Next gen of weapons against antibiotic-resistant superbugs

For four out of five of them, surgery is the
answer. Wormald carves away inflamed tissue, widens
sinus openings and flushes out accumulated pus.
For the stubborn one in five, however, Wormald is
conducting one of the world’s first clinical trials into
phage therapy, a century-old idea that predates modern
antibiotics.

Such trials are desperately needed. We are on the
threshold of returning to the dark ages that preceded
antibiotics. In the late 19th century, tuberculosis
was humanity’s greatest scourge. Robert Koch, who
identified the causative Mycobacterium tuberculosis,
estimated that “one-seventh of all humans die
of tuberculosis”. The disease is now on its way to
becoming untreatable once more. Every year, nearlyhalf a million new cases of multidrug-resistant
tuberculosis (MDR-TB) occur world-wide. Extensively
drug-resistant tuberculosis (XDR-TB) strains,
impervious to the most potent antibiotics in our
arsenal, have already reared their head.

Even normally benign bacteria like Staphylococcus
aeureus – golden staph – which harmlessly colonises
our skin and nostrils, can cause lethal infections if
they hitch a ride into the bloodstream on a catheter or
through a surgical incision.

In the post-antibiotic era, drug-resistant strains
could render elective surgery, like knee or hip
replacements, too risky. According to a 2016 review
from Britain led by economist Jim O’Neill, by 2050
drug-resistant infections could kill 10 million people
each year – higher than the toll from cancer.

Our profligate use of antibiotics is responsible.
Antibiotics unleash massive die-offs within
bacterial ecosystems. In a textbook case of evolution,
that antibiotic-laden environment selects for the rare
bacterium that happens to have acquired a resistance
gene. By mechanisms that range from shredding or
pumping out the antibiotic to shielding vulnerable
targets, resistance genes enable bacteria to dodge
whatever weapons we throw at them.

Thus armed, a single bacterial cell can quickly
blossom into a resistant army of trillions. The
resistance genes, which are carried on rings of DNA
called plasmids, can be shared with unrelated bacteria
like the latest piece of malware. Since the first use
of penicillin more than 70 years ago, this story has
played out for every antibiotic deployed. In most cases,
resistance emerges within a few short years.

In 2015 a new shock emerged. Researchers in China
reported finding E. Coli bacteria in pigs, chicken and
humans that had acquired a plasmid that made them
resistant to colistin, an antibiotic of last resort. It’s
not often used in humans because it causes kidney
damage, which is why it had remained effective. But in
China, and other places, this cheap antibiotic has been
a mainstay of animal farming. Indeed 70% of our global
use of antibiotics is for the purpose of accelerating
growth in farm animals, reducing the time needed to get them ready for market. The 2015 report in Lancet
Infectious Diseases made it clear that resistant bugs in
farm animals could spread their malware to bacteria
that infect humans – till then a hypothetical risk. China
banned the use of colistin in farm animals a year later.

Until recently, we’ve managed to outmanoeuvre
disease-causing bacteria. When one antibiotic
succumbed to resistance, there was another popping
out of the pipeline. Over the past few decades, however,
the steady flow has dried to a trickle.

Pharmaceutical makers see little profit in the costly
development of new antibiotics. That’s because, at
least in the near future, the majority of infections will
still be treatable by available low-cost antibiotics. That
leaves a relatively small market for the new drug. “For
a pharmaceutical company, the economics just don’t
make any sense,” says chemist Mark Blaskovich from
the University of Queensland. “Why would you invest
in something where it’s a single two-week course and
you’re cured, as opposed to an ongoing therapy [like
new treatments for cancer] costing thousands, or
hundreds of thousands, of dollars a year.”

According to a recent report from the PewCharitable Trust, just 40 antibiotics are chugging
along the drug development pipeline, compared to
several hundred drugs for cancer. To make matters
worse, bacteria are increasingly arming themselves
with multiple resistance mechanisms. When it comes
to treating gonorrhoea and tuberculosis, for example,
doctors now have few drugs that still work.

While health authorities like the World Health
Organisation exhort the community to limit their use
of antibiotics to slow the spread of resistant bacteria,
it won’t eliminate the hordes of resistant microbes
already in our midst.
In 2014, at the time of announcing the O’Neill-led
review, then British prime minister David Cameron
warned: “If we fail to act, we are looking at an almost
unthinkable scenario where antibiotics no longer work
and we are cast back into the dark ages of medicine.”.
Now we are “beyond a tipping point”, according
to Michael Gillings, a microbiologist at Macquarie
University, Sydney. “It might have been possible to
stop this 40 to 50 years ago,” he says, “now we have the
problem forever.”

As antibiotic after antibiotic invariably fails,
scientists are searching for alternative weapons.
One of those weapons was discovered amid the fog
of World War I. In the summer of 1915, an outbreak
of severe haemorrhagic dysentery raged through the
ranks of French soldiers stationed at Maisons-Laffitte
on the outskirts of Paris. Several of the soldiers were
hospitalised, and French-Canadian microbiologist
Félix d’Hérelle, working at the Institut Pasteur in
Paris, was sent to investigate. He discovered that
stool samples from the soldiers not only contained
the dysentery-causing bacterium Shigella but also the
antidote – “un microbe invisible” which, when added
to Shigella in a dish, killed it.

Across the channel, British microbiologist
Frederick Twort had also stumbled across bacteria-killing
agents in his culture dishes. Both turned out
to be bacteriophages, or ‘phages’ for short. These
‘bacteria eaters’ are viruses that specifically infect and
kill bacteria, much as the flu virus infects our own cells.

It was d’Hérelle that first had the idea of harnessing
phages as a clinical treatment. In 1919, he unleashed
his poo-derived concoction on a small group of Parisian
children with dysentery. The trial was a success, and
phage therapy quickly gained the attention of the
medical community. By the 1940s, however, it had
all but been abandoned in the West in favour of the
newfangled – and less finicky – antibiotics.

In the former Eastern bloc, phage therapy is alive
and kicking. Specialist institutes in Georgia and Poland
have carved out a niche supplying personalised phage
remedies for stubborn bacterial infections. Now, in
the face of failing antibiotics, researchers in Western
countries are following their lead.

Nevertheless, rigorous clinical trial data remains
sparse. Researchers like Wormald, who also leads
otolaryngology head and neck surgery at Adelaide and
Flinders universities, are now playing catch-up to test
whether phage therapy is as effective as its proponents
have long suggested.

Twice a day for two weeks, nine of his patients
flush out their sinuses with a briny solution containing
phages that kill golden staph, the most common culprit
in chronic sinusitis. This usually harmless microbe lives
on most people’s skin and nostrils, but can overrun
nasal cavities, wounds or surgical incisions when a
person’s immune system is at a low ebb or the microbial
ecosystem has been thrown out of whack with
antibiotics. At the end of the two weeks, Wormald sees
modest improvement. Three months on, the results
are dramatic. “They are absolutely 100%,” he says. The
likely explanation is that phages stay on the job: as long
as there are bacteria, they hang around and attack.

Wormald uses a cocktail of four different phages
that together kill about 95% of golden staph strains
circulating in the human population. Other cocktails
– such as one used to treat leg ulcers – also combine
phages to target several different bacterial species
at once. Cocktails guard not only against treatment failure but against resistance, says Wormald: “While
[the bacteria] might try to become resistant to one
strain of the phage, they’re likely to be hammered by
the others.”

In another recent trial conducted at wound centres
in the US state of Washington, phages were dabbed
onto the gangrenous toes of six people with diabetes. It
was a last-ditch attempt to spare their toes. In all cases
the phage preparation – obtained from the George
Eliava Institute in Tbilisi, Georgia – did the trick.

Even more promising, researchers in the US
announced in April 2017 the successful deploymentof phages to treat a man on the brink of death due to a
multidrug-resistant Acinetobacter baumannii infection.

The phages were introduced via catheters into the
man’s abdominal cavity, and injected intravenously. It
is the first report of phage therapy thwarting a systemic
infection with no apparent side-effects; the caveat is it
was a single case and is yet to be published in the peer-reviewed
literature.

Like guided missiles, phages target enemy bacteria
with great precision. In principle that makes them safe
– both for us and for the legions of beneficial microbes
that inhabit our bodies. “They have a very low potential
to do harm,” says phage researcher Steve Abedon of
Ohio State University.

As phage therapy becomes more widespread, will
phage-resistant bacteria emerge? Yes, but unlike the
arms race between bacteria and antibiotics, which
requires humans to keep upgrading their weaponry
to stay in the game, phages do it by themselves. As
bacteria evolve resistance to the phages that prey on
them, phages evolve new ways to target them.

Also, when it comes to new phage varieties, nature
has been prodigious. Phages are the most abundant
life form on the planet and they are everywhere. A
drop of seawater, a smear of poo, a clump of dirt – all
teem with a multitude of phage types. This makes for
an essentially limitless pool from which to fish for new
weaponry. In theory, for every bothersome bacterium
there should be a phage to prey on it.

That said, it hasn’t all been smooth sailing for
the phage field. The largest randomised clinical trial
of phage therapy to date – carried out in 2016 in
Bangladesh with 100 children suffering diarrhea – was a failure, with the phage cocktail providing no benefit.
There were, however, mitigating factors. The phages
only targeted Escherichia coli (E. coli) and it turned out
that more than a third of the children weren’t infected
with this bacterium. For the rest of the children, the
phage dose was too low to be effective. Whatever the
reason for the trial’s failure, the results played to the
perception of phages as a finicky therapy that won’t
easily replace antibiotic pills.

Phage therapy faces other hurdles. One is finding
commercial backers. “They’re the most ubiquitous
biological entity on Earth,” says Abedon, “so they’re
just free for the taking.” This makes them unattractive
to pharmaceutical companies. Without investment to
cover the cost of conducting expensive clinical trials,
phage therapy will struggle to become anything more
than a niche treatment.

Vincent Fischetti, a phage researcher at Rockefeller
University, New York, also predicts “an uphill battle”
in gaining regulatory approval. Regulators favour welldefined
single-molecule drugs. A complex cocktail of
viruses could prove challenging, he says.
Once approved, the effectiveness of phage
formulations would also need to be carefully monitored
and modified in step with the march of bacterial
evolution. This is similar to the annual revamp that the
flu vaccine gets – and why you need a fresh jab each
year – but it’s another mark against phages, potentially
making them less attractive to investors.

If phages themselves are too messy, Fischetti
has another solution: commandeer their weaponry. 

Once phages home in on their target, they act like
hypodermic syringes, injecting their genetic blueprint
into their bacterial host. Within minutes that blueprint
is directing the assembly of dozens of new phage
progeny. To break out, they drill holes in the tough
outer wall of the bacterial cell by deploying deadly
enzymes called lysins. These lysins themselves are
being developed as single-molecule patentable
drugs, closer to what pharmaceutical companies and
regulatory agencies are accustomed to.

Lysins also have the advantage over phages – and
traditional antibiotics – of being extremely efficient
killers. In 2001, Fischetti’s team showed that, within
seconds, a purified phage lysin obliterated 15 different
strains of the pneumonia-causing bacteria Streptococcus
pneumoniae in test tubes but were less deadly towards
harmless throat bacteria.

Their ability to specifically target bacteria is not
as finely honed as that of phages, but is superior to
antibiotics. For instance, Fishcetti says it is possible to
direct specific lysins to wipe out all streptococci, or all
staphylococci, or all pneumococci. Nor do lysins just
work in test tubes; they have rescued mice from death
by multidrug-resistant golden staph infections.

In 2016, Fischetti and colleagues unexpectedly
found that lysins could even chase down and kill
Streptococcus pyogenes, the bacterium responsible for
“strep throat”. The pyogenes hide away inside throat
cells, where antibiotics are unable to reach them,
making strep throat highly resistant to treatment.
Remarkably the lysin did not harm the throat cells. 

“Lysins are right up there as probably the best chance of
killing organisms at least as well as current antibiotics,”
Fischetti says.

Lysins are not only potent antimicrobials; they also
have a reputation for being evolution-proof. That’s
because lysins target peptidoglycan, a fundamental
building block of the bacterial cell wall. Any tweaking
of these building blocks to evade lysins would likely be
deadly to the cell, too. “Lysins have evolved to target
substrates that the bacteria can’t change very easily,”
Fischetti explains. Of course, he and others aren’t
taking any chances. They look all the time, he says, and
haven’t found one organism that’s resistant to lysin.

Despite the impressive results coming out of preclinical
trials, progress towards human trials of lysins
has been sluggish. That’s about to change. Fischetti
has been working with the company ContraFect on a
lysin treatment for golden staph blood infections. A
phase II clinical trial will kick off mid-2017, following
on from a successful phase I safety trial that ended in
2016. Fischetti expresses confidence that the trial,
which will take about two years to complete, will be a
success: “From what I see in animal studies and [other]
experiments, it works every time.”

One of the reasons that superbugs emerge is
because antibiotics are so deadly. In the wake of the
microbial holocaust, resistant organisms thrive. Roy
Robins-Browne at Melbourne’s Doherty Institute
thinks there’s a better way to treat the troublesome
bacteria that cause infections. Instead of trying to kill
them, just defang them.

In 2013, Robins-Browne and his team unveiled regacin, a molecule that effectively defangs the deadly
diarrhoea-causing enteropathogenic E. coli (EPEC).
Regacin, turns off the “virulence” genes that make this
bacteria such a bad ass, preventing them from setting
up camp in the intestine and pumping out poisonous
toxins. In mice, regacin works against an EPEC-like mouse pathogen. So far, Robins-Browne hasn’t found
any regacin-resistant mutants. In humans, he says,
using a drug like regacin could turn the deadly EPEC
back into a harmless strain of E. coli, without fear of
resistance emerging. But Robins-Browne is yet to find
backing from the pharmaceutical industry to develop
the drug further. “You can argue till you’re blue in the
face about how this doesn’t select for resistance,” he
says, “but they don’t believe you.”

While Robins-Browne’s strategy is to disarm
bacteria, there is another way of curbing their
aggression: make them think they don’t have the
numbers to mount a successful attack. 

Some bacteria have a clever way of sensing the size
of their ranks. Known as “quorum sensing”, researchers
first stumbled on this phenomenon in the 1960s in an
unlikely place: the bobtail squid. It needs camouflage
from predators below that can see it silhouetted against
the light. The squid solves that problem by virtue of a
light organ on its underbelly that houses luminescent
bacteria. These microbial light bulbs glow only once
they reach a threshold population. The bacteria ‘ping’
each other with a protein that lets the others know they
are there. The more ‘pings’, the greater their number.
When there are enough ‘pings’, the whole group turns
on its bioluminescence.

Researchers subsequently discovered quorum
sensing can be used for more aggressive purposes.
Disease-causing bacteria use it to coordinate a
successful invasion. As soon as there’s a ‘quorum’,
they pump out toxins and tissue-digesting enzymes.
In about two-thirds of infections, the bacteria also
hunker down into resilient, slime-shrouded biofilms
that protect them against the immune system and
antibiotics.

It wasn’t long before scientists were looking for
ways to silence this microbial chatter. Drugs that do
this are called quorum quenchers. “Quorum sensing
inhibition jams the communication lines,” explains microbiologist Tom Coenye from the University of
Gent in Belgium.

This tricks the bacteria into acting as if they don’t
have the numbers to mount an offensive or build a
biofilm. That makes it easier for the immune system –
or antibiotics – to come in and counter the would-be
invaders.

Dozens of quorum quenchers have been identified.
In petri dishes, Coenye has found, they prevent bacteria from building biofilm fortresses. In mice, quorum
quenchers have reduced the severity of Pseudomonas aeroginosa lung infections.

But quorum quenchers have their limitations. Most
people seek treatment when their infections are well
and truly established – too late for quorum quenchers
to work. Their role, therefore, will be in preventing the
spread of infections in the first place.

One notorious source of drug-resistant infection
in hospitals is via medical devices such as catheters
or replacement joints. That’s why Helen Blackwell, a
chemist at the University of Wisconsin, is developing
ways of impregnating catheters and replacement
hips with chemicals that act as quorum quenchers.
Preventing post-operative infections could help
eliminate the need for antibiotics and reduce the
chance for resistance to evolve and spread.

Meanwhile, Coenye is hoping quorum quenchers
will make current antibiotic therapies more effective.
His work on hamamelitannin – a naturally occurring
quorum quencher found in the bark of witch hazel
– makes golden staph biofilms more susceptible to antibiotics.

The upshot would be that antibiotics could be used
at lower doses and for shorter durations, reducing the
chance of antibiotic resistance and extending the useful
life of the antibiotics we currently rely on. 

With deaths from drug-resistant infections now
estimated at 700,000 a year globally, there’s no doubt
our seven-decade dream run with antibiotics is drawing
to a close.

Recognising the dangers, governments and
pharmaceutical companies are beginning to respond.
In 2016, nearly 100 pharmaceutical companies
pledged to work with governments to reinvigorate the
antimicrobial development pipeline.

Overall scientists are thinking broadly. In addition
to phages, lysins, quorum quenchers and virulence
disruptors, the war chest includes probiotic capsules
packed with beneficial bacteria to edge out troublemakers,
as well as vaccines and drugs such as host
defence peptides that ramp up the body’s own natural
defences.

For now this is an arms race that we are losing. To
buy time, our best bet is to rob resistant bacteria of
their evolutionary advantage by minimising the use of
antibiotics.

With sufficient investment in research and
development, the next generation of smart weapons
will hopefully be ready before antibiotics are rendered
useless. If the researchers are right, our new weapons
should protect us a lot longer than 70 years.