You’ve narrowed the issue down to mysql/php and since you are running WordPress my guess would be that you have a plugin or theme that is doing something to max out your resource usage.

Do these spikes occur only when someone is viewing the site or randomly even when there is no traffic? If it’s the later I would recommend checking any cron jobs (scheduled tasks) that your plugins may be using. A plugin designed to back up your WP site could potentially cause a spike like this when it dumps the whole database through php to a file.

If you are running 3rd party plugins the best way to determine the source of the issue would be to disable these plugins and re-enable them one at a time to see if the issue recurs after a particular one is running. You can also check your access and error logs during the times of the spikes to see if anything is recorded.

Nginx access/error logs are in:

/var/log/nginx/

PHP-fpm logs can be found in:

/var/log/php-fpm/