OpenSSH and X509 Authentication
Using SSH with SSH certificates
OpenSSH itself supports SSH Certificates that are not X.509 Certificates. As of EJBCA 7.4, basic issuance of SSH certificates are available in EJBCA.
Using SSH with X.509 certificates
The following resources provide some guidance for using SSH with X.509 certificates, or more commonly with smart cards and USB tokens:
https://github.com/OpenSC/OpenSC/wiki/OpenSSH-and-smart-cards-PKCS%2311
https://developers.yubico.com/PIV/Guides/SSH_with_PIV_and_PKCS11.html
For information on using SSH with X.509 certificates there are a number of (mostly outdated) resources you can find, for example this OpenSSH and X509 authentication guide by Bruno Bonfils.