Helicobacter pylori

What Helicobacter pylori is

Helicobacter pylori is a bacterium that has adapted to live in one of the most hostile places in the body, the acid lining of the stomach. It survives there by burrowing into the mucous layer and neutralising the acid immediately around itself. Once it settles in, it stays, often for life, unless it is deliberately treated.

Almost everyone who carries it was infected as a child, usually from close household contact. Catching it as an adult is uncommon. Exactly how it passes from person to person is still not settled, which is part of why there is no practical way to prevent it.

It causes inflammation of the stomach lining in everyone it infects. That inflammation is usually silent. The bacterium was only identified in 1982, by Barry Marshall and Robin Warren in Perth, work that overturned the belief that ulcers were caused by stress and acid alone and that earned them the Nobel Prize in 2005.

How common it is in Australia

Worldwide it is one of the most common chronic infections in humans. In Australia it has become steadily less common over the past few decades, which is thought to reflect better housing, smaller households and cleaner water supply during childhood rather than anything doctors have done.

Australian population studies collected between 1991 and 2002 showed the rate falling from 38 per cent to 15 per cent. Because the infection is acquired in childhood, that fall shows up as a difference between generations rather than a change within one person's lifetime. Studies in the early 2000s found around 40 per cent of Australians over 65 infected, and because the fall is generational rather than something that happens with age, the figure for today's older Australians is lower again. Rates in younger Australians are lower still.

It remains more common in Aboriginal and Torres Strait Islander communities, and in people who grew up in parts of Asia, the Middle East, Eastern Europe and South America. Men are slightly more likely to carry it than women, though the difference is small and it is common in both. For a gastroenterologist working in Western Sydney, where a large proportion of patients were born overseas, this is not a rare finding.

What it can cause

Most people who carry Helicobacter pylori have no symptoms and no disease from it. The reason it is taken seriously is that a minority develop something significant, and there is no reliable way to tell in advance who that will be.

Peptic ulcers

An ulcer is a break in the lining of the stomach or of the duodenum, the first part of the small bowel. Helicobacter pylori is the commonest cause worldwide, behind roughly 70 per cent of stomach ulcers and 90 per cent of duodenal ulcers. Someone who carries the bacterium has something like a 10 to 20 per cent chance of developing an ulcer at some point in life.

Most of the remaining ulcers are caused by anti-inflammatory painkillers, including ibuprofen (commonly known as Nurofen) and low-dose aspirin. Modern acid-lowering treatment heals almost all ulcers, but if the bacterium is left in place the ulcer is very likely to come back. Clearing it makes recurrence uncommon.

Stomach cancer

Helicobacter pylori is the single largest known risk factor for cancer of the stomach. Even so, the individual risk is low. The large majority of people who carry it never develop stomach cancer, and most of those who do are over 60. The risk is higher where the stomach lining has already changed, and a family history of stomach cancer raises it further.

Stomach cancer is uncommon in Australia but not negligible. Around 2,740 new cases and 1,187 deaths were estimated for 2025, and five-year survival was 40 per cent for people diagnosed between 2017 and 2021. That survival figure is the reason prevention matters more here than early detection does.

The bacterium is also the cause of a rare stomach lymphoma known as MALT lymphoma, which in its early stages can sometimes be treated by clearing the infection alone.

Other associations

Long-standing infection is one of the recognised causes of iron deficiency that has no obvious source of blood loss, so it is often tested for as part of that work-up. It is also associated with a low platelet count in a small number of people.

Who should be tested

Testing is worth doing when the result will change what happens next. In practice that means:

• Anyone with a peptic ulcer now, or a history of one.
• Anyone with ongoing indigestion, as an early step before or instead of a gastroscopy.
• People with a first-degree relative who has had stomach cancer.
• People found to have certain changes in the stomach lining on biopsy, such as atrophy or intestinal metaplasia.
• People with iron deficiency for which no other cause has been found.
• People about to start long-term anti-inflammatory medication or aspirin, in some circumstances.
• Anyone previously treated for it, to confirm the treatment worked.

The international position has shifted. Helicobacter pylori is now formally classed as an infectious disease, which carries the principle that anyone found to have it should be offered treatment rather than watched. In Australia that principle is applied with judgement: in an older person with no symptoms and other health problems, the side effects of a course of antibiotics may reasonably outweigh a small long-term benefit.

Testing everybody is a different question again. Some countries with high rates of stomach cancer, notably Japan and Korea, screen the population. Australia does not, because stomach cancer here is too uncommon for that to make sense.

How it is tested for

There are four tests in common use, and they answer slightly different questions.

Urea breath test

The most useful test for most people. It detects bacteria that are alive and present now, it is accurate and it involves nothing more than drinking a solution and breathing into a container. It is the test of choice both for making the diagnosis and for confirming that treatment has worked.

Stool antigen test

Also detects current infection, with accuracy close to the breath test. It is a practical alternative, and it is the usual choice in children.

Gastroscopy with biopsies

If a gastroscopy is being done anyway, for indigestion or for another reason, small biopsies answer the question at the same time and show the state of the stomach lining, which the other tests cannot. Several methods can be used on the sample, including a chemical test done during the procedure and examination under the microscope. A gastroscopy is not needed purely to look for the bacterium.

Blood test

A blood test detects the antibody the body makes in response to the infection. That antibody persists for months or years after the bacterium has gone, so a positive blood test cannot distinguish a current infection from an old one, and it is of no use for checking whether treatment succeeded. It still has a place in specific situations, such as during active bleeding from an ulcer, when the other tests become unreliable.

How it is treated

One medicine alone will not clear it. Treatment combines a medicine that strongly suppresses stomach acid with two or more antibiotics, taken together for a set course. The acid suppression is not there for symptom relief; the antibiotics work far better in a less acidic stomach.

The combinations in current use clear the infection in roughly 80 to 90 per cent of people, and that figure falls sharply if doses are missed. The course is short and the tablets are frequent, which makes it easy to lapse in the last few days once symptoms have settled. Finishing it exactly as prescribed is the single thing a patient controls that most affects whether it works.

Side effects are common and usually mild. A metallic taste, nausea, loose bowels and, less often, a rash. Some of the antibiotics used react badly with alcohol, so alcohol is avoided for the duration. Anyone who has reacted to an antibiotic before should say so before starting, because it changes which combination is chosen.

Why the recommended course has been getting longer

The bacterium has become harder to clear, because it has become resistant to one of the antibiotics most often used against it. Guidelines internationally have responded by lengthening the course to fourteen days and, in many cases, adding a fourth medicine. The standard Australian first course has been shorter.

Australian resistance has been rising too. Testing at one Australian centre over twenty years found resistance to that antibiotic climbing steadily and sitting above 20 per cent since 2010, and most of those patients had never been treated before, so this is resistance people already carry rather than resistance they acquired from a failed course. Among Australians whose first course has already failed, the figure is above 80 per cent.

The practical consequence is not alarming, but it is worth understanding. It means a first course is less certain than it once was, and it means the step that actually protects a patient is the test afterwards rather than the choice of tablets.

Why the test is repeated afterwards

This is the step most often missed, and it is the one worth insisting on.

Everybody treated for Helicobacter pylori should have a test afterwards to confirm it has gone. Symptoms are not a guide. Someone whose indigestion settles may still be carrying the bacterium, and someone whose symptoms persist may have cleared it and have a separate problem that needs a different answer. Without the test, neither is distinguishable.

The timing matters. The repeat test, usually a breath test, is done at least four weeks after the last antibiotic, and acid-lowering medication is stopped for two weeks beforehand. Testing earlier or while still on acid suppression can produce a negative result in someone who is still infected, which is the worst of both worlds.

When the first course does not work

In between one in ten and one in five people, a standard first course fails to clear the infection, and the figure is higher in some groups. That is expected rather than a sign that anything went wrong, and it is not a reason to give up.

The second course uses different antibiotics, chosen so as not to repeat what has already failed, and usually with stronger acid suppression and a longer duration. Success rates remain good at this stage.

Why later courses are harder to arrange

Some of the medicines used in second and third courses are not stocked by every pharmacy, are not covered by the Pharmaceutical Benefits Scheme, or are not registered for general use in Australia and have to be obtained through a special access pathway or a compounding pharmacy. None of that is a reflection on the medicines. It reflects how uncommon these courses are, and it is one of the practical reasons this point is where a gastroenterologist becomes useful.

Testing the bacterium rather than guessing again

If two properly taken courses have both failed, the approach should change. Rather than trying a third combination on probability, the bacterium itself can be tested to see which antibiotics it still responds to, either on a stool sample or on tissue taken at gastroscopy, and the next course chosen from that result.

This matters more than it used to. Australian work has found that among people whose treatment has already failed, resistance is common not only to the antibiotic used first but to several of the ones a second or third course would normally fall back on. Choosing blind at that stage risks another failed course and another round of side effects. Testing first is slower to arrange and considerably more likely to work.

Whether clearing it makes reflux worse

This question comes up often, usually because someone has read that the bacterium protects against reflux. The concern has a real origin. Long-standing infection can reduce how much acid the stomach produces, and in theory removing it allows acid production to recover.

The evidence does not bear out the worry in practice. In people who already have reflux, clearing the infection has not been shown to make the disease worse, and in some it improves. Reflux that appears after treatment is usually reflux that was already there, unmasked once the indigestion it was hiding behind has gone.

There is a consideration that runs the other way. In people who take acid-lowering medication continuously for years, carrying Helicobacter pylori at the same time is associated with more inflammation in the body of the stomach, which is why testing is often suggested before settling into long-term acid suppression.

More on this on the reflux and Barrett's oesophagus page.

After it has been cleared

Once the infection has genuinely gone, catching it again is unusual. The risk is in the order of half a per cent to one per cent a year, because most infections are acquired in childhood and adult transmission is uncommon.

Whether anything further is needed depends on what the stomach lining looked like. In most people the inflammation resolves and no follow-up is required. In a smaller group the biopsies show changes that have not fully reversed, such as atrophy or intestinal metaplasia, and those people are usually offered periodic gastroscopy because their long-term risk of stomach cancer stays somewhat above average.

Testing family members is not routine. It is worth discussing where there is a family history of stomach cancer, or where a household member has symptoms of their own.

If the symptoms persist after it is cleared

A proportion of people are treated successfully, confirmed clear and still have the indigestion that led to the test. That is a common and frustrating outcome, and it does not mean the treatment failed or that something has been missed.

Clearing the bacterium relieves symptoms in some people with indigestion, but not in most. Where symptoms persist and the tests are normal, the diagnosis is usually functional dyspepsia, which is a different problem with different treatment. That is covered on the indigestion and functional dyspepsia page.

Where Helicobacter pylori is managed in Sydney

A/Prof Viraj Kariyawasam is a consultant gastroenterologist and hepatologist. Helicobacter pylori, including infections that have not cleared after a first course of treatment, is managed at consultation in Norwest, Rouse Hill, Pennant Hills and Macquarie Park.

Where a gastroscopy is needed, it is performed at Norwest Private Hospital, Macquarie University Hospital and Pennant Hills Day Surgery. A referral from your GP is needed for a consultation.