Bacteriophages – Fighting antimicrobial resistance

Bacteriophages (phages) are viruses infecting bacteria and can be used as an alternative to antimicrobials. But how can we use viruses to kill bacterial pathogens? AVANT will develop and test anti-ETEC phages based products to reduce the use of colistin and other highest priority critically important antimicrobial HP-CIAs for the treatment of enterotoxigenic Escherichia coli infections in pigs. This will reduce the spread of antimicrobial resistance in humans and animals.

Equivalent to many bacteria associated with our body, forming the microbiome, phages are part of the microflora too. In fact, they are an integral part of our physiology. Phages control the population of bacteria in the gut and prevent certain species to dominate the flora. Consequently, they help to maintain a healthy balance. In essence, phages are as abundant as bacteria in the human body, where they accumulate in the gut mucosa for example [1]. Additionally, phages constitute a fundamental part of the virome, which is the total population of viruses deeply associated and interacting with our cells and organism [2].

Bacteriophages as antimicrobials

Depending on how phages infect bacteria, they are referred to as ‘lytic’ or ‘temperate’. Lytic phages break bacterial cells open (lytic cycle) and destroy them after immediate replication of new phage progeny, which represent complete particles made of nucleic acid (RNA or DNA) and a protein coat. After destroying the bacterial cell, the phage progeny can ultimately find new host cells to infect. Bacteriophage T4 for example, infects E. coli and can actually be found in the human intestinal tract [3]. At the moment, lytic phages are the only phages suitable for the so called phage therapy.

In contrast, temperate phages can undergo a lysogenic cycle, which does not lead to an immediate lysis of the bacterial host cells, instead their DNA will integrate with the bacteria DNA and replicate along with it until the conditions surrounding the bacteria will change and the phage will eventually be released by lysating the cell [4]. However, the use of native temperate phages as antimicrobials is currently not considered safe. Phage lambda of E. coli is an example of a bacteriophage following the lysogenic cycle as well as the lytic cycle.

A targeted treatment by using bacteriophages

Generally speaking, phages detect host cells by recognizing specific proteins on the bacteria surface, which ensures that each phage type usually attacks only one gut bacterium species. In return, this is a huge advantage for using them as a targeted treatment. Altogether, the use of bacteriophages enables a targeted destruction of pathogenic microbes without damaging the remaining microbiome, as it is the case for antibiotics. Moreover, phages are subject to evolution and quickly adapt to changing environmental influences, which enables them to overcome mutations, that bacteria develop to escape infections. Obviously, a fundamental difference to antibiotics.

A recognised contribution to the gut health is definitely represented by phage genes which are coding for enzymes, that are important for the microbiome’s amino acid and carbohydrate metabolism [5]. Apart from that, some phages can even degrade polymeric substances produced by bacterial communities to defend themselves, also referred to as biofilms. While the polymeric substances are very efficient in reducing the antibiotic concentration that will reach the bacterial cells within a biofilm, it has been demonstrated that phages can permeate this barrier and infect their host [6].

Phages as allies in fighting antimicrobial resistance

  1. In total, our organism contains about as many bacterial as human cells, and at least the same number of phages
  2. Phages not only balance our microbiome, but significantly advance its development and presumably fulfil further, as yet unknown functions
  3. Ultimately, bacterial infections can be controlled with selected phages, which is a chance to push back antibiotic-resistant germs

 

(C) UCPH, Plate with phages isolated against porcine ETEC strains.

 

The use of phages to treat diseases is an effective weapon in the fight against antimicrobial resistance. Nonetheless, there are still numerous regulatory hurdles that need to be overcome in order to ensure the safety of their use and effectiveness. Hence, AVANT will use state-of-the-art tools under the guidance of University of Copenhagen (UCPH) in clinical testing of phage formulations. The research approach basically builds on testing and optimising phage-based products to target ETEC clinical strains. In brief, it includes metagenomics profiling by 16S rDNA and shotgun sequencing and susceptibility testing in porcine infection models. Furthermore, the UCPH provides porcine ETEC infection models and animal facilities for in vivo testing of phage products among others.

Involved Partners: University of Copenhagen, Easy AgriCare, Schothorst Feed Research, SEGES: AVANT Consortium.

Find out more about AVANT’s Research Plan here.

 

Authors: Assistant Professor Michela Gambino, PhD

University of Copenhagen, Department of Veterinary and Animal Sciences

Dr. Stefan Weiss, Dipl. Biol.

RTDS Group, Dissemination & Communication

Related articles: “Status Quo of Alternatives to Antibiotics in Pig Farming”

 

References

[1] Ogilvie, L.A. and Jones, B. V (2015) The human gut virome: A multifaceted majority. Front. Microbiol. 6, 1–12.

[2] Breitbart, M., Hewson, I., Felts, B., Mahaffy, J. M., Nulton, J., Salamon, P., et al. (2003). Metagenomic analyses of an uncultured viral community from human feces. J. Bacteriol. 85, 6220–6223.

[3] Ken Cadwell “The Virome in host health and disease” NCBI 2015 Immunity 42 (5), 805-813.

[4] Biology LibreTexts “The Lytic and Lysogenic Cycles of Bacteriophages” (August, 2020).

[5] Frederic D. Bushman & Team (The Bushman Lab, University of Pennsylvania, 2011).

[6] Azeredo, J. and Sutherland, I. (2008) The Use of Phages for the Removal of Infectious Biofilms. Curr. Pharm. Biotechnol. 9, 261–266.

Status Quo of Alternatives to Antibiotics in Pig Farming


AVANT Project – Alternatives to Veterinary ANTimicrobials 

The AVANT project explores viable alternatives to Colistin & Zinc Oxide, urgently needed for European swine industry. AVANT is a new 5-year, multi-actor inter-sectorial EU-funded research project and will bring forward new technologies and products to the market that allow modern pig farms to wean healthy piglets without the use of antibiotics, or at least with very limited use.

“Prevention is better than cure” 

(European Commission motto on the One Health Initiative and animal health strategy)

Potentially, any use of antibiotics in animals could eventually affect the future treatment efficacy in the individual animal or herd, but also in consumers. This is due to the connectedness and direct contact of microbial populations and the environment. Thus, the use of antibiotics needs reducing in both treatment groups, animals and humans to ultimately preserve their effectiveness.

As shown by the European Innovation Partnership for Agricultural Productivity and Sustainability (EIP-AGRI, launched by the European Commission in 2013) several preventive non-medication actions reducing the risk of infectious diseases transmission besides infectious factors have been identified. The three main areas, where practical solutions already exist or may be further developed to strategically reduce antibiotic usage in EU pig farming are:

  • General enhancement of animal health and welfare by improved biosecurity, husbandry management, facility design, and training of personnel, veterinarians and other advisers
  • Feed supplements and techniques including vaccination, breeding and feeding programmes promoting pig health (certain feed structure & viscosity can reduce the risk of e.g. Salmonella infections)
  • Balanced and sustainable use of antibiotics by changing human behaviour, habits and attitude through improved information dissemination, education and training

“The key to reducing the need for antibiotics in the pig sector is improving the pig health.”

(Christelle Fablet, Coordinating Expert, EIP-AGRI Focus Group on Animal Husbandry)

Expert focus group has proposed several ways to promote and implement best practices for each cluster, i.e. sow and piglet management, biosecurity, housing conditions and human attitudes and behaviour determinants, to contribute to cost-effective practical solutions that leads to the reduction of antibiotics use. The group also proposed the use of interactive tools for farmers and farm advisors for improved husbandry management, using standardised risk-based analyses.

Since improvements of animal health and welfare also results from social and human sciences, further education and information, advisory task forces, bench-marking systems (data collection and transfer), consulting boards and special training schemes for farmers and veterinarians are recommended. This includes also economic evaluations and required demonstrations of research results in field testing. The EIP-AGRI focus group concluded:

“A multidisciplinary research approach should be adopted to develop solutions and strategies to prevent and manage multi-factorial respiratory and enteric diseases. Communication strategies and coaching should also be implemented across Europe […] planning an EU-wide guidance and demonstration of good biosecurity and health management practices

Here is where the AVANT project sets in, following recommendations for future projects with concrete action plans to catalyse innovation. The main innovation development activities focus on these treatment and prevention targets as alternatives for antibiotics:

    • Innovative synbiotic feed additives (BIOMIN)
    • Faecal transplantation and in-farm protocols to treat certain enteric infections in pigs (University of Copenhagen)
    • Anti-ETEC phages for the targeted host species specific intervention bringing ETEC-targeting phage products close to the market (Easy Agricare)
    • Advanced Anti-ETEC polymers regarding optimised dosage requirements, safety and efficacy as well as improved mode of action (Royal Veterinary Collage)
    • New oral & injectable immunostimulants will signify a major breakthrough in immunomodulation approaches (Ovejero Laboratories)
    • Alternative feeding strategies modulating the pig gut microbiome to prevent post-weaning diarrhoea (Schothorst Feed Research, Wageningen Research)

AVANT’s project partners from industry, research and associations (in total 14 from 9 different European countries) now work together in a multi-actor approach to reach the afore mentioned goals within the next five years, with an overall budget of € 6,5 Mio (EU Contribution: € 5,99 Mio). Here we will keep you informed about the project’s progress, ongoing activities, networking events and press releases. Please subscribe to our upcoming AVANT newsletter to keep informed!

 

Further information:

Find our project entries on EIP-AGRI and  CORDIS here.

Author:

Dr. Stefan Weiss, Dipl. Biol.

RTDS Group, Dissemination & Communication

AVANT – Follow us on LinkedIn!

Introducing the new H2020 project on alternatives to antibiotics in pig farming. AVANT is a multi-actor inter-sectorial project aimed at developing alternatives to antimicrobials for the management of bacterial infections in pigs, especially diarrhoea during the weaning period, as the major indication for antimicrobial use in livestock in Europe. During pre-clinical studies, efficacy, toxicity, and mode of action of these interventions is tested, and their dosage and formulation optimized. The results and a survey for veterinarian-, farmer- and consumers perception of antimicrobial alternatives, will be used together with legal and economic considerations to select three interventions for large-scale farm trials, assessing clinical efficacy and impact on antimicrobial use. The main impacts: The AVANT portfolio comprises a variety of alternatives for treatment or prevention of diarrhoea and/or respiratory infections, namely: gutstabilizing interventions based on a symbiotic product and faecal microbiota transplantation; Novel veterinary medicinal products containing bacteriophages and polymers for targeted treatment of enterotoxigenic E. coli infections; Immunostimulating injectable and feed additive products; Alternative feeding strategies targeting sows and piglets.

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New Social Media Profile – AVANT on Facebook!

In order to introduce our AVANT project to a wider audience, our channel on Facebook informs about current activities and upcoming events such as the virtual kick-off meeting. Here we also present stories from the project context, such as this one about the latest findings of MIT:

What do antibiotics have to do with Stanley Kubrick’s “2001: A Space Odyssey”?

Although AVANT is striving for alternatives to antibiotics, Massachusetts Institute of Technology (MIT) researchers impressively demonstrate how AI can be used to identify new powerful antibiotic compounds using machine learning algorithms.

“We wanted to develop a platform that would allow us to harness the power of artificial intelligence to usher in a new age of antibiotic drug discovery […] Our approach revealed this amazing molecule which is arguably one of the more powerful antibiotics that has been discovered.” (James Collins, Professor of Medical Engineering & Science in MIT’s Institute for Medical Engineering & Science [IMES] and Department of Biological Engineering)

A predictive computer model was trained for in silico screening, which were until now not sufficiently accurate to transform drug discovery. Testing a library of about 6,000 compounds, the model picked out one molecule with strong antibacterial activity against resistant Clostridium difficile, Acinetobacter baumannii and Mycobacterium tuberculosis.

Interestingly, the scientists decided to call it halicin (formerly tested as possible diabetes drug), after the fictional artificial intelligence system “H.A.L. 9000” from Stanley Kubrick’s 1968 science-fiction movie.

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