The largest private provider of NHS out-of-hours GP services is facing allegations by senior doctors that its service in London is so short-staffed it is regularly unsafe.

Harmoni, which has contracts covering 8 million patients across large areas of London and southern England, is also alleged to have manipulated its performance data, masking delays in seeing patients and other missed targets.

A seven-week-old baby with a suspected respiratory infection died in November after repeated calls to the service over several days, during which it is alleged to have failed to follow protocols in key areas. Sources with knowledge of the case say they fear a four-hour wait for a doctor to see the baby at a Harmoni-run clinic at the Whittington hospital in London on the Saturday he died may have contributed to the tragedy.

The allegations come as the number of NHS contracts being put out to competitive bidding is rising sharply under the government's controversial Health and Social Care Act. Harmoni has been one of the most successful private sector bidders in the recent tendering. It has won more than a quarter of the contracts for the new NHS 111 service, which will be introduced nationwide from next spring.

Documents seen by the Guardian, and sources close to the service, indicate that Harmoni has frequently operated in the capital with shifts unfilled, both recently and over an extended period.

Dr Fred Kavalier, the former clinical lead at Harmoni, said he resigned in January last year because he felt unable to be responsible for the service, which he believed had become unsafe after cost-saving cuts in clinicians' shifts and the length of time allowed for GPs to see patients, and a failure to recruit and pay GPs sufficiently.

A Norfolk family is suing Harmoni's out-of-hours service and one of its nurses after the death of a 19-year-old woman. Although the nurse has admitted being in breach of her duty, she claims the company should have indemnified her. Harmoni says its insurance excludes responsibility for negligence by nurses.

In the Whittington case, crucial checks are said to be missing from the notes of the doctor who first saw the baby. A second doctor, who assessed the case by phone from another site a couple of days later and downgraded it from urgent, failed to record his call, as is required.

Local doctors were receiving frantic texts from a Harmoni rota co-ordinator for north central London on the Friday and Saturday in question, asking for help with unfilled shifts that weekend, one recipient told the Guardian. Sources say the baby died shortly after arriving at the clinic, which has been regularly overbooked or closed because of staff shortages. The baby was transferred at the last minute to the NHS A&E department next door, but by then medics were unable to save him.

Harmoni acknowledged that a baby had died in a "serious incident" but said it was unable to comment on the case while it was the subject of formal investigation. The incident has been reported to the NHS regulator, the Care Quality Commission, and the General Medical Council.

Harmoni did not deny staff shifts had been unfilled, or that London clinics including the Whittington had been closed for several hours on recent occasions because clinicians had not been available to run them. But the private equity-owned company, which was sold for £48m to Care UK in November, categorically denies that the service has been unsafe or failed to meet contractual obligations on clinic opening and response times. Care UK told the Guardian it was, as a routine part of its takeover, reviewing Harmoni's performance and practices to make sure they were safe, met contractual requirements and provided the expected quality of care.

Sources described Harmoni data being "cleaned up" by blaming delays on patients not wanting to take appointments many miles from home, or by recategorising them. Local GPs have reported being puzzled by repeated evidence that targets were regularly missed, despite reports suggesting all was well.

Harmoni said it believed reporting of its performance to the NHS was accurate and complied with the process agreed by commissioners, but it had instigated an audit following allegations put to it by the Guardian. It confirmed that raw data had sometimes been changed but said: "We believe the allegations have arisen as a result of a misunderstanding of the process we use to review raw data. In order to produce an accurate report for commissioners that reflects both performance of the service and patients' preferences, the data is checked for duplications and inaccuracies."

We put a sample of shortfalls in recent weeks to Harmoni. The Guardian was told of the routine overnight report prepared for management each morning, which says that on the night of Saturday/Sunday 10/11 November, owing to staff shortages, for most of the night only one advanced nurse practitioner was exclusively designated to assess the seriousness of calls from patients to the out of hours service for the whole of Harmoni's London contract area. This covers Brent, Barnet, Camden, City and Hackney, Ealing, Haringey, Harrow, Hillingdon, Hounslow, Islington, Kingston, Richmond, Twickenham, and Wandsworth, a population of more than 3 million. In response, Harmoni said four GPs assigned to cars for home visits for the London area were able to cover some of the triage work, taking half of the calls from their vehicles in between home visits to assess the urgency of cases.

In another example, sources say on 26, 27, 28, 29 and 30 November shifts were unfilled overnight at a Harmoni clinic in St Pancras, with no qualified medic or nurse to see patients. They also allege that clinics the Harmoni service is expected to run at the Whittington hospital for patients who need an urgent out-of-hours appointment have been closed repeatedly for several hours, including on 30 November and 1 and 2 December. Harmoni did not dispute the allegations but said it did not believe safety had been compromised.

Kavalier's resignation letter detailed numerous complaints from GPs, including a booked home visit to an elderly patient which never took place, and a child under two, who later needed hospital admission, being directed by a nurse on the phone at Harmoni West Sussex from the family home in south-west London to north London, many miles away. "If the child had been more ill the journey could have had serious consequences … The service is leading to patient complaints and I fear it is only a matter of time before this low level of service leads to a serious clinical incident," Kavalier wrote.

Concerns about the safety of the service, the number of complaints about its quality, and allegations that its performance data were being "cleaned up" have also been made by the local GPs' representative body, the Local Medical Committee (LMC). Dr Paddy Glackin, who was secretary of the LMC until this summer, said concerns about each of these three issues had been brought to him by several local GPs and staff. Dr Tom McAnea, a GP in Islington who works home-visiting shifts for the service, wrote to Harmoni's regional director in autumn 2010 saying he feared the service had become unsafe because of an aggressive cost-cutting agenda. He decided not to work shifts at Harmoni clinics after it cut the time available for appointments, because he felt it put patients at risk.

Harmoni told the Guardian none of these concerns had been raised with it by the primary care trust or the LMC. It said it had adjusted GP consultation times from 15 minutes per patient to 12 minutes to bring them in line with the average of 10 minutes elsewhere and its own surveys of what was typically needed. It said its "safety record, incidents, complaints, response times to patients and rota fills all indicate a safely run service. We refute entirely any suggestion that we have cut costs in a way that compromises the quality of the service".

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