What is broken or how was I hacked?

When our developers edit a page, review posts (wp-admin/edit.php), look at users (users.php) or some other wp-admin dashboard actions, the following query is issued:
SELECT wp_users.ID,wp_users.user_login,wp_users.display_name FROM wp_users INNER JOIN wp_usermeta ON (wp_users.ID = wp_usermeta.user_id) WHERE 1=1 AND ( (wp_usermeta.meta_key = 'wp_user_level' AND CAST(wp_usermeta.meta_value AS CHAR) != '0') ) ORDER BY display_name ASC /* From [vivinow.com/wp-admin/edit.php] in [N/A] */
With 195,000 registered users, this query has a network timeout at about 100,000 users downloaded
. How do I fix it?