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What's the problem?

Antimicrobial resistance

Life-threatening pneumonia, deadly wound infections - what sounds like a scenario from the 19th century is turning into an increasingly realistic future, as the weapons we have at command to fight such diseases are getting blunt.
Infectious diseases are caused by microorganisms like bacteria or viruses and were mostly impossible to cure a hundred years ago. The discovery of penicillin in the late 1920s gave rise to a completely new class of medicines, so called antimicrobials, which allowed for the first time selective targeting of microorganisms, in case of antibiotics specifically bacteria. In the following decades, development of a wide range of antimicrobials enabled successful treatment of formerly life-threatening diseases and significantly increased global health and life expectancy.
However, fighting microorganisms has never been a completed task but rather an always ongoing race between drug development and pathogen evolution, a race in which microorganisms are more and more taking the lead. Resistance of bacteria against all known antibiotics are no longer gloomy visions of the future but already detected in some of the most widespread genera [1, 2]. The World Health Organization (WHO) even warns of a post-antibiotic era, in which common infections once again become deadly threats, if no efficient countermeasures are taken within the next years [3].

Development gap

Two aspects mainly contribute to the worsening situation. On the one hand, emergence and spread of antimicrobial resistance speeds up, while on the other hand the development of new antimicrobial agents slows down. Reasons for both aspects are numerous and will be highlighted with focus on antibacterial compounds.

Lack of new antimicrobial drugs

Economic reasons: Drug development is economically unviable.
Newly introduced antibiotics are used only sparingly to prevent development of new resistance, they are likely to be kept as second or third-line drugs, in case conventional treatment fails. Thus, profit potential of such compounds is low [5, 6].

Scientific reasons: New classes of antibiotics are hard to discover.
Targets for antibacterial drugs have to fulfil a range of criteria like essentiality to the organism, conservation across bacterial species or ‘druggability’ by small molecules blocking the target’s function. Despite new technologies like the ‘-omics’, bioinformatics or high-throughput methods, researchers are struggling to find potential drug targets meeting these requirements and no significant scientific progress has been made in the field of antibiotics over the past 25 years [7].

Regulatory Reasons: Established antibiotics set high standards regarding toxicity.
High demands are placed on newly developed compounds in terms of toxicity, as known antibiotics generally show very few side effects. Thus, investors face the risk that their agent is withdrawn from the market.

Increased development of antimicrobial resistance – a natural phenomenon strongly accelerated by human action

‘Inappropriate use of antimicrobials’ in humans is considered the ‘most important cause’ for AMR emergence by the WHO [8]. This includes both over and underuse. Every use of antimicrobials puts the human microbiome under selective pressure, enhancing selectively the proliferation of resistant strains. Thus, over-prescription of antibiotics unnecessarily intensifies the selective pressure and promotes AMR development without benefit for the patient.
However, underuse in case of a bacterial infection is no less harmful. Intake of the right antibiotic for sufficient time and dosage is required to ensure complete elimination of the pathogenic bacteria. Non-lethal quantities of an antimicrobial drug enables pathogens to develop resistance and prolongs the infection, giving resistant organisms increased possibility to spread [9].

Not only human health is achieved by use of antimicrobial compounds, antibiotics are also applied in a large scale in animal husbandry for healing or preventively avoiding diseases. Moreover, their ability to promote animal growth and improve production performance makes them attractive feed additives especially for factory farming [10].
Such non-therapeutic antimicrobials have been shown to be associated with AMR development, promoting even multi-drug resistance to compounds that were not used at the farm at all. Especially the low-dose, long-time application of antibiotics as feed additives selects strongly for resistant strains. Animal-to-human transfer of such strains may happen by direct contact or indirectly through the food chain [11].

Global challenges regarding faster and wider spread of antimicrobial resistance

Global trade and travel have increased significantly in the last decades, while urbanization leads to higher population density in cities. Both factors enhance spreading of resistance microorganisms between individuals, communities and nations. Additional trends like the AIDS epidemic or ageing populations in industrial countries increase the number of immunocompromised and hospitalized people, two groups at particularly high risk of exporsure and opportunistic infections [8].
Detailed knowledge about emerging resistance and its spread is crucial for correct risk assessment and appropriate countermeasures. Thus, surveillance of antimicrobial resistance is a basis for global health. It is, however, neither coordinated nor harmonized globally and often incomplete in many countries of the world. The lack of representitive data hampers development and implementation of effective strategies against AMR [3].

A problem-solving approach

The BaKillus strategy

Increasing bacterial resistance to classical antibiotics is a serious threat to global health and urges the development of novel pathogen-killing strategies. To address this need, we, the iGEM team LMU-Munich, develop BaKillus, a pathogen-hunting microbe. Our genetically modified Bacillus subtilis is able to detect pathogens by eavesdropping on their communication system which is based on quorum sensing (QS). This is a promising target, as many pathogens synchronize their pathogenicity using quorum sensing. In response to the sensing of the pathogen, BaKillus produces various killing factors such as peptide antibiotics or toxins to extinguish it. Additionally, BaKillus is able to adhere to the pathogen and after fulfilling its purpose, it drives itself into suicide by a delayed loss of immunity against its own killing factors.

How BaKillus decelerates the development of antimicrobial resistance

By operating via an innovative pathogen-killing strategy, Bakillus aims to decelerate the spread of bacterial resistance to antibiotics. With our strategy, we will be able to avoid one of the main reasons for antibiotic resistance, namely the mis-/overuse of antimicrobial agents. This is primarily accomplished through reduction of inappropriate use of antibiotics and a higher degree of treatment efficacy.

The first part our project, the detection of quorum sensing molecules, enables a time-limited application, as antibiotics are only produced if the QS-molecule threshold is reached. In contrast, common antibiotic therapies are administered over a longer period of time.

Bacteria regulate and synchronize energy-consuming mechanisms like pathogenicity and biofilm formation via quorum sensing in dependence on a certain cell density. Thus, only bacteria on the cusp of pathogenicity are targeted. Commensals and probiotic microorganisms residing the human body or even providing benefits, can escape the killing factors. This forms a striking contrast to the administration of broad-spectrum antimicrobials, which do not distinguish between their targets when applied, and which may lead to undesirable side effects. Therefore, the QS-dependent detection is an excellent feature to reduce the misuse of antimicrobials.

The adhesion module of BaKillus also contributes to the reduction of inappropriate use of antimicrobial agents. Our BaKillus is able to adhere to the surface of a specific pathogen, which allows a precise and localized application of the killing factors. This shelters commensals and probiotics from the exposure to antibiotics. Furthermore, the attachment to the surface of the pathogen leads to a higher treatment efficacy. A high dose of antimicrobials is released in close proximity to the target pathogen in order to efficiently kill it. In contrast, classical treatments lack this precision and pathogens can evade the drugs more easily. As adhesion happens regardless of the QS-threshold of the pathogens, this provides an excellent control strategy against opportunistic pathogens. If the cell density of the pathogen population increases and becomes pathogenic, BaKillus is already at the right spot of intervention.

Moreover, killing strategies used by BaKillus frequently have high target specificities and are only active against a certain pathogen, but spare other residents from harm. The specificity is further supported by the modularity of the systems, allowing the simple exchange of killing and sensing devices. This also helps to reduce the use of antibiotics, since it once more minimizes the exposure of antimicrobials to commensals. Another attribute of BaKillus is the usage of complementary combat strategies. Similar to classical therapies with combination products, BaKillus can produce more than one killing factor, which operate in a complementary fashion. Thereby, the concentration required for killing the pathogen is reduced for both agents. Furthermore, complementary substances, such as biofilm-degrading agents could be used as supplements to contribute to a higher efficacy of the treatment.

In conclusion, our BaKillus strategy increases the efficiency of antimicrobial treatments and strongly reduces the mis- and overuse of antibiotics, the main reason for increasing antimicrobial resistance. Thus, BaKillus is able to decelerate the development of this fast-growing, global threat.