 0, 5, 1

  • a.Find the average (mean) number of colonies in each set.
  • b.Which set fits the idea that the antibiotic causes resistance, and which fits the idea that resistance arises by chance mutations while the bacteria grow? Explain.
Answer
  • a.Set A: total 110, mean 110 ÷ 10 = 11. Set B: total 119, mean 119 ÷ 10 = 11.9. The means are nearly the same.
  • b.Set A fits “the drug causes resistance”: if every bacterium has the same small chance of being changed when it meets the drug, every dish gets about the same number, with a small spread (8 to 14). Set B fits “chance mutations before the drug”: in most cultures a mutation happened late, or not at all, giving few or no colonies; in one, a mutation happened early, and its descendants doubled many times, giving a “jackpot” of 107. The huge spread, not the average, is the evidence. Luria and Delbrück’s real results looked like Set B.
c.

In Finland, macrolide antibiotic use fell from 2.40 to 1.38 doses per 1,000 people a day between 1991 and 1992, and stayed low. Erythromycin resistance in streptococci was 16.5% in 1992 and 8.6% in 1996.

  • a.By what percentage did the use of macrolides fall?
  • b.By what percentage did the share of resistant bacteria fall between 1992 and 1996?
  • c.Explain the change in resistance using natural selection.
  • d.Why can’t these numbers alone prove that using less of the drug caused the fall?
Answer
  • a.(2.40 − 1.38) ÷ 2.40 × 100% = 1.02 ÷ 2.40 × 100% ≈ 43%.
  • b.(16.5 − 8.6) ÷ 16.5 × 100% = 7.9 ÷ 16.5 × 100% ≈ 48%: resistance almost halved.
  • c.With less of the drug around, resistant bacteria had less advantage, while resistance still had a small cost. Susceptible bacteria left slightly more offspring each generation, so their share rose and the resistant share fell. The fall took years because the cost is small: selection without the drug is weak.
  • d.Something else might also have changed in those years, for example which strains of streptococci were spreading. A fall in resistance at the same time as a fall in use is evidence, and it fits what selection predicts, but stronger evidence would come from comparing places that cut their use with places that didn’t, or from following the same strains over time.
d.

A TB patient feels better after two weeks and starts taking only one of his four drugs, to “save money”. Using the idea of chances, explain why this is dangerous.

Answer

In a large TB infection, there are almost certainly some bacteria resistant to any one drug: for isoniazid, about 1 in a million, so about 100 in a cavity of 100 million. While all the drugs are taken together, each drug kills the bacteria that resist the others; a bacterium resisting all of them at once is so unlikely (around 1 in 10¹⁹ for three drugs) that there is almost certainly none. With one drug alone, the bacteria resistant to it survive and multiply, and the patient’s TB becomes resistant to that drug. Later, the same can happen with another drug, step by step, until he has multidrug-resistant TB, which is harder to cure and can spread to his family. (He should go back to his health worker, who can help with the cost: TB treatment in Nepal is free.)

e.

The WHO reported that in 2023 about 1 in 3 laboratory-confirmed bacterial infections in its South-East Asia Region was resistant, compared with about 1 in 10 in Europe.

  • a.Give two possible reasons, linked to natural selection, for the difference.
  • b.Only infections tested in a laboratory are counted. Why might this make the share of resistant infections look higher than it is among all infections, especially where tests are less common?
Answer
  • a.Possible reasons: antibiotics may be used more, or more often without a prescription, so resistant bacteria are favored more often; more infections spread through unsafe water and crowding, so resistant bacteria pass between people more; antibiotics may be used more on farms. More selection and more spread both raise the share of resistant bacteria.
  • b.Where laboratory tests are expensive or far away, people are often tested only when they are very ill, or when a first antibiotic has already failed. Those are exactly the infections most likely to be resistant. So the tested infections are not a fair sample of all infections, and the share of resistant ones among them may be higher than among all infections. Comparing regions needs samples chosen in the same way.
f.

The model in “Watch the share change” is simple. List three of its simplifications, and say for each how a real infection is different.

Answer

Any three of these, or others that are true:

  1. The numbers are fixed (the drug kills exactly 9 in 10 susceptible bacteria; resistant ones always leave 1.9 offspring). In real life the drug’s level in the body rises and falls between doses, and so does how many it kills.
  2. It has only two kinds of bacteria. Real resistance often comes in degrees, built up mutation by mutation, as on the MEGA-plate.
  3. It ignores chance: with only one resistant bacterium at the start, in reality it might die before dividing, and the infection could be cured.
  4. It ignores the immune system, which kills bacteria of both kinds and often finishes off a small infection.
  5. It ignores plasmids passed between bacteria, new mutations during treatment, and bacteria arriving from other people.
  6. It holds the population’s shares only, as if there were always room for the survivors to multiply; in the body, numbers fall as the drug works.

Where to go next