Independent experts have tested food, water and air samples from the Steigenberger Aqua Magic hotel, where Cook agent Susan Cooper and her husband John died on August 21.
The examination included the hotel’s pool, carbon monoxide and carbon dioxide levels at the hotel, air conditioning units, and a “thorough audit of food storage, preparation, presentation and equipment”.
However, specialists were unable to access the Cooper’s hotel room, which has remained under the control of the Egyptian authorities due to their ongoing investigation.
Cook’s experts found:
Tests results were verified by a team at University College Hospitals in London, led by Dr Vanya Gant.
The operator said in a statement: “It is clear from these results something went wrong in August at the Steigenberger Aqua Magic Hotel in Hurghada and that standards fell below what we expect from our hotel partners.
“This is also supported by a review we have conducted of our customer satisfaction scores [at the Steigenberger Aqua Magic hotel], which fell sharply during this month.
"It is likely the presence of E. coli and staphylococcus would explain the raised level of illness reported among guests at the hotel during this time, supporting Thomas Cook’s decision to remove our 300 customers.
“However, neither our independent specialists nor Dr Vanya Gant believe that these results shed any light on the still unexplained cause of death of Mr and Mrs Cooper.
"We await the results of the autopsies being conducted by the Egyptian authorities.”
Thomas Cook chief executive Peter Fankhauser added: “We continue to await the results of the investigation being conducted by the Egyptian authorities and are working closely with the Foreign and Commonwealth Office to ensure we prioritise the very best interests of the Cooper family.
“However, the tests that Thomas Cook commissioned and announced today show hygiene at the Steigenberger Aqua Magic Hotel during the month of August did not meet the standards we expect.
"I am very sorry for all our customers who fell ill while on a Thomas Cook holiday at this hotel.”
Cook said it would continue to send clients to the hotel despite offering a compensation package to those affected by illness in August.
The operator added that it would start specialist hygiene assessments at all its hotels with an abnormal level of sickness.