What is the ruling on one who believes that diseases are contagious by their very nature, by the permission of Allah Almighty, meaning that Allah has made their transmission part of their natural course, and is this considered major shirk (polytheism)?

What the questioner mentioned, that diseases inherently transmit, while linking that to God's permission and command, and that it is a common characteristic of diseases, is a combination of contradictions. The pre-Islamic era (Jahiliyyah) believed that contagious diseases transmitted inherently, without attributing it to God, and this is what is meant by the denial of contagion in the Hadith. As for the prohibition of bringing the diseased to the healthy, it is a guidance to avoid what usually causes harm by God's decree. So, the first Hadith denied contagion by its inherent nature, but did not deny the occurrence of harm by God's decree. And the second Hadith guided to take precautions against what causes harm by God's action. Whoever believes that diseases transmit by God's command, and that God has made that their common characteristic, does not hold the belief of the Jahiliyyah.