CRISPR, the New Antibiotics Generation – Resistance is Futile!

A computerised imaged of MRSA (Methicillin Resistant Staphylococcus Aureus).Seek-and-Destroy Antibiotics

Forget about the threat of Ebola for a moment and consider something much closer to home…  Meet MRSA – a “superbug”, the bacterium of the decade, the Nemesis of hospitals and operating theatres.  A single cell organism that can colonise the living tissues and have a devastating or even fatal impact on the human body.  Now.  Meet CRISPR – also bacteria.  A friend that can potentially help you fight and repel an otherwise deadly bacterial invasion…

Surprisingly perhaps, the human body houses ten times more bacterial cells than human ones.  This community of bacteria is called the microbiome and its importance is being increasingly recognised.  Most of these bacteria help our bodies function and remain healthy.

Often, we encounter a bug that triggers our body’s immune defences.  Occasionally, the biological agent is powerful enough that our bodies cannot deal with it and need assistance in the form of antibiotics drugs.

One of the problems with current antibiotics is that they also target the good bacteria, as well as the bad bacteria.  This allows the bad bacteria to flourish.  Scientists and politicians have warned that we face a return to the medical “dark ages” if action is not taken against antibiotic resistance of exogenous agents.

 

MRSA: A Clear and Present Danger

A map showing the Prevalence of Healthcare Associated Infections, including MRSA in 2006, in Western Europe.
Prevalence of Healthcare Associated Infections $ ($including MRSA$ )$ in Western Europe $ ($2006$ )$

Methicillin-resistant Staphylococcus aureus (MRSA) has rapidly become the bacteria of the decade.  MRSA infections now respond only to very advanced antibiotics that were never meant to be a first-line of defence.  The drugs have to be delivered intravenously, often meaning spending nights in the hospital.  And it doesn’t help that the state of antibiotics is falling behind.  With new antibiotics being approved at slower and slower rates, the battle against MRSA has many doctors worrying about creating the next deadly superbug – one that they can’t kill at all.  And new data suggest that the MRSA problem may even be far worse than we thought.

A recent study by researchers at the University Health System Consortium (UHC) and the University of Chicago Medicine, the rate of MRSA infections was recorded at U.S. academic hospitals to have doubled in the five years between 2003 and 2008.  Nearly 1 in 20 in-patients are now either battling an invasive infection or have been colonised by the bacteria (meaning that patients can carry the bacteria, but do not suffer from any symptoms).

The study also found that more MRSA-infected people have checked into the hospital than either HIV-positive or influenza-afflicted patients combined, in each of the last three yearsMost of these patients are likely to have picked up the germs before they reach the hospital grounds.  According to a 2010 Centers for Disease Control (CDC) report, infections of invasive MRSA acquired in-hospital fell by 28 percent from 2005 through 2008.

A graph showing the number of Community-Associated MRSA Infections per 1,000 Emergency Department Visits between 2001 and 2009.The CDC report also found an increase from 21 infections per 1,000 people to 42 cases per 1,000 peopleGiven such a rapid advance of MRSA, we can safely conclude that the increases seen can be blamed on community-associated MRSA, a different strain of the bacterium.

Most MRSA infections in the community are skin infections.  In medical facilities, MRSA causes life-threatening bloodstream infections, pneumonia and surgical site infections.

Together, the CDC report and the newer study from the University of Chicago paint two different portraits of the MRSA problem:

  • The first describes the extent of the illness as it actually affects victims today.  It only counts serious infections that have penetrated deep into blood or spinal fluid, and makes a point of excluding cases of colonisation.
  • The second tries to account for all cases of infection, including colonisation, and winds up capturing MRSA’s full potential. Knowing how many people have been colonised by MRSA implies just how many are at risk for consequential illness.

 

According to the Chicago scientists, the new estimate might even be low-balling the disease’s pervasiveness because the database they use – a collection of insurance bills – tends to under-report instances of MRSA if patients were hospitalised for some other ailment.  When the researchers went back to correct for the statistical inaccuracy, they discovered that the insurance claims missed between a third to one-half of MRSA cases as recorded by the hospitals’ own records.

We are now more alert to the risk of contracting MRSA than we used to be.  Better screening guaranties we find more of what we are looking for.  Still, that doesn’t change the problem that more people are becoming carriers for MRSA.  Getting infected may not guarantee illness in a specific patient, but it increases the bacteria’s chances of eventually being spread to someone who will fall ill from an infection.  And that’s why understanding the scope of MRSA’s potential – instead of measuring only the immediately-consequential cases of MRSA infection – is so important.

 

If We Do Not Act Now…

The predictions are stark.  No new classes of antibiotic drugs have been developed for over a quarter of a century.  Meanwhile, the overuse of available antibiotics favours the survival of drug-resistant bacteria.  These bacteria can then go on to transmit their resistance genes to other bacteria using tiny circles of DNA called plasmids.  This process effectively speeds up evolution to produce bugs that cannot be killed when they cause disease.  The problem is huge and requires a new interdisciplinary approach.

If we fail to act now, we are looking at an almost unthinkable scenario where antibiotics no longer work and we are cast back into the dark ages of medicine where treatable infections and injuries will kill once again.  The consequences would be chilling!!

The new CRISPR system is a new type of antimicrobial that really acts very differently to previously developed antibacterials.

 

Meet CRISPR / Cas9

The new antibiotic uses an RNA-guided nuclease called a “Crispr” to hunt down and chop up target genes inside bacterial cells.

A diagram explaining how Crispr works.
How CRISPR/Cas9 works: 1. A Crispr is designed to target a specific bacterial DNA sequence.  2. The molecule is packaged into a bacteriophage carrier to enter the target cell.  3. The CRISPR system finds the gene target, cuts the DNA strand at the specified location, and deletes the plasmid – with or without cell death occurring. 4. Targeted chromosomal DNA cuts always lead to cell death.

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), mostly found in bacteria, is a form of acquired prokaryotic immune system, conferring resistance to exogenous sequences, such as plasmids and phages.

In an account of laboratory experiments published in Nature Biotechnology, the researchers showed they could produce a molecular “conditional-lethality device” capable of highly targeted action against the “bad” bacteria in a consortium of different strains.

Crispr systems are designed to go into bacteria and specifically kill only bacteria that contain antibiotic resistance genes or virulence genesThe bacteria targeted in the experiments included a strain of E. coli which can cause severe diarrhoea and kidney failure.

But the researchers are not only interested in killing the deadly bacterium.  They also seek to rehabilitate it.  In separate experiments, the researchers showed they could change the genetic makeup of the bacteria without killing them.  Targeting the bad genes, instead of killing the good and bad bacteria alike, is a new approach which imposes direct evolutionary pressure at the gene level.

 

Vaccinating Bacteria

Like a vaccine, the technology could eventually be given to healthy people to prevent antibiotic resistance developing.  A probiotic bacteria could distribute these Crispr constructs into your natural bacterial population, and immunise them from being able to pick up bacterial resistance genes – effectively making it a vaccine for your bacteria, not for you.

Since antibiotic resistance plasmids naturally spread in a population, these Crispr we could also potentially be designed to spread… like a benevolent parasite that hops from bacteria to bacteria.  However, self-replicating gene treatments might not be without risk, and the idea must be carefully considered.  Introducing self-replicating gene treatments into our microbiome could have unforeseen consequences.

The use of antimicrobial agents based on DNA has exciting potential that remains to be harvested.  The greatest challenge is how to deliver a DNA-based agent into the bacteria to be targeted.  The MIT team explored two approaches:

  • One idea is that you can hijack the system that bacteria use to trade resistance genes.  The target cell accepts a Trojan horse-type plasmid of DNA from another bacteria, with the Crispr hidden inside it.  But as this would require live bacteria to be given to a patient, it is unlikely to be the best solution for the best outcome in the case of an acute infection.
  • Bacteriophages are natural virus predators of bacteria, highly adept at injecting
    An electron microscope photograph (or micrograph) of a T4 Enterobacteria Phage (or bacteriophage).
    Annotated Electron Micrograph of a T4 Phage

    DNA into host cells.  Using bacteriophages is also not without difficulties.  The right type of phage must be found to bind to each type of bacteria.  How easily phage can reach the site in the body where the bacteria are causing an infection, and whether they will be blocked by antibodies remain big issues.

 

The benefits of manipulating the balance of “good” and “bad” bacteria in the human body might extend beyond fighting infection.  Certain classes of bacteria in the gut are known to be over-represented in people who are obese or suffer from metabolic diseases.

A specific CRISPR-based system could be designed to target certain subsets of bacteria and only activate when they recognise the genes we know to be correlated with a particular human disease.

Until then, Nissim et al. (2014) are confident that the new Crispr-type antibiotics could be ready for clinical trials in some infections within a few years.

Effectively, a new technological arms race against bacteria has begun.