@ChristianEhrhardt: I'm not sure how to determine whether systemd-
resolver is forwarding back to dnsmasq, hopefully it's clear from the
output:

mdroth@sif:~$ cat /etc/resolv.conf 
# Dynamic resolv.conf(5) file for glibc resolver(3) generated by resolvconf(8)
#     DO NOT EDIT THIS FILE BY HAND -- YOUR CHANGES WILL BE OVERWRITTEN
# 127.0.0.53 is the systemd-resolved stub resolver.
# run "systemd-resolve --status" to see details about the actual nameservers.

nameserver 127.0.0.1

mdroth@sif:~$ ps aux | grep dnsmasq
dnsmasq   1122  1.6  0.0  55276  2864 ?        S    Sep18  10:11 
/usr/sbin/dnsmasq -x /run/dnsmasq/dnsmasq.pid -u dnsmasq -r 
/run/dnsmasq/resolv.conf -7 /etc/dnsmasq.d,.dpkg-dist,.dpkg-old,.dpkg-new 
--local-service 
--trust-anchor=.,19036,8,2,49AAC11D7B6F6446702E54A1607371607A1A41855200FD2CE1CDDE32F24E8FB5
libvirt+  1794  0.0  0.0  52380   396 ?        S    Sep18   0:00 
/usr/sbin/dnsmasq --conf-file=/var/lib/libvirt/dnsmasq/default.conf 
--leasefile-ro --dhcp-script=/usr/lib/libvirt/libvirt_leaseshelper
root      1795  0.0  0.0  52352   396 ?        S    Sep18   0:00 
/usr/sbin/dnsmasq --conf-file=/var/lib/libvirt/dnsmasq/default.conf 
--leasefile-ro --dhcp-script=/usr/lib/libvirt/libvirt_leaseshelper
mdroth    7792  0.0  0.0  14244  1028 pts/6    S+   06:43   0:00 grep 
--color=auto dnsmasq

mdroth@sif:~$ cat /run/dnsmasq/resolv.conf 
nameserver 127.0.0.53

mdroth@sif:~$ systemd-resolve --status
Global
         DNS Servers: 127.0.0.1
          DNSSEC NTA: 10.in-addr.arpa
                      16.172.in-addr.arpa
                      168.192.in-addr.arpa
                      17.172.in-addr.arpa
                      18.172.in-addr.arpa
                      19.172.in-addr.arpa
                      20.172.in-addr.arpa
                      21.172.in-addr.arpa
                      22.172.in-addr.arpa
                      23.172.in-addr.arpa
                      24.172.in-addr.arpa
                      25.172.in-addr.arpa
                      26.172.in-addr.arpa
                      27.172.in-addr.arpa
                      28.172.in-addr.arpa
                      29.172.in-addr.arpa
                      30.172.in-addr.arpa
                      31.172.in-addr.arpa
                      corp
                      d.f.ip6.arpa
                      home
                      internal
                      intranet
                      lan
                      local
                      private
                      test

Link 5 (virbr0-nic)
      Current Scopes: none
       LLMNR setting: yes
MulticastDNS setting: no
      DNSSEC setting: no
    DNSSEC supported: no

Link 4 (virbr0)
      Current Scopes: none
       LLMNR setting: yes
MulticastDNS setting: no
      DNSSEC setting: no
    DNSSEC supported: no

Link 3 (wlp4s0)
      Current Scopes: DNS LLMNR/IPv4 LLMNR/IPv6
       LLMNR setting: yes
MulticastDNS setting: no
      DNSSEC setting: no
    DNSSEC supported: no
         DNS Servers: 192.168.2.254
                      fd6d:6e53:4042::1
          DNS Domain: lan

Link 2 (enp0s31f6)
      Current Scopes: none
       LLMNR setting: yes
MulticastDNS setting: no
      DNSSEC setting: no
    DNSSEC supported: no

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https://bugs.launchpad.net/bugs/1670959

Title:
  systemd-resolved using 100% CPU

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