Such advice is deeply ingrained in medical policy and practice.
The longer these bacteria are exposed to antibiotics, the greater the pressure to select for resistance to the drugs, which can then be passed on to other bacteria of different species.
Those numbers are expected to increase significantly in the coming years.
Researchers say it is now time to drop the "complete the course" message for antibiotics as it is not backed up by evidence and should be replaced.
There was no evidence that this was because of resistance, but the experience may have planted the idea that prolonged therapy was needed to avoid treatment failure.
Nearly 90 years ago, Scottish researcher Alexander Fleming discovered penicillin and ushered in a wave of new medications, all derived from bacteria in the soil beneath our feet.
The HSE said it could not comment.
This review challenges current medical advice by suggesting that concerns around antibiotic treatment are driven by fears of "under-treatment", where the course of antibiotics doesn't last long enough to clear any infection, when the concern should be more about over-use.
"Any implementation in a change of national guidance needs to be explicit on the information given to patients by pharmacists dispensing antibiotic prescriptions, but more importantly to ensure that any leftover antibiotics are returned to a pharmacy for destruction, and not re-used for new infections by the patient or others", he said.
In hospitals, patients are often treated with antibiotics only until tests show they have recovered from infection. In many previously healthy patients with acute infections, letting them stop the antibiotics once they feel better has considerable appeal.
Completing the course also contradicts one of the most fundamental and widespread medication beliefs people have, which is that we should take as little medication as necessary, they argued.
Royal Pharmaceutical Society spokesman and consultant pharmacist Dr Kieran Hand, said the article was a welcome opening of the debate in the United Kingdom on the relationship between the length of a course of antibiotics, efficacy and resistance.
"The relation between antibiotic exposure and antibiotic resistance is unambiguous both at the population level and in individual patients".
Bacteria have developed multiple tactics to boost their resistance, depending on the infection and antibiotic involved.
Public health education around antibiotics needs to highlight that antibiotic resistance is the result of the overuse of antibiotics by patients, and that it can not be prevented by completing a course.
But she agreed that more clinical trials are needed to understand more about whether courses should be completed, and that people should then take any new evidence into account when guidelines are updated.
Overprescribing antibiotics to a patient raises concerns not only about antibiotic resistance, Osterholm explained, but also about disrupting the patient's microbiome - the normal, healthy and protective organisms that live on and within each of us.
However, Seamus Martin, Smurfit Professor of medical genetics at Trinity College in Dublin, said last night he believed patients should finish the course.
"We don't want, in some instances, to cause patients to have a relapse in their infection", he said.
The researchers say that some diseases such as tuberculosis can become resistant if the drugs are not taken for long enough - but this is not the case with most illnesses. "We always need to be asking, 'What do we know?' 'How do we know it?' and 'Why do we know it?'"
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