Q:

If part of halal food becomes changed in colour,toxic & harmful to eat for microbes or other reasons, does it become impure & haram to hold these by hands before discarding? Is there scholarly consensus about this impurity? What is told in Quran & hadith about it? 

A:

In the Name of Allah, the All-Merciful, the Mercy-Giving.

All praise is due to Allah. Peace and blessings be upon his Prophet Muhammad.

There is no correlation between harmfulness or toxicity of a substance and its najasah (ritual impurity). The circle of harmful substances is much wider than the circle of ritually impure ones. To judge a substance as najis (ritually impure) requires a Shariah textual evidence.  

Almighty Allah knows best.