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Most GPs will be forced to change their computer software in as little as two years under Government plans to abandon almost all existing practice IT systems.
A document released by the NHS's National Programme for IT last week said two systems, neither of which yet exists, will replace the majority of products used by GPs.
Under the new GP contract, primary care organisations would have to give practices a choice between one of the new systems and at least one alternative.
But this alternative would almost certainly not include EMIS, used by 56 per cent of GPs, because it has refused to sign 'onerous' contracts with local service providers delivering the national programme.
Practices that wanted to keep a system not offered by their PCO would be forced to pay for it themselves.
GPs said such wholesale change of computer systems would bring massive disruption and warned it could harm clinical care due to loss of patient data and threaten practices' quality achievement.
Practices would also face crippling costs to train staff on the new systems.
The National Programme for IT said the majority of the work would be done in the next two to five years.
'The majority of existing systems will have been replaced or integrated within a local service provider solution,' it said. 'It must be accepted some existing systems will not be integrated to local service provider solutions.'
Dr Manpreet Pujara, chair of the EMIS national users group and a GP in Carshalton, Surrey, said it was 'clear the programme saw no future for any of the current suppliers'.
He added: 'It's very unlikely EMIS will be offered as a choice. The bottom line for GPs will then be whether they are prepared to pay.'
EMIS managing director Sean Riddell admitted GPs would find it hard to convince PCO finance directors to pay for its systems when there was a 'free' alternative.
Dr Paul Cundy, joint-chair of the GPC/RCGP IT subcommittee, said the burden of implementing a new system was staggering, but he doubted all the work could be done by 2009. 'It took my practice a year and if we are not cutting edge I don't know what is.'
By Ian Cameron