Modified viruses deliver death to antibiotic-resistant bacteria

Engineered microbes turn a bacterium’s immune response against itself using CRISPR.

Genetically modified viruses that cause bacteria to kill themselves could be the next step in combating antibiotic-resistant infections.

Several companies have engineered such viruses, called bacteriophages, to use the CRISPR gene-editing system to kill specific bacteria, according to a presentation at the CRISPR 2017 conference in Big Sky, Montana, last week. These companies could begin clinical trials of therapies as soon as next year.

Initial tests have saved mice from antibiotic-resistant infections that would otherwise have killed them, said Rodolphe Barrangou, chief scientific officer of Locus Biosciences in Research Triangle Park, North Carolina, at the conference.

Bacteriophages isolated and purified from the wild have long been used to treat infections in people, particularly in Eastern Europe. These viruses infect only specific species or strains of bacteria, so they have less of an impact on the human body’s natural microbial community, or microbiome, than antibiotics do. They are also generally thought to be very safe for use in people.

But the development of phage therapy has been slow, in part because these viruses are naturally occurring and so cannot be patented. Bacteria can also quickly evolve resistance to natural phages, meaning researchers would have to constantly isolate new ones capable of defeating the same bacterial strain or species. And it would be difficult for regulatory agencies to continually approve each new treatment.

CRISPR-fuelled death

To avoid these issues, Locus and several other companies are developing phages that turn the bacterial immune system known as CRISPR against itself. In Locus’ phages, which target bacteria resistant to antibiotics, the CRISPR system includes DNA with instructions for modified guide RNAs that home in on part of an antibiotic-resistance gene. Once the phage infects a bacterium, the guide RNA latches on to the resistance gene. That prompts an enzyme called Cas3, which the bacterium normally produces to kill phages, to destroy that genetic sequence instead. Cas3 eventually destroys all the DNA, killing the bacterium. “I see some irony now in using phages to kill bacteria,” says Barrangou.

Another company, Eligo Bioscience in Paris, uses a similar approach. It has removed all the genetic instructions that allow phages to replicate, and inserted DNA that encodes guide RNAs and the bacterial enzyme Cas9. Cas9 cuts the bacterium’s DNA at a designated spot, and the break triggers the bacterium to self-destruct. The system will target human gut pathogens, says Eligo chief executive Xavier Duportet, although he declined to specify which ones.

The two companies hope to start clinical trials in 18–24 months. Their first goal is to treat bacterial infections that cause severe disease. But eventually, they want to develop phages that let them precisely engineer the human microbiome by removing naturally occurring bacteria associated with conditions such as obesity, autism and some cancers.

Both Barrangou and Duportet acknowledge that for now, causal links between the human microbiome and these conditions are tenuous at best. But they hope that by the time their therapies have been proved safe and effective in humans, the links will be better understood. Phages could also allow researchers to manipulate the microbiomes of experimental animals, which could help them to untangle how certain bacteria influence conditions such as autism, says Timothy Lu, a synthetic biologist at the Massachusetts Institute of Technology in Cambridge and a co-founder of Eligo.

An engineered solution

Other companies are working to get phages to perform different tasks. ‘Supercharged’ phages, created by a group at Synthetic Genomics in La Jolla, California, could contain dozens of special features, including enzymes that break down biofilms or proteins that help to hide the phages from the human immune system.

But engineered phages still have to overcome some hurdles. Treating an infection might require a large volume of phages, says Elizabeth Kutter, a microbiologist at Evergreen State College in Olympia, Washington, and it’s unclear whether this would trigger immune reactions, some of which could interfere with the treatment. Phages could also potentially transfer antibiotic-resistance genes to non-resistant bacteria, she notes.

Lu adds that bacteria may still develop resistance even to the engineered phages. So researchers might have to frequently modify their phages to keep up with bacterial mutations.

But as antibiotic resistance spreads, Kutter says, there will be plenty of space for both engineered phages and natural phage therapies, which are also growing in popularity. “I think they’ll complement the things that can be done by natural phages that have been engineered for hundreds of thousands of years,” she says.

Reardon, S. Modified viruses deliver death to antibiotic-resistant bacteria. Nature 546, 587–588 (2017).


FOLIUM Science CEO Interviewed by FeedInfo

UK-based FOLIUM Science has developed a unique way to fight unwanted bacteria in animal production; remove the organisms from an animal’s gut by causing them to self-destruct.

The patented technology, being developed at the company’s research and development laboratory in Bristol, could potentially reduce the need for antibiotics in farmed animals and, therefore, help stem the growing problem of anti-microbial resistance. Its targeted action against unwanted bacteria could also be employed to maintain a healthy microbiome, which, the company believes, could mean that current antibiotic alternatives, like pre- and probiotics, will no longer be needed in the future.

This selective removal of the bacteria responsible for production issues in animal agriculture and how the process could be used to fight anti-microbial resistance was the idea behind FOLIUM Science’s creation in 2015. Founded by CEO Ed Fuchs, a former food industry executive, along with systems biology professor Morten Sommer, veterinary and human medicine expert, Dr Christian Grondahl, and patent attorney, Jasper Clube, the company has turned this concept into its own patented system called ‘Guided Biotics™’, which it plans to develop into zootechnical additives that can be added to feed or drinking water.

Through the use of CRISPR, the biological sequences that make up the bacterial immune system, FOLIUM’s system directs the organism into believing it is being attacked thereby causing it to self-destruct. FOLIUM can tailor the technology to target a specific bacterium or a defined range of bacteria, which means that, unlike the kill-all approach of many antibiotics, it can be used to remove only the unwanted bacteria in the animal’s digestive tract and leave beneficial gut flora unchanged.

Feedinfo News Service recently caught up with the company’s CEO to find out how the company sees its technology affecting the animal agriculture industry when it hits the market in late 2020 and what its role in the fight against anti-microbial resistance will be.

[Feedinfo News Service] You credit antibiotic/antimicrobial resistance in animal agriculture as a reason for establishing FOLIUM Science. In your view, has the industry made sufficient changes to slow its growth?

[Ed Fuchs] The link between the use of antibiotics in animal rearing and the rise in anti-microbial resistance is now widely recognised, hence the move away from sub-therapeutic use in feeds in many parts of the world. Recent studies have shown that many salmonella and E.coli found in chickens are resistant to a range of commonly used antibiotics. Importantly, these bacteria enter the human food chain and are potential zoonotics, meaning they can cause health problems in humans. Antibiotic resistance is estimated to contribute to the death of approximately 700,000 people at a cost of USD 40 billion annually across the globe, and is predicted to increase if current practises do not change.

Since restrictions came into force in Europe and the United States on the use of sub-therapeutic antibiotics, the industry has focused on trying to find viable and effective alternatives that will prevent the proliferation of undesirable gut bacteria and promote animal health. However, the range of options currently available to producers, whilst supportive of gut health, are less than fully effective in removing unwanted bacteria.

[Feedinfo News Service] Your approach to helping them fight these unwanted bacteria involves CRISPR. Most people will probably know it as a gene editing tool, but in bacteriology it is something different. Can you take us through what it is and how FOLIUM Science is applying it to livestock production? How reliable is this technology?

[Ed Fuchs] Guided Biotics™ are based on patented CRISPR-Cas technology. CRISPR is an acronym that describes repeating sequences of DNA that form part of the bacterial natural immune system that has developed to recognise and destroy the DNA of invading elements, such as bacterial viruses. Guided Biotics™ use CRISPR to identify and target specific sequences of DNA only in the targeted undesirable bacteria.

This natural bacterial immune system involves a nuclease enzyme (Cas) that cuts the DNA of an attacking virus. Guided Biotics™ redirect this enzymic mechanism so that undesirable bacteria cut their own DNA. This causes bacteria to self-digest, meaning that the specific unwanted bacterium is removed from the animal gut.

Although CRISPR is more widely known as a gene editing tool, the action of our technology does not involve any gene editing of the target bacteria. Guided Biotics ™ are designed to be extremely specific in targeting the unique sequences of DNA that are found only in the target organism. The data from our in-vitro and in-vivo studies shows that this can be achieved consistently and repeatedly.

Three independent in-vivo studies have conclusively proved that Guided Biotics™ can dramatically reduce salmonella bacteria in poultry. In these three studies, Guided Biotics™, designed to target all 2,400 serotypes of salmonella, were given to test groups of birds as an additive to the drinking water whilst the control groups were not given the Guided Biotic™. All birds were then exposed to a severe salmonella challenge.

Collectively, the data showed statistically significant reductions (p=0.001) in colony forming units (CFUs) of salmonella bacteria in caecal samples when comparing colonisation levels in the test groups with those of the control groups. There was an overall drop in colonisation of at least log 2 across the flock given the Guided Biotic™. Furthermore, salmonella could not be detected in 50% of the birds given the Guided Biotic™ compared to 100% detection in the control animals.

[Feedinfo News Service] Let’s turn to antibiotic/anti-microbial resistance, a subject you’ve obviously considered while developing your Guided Biotics technology. What are some of the developments that you’ve noticed while researching this field?

[Ed Fuchs] Every geography and animal group has unique issues when it comes to antimicrobial resistance and also zoonotic contamination. For example, there are, to a greater or lesser extent, issues with salmonella globally, particularly in poultry products. In regions raising broilers without sub-therapeutic antibiotics, Clostridium perfringens-mediated necrotic enteritis has become a major problem.

Conversely, in piglets Escherichia coli-mediated diarrhoea can cause serious economic losses, while Vibrio species are a particular problem in shrimp production. The list of undesirable bacteria that need control is extensive.

[Feedinfo News Service] And for a long time antibiotics was the way to do this. But, as a result of antibiotic resistance and restrictions on antibiotic use, more and more producers are turning to gut health products, like pre- and probiotics, and phytogenics. How does your technology differ from these alternative solutions in ensuring livestock health?

[Ed Fuchs] What makes our Guided Biotics™ different is that alongside being delivered via a standard probiotic, they also selectively remove undesirable bacteria from the gut, leaving the beneficial and commensal bacteria intact. This supports a positive gut microbiome by allowing these beneficial bacteria to thrive.

No other feed additive is this specific. Whilst some phytogenics, probiotics and prebiotics may have marginal suppressive and competitive exclusion effects on some pathogens this reduction is never more than marginal.

[Feedinfo News Service] In terms of cost, how competitive will your solution be when it is launched? Especially compared to these antibiotic alternatives that are already on the market?

[Ed Fuchs] Guided Biotics™ will be priced competitively with current feed additives such as pre- and probiotics. We are developing our manufacturing capability to ensure our costs of production will support this goal and we have sufficient capacity to meet projected global demand.

[Feedinfo News Service] In your opinion, will your technology replace, to some extent, current nutritional antibiotic alternatives in the future? Or do you see it playing more of a complementary role?

[Ed Fuchs] Because Guided Biotics™ will be effective in removing the undesirable bacteria in the animal gut and thus supporting the growth of positive bacteria, it will mean that some additives such as the probiotics that are currently used to give support to the gut microbiome will no longer be necessary.  For this reason we consider Guided Biotics™ as “next generation” probiotics.

[Feedinfo News Service] We understand that the first version of your technology will focus on eliminating salmonella in chickens. How far away are you from adapting it for other bacteria (like E.coli) and for the beef, pork and aquaculture industries?

[Ed Fuchs] Applications are in development for use in poultry, cattle, swine and aquaculture. Phase one priority targets for poultry applications are salmonella (all serotypes) and then C. perfringens. Salmonella can cause bird production losses and is a major zoonotic human health issue globally. C. perfringens causes necrotic enteritis that has become a significant cause of productivity losses in markets where antibiotic-free poultry is an increasingly important consumer requirement.

Subsequent products are under design for a wide range of pathogens, spoilage and wastage bacteria in all parts of animal production, agriculture and aquaculture.


FOLIUM Science granted third Innovate UK award

Innovate UK, the UK’s innovation agency has confirmed its support for agri-technology that can help in the fight against anti-microbial resistance (AMR) by awarding a third grant to FOLIUM Science.

FOLIUM Science has developed unique and patented technology in the form of Guided Biotics ™ that selectively removes unwanted bacteria by harnessing enzymes in the bacteria. The three Innovate UK supported projects will develop the application of Guided Biotics ™ in the agricultural sector in partnership with leading science institutions and technology businesses.

The third grant has just been confirmed as part of a £22 million government investment in new agricultural technology. This latest project aims to identify and control bacterial blight in world crops. For this work, FOLIUM Science will be working in partnership with the John Innes Centre(JIC), the University of East Anglia (UEA) and Rinicom Ltd. The project will develop Unmanned Aerial Vehicle (UAV) systems to detect sites of Xanthomonas and other bacterial infection within a crop and deliver a precise application of FOLIUM Science’s Guided Biotics ™ as a localised liquid spray. The team aims to develop a prototype for demonstration in a crop production system.

Xanthomonas blight is a significant challenge to sustainable food production, affecting more than 400 species of plants. Once established,the bacteria can infect the entire crop within six weeks resulting in substantial, often devastating losses to crop yields. Staple world food crops such as rice, soybean and cassava have recorded yield losses of between 50% and 75% due to Xanthomonas infection.

Despite the scale of the challenge, current treatment options have had only moderate success.

Xanthomonas infected plants will be treated by precise local spot spray application of Guided Biotics™ delivered precisely and accurately to only those plants identified as carrying the infection. Guided Biotics ™ have proved to be highly effective against bacteria, with up to 6log reduction in bacterial colony forming units (CFUs), are equally effective against bacteria that are resistant to antibiotics yet result in no build up in resistance to their action. They remove only the target pathogen leaving a healthy plant and no residual material.

Rinicom’s UAV system will employ advanced AI driven video analytics and proprietary algorithms to detect, track and classify early signs of Xanthomonas infection in a crop. Using high resolution imaging to identify physiological measures such as foliage colour and plant height, susceptible plants will be located by the UAV within exact GPS coordinates. Once an infection is suspected, analysis can occur within 15 minutes and the Guided Biotics ™ aerosol spot treatment deployed to the infected site.

FOLIUM Science’s CEO Ed Fuchs says “The combination of our Guided Biotics ™ with Rinicom’s state-of-the-art technology has the potential to revolutionise the treatment of this persistent and damaging bacterial blight. Not only will crop yields improve as a result but Guided Biotics ™ but this technology supports a sustainable environment by reducing the need to use chemicals or antibiotics.We are establishing a new gold standard in environmentally friendly, highly specific crop treatment solutions.”

“We are pleased and honoured to be part of this exciting and challenging project where our AI and video analytics know-how can make positive impact to a global problem”, said Professor Garik Markarian, CEO of Rinicom. “Working with FOLIUM and UEA will ensure the success in establishing UK’s leading role in environmentally friendly crop treatment” 

This project is focused on Xanthomonas blight in UK brassica crops and the team will be working with local farm communities to execute field trials.

This third award builds on the two previous Innovate UK grants for Guided Biotics ™ applications.

The first, awarded in April 2018 seeks to develop a treatment spray for use on fresh fruit and vegetable crops. Using FOLIUM Science’s Guided Biotics ™ technology, and in partnership with the University of East Anglia and the John Innes Centre (JIC), the aim is to disrupt and prevent the formation of Pseudomonas biofilms on plant surfaces. The work will also explore the options for manufacture and commercial scale up of the Guided Biotics ™ treatment.

The second, awarded in September 2018 seeks to demonstrate that FOLIUM Science’s Guided Biotics ™ can reduce the need to use antibiotics in the production of farmed animals. For this project FOLIUM Science is working in partnership with the University of Bristol, and the Quadram Institute Bioscience to evaluate the effectiveness of Guided Biotics ™ to control specific pathogens and demonstrate superior effectiveness compared to other non-medical interventions.

“Innovate UK has recognised one of the greatest challenges of modern times represented by antimicrobial resistance and the potential contribution of Guided Biotics ™” says Ed Fuchs. “The specificity of our biotechnology allows us to target only those bacteria that are harmful to plant or animal health, leaving the good bacteria intact. The funding from Innovate UK in these three critical areas of challenge will support the development of UK led biotechnology that can be of long-term benefit to the food supply chain.”


FOLIUM Science at Alltech ONE Ideas Conference

As part of the Pearse Lyons Accelerator programme for agribusiness innovators, FOLIUM Science  showcased their Guided Biotics ™ technology at the ONE19 Alltech Ideas Conference in Lexington, Kentucky 19th – 21stMay 2019.

FOLIUM Science was selected as one of ten start-up businesses from over 250 applications with mentoring and support from Alltech’s management team and accelerator experts Dogpatch Labs. The programme culminated in attendance at the Alltech One conference and an opportunity for FOLIUM Science to exhibit their technology to more than 4,000 conference delegates from across the animal nutrition and animal rearing industries.

FOLIUM Science’s new technology, Guided Biotics ™ can remove the need to use antibiotics in animal rearing and has the potential to contribute to the fight against antimicrobial resistance.  

Guided Biotics ™ remove unwanted bacteria from an animal’s gut by turning the bacteria’s own natural defence against itself. The first product to market will be in 2020 and will target specific pathogens and spoilage bacteria. Further product development will target bacteria in poultry, cattle, swine, aquaculture and plants.

FOLIUM Science CEO Ed Fuchs says “ We very much enjoyed participating in the Alltech Ideas Conference and specifically meeting with a wide range of potential users of our Guided Biotics™ . Our technology is proven in live poultry trials, and we are now on the pathway to commercialisation so the opportunity to showcase our Guided Biotics ™ amongst the global agribusiness community and to meet with journalists and potential partners was of great value to us”


Hadden Graham joins FOLIUM Science as Chief Technology Officer

UK based biotechnology business FOLIUM Science is delighted to announce the appointment of Dr Hadden Graham as Chief Technology Officer, to lead the development of its Guided Biotic™ next generation probiotic technology. FOLIUM Science’s Guided Biotic™ technology is part of a multi-platform approach to replace the use of antibiotics in farmed animal production.

Hadden joins the business from AB Vista, where he was a founding employee and head of the global technical team. Alongside his role within AB Vista, Hadden was President of the FEFANA, the EU Association of Specialty Feed Ingredients and their Mixtures, from 2007-9. Prior to that,Hadden filled various research, technical and regulatory roles in Finnfeeds International/Danisco Animal Nutrition

FOLIUM Science CEO Ed Fuchs says “We see this as a significant strategic appointment in the continued development of our business model. Our Guided Biotic™  technology is already proving successful and the addition of Hadden’s experience, skills and connections represents the next phase in our growth plan. Hadden is well known across the industry, and his decision to join us reflects the size of the market opportunity and the excitement associated with this new technology”.

Hadden commented “FOLIUM Science has novel and patented technology with numerous applications within the agricultural space and I am very much looking forward to working with the team.The marketplace needs products that will address the challenges faced by our farmers and consumers, and I believe that FOLIUM Science’s technology has real potential”.

Hadden joins FOLIUM Science on 1st April and will lead the development of the technology through the process of commercialisation and market entry.


Watch the FOLIUM Science video

CEO Ed Fuchs and Chief Scientist Professor Martin Woodward explain how Guided Biotic technology works.


BBC Documentary on new ways that scientists are trying to fight bacterial infections, as they try to combat antibiotic resistance


FOLIUM Science demonstrate their Guided Biotic™ technology controls Salmonella in three successful poultry trials

FOLIUM Science continues to prove the efficacy of its unique and patented Guided Biotic™ technology to counter productivity losses associated with the burden of bacterial pathogens in farmed animals. This novel technology is part of the multi-platform approach to replace the use of antibiotics in farmed animal production.

Folium Science has designed its Guided Biotic™ technologies to selectively remove unwanted organisms that are detrimental to productivity. Three independent in-vivo studies have conclusively proved that Guided Biotics™ can dramatically reduce Salmonella bacteria in poultry.

In these three studies, Guided Biotics™ were given to test groups of birds as an additive to the drinking water whilst the control groups were not given the Guided Biotic™. All birds were then exposed to Salmonella.

Collectively, the data showed statistically significant reductions(p=0.0001) in colony forming units (CFUs) of Salmonella bacteria when comparing colonisation levels in the test groups with those of the control groups. These reductions were seen in two key parameters. Whereas every bird (100%) in the control groups without Guided Biotic™ were colonised with ~106 Salmonella per gram of gut contents there was an overall drop in colonisation of at least log 3 across the flock given the Guided Biotic™ and furthermore Salmonella could not be detected in 50% of the birds given the Guided Biotic™.

Chief Scientific Officer Professor Martin Woodward says “Having been involved in animal vaccine development for many years, these are quite stunning data. The data shows the huge potential for GuidedBiotics™ to be a very meaningful tool in the selective removal of unwanted bacteria in poultry and other livestock. To have in-vivo data that reinforces ourin-vitro data where reductions of log 6 have been achieved is a very exciting step forward in the translation of this technology to a much-needed non-antibiotic commercial solution. Not only are birds healthier as a result of a reduced bacterial pathogen burden but the reduced shedding of bacteria carries with it a reduced risk of cross contamination, environmental spread and significantly less entry into the human food chain. We have also designed GuidedBiotics™ to tackle the productivity issues caused by Campylobacter, AvianPathogenic E. coli and Clostridium perfringens and other pathogens that confound poultry production. We are very excited about achieving these truly remarkable data in-vivo in poultry and this encourages us to make the necessary design changes for other production issues in pigs, cattle, fish and shrimp”.

FOLIUM Science remains committed to developing this technology across a broad range of applications to selectively remove unwanted bacteria with products in development for pigs, cattle and aquaculture. For example, GuidedBiotics™ have the potential to address scouring in cattle, neonatal diarrhoea in pigs, Campylobacter colonisation of poultry, Vibrio parahaemolyticus in shrimp amongst others. Additional work includes the development of treatment sprays and biocides for bacterial blights in fruit, vegetable and other staple food crops.

FOLIUM Science CEO Ed Fuchs says “We recognise one of the greatest challenges of modern times in production is the spectre of antibiotic resistance and we have just demonstrated in these poultry trials the ground-breaking potential of our Guided Biotics™. The specificity of our technology allows us to target only those bacteria that reduce animal or plant productivity, leaving the good bacteria intact and stabilising the microbiome. Farmers are having to deal with many persistent problems, so we are aspiring to give them a productivity benefit of several percentage points. By feeding Guided Biotics™, farmers will improve productivity and give themselves an insurance against the associated financial losses that these inherent issues can drive. The data from this project demonstrates the effect on a major poultry issue however Guided Biotic™technology can be equally effective on a broad range of bacterial species found in agriculture and aquaculture and we are already working on further solutions to support greater productivity across the food supply chain”.


FOLIUM Science selected as Pearse Lyons Accelerator finalist

As one of ten finalists, FOLIUM Science has been selected from more than 250 applications across 53 countries to take part in this forward-thinking programme for innovative Agri-Tech businesses.

The Pearse Lyons Accelerator aims to discover the brightest ideas in agriculture and technology and to equip future AgTech entrepreneurs to develop successful, sustainable businesses. Being part of the Pearse Lyons Accelerator provides access to expertise, mentors and resources to speed the development process, challenge traditional thinking and make great ideas a commercial reality.

Alltech, the global animal nutrition and agri-business created the Accelerator as part of its vision to feed the world, raise healthy plants and animals and protect the environment through nutrition and scientific innovation.

FOLIUM Science’s biotechnology impressed the judges with its potential to contribute to the fight against antimicrobial resistance. FOLIUM Science has developed Guided Biotics ™; unique technology that can reduce the need to use antibiotics in food and farming. Guided Biotics ™ harness naturally occurring enzymes to weed out unwanted bacteria in any microbiome where they impact plant or animal health.

The use of Guided Biotics ™ in animals is as an additive to feed or drinking water with applications in development for poultry, cattle, swine and aquaculture as well as applications in plants that will support greater productivity.

To be selected as part of the Pearse Lyons Accelerator will allow us to build on our proof of concept and quickly establish the commercial route to market” says FOLIUM Science CEO Ed Fuchs “This will extend our access to feed and feed additives markets and we can clearly see a path to the US via registrations in key territories such as South East Asia and India.The expertise and resources that the programme provides all finalists will bring added traction to the commercial opportunity represented by our Guided Biotics ™”

The Pearse Lyons Accelerator runs over 16 weeks and is comprised of workshops, strategy sessions and mentoring culminating in a pitch to more than 4,000 potential customers and investors at the Alltech One conference in May in Kentucky.