Adding back "[NOTFOUND=return] resolve" to /etc/nsswitch.conf, setting 
DNSSEC=no in /etc/systemd/resolved.conf, restarting systemd-resolved process 
and then:
> $ getent ahosts irc.freenode.net
Gives proper list of hosts

Commenting again the DNSSEC line of resolved.conf, restarting the
service, and the resolution is still working. I'm a bit puzzled.

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https://bugs.launchpad.net/bugs/1665394

Title:
  DNS resolution of irc.freenode.net or chat.freenode.net fails

Status in systemd package in Ubuntu:
  Confirmed

Bug description:
  I am running Ubuntu 16.10 (from a base install upgraded several
  times), with proposed-updates enabled. Recently, I started having
  problems where I am unable to resolve irc.freenode.net.

  This is unrelated to the networks. I have been able to confirm that
  systemd-resolved is able to perform the name resolution. Yet,
  getaddrinfo() call returns -EAI_AGAIN error.

  This can be reproduced using getent:
  > $ getent ahosts irc.freenode.net
  > $

  While testing v4 or v6 directly returns something valid:
  > $ getent ahostsv4 irc.freenode.net
  > 38.229.70.22    STREAM chat.freenode.net
  > 38.229.70.22    DGRAM  
  > 38.229.70.22    RAW    
  > 130.239.18.119  STREAM 
  > 130.239.18.119  DGRAM  
  > 130.239.18.119  RAW    
  [...]
  > $

  > $ getent ahostsv6 irc.freenode.net
  > 2001:5a0:3604:1:64:86:243:181 STREAM chat.freenode.net
  > 2001:5a0:3604:1:64:86:243:181 DGRAM  
  > 2001:5a0:3604:1:64:86:243:181 RAW    
  > 2001:6b0:e:2a18::118 STREAM 
  > 2001:6b0:e:2a18::118 DGRAM  
  > 2001:6b0:e:2a18::118 RAW    
  [...]
  > $

  dpkg.log shows there has been some upgrade of systemd recently, though
  I cannot tell for sure if that directly relates to the problem, I do
  use suspend-to-ram a lot and reboot not that often.

  > $ lsb_release -a
  > LSB Version:        
core-9.20160110ubuntu5-amd64:core-9.20160110ubuntu5-noarch:printing-9.20160110ubuntu5-amd64:printing-9.20160110ubuntu5-noarch:security-9.20160110ubuntu5-amd64:security-9.20160110ubuntu5-noarch
  > Distributor ID:     Ubuntu
  > Description:        Ubuntu 16.10
  > Release:    16.10
  > Codename:   yakkety

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