When Abbas Pasha came to rule Egypt, he tried to pull down all that was French according to the British councilor' 5 advice. As a result, Clot Bey resigned in 1849, and was succeeded by Dr. Duvigneau, then Peron Bey, and then Shafir Bey, who was the first Egyptian President of the School. During his days, the German Professor, Alexander Reyer, was invited. He recommended sending missions, similar to those of Mohamed Aly Pasha, to Austria.
This was achieved, and the school came under the control of the German administration.
Then came Professor Lightner and Dr. Tudor Bihlarz. Although the Shistosoma Heamatobium was discovered at that time, the school did not make any progress : sound planning was missing at this stage, and so the school started to deteriorate.
In 1854, Abbas Pasha tried to exchange Germans with Italians: Dr. Raggi and Dr. Ranzi. As a matter of fact, Dr. Ranzi tried to improve the conditions of the School and to convince Abbas Pasha, then Said Pasha, to go back to Clot Bey's system, but his advice was not carried out at first .