Here is the procedure that I've used to create a letsencrypt certificate in manual mode using a DNS record for registration.
sudo letsencrypt certonly -d example.com -d www.example.com --manual --preferred-challenges dns
The procedure will guide to the creation of a DNS TXT record used to verify the ownership of the domain.
After that the certificate can be found in /etc/letsencrypt/live/www.example.com
For any of you using Plesk remember that privkey.pem is the privateKey, cert.pem is the Certificate and chain.pem is the CA