Thousands of women were taken to hospital with chronic urinary tract infections in the past year, according to NHS figures that reveal a striking rise in the numbers seeking medical help for the condition.

More than 12,000 patients, the majority women, attended hospital with persistent urinary tract infections (UTIs) or cystitis last year, up from around 4,500 in 2001.

Experts warned that the increase could be linked to a crackdown on the prescribing of antibiotics by GPs owing to fears about antimicrobial resistance (AMR), resulting in some patients developing intractable infections that require admission to hospital.

Prof Jonathan Duckett, a consultant urogynaecologist and chair of the British Association of Urogynaecologists, said: “We’re on a drive to decrease antibiotic prescriptions … and the side-effect of the drive to cut antibiotic use is that you see more serious infections. That’s how I interpret it.”

Others said that antimicrobial resistance itself, which means that some infections can no longer be treated with first line drugs, could also be driving the trend.

Meghan Perry, a senior clinical research fellow at the University of Edinburgh, said there is evidence that the more courses of antibiotics a patient receives, the more likely they are to have a multi-drug resistant infection. “Sometimes that means you run out of options that are able to treat the infection in the community and you need to come in for an IV drug,” she said.

Perry said this did not rule out prescribing practices also playing a role. “It’s hard to dissect and there could be multiple factors,” she said.

Overall admissions for UTIs generally (as opposed to persistent infections) also more than doubled, from 73,000 in 2001 to 172,000 last year and the figures ramp up steadily year on year.

Figures obtained independently by the patient campaign group Cutic also showed a 54% increase in A&E admissions for UTI between 2012 and 2016 and a 34% rise in diagnoses of urosepsis, a life threatening complication.

For most women getting a UTI is an unpleasant, but short-lived experience. The symptoms include blood in the urine, a burning sensation when peeing and feeling like you need the toilet all the time. But a small proportion – about 2% – develop recurrent or continuous infections, which can have a major impact on their lives.

There are no Nice guidelines for how to treat chronic UTIs and there is disagreement among doctors. Patients have described the difficulty in getting their condition diagnosed and navigating between GPs and specialists to get treatment.

Recent research has revealed that a dipstick urine test that is widely used by GPs is hugely unreliable, missing up to 50% of infections. Even when samples are sent for full analysis at microbiology labs, there are limits to which bacteria can be detected: common pathogens like E coli will normally be spotted, but if a rarer bacterial species is causing the infection, this might not be flagged.

Prof James Malone Lee, a recently retired NHS consultant who continues to run a private practice in London said a continued reliance on inadequate tests means that patients are sometimes wrongly told that antibiotic medication won’t help. Many of these women, he said, are being diagnosed with “interstitial cystitis” (meaning cystitis symptoms, but with no evidence of an infection) or painful bladder syndrome.

“It is a dreadful psychological ordeal to suffer like this and yet be told by your doctor that there is nothing wrong because of the result of a test,” he said.

Malone Lee has pioneered an approach that involves giving women months or even years of antibiotics to patients until their symptoms clear and a published review of outcomes for 624 women treated over 10 years at his Hornsey central health centre clinic suggests the approach has been effective.

However, some doctors are concerned about potential side-effects for patients and the risk of fuelling the problem of antimicrobial resistance and believe more extensive trials are needed.

Malone-Lee said that the requirement for very long courses of treatment is supported by research showing that bacteria can colonise the bladder wall, rather than simply floating around inside. In some patients, the bacteria form biofilms or even burrow inside cells to form “nests” which lie dormant and untreatable for months at a time. When cells in the bladder wall are shed during the tissue’s natural regeneration process, the dormant bacteria is released, re-activating the infection.

Dr Catriona Anderson, a GP specialised in treating UTIs agreed that a shift towards prescribing three-day courses of antibiotics meant that some patients were being left with residual infection.

“If you have a thousand enemy soldiers coming over the hill, you don’t just send in a single sniper,” she said. “You need to go in and hit the infection hard. If you just tickle the bug with an insufficient dose of antibiotic, you drive resistance.”

Duckett said that despite the increase in numbers being admitted to hospital there has not been major progress in developing new drugs or treatment strategies in what some view as an “entirely unglamorous” area of medicine.

Case study

Kirstin Lavender: ‘I woke up with an infection and it didn’t leave for four years.’ Photograph: Christopher Thomond/The Guardian

When Kirstin Lavender, 46, woke up with a low, dull stomach ache a couple of weeks after her 40th birthday, she was not unduly alarmed. “I said to my husband, ‘I think I’ve got a UTI coming on’,” she recalls. Like most women, she’d had the occasional bout of cystitis, but this time things were different.

At the GP surgery, she was given a dipstick test which suggested a low level infection and was given a three-day course of antibiotics. But instead of clearing the infection, she began to feel worse. “The pain was going up into my kidneys,” she says.

When she returned to the doctors and had another urine test it came back negative and she was told to head home and return if she was still feeling unwell in a week. “I thought, ‘But I’m unwell right now,’” she says.

This marked the beginning of a four-year ordeal, during which her illness never went away. “I woke up with an infection and it didn’t leave for four years,” she says.

After taking time off sick, Lavender eventually handed in her notice at the hospital where she worked as a mortician. She lost friends because she couldn’t go out and socialise and missed out on spending time with her then three-year-old daughter.

She was plagued by bladder pain and the constant sensation of being desperate for the toilet. But urine tests came back as negative for an infection and repeated short courses of antibiotics seemed to barely touch her symptoms. “It was just getting gradually worse and worse,” she says.

The lack of any concrete diagnosis and the frequency of her visits led one GP to suggest, while pointing to his own stomach, “The problem’s not in here, I think it’s in here,” moving his finger to tap the side of his head.

“You get treated basically like a hypochondriac,” she says. “You feel ashamed.”

Eventually, after advice on patient forums, she sought an appointment with Prof James Malone Lee, who runs a specialist clinic in London. His approach of prescribing long courses of antibiotics has won support among patients, but remains controversial within the medical profession.

Lavender ended up taking antibiotics almost continuously for 26 months before she came off drugs completely and says that she has now made a full recovery. “I cycle into Leeds every day, I run, I swim, I’ve got a completely normal life now,” she says. “I do everything with my daughter that I couldn’t do for a few years.”

The latest NHS Digital data gives a breakdown of figures for both chronic cystitis and chronic interstitial cystitis. These numbers were combined to give the chronic UTI figures in this piece (both diagnoses, taken separately, also show an increase).