Since Jehovah is the designer and creator of all things, including viruses, flesh eating bacteria, ticks mosquitos and other blood thirsty pestilence..
Jehovah isn't a literal creator of ALL living things, he laid down a FOUNDATION for all living things, called the DNA.
The DNA is capable of astonishing feats that adjust to it depending on the situation and the need.* Yes, the micro evolution as noted by Darwin exist. What's wrong is the species-jumping macro evolution every so-called "Scientist" like to believe.
We don't know how much the spiritual component plays here. Since the spirit, or the life-force guides and drives us, it's not implausible to assume a bad spirit can affect the DNA of living things to micro evolve in such a manner.
Hence, in the new world when the whole "spirit" is subdued, then it would go away from carnivorous, blood sucking creatures to harmless plant eating ones like it did originally. The world is going to look completely different than it does today.
The ones you are annoyed at and people call pests, and nuisances also play a very important role. When the environment is out of balance, it brings out the lowest form of creatures such as bacteria, and then what we call "pests". Then those "pests bring in higher level creatures that eat them such as spiders, ladybugs, and animals such as birds that eat them too. The low-level creatures try to kick out the problem, whether that be polluting humans, garbage, or dung on the ground. It can take years to do so, which after the balance of nature is established. Mosquitoes, Cockroaches, horseflies, rats and mice mostly disappear, the land quality goes from bad to fertile and everything becomes strong again.
This is likely the reason why the low-level creatures all spread disease. They try to eliminate(kill) the problematic source. Big(not the only) reason why they are prevalent is because of terrible, short-sighted farming/gardening practiced by 99.99% of the population. One of the most idiotic things ever done is in the US of A where farmers would burn swathes of forests indiscriminately, and plant, which would cause it to flourish for few years, but after that turns the land into deserts. Most of US deserts are due to 18-19th century farming practices. We as humans do many brain-dead things today.
*For some examples, the liver creates the protein needed to filter out what's there, and when it's done, the protein disappears. Second example is the creatures living in the Chernobyl zone. There are mushrooms that live by EATING radiation. The environment adapted to something that we thought inhospitable forever. Also in Hiroshima and Nagasaki, the cities are flourishing with hundreds of thousands of humans. Traces of radiation virtually disappeared after 10 years.