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Authorities in Karlsruhe found that several workers at the clinic were not properly qualified and a number of the clinic's specialist machines for washing surgical instruments were no longer certified for use, Spiegel Online reported.
State prosecutors are investigating the clinic on suspicion of infringing the Medical Devices Act.
The hospital, which normally performs 60 operations a day, has been stripped of all non-emergency surgery in the meantime and is operating a reduced service.
Medics who were not properly qualified have been sent home.
The latest allegations of poor hygiene come after a doctor at the clinic noticed that one of his instruments was dirty before using it, causing state prosecutors to begin an investigation last month.
In a statement on Friday, clinic authorities said that they would “act promptly on the indications of deficiencies in the preparation of instruments.”
“Patients have neither been endangered nor hurt,” the statement continued.
All the machines which haven't been properly checked have been taken out of service and the clinic will reduce the number of elective surgeries it carries out while they are being returned to use.
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