What is the best way to issue one certificate for one domain that is spread across multiple servers?

I have a domain, with subdomains that have different IPs (different servers). I want to generate one certificate for this domain, for all the subdomains.

What is the best way to do this?

I have been using manual mode, but this is tedious and is a lot of work each time the certificate is renewed or a subdomain is added, so I want to find a simple way of doing this.

Ether use a client that supports the DNS challenge, or redirect /.well-known/acme-challenge/ on each of the subdomains to the main server

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Which is the best client to use for the DNS challenge? I run BIND nameservers for the domain.

GetSSL is a good one, especially if you have BIND configured to work with nsupdate.

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