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From a single plugin you cannot monitor all MySQL instances. You can reuse the same MySQL plugin by renaming it and editing the configuration.
Using MySQL for monitoring multiple instances:
#1) Copy the mysql/ folder to mysql_instance/
#2) Rename the mysql.py to mysql_instance.py present under mysql_instance/
Commands to execute in your server to achieve the above steps
cp -r mysql/ mysql_instance/
mv mysql.py mysql_instance.py
#3) Edit the mysql_instance.py to change the mysql configurations.
Agent will pick this up in the next data collection and you can view your plugin under server monitor details page.
If you have many instances, please follow the steps listed above (i.e rename the plugin file and its configurations).