Three-quarters of Year 13 students eligible for the meningitis B vaccine have not taken up the offer available through pharmacies, public health officials warn.

Raising concerns about the numbers left unprotected, the UK Health Security Agency (UKHSA) urged individuals to seek out the jab – especially university freshers who are at particular risk.

The figures come from the first interim report on MenB vaccine uptake for the one-off campaign targeting 17 and 18-year-olds in Year 13 and young adults under 25 years starting university or further education colleges.

By 20 September only 212,549 of the 799,840 17 and 18-year-olds eligible for the vaccine (26.6%) had been vaccinated, uptake figures show.

The vaccination offer – in which young people are being encouraged to book with pharmacies through an NHS booking system – was introduced after a large outbreak in Kent in March which led to 21 cases and two deaths.

Two further clusters had been reported in Weymouth and Reading in which another young person died.

UKHSA researchers have identified genomic changes in the bacteria that they believe enabled it to spread so quickly and cause severe disease. Similar outbreaks could happen again, they said.

GP leaders had already warned that pharmacies were struggling with the rollout of the one-off vaccination campaign from which general practice was excluded.

The BMA’s GP Committee expressed that this added to its ‘growing concerns’ over the direction of travel for vaccination commissioning in recent years.

Data show that young people starting at university are at increased risk of meningococcal disease due to social mixing patterns and other risk factors – with the risk for students in their first year of university around seven times higher than young people of a similar age who do not go to university.

UKHSA said individuals needed two doses of the vaccine to be fully protected and uptake is gradually increasing.

But they also found stark variation by geography, sex, deprivation and ethnicity.

London had the lowest uptake at 21% and across the country vaccine coverage varied from 11.8% in the most deprived areas to 45% in the least deprived.

Young women were more likely to have taken up the first dose (31.5%) than men (21%), the report found.

The Joint Committee on Vaccination and Immunisation has recommended a MenB routine programme for 15-year-olds but a final decision is up to the Government.

Dr Sharif Ismail, consultant epidemiologist at UKHSA, said: ‘We know how devastating meningitis B can be.

‘The outbreaks in England this year tragically caused three deaths and left some who survived now facing life-long health consequences. There is a particular risk for students in their first year of university.

‘Our recent genomics study also highlights how suddenly and unpredictably dangerous new strains of meningitis B can emerge, such as the one seen in the Kent outbreak.’

NHS Director of Vaccination Caroline Temmink said: ‘The NHS worked hard to quickly establish and deliver this first-ever potentially life-saving programme, and it’s great that in the eligible cohort as a whole, more than a quarter of a million young people have already received vital protection.

‘But we want to reach more young people, which is why the offer of MenB vaccination remains in place at high street pharmacies across the country and we’re encouraging anyone who is eligible, particularly young people starting university for the first time, to come forward and get protected as soon as possible.’

Note: This article was updated at 12.45 on 1 October to clarify that the 26.6% uptake figure is for Year 13 students only.

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MenB vaccination only taken up by a quarter of students heading for university