How sea sponges could be the answer to antibiotic resistance

By Madeleine Eaton

In the past century, antimicrobial resistance (AMR) has emerged as a critical global public health threat, threatening our ability to prevent and treat infections ranging from bacterial to fungal. AMR develops in microorganisms due to many reasons including drug efflux pumps, antibiotic inactivation by enzymes, and alterations in metabolic pathways or cell membrane permeability.3 The “2020 antibacterial agents in clinical and preclinical development” report by the WHO stated that “the clinical pipeline and recently approved antibiotics are insufficient to tackle the challenge of increasing emergence and spread of antimicrobial resistance”.1 In fact, only 11 new antibiotics have been approved since July 2017, with the majority having limited impact because they are part of existing antibiotic classes. Because many existing antibiotics were derived from terrestrial bacteria, continuing research continues to discover the same antimicrobial agents, a ‘rediscovery problem’ so to say.2 The importance of isolating novel compounds that are active against antimicrobials cannot be overstated, and surprisingly, marine life such as sea sponges could be the solution. 

The range of conditions in the marine environment such as temperature, pressure, and light (to name a few) is enormous, meaning its colonization by organisms has led to wide biodiversity, especially metabolic and chemical diversity in terms of production of secondary metabolites. The combination of technologies such as DNA sequencing, high resolution mass spectrometry, liquid chromatography, and high-power bioinformatics allows research and insight into these novel compounds.2 Some of these have been identified to be biologically active against several pathogenic organisms by inhibiting quorum sensing, and oxidative phosphorylation, as well as increasing cell permeability and binding cytoplasmic membranes. In addition, they are extremely chemically diverse, comprising of peptides, sterols, lactones, polyketides, and more3, meaning they hold the potential to develop new antibiotic classes. 

In the past 50 years, more than 600 novel natural products (NPs) have been derived from deep-sea bacteria and fungi.8 For example, deep-sea sponges have been found to contain over 1,000 novel strains of actinobacteria. Actinobacteria are a gram-positive bacteria phylum that produce many metabolites identified to be useful in humans as antibiotics, antifungal agents, antitumor compounds, and more. Almost 2/3 of current drugs used against microbes were isolated from terrestrial actinobacteria, such as streptomycin.4 A study in Frontiers in Microbiology screened the metabolites of 50 marine actinobacteria strains against several common pathogens such as methicillin-resistant S. aureus and C. difficile. The results showed that 50% of these strains had anti-microbial and antifungal activity. One strain was even shown to be more effective than vancomycin, a common antibiotic, against C. difficile bacteria5, a bacterial pathogen infecting the bowels with reported resistance to a number of antibiotics including penicillin and clindamycin.6 Marine fungi also represent a promising new area of research. In 1948, the B-lactam antibiotic cephalosporin was discovered in the Sardinian sea from fungi and has become a key treatment for Gram-positive bacteria such as Streptococcus. It has a similar mechanism of action as penicillin (disrupting the peptidoglycan layer) but are not as susceptible to B-lactamases.7 Additionally, the analysis of fungal genomes has shown that the amount of predicted biosynthetic genes is more than those currently identified, meaning there are potentially hundreds of biologically active compounds yet to be discovered.8 These are just a few key examples example of how the wide diversity of marine life is used for isolation of novel compounds that enter the drug development pipeline. 

When it comes to the discovery and isolation of these marine compounds, traditional methods such as bioassay guided isolation are insufficient.9 Genome mining has been identified as the current most useful approach to identify novel compounds in biosynthetic pathways of marine microorganisms. It uses computing and bioinformatics tools to identify genes likely to encode enzymes useful for further research by exploiting sequence comparison with existing DNA sequence data publicly available. This comparison is used to identify useful gene clusters in the marine organism genomes and identify/analyze the products encoded in them.10 An example of how this has been used to enhance natural product discovery is the research into the marine actinomycete genus Salinispora. As previously mentioned, marine strains of actinobacteria are key research targets when looking to isolate products active against pathogens. Initial probing into potential secondary metabolites of Salinispora strains used traditional bioassay, cultivation, and screening approaches, however more recent work has focused on using genome mining as a more effective tool. Through this, researchers were able to elucidate 2 potent antibacterial agents: lomaiviticins A/B and salinisporamide A. Salinisporamide A, in particular, was identified to be a highly potent proteasome inhibitor and has entered phase 1 clinical trials for multiple myeloma treatment.11 Additionally, DNA sequencing tools have revealed that many bacteria contain gene clusters that are ‘silent’, ie. inactivated, yet that encode novel antibiotic compounds. As antibiotic production is energetically costly to a bacterium, these genes would only be switched on when a competing bacterium is encountered. Researchers are now attempting to induce microbes into activating the gene clusters and producing these compounds, for example by coculturing two bacteria and forcing them to produce these uncharacterized antibiotics to compete for survival.12 The products can then be purified and analyzed further to determine structure, method of action, and drug development potential. As we can see, gene mining eliminates the randomness of traditional discovery methods, saving time and resources, as well as speeding up the ability of researchers to put promising compounds into the pre-clinical pipeline. 

Overall, it is evident how marine life is a reservoir for the reinvigoration of the currently dry antibiotic development pipeline. The discovery of novel biologically active compounds is key to tackling the critical issue of antimicrobial resistance and exploiting the rich biodiversity of marine life is a step in the right direction. 


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