There was a second creation wherein God created these organisms to plague mankind? Where does the Bible mention that?
The fundamental nature of God's creation was changed with the fall. Animals began to eat other animals and fear humans. That didn't happen before the fall. Humans began to hunt and to desire sin. The organisms which cause the diseases which you mentioned were present at creation. However, they weren't dangerous then. God said all of his creation was "very good". Death did not exist, nor disease. Then man sinned. The Bible said that act cursed creation, and suddenly harmless organisms became dangerous. As mutation occurs, they become even more dangerous.
Today, a lot of diseases are likely started and spread through sinful activity. Example being, the origins of Aids. Other STDs no doubt started from sex with animals. It's hard to find information on this on the internet, but that is the rumor with Syphillis. (There is also another article on the net tracing it to an entirely different disease, so I'm really unsure on that). God punished sexual relationships that were viewed as depraved. The penalty for bestiality was death. Why? Because God is just a cosmic kill-joy who doesn't want a guy to relieve a little tension when a woman isn't around? No. Because it is harmful to his creation (not to mention disgusting and vile). God also forbad homosexuality and mentioned that men having sex with men would bring about a just reward within their bodies. I didn't write the book. It is in Romans 1. You can read it
with the referencing footnotes
The point is, God did create everything lovely and perfect and man did screw it up, but God has promised to fix it back the way it was supposed to be. That's good news and a testimony to God's love. He is allowing man the run of his free will now, but the time will come where he allows such no longer. All will be judged, according to His righteousness spelled out in Scripture. Since no man is righteous, only those robed in the righteousness of His Son will be accepted.
As Peter said in Acts 4 when speaking to an audience of Jews:
10 Be it known unto you all, and to all the people of Israel, that by the name of Jesus Christ of Nazareth, whom ye crucified, whom God raised from the dead, even by him doth this man stand here before you whole.
11 This is the stone which was set at nought of you builders, which is become the head of the corner.
12 Neither is there salvation in any other: for there is none other name under heaven given among men, whereby we must be saved.
The good news is that we are all sinners and under a curse, but we can be freed from that curse by accepting Him. Jesus loves gay and straight, adulterers, murderers, and just your average "nice guys". But our best isn't enough to match God's standards of holiness- but Jesus's is and he offers that gift freely to you (John 3:16).