Antibiotic Resistance: Advances in Understanding and Drug Development

Bacterial resistance to antibiotics, including last-resort therapies, is a major global public health threat. Few truly novel antibiotics have been introduced in recent years, and most candidates in current pipelines are derivatives of existing molecules. However, promising research continues in the space. Scientists are leveraging advanced digital technologies, gene-editing techniques, and a variety of other strategies that take advantage of growing knowledge about how antibiotic resistance evolves. Even so, significant policy shifts are needed to mend the broken antibiotic market if the spread of antimicrobial resistance is to be halted.

The Costs of Antimicrobial Resistance

COVID-19 drew the world’s attention and government funding, leading to the development of effective treatments and vaccines in record time. There is an even greater threat lurking in the wings, however — one that has been building for years but has largely been ignored by much of the industry and policy makers. If not addressed soon, antibiotic resistance could eventually make even the simplest infection a life-threatening experience.

As one example, consider urinary tract infections, which had been on the decline. In 2020, however, a 15% increase in infections by antimicrobial-resistant organisms occurred.¹ The primary causes were misuse and overuse of antibiotics in COVID-19 patients — theses two main factors (along with agricultural use of antibiotics) have contributed to the steady spread of antimicrobial resistance over the last several years.²

Overall, well more than 1 million people die each year worldwide from infections caused by antibiotic-resistant bacteria.¹ It isn’t just multidrug-resistant bacteria causing the problem, either. The majority of fatal infections are caused by bacteria that are hard to treat for different reasons, often related to the condition of the patient.

Most large pharmaceutical companies no longer have antibiotic development programs, and seven of the 12 companies that have successfully developed and commercialized new antibiotics have gone bankrupt or exited the market owing to poor sales.³ The antibiotic market is considered to be broken, because physicians often avoid using new, more expensive antibiotics until it is absolutely necessary.¹ That hinders new drug development and encourages further expansion of resistant microbes.

Antimicrobial resistance (AMR) carries three types of costs: to the patient, the healthcare system, and the general economy. Patients can develop serious health issues or die. It is predicted that AMR infections could cost hospitals up to $2 billion annually in the United States and $300 billion to $1 trillion worldwide.²

A 2021 Centers for Disease Control and Prevention (CDC) study found that treating six antibiotic resistance bacterial infections costs the healthcare system more than $4.6 billion annually.⁴ Another 2021 study found that, in 2017 alone in the United States, AMR infections led to 10,000 deaths among older adults and $1.9 billion in health care costs.⁵

The overall cost of AMR in the US is estimated to be $55 billion per year, more than half of which is attributed to loss of productivity. AMR is also believed to be contributing to expansion of the gap between developed and developing countries.

More Knowledge about Resistance Mechanisms

To combat AMR, it is essential for researchers to better understand the mechanisms involved in the development of resistance to antibiotics. Much progress has been made in recent years as genetic technologies have enabled investigation of genetic causes and other previously unknown mechanisms that bacteria use to develop and spread resistance.

Antibiotic resistance is generally established in bacteria through the acquisition of resistance genes from other bacteria that encode for proteins or peptides that degrade or reduce the concentration of specific antibiotics or alter the target of the antibiotic so it cannot bind and halt growth.⁶

Scientists at the University of Gothenburg have, by comparing thousands of bacterial genomes, outlined how antibiotic resistance genes have evolved.⁷ Most initially spread across species from disease-causing bacteria, a phenomenon that has been facilitated by the misuse and overuse of antibiotics. Another group of researchers in Sweden and the United States found that some resistance genes emerge from completely random DNA sequences.⁶

University of Exeter scientists observed that plasmids can spread rapidly within bacterial communities that have been treated with antibiotics, which is why resistance can spread rapidly within hospitals.⁸ Duke University scientists, meanwhile, determined that “jumping genes” or transposons are responsible for the physical spread of antibiotic resistance between bacteria when high doses of antibiotics are used.⁹ The transposons “jump” around in the cell and ultimately transfer the genetic instructions for resistance from the source code within cells to the DNA plasmids that move from cell to cell. Imperial College London researches have added to this knowledge by identifying the proteins that mediate the exchange of DNA.¹⁰

Various research groups have explored the behavior of bacteria in response to specific classes of antibiotics. Bacteria resistant to rifamycin-related antibiotics, which work by binding to the protein RNA polyermase, produce a protein that displaces rifamycin compounds from RNA polymerase and other proteins that degrade the antibiotics.¹¹ Separately, new resistance genes responsible for antibiotic resistance in Mycobacterium tuberculosis bacteria to 13 first- and second-line new and repurposed antibiotics were identified by an international consortium.^12,13 The bacterium Pseudomonas, which often causes lung infections, when in the presence of colistin, a “last-resort” antibiotic, was found to have a resistance gene that mutates extremely rapidly and thus evolves its resistance capabilities quite quickly.¹⁴ Separately, a hospital strain of Acinetobacter baumannii and its cellular response to colistin uncovered the existence of a “two-component signal transduction” that includes a response regulator protein in the StkR/S system that when removed allows hundreds of transcriptional changes to take place.¹⁵ Some of these changes include modifications of the other cell membranes of the bacteria that lead to colistin resistance.

Non-genetic factors that play a role in AMR have also been identified. For instance, decreasing bacterial acidity can reduce the likelihood of persistent bacterial infections by eliminating bacteria that survive following treatment with antibiotics.¹⁶ Another example relates to the gut microbiome; healthy people that eat a varied diet including at least 8–10 grams of soluble fiber per day typically have fewer antibiotic-resistant microbes in their stomachs.¹⁷

Other scientists are developing methods to facilitate the rapid analysis of bacterial resistance development. Rice University researchers, for instance, have created a high-throughput microfluidic platform that encapsulates bacteria with varying concentrations of antibiotics to evaluate their evolution, applying biomarker discovery to antibiotic resistance.¹⁸ The microdroplets generated by the system are also thought to better mimic the early stages of infection. They are also stable for 24 hours, allowing extraction of DNA for whole-genome sequencing.                                                                           

Scientists at American University, meanwhile, have developed a new, highly sensitive rapid genetic test that enables determination in minutes of antibiotic resistance in bacteria to two antibiotics commonly used to treat respiratory infections.¹⁹ Current culture-based methods require hours or days.

Interesting Clinical Pipeline

A few new antibiotics have been approved by the U.S. Food and Drug Administration in recent years, including some that target gram-negative bacteria, which cause many hospital infections. Examples of newly approved antibiotics include eravacycline (a tetracycline derivative), cefiderocol (a siderophore cephalosporin), fourth-generation fluoroquinolones (delafloxacin), new combinations between one β-lactam and one β-lactamase inhibitor (meropenem and vaborbactam), new aminoglycosides (plazomicin), ceftazidime/avibactam, ceftolozane/tazobactam, and imipenem/relebactam.^20,21

Several innovative chemical compounds are in clinical development as well, many of which target multidrug-resistant organisms and rely on novel mechanisms of action.²¹ Phase III candidates include zoliflodacin, the first synthesized spiropyrimidinetrions, for the treatment of multidrug-resistant Neisseria gonorrhoeae, and ridinilazole (a bis-benzimidazole) and bezlotoxumab (Zinplava^®, a human monoclonal antibody against toxin B) for the treatment of gram-positive, spore-forming, toxin-producing Clostridioides difficile.

An assessment of the antibiotic candidate pipeline as of December 2020 found 43 new antibiotics (15 in phase I, 13 in phase II, and 13 in phase III) in clinical development, some of which are being developed to address resistant bacteria.²² At least 19 of the candidates target Gram-negative ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens, 15 have potential activity against carbapenem-resistant/extended spectrum β-lactamase (ESBL)-producing Enterobacteriaceae, at least 10 could address infections caused by drug-resistant N. gonorrhoeae or C. difficile.

 A WHO report published in August 2022 identified 77 antibiotics and antibiotic combination products in clinical development, 45 of which are traditional antibacterial agents and 32 that are considered non-traditional.²³ Of the traditional candidates, 27 target WHO priority pathogens. The nontraditional candidates are based on antibodies, bacteriophages or phage-derived products, microbiome-modulating agents, immunomodulating agents, and other technologies.

The preclinical pipeline includes 217 antibacterial agents/programs being pursued by 121 commercial and non-commercial entities.²⁴ Fabimycin is one example. It is a preclinical candidate derived from Debio-1452, a FabI inhibitor highly potent against Gram-positive Staphylococcus aureus that may be effective against drug-resistant gram-negative bacteria.²⁵

Using Computational Approaches to Identify New Antibiotics

The complexity of bacterial resistance development makes this problem an ideal one to tackle with advanced digital tools, including artificial intelligence (AI) and machine learning (ML).

Using ML to analyze the ATLAS database of minimum inhibitory concentration (MIC) data (managed by Pfizer) as an indication of the resistance of pathogens to antibiotics in a clinical environment, researchers have been able to predict the development of resistance and design more effective antibiotic treatments with respect to treatment of infections and reducing resistance.²⁶ Another group has used ML analysis of bacterial genomic sequence data and patient records to develop an antibiotic prescribing algorithm that reduces the risk of the emergence of antibiotic resistance by up to 50%.²⁷ In a similar approach, researchers have combined ML with DNA sequencing to identify when and where antibiotic resistance is spreading between humans, animals, and the environment.²⁸

In another example, a deep learning computer model developed at the Massachusetts Institute of Technology that can in days screen more than one hundred million compounds to identify those with novel antibiotic mechanisms has been used to elucidate several promising candidates, one of which has been shown in the laboratory setting to kill many of the most difficult bacterial strains, including those that are resistant to all known antibiotics.²⁹ A different mathematical model has been developed to predict how the number and effects of bacterial mutations leading to drug resistance will influence the success of antibiotic treatments.³⁰

Two sets of researchers have used computational methods to design promising new antibiotics. One group uses a multi-pronged computer-guided strategy in their antibiotic design efforts, which involve modification of existing antibiotics, and has developed one candidate that exhibited activity 56 times that of erythromycin and clarithromycin when tested in the lab.³¹ The other group uses computational models of bacterial gene products to design new antibiotics.³² They identified genes within bacteria that are predicted to be involved in killing other bacteria but have not been previously investigated, with the “cil” cluster attractive given its proximity to other genes involve in masking antibiotics. Cilagicin, one of its promising candidates that works by a novel mechanism (binding C55-P and C55-PP, which help maintain bacterial cell walls), has been shown in mice to be effective against many different resistance bacteria. Yet another new software solution has been developed to aid in the design of enzyme inhibitors that fight methicillin-resistant Staphylococcus aureus (MRSA). Even single, small mutations can have a measurable impact on efficacy.³³

Applying Gene Editing Tools to the Development of New Antibiotics

Advanced digital technologies are not the only modern research tools being applied to the development of novel antibiotics. Many researchers are also leveraging gene-editing techniques. In one case, researchers used CRISPR-Cas9 gene-editing technology to remove an antibiotic resistance gene from a plasmid within the bacterium Enterococcus faecalis.³⁴ The engineered E. faecalis strains delivered the modified plasmids to resistant to E. faecalis organisms, leading to a three-fold reduction in resistance within mouse models.

Other scientists are using CRISPR-Cas9 gene editing tools to create new non-ribosomal peptide synthetase (NRPS) enzymes, efficient producers of natural antibiotics, to express novel antibiotics that can potentially fight against drug-resistant pathogens.³⁵ A third group has developed customized CRISPR tools to control the expression of “silent” genes in Streptomyces bacteria that are not expressed naturally unless needed –– genes that code for the production of many interesting molecules, including antibiotics. Their approach involves the addition of synthetic regulators into bacterial cells to stimulate expression.³⁶

Many Other Promising Strategies

Beyond the use of advanced data analytics and gene editing, researchers are leveraging multiple strategies for the development of novel antibiotics. A team of researchers has made resistant bacteria, including E. coli, K. pneumoniae and P. aeruginosa, vulnerable again to antibiotics by inhibiting the protein DsbA, preventing the assembly of antibiotic-resistance proteins. The goal is to combine these inhibitors with existing antibiotics.³⁷ Indole carboxylates screened for their ability to bind metallo-beta-lactamases (MBLs) that break down carbapenem antibiotics had their chemical structures optimized for binding. They were shown to bind to MBLs by imitating the binding of carbapenems. When used in combination with carbapenems, the effectiveness of the antibiotics was significantly boosted.³⁸

Hydroquinine, a naturally occurring compound found in the bark of some trees and used as an effective treatment for malaria, has recently been shown to exhibit antibacterial activity in lab test, including multidrug-resistant P. aeruginosa.³⁹ Another study of P. aeruginosa revealed the existence of a new mechanism of bacterial killing that involves ADP-ribosyltransferases (ARTs), which modify RNA. The bacteria produce the toxin RhsP2, which kills other species of bacteria by modifying RNA via ADP-ribosylation. These targets could potentially be targets of novel antibiotics as well.⁴⁰

Hemithioindigo (HTI) molecules when activated by light act as molecular motors that enhance the generation of reactive oxygen species (ROS) that attack and destroy gram-positive bacteria and the biofilms they form.⁴¹ Other scientists found that blanket inhibition of all caspases, enzymes that mediate programmed cell death and remove old cells, can be an effective means of boosting immune responses against MRSA and other bacterial skin infections.⁴²

Gold nanoclusters, meanwhile, have been shown to disrupt bacterial cells, making them more susceptible to standard antibiotic treatments.⁴³ Silver (Ag)-based nanoparticles have also been shown to effectively bind to Ag⁺-binding proteins in S. aureus and disrupt antibiotic resistant by interfering with multiple biological pathways.⁴⁴ A combination of antibiotics with silver nanoparticles is thus a promising approach to increasing the effectiveness of existing antibiotics.

Finally, the efficacy of bacteriophages –– viruses that attack bacteria –– can be boosted by subjecting them to evolutionary training.⁴⁵ Phages designed to adapt and evolve to host bacteria can, more specifically, delay the onset of resistance.

Uncertain Future Despite Antibiotic Developments

Although many new possibilities for antibiotic development have been identified in recent years, the World Health Organization’s (WHO) 2021 antibiotic pipeline analysis concluded that little progress had been made to develop antibiotics effective against drug-resistant bacteria, particularly oral drugs that could be taken outside of the hospital setting.³ In addition, 11 of the 13 drugs approved in the past few years are all derivatives of existing products with similar mechanisms of action and efficacy, with only two truly novel antibiotics.

The reasons for the limited progress include the difficulty of developing new solutions using existing screening approaches and the constant evolution of pathogenic bacteria, but the largest contributor is lack of financial incentive for pharma companies.^3,46-48 It is believed that, if the same level of supportive funding and financial returns could be achieved for antibiotics as is garnered for cancer drugs, a similarly high level of innovation would occur in the antibiotic field. However, if things remain the same, Henry Skinner, CEO of the AMR Action Fund, believes that a decade will pass before the next truly novel antibiotic reaches the market.⁴⁷

Significant changes in policy are needed, along with a much greater public understanding of the value of antibiotics to society.^46–48 Even the G7 countries are aware of the issue, with the finance ministers committing to address antibiotic market failure and create the right economic conditions to preserve essential existing antibiotics.”⁴⁹ One proposed solution is to guarantee “subscription-style” government contracts for new antibiotics if they are able to treat drug-resistant infections. The U.K. announced such a framework in 2019 and is evaluating antibiotics for inclusion in its program.

In the United States, the Pioneering Antimicrobial Subscriptions to End Up surging Resistance (PASTEUR) Act would create a subscription model. Separately, Reps. Diana DeGette, D-Colo., and Fred Upton, R-Mich., are developing a bill called “21^st Century Cures 2.0” that would, among many other things, establish an $11 billion fund for antibiotic purchases and outline a plan for determining which antibiotics would qualify. The proposed legislation currently focuses on novel chemistries/classes. The DISARM Act, meanwhile, would provide an extra Medicare payment when new, more expansive antibiotics with special status granted by the FDA are used appropriately. The hope is private insurers would take similar action. No hearings had been held for either bill, however, as of early October 2022.

The biopharma industry has taken some steps as well. The AMR Action Fund was established in July 2020 by 20 leading biopharma companies. in conjunction with the WHO, the European Investment Bank, and the Wellcome Trust to support the development of innovative antibiotics.⁴⁷ Its first investees include Adaptive Phage Therapeutics and Venatorx Pharmaceuticals.

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