Hmm I knew I remembered something related ...
In bug 1694156 we have had a - what appears to me as - similar case.
There we could track it down to a config issue, but maybe you here are affected 
by the same issue yet without a simple config issue to fix.

The clue there was, that that dnsmasq was configured as global dns server to 
resolved in a manually added /etc/resolvconf/resolv.conf.d/tail. Due to that 
searches to the local search domain that failed started to be passed back and 
forth between dnsmasq and systemd-resolvd.
Does anybody affected here have the same setup of dnsmasq being registered as 
global dns? You can check with:
 $ systemd-resolve --status
The local dnsmasq should not more be listed in there.

Not sure - but if all affected users would have such a "local dnsmasq is
configured as global dns in systemd-resolved" then we will have to find
which package/config/guide/upgrade-path sets it up that way and resolve
that - but first of all please verify that this would help you.

Also as another option if you explicitly want your local dnsmasq to be
configured in resolved as global dns server - then you might want to
check if dnsmasq's option "--dns-loop-detect" via DNSMASQ_OPTS in
/etc/default/dnsmasq.

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

Title:
  systemd-resolved using 100% CPU

Status in dnsmasq package in Ubuntu:
  Confirmed
Status in systemd package in Ubuntu:
  Confirmed

Bug description:
  Sometimes systemd-resolved process is using 100% CPU.
  After a while it changes back to normal.

  It happens usually after connecting to the (wifi) network, like
  starting the OS.

  strace output:

  sendmsg(12, {msg_name(16)={sa_family=AF_INET, sin_port=htons(33589), 
sin_addr=inet_addr("127.0.0.1")}, 
msg_iov(1)=[{"6\215\201\200\0\1\0\1\0\0\0\1\4cs41\3wac\vedgecastcdn\3net\0\0\34\0\1\300\f\0\34\0\1\0\0\10\235\0\20&\6(\0\0024\0Y%L\4\6#f&\214\0\0)\377\326\0\0\0\0\0\0",
 81}], msg_controllen=28, [{cmsg_len=28, cmsg_level=SOL_IP, 
cmsg_type=IP_PKTINFO, {ipi_ifindex=if_nametoindex("lo"), 
ipi_spec_dst=inet_addr("127.0.0.53"), ipi_addr=inet_addr("127.0.0.53")}}], 
msg_flags=0}, 0) = 81
  sendmsg(3, {msg_name(0)=NULL, 
msg_iov(4)=[{"PRIORITY=6\nSYSLOG_FACILITY=3\nCODE_FILE=../src/resolve/resolved-dns-stub.c\nCODE_LINE=363\nCODE_FUNCTION=dns_stub_process_query\nSYSLOG_IDENTIFIER=systemd-resolved\n",
 160}, {"MESSAGE=", 8}, {"Processing query...", 19}, {"\n", 1}], 
msg_controllen=0, msg_flags=0}, MSG_NOSIGNAL) = 188
  epoll_wait(4, [{EPOLLIN, {u32=3176459184, u64=94565471415216}}], 16, -1) = 1
  clock_gettime(CLOCK_BOOTTIME, {44665, 938069872}) = 0
  recvfrom(12, NULL, 0, MSG_PEEK|MSG_TRUNC, NULL, NULL) = 53
  recvmsg(12, {msg_name(16)={sa_family=AF_INET, sin_port=htons(33589), 
sin_addr=inet_addr("127.0.0.1")}, 
msg_iov(1)=[{"Z\262\1\20\0\1\0\0\0\0\0\1\4cs41\3wac\vedgecastcdn\3net\0\0\34\0\1\0\0)\2\0\0\0\0\0\0\0",
 3936}], msg_controllen=56, [{cmsg_len=28, cmsg_level=SOL_IP, 
cmsg_type=IP_PKTINFO, {ipi_ifindex=if_nametoindex("lo"), 
ipi_spec_dst=inet_addr("127.0.0.53"), ipi_addr=inet_addr("127.0.0.53")}}, 
{cmsg_len=20, cmsg_level=SOL_IP, cmsg_type=IP_TTL, {ttl=64}}], msg_flags=0}, 0) 
= 53
  stat("/etc/resolv.conf", {st_mode=S_IFREG|0644, st_size=303, ...}) = 0
  getrandom("\365I", 2, GRND_NONBLOCK)    = 2
  stat("/etc/resolv.conf", {st_mode=S_IFREG|0644, st_size=303, ...}) = 0
  getrandom("\203;", 2, GRND_NONBLOCK)    = 2
  clock_gettime(CLOCK_BOOTTIME, {44665, 938446937}) = 0
  open("/run/systemd/netif/links/3", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such 
file or directory)
  stat("/etc/resolv.conf", {st_mode=S_IFREG|0644, st_size=303, ...}) = 0
  stat("/etc/resolv.conf", {st_mode=S_IFREG|0644, st_size=303, ...}) = 0
  socket(AF_INET, SOCK_DGRAM|SOCK_CLOEXEC|SOCK_NONBLOCK, IPPROTO_IP) = 18
  connect(18, {sa_family=AF_INET, sin_port=htons(53), 
sin_addr=inet_addr("127.0.0.1")}, 16) = 0
  epoll_ctl(4, EPOLL_CTL_ADD, 18, {EPOLLIN, {u32=3176610576, 
u64=94565471566608}}) = 0
  write(18, 
"\203;\1\20\0\1\0\0\0\0\0\1\4cs41\3wac\vedgecastcdn\3net\0\0\34\0\1\0\0)\2\0\0\0\0\0\0\0",
 53) = 53
  clock_gettime(CLOCK_BOOTTIME, {44665, 938833717}) = 0
  clock_gettime(CLOCK_BOOTTIME, {44665, 938875138}) = 0
  epoll_ctl(4, EPOLL_CTL_DEL, 18, NULL)   = 0
  close(18)                               = 0

  journalctl output:

  Mar 08 08:25:35 parsec systemd-resolved[1512]: Processing query...
  Mar 08 08:25:35 parsec systemd-resolved[1512]: Processing query...
  Mar 08 08:25:35 parsec systemd-resolved[1512]: Processing query...
  Mar 08 08:25:35 parsec systemd-resolved[1512]: Processing query...
  Mar 08 08:25:35 parsec systemd-resolved[1512]: Processing query...
  Mar 08 08:25:35 parsec systemd-resolved[1512]: Processing query...
  Mar 08 08:25:35 parsec systemd-resolved[1512]: Processing query...
  Mar 08 08:25:35 parsec systemd-resolved[1512]: Processing query...
  Mar 08 08:25:41 parsec dnsmasq[1545]: Maximum number of concurrent DNS 
queries reached (max: 150)

  As you can see, I would use it together with dnsmasq.

  ProblemType: Bug
  DistroRelease: Ubuntu 17.04
  Package: systemd 232-18ubuntu1
  ProcVersionSignature: Ubuntu 4.10.0-9.11-generic 4.10.0
  Uname: Linux 4.10.0-9-generic x86_64
  NonfreeKernelModules: zfs zunicode zavl zcommon znvpair
  ApportVersion: 2.20.4-0ubuntu2
  Architecture: amd64
  Date: Wed Mar  8 08:20:18 2017
  MachineType: Hewlett-Packard HP EliteBook Folio 1020 G1
  ProcEnviron:
   LANGUAGE=en_US:en
   TERM=xterm
   PATH=(custom, no user)
   LANG=en_US.UTF-8
   SHELL=/bin/zsh
  ProcKernelCmdLine: BOOT_IMAGE=/@/boot/vmlinuz-4.10.0-9-generic 
root=UUID=a54fe703-35d4-47ac-9c6e-4034421531fb ro rootflags=subvol=@
  SourcePackage: systemd
  UpgradeStatus: Upgraded to zesty on 2015-05-24 (653 days ago)
  dmi.bios.date: 03/09/2015
  dmi.bios.vendor: Hewlett-Packard
  dmi.bios.version: M77 Ver. 01.05
  dmi.board.name: 2271
  dmi.board.vendor: Hewlett-Packard
  dmi.board.version: KBC Version 91.4C
  dmi.chassis.asset.tag: CNU51199KV
  dmi.chassis.type: 10
  dmi.chassis.vendor: Hewlett-Packard
  dmi.modalias: 
dmi:bvnHewlett-Packard:bvrM77Ver.01.05:bd03/09/2015:svnHewlett-Packard:pnHPEliteBookFolio1020G1:pvrA3009DD18303:rvnHewlett-Packard:rn2271:rvrKBCVersion91.4C:cvnHewlett-Packard:ct10:cvr:
  dmi.product.name: HP EliteBook Folio 1020 G1
  dmi.product.version: A3009DD18303
  dmi.sys.vendor: Hewlett-Packard

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