The Battle Against Bacteria
Since bacteria met antibiotics, we have been facing antibiotic resistance. How is resistance passed on between bacteria? How has it been accelerated? And most importantly, how can we fight the danger it poses to our society? One way is to find new antibiotics. We investigate an exciting study that focuses on antimicrobial peptides found in the human proteome.
Microbiology | Riya Balia
“When I woke up just after dawn on September 28, 1928, I certainly didn’t plan to revolutionise all medicine by discovering the world’s first antibiotic, or bacteria killer.”
— Alexander Fleming [1]
Fleming’s discovery of penicillin did, in fact, transform the entire field of medicine— he had introduced a completely new area of study in medicinal research. In World War II, antibiotics proved crucial in saving the lives of soldiers from bacterial infections caused by wounds or the consumption of contaminated food and water. Today, they are used to protect us from previously more dangerous and common diseases, including [2]:
Tuberculosis
Strep throat
Whooping cough
Urinary tract infection
Sepsis
Pneumonia
There are many specific means by which antibiotics inhibit bacteria. Penicillin, for example, impedes cell wall synthesis by interfering with the production of peptidoglycan, a molecule that urrounds the cytoplasmic membrane, protecting some bacterial cells from environmental stresses and providing cell stability. Other antibiotics can disrupt cell membranes or hinder folate, DNA, RNA, or protein synthesis. Each method of attack violates a significant function without which the targeted bacteria cannot survive.
Although antibiotics have inhibited many species of bacteria, thereby saving many millions of lives, Fleming foretold their demise. He had warned that it would not be difficult to make microbes
resistant to penicillin in the laboratory. Indeed, in 1940, it was reported that an E. coli strain inactivated penicillin by producing penicillinase [3]. Resistance has since been seen to nearly all antibiotics that have been developed. The timeline for a few antibiotics is shown in Figure 1.
Resistance to antibiotics appears due to genetic mutations and is passed on by vertical and horizontal gene transfer. Mutations occur following errors in DNA replication while a bacterium rapidly reproduces. With a bit of luck, one mutation may prove beneficial against an antibiotic the bacterium is facing. This beneficial mutation can be passed down vertically through the bacterium’s following generations or to any species of bacteria in the local proximity by methods of horizontal gene transfer: transduction, transformation, and conjugation, as shown in Figure 2.
Figure 1: A timeline showing the rate at which resistance to some antibiotics has developed [4]. Note: Penicillin was discovered in 1928 but was not widely used by the general population until 1943.
Figure 2: A diagram showing the methods of horizontal gene transfer [5].
Rapid resistance rates have been accelerated by our misuse and overuse of antibiotics. According to the New Zealand Ministry of Health, about half of the people who visited their GP in 2017 were dispensed with at least one antibiotic [6]. Antibiotics are prescribed more often than necessary because doctors feel pressured to provide a solution to common problems [7]. Examples of misuse include flu sufferers who take antibiotics without realising that the drugs are ineffective against viruses. In the agriculture industry, antibiotics are used excessively in livestock to promote growth and prevent the spread of disease [8]. Using antibiotics when not needed may lead to health consequences for individuals and increase the burden of antimicrobial resistance in the long term. Even now, the rise of antibiotic-resistant bugs has led to severe infections, killing about 700,000 people worldwide each year, with the number expected to rise to ten million by 2050 if no action is taken [9]. In short, increased mortality, prolonged hospital stays, and higher medical costs are the consequences of drug-resistant infections [10].
Several measures can be taken to address the issue of antibiotic resistance. Campaigning for awareness, creating guidelines for prescriptions, and placing restrictions on drug use in agriculture are a few ideas. Another approach would be to hunt for new antibiotics. Scientists are doing exactly that. Not only have we developed new scaffolds in labs, we have also found more in nature. Potential antibiotics have been discovered in bacteria itself, fungi, and now in a previously untapped source — our very own bodies.
“The human body is a treasure trove of information, a biological dataset. By using the right tools, we can mine for answers to some of the most challenging questions.” says Dr Cesar de la Fuente, the leader of an exciting study at the University of Pennsylvania [11]. De la Fuente’s team identified encrypted* peptides with antimicrobial characteristics by using artificial intelligence (AI) to screen the human proteome [12].
AI technology used a specific algorithm to find encrypted peptides based on their ability to fit into the parameters of the search. The parameters focused on physiochemical characteristics all antimicrobial peptides have in common: 8 to 50 amino acids in length, positively charged and possessing both hydrophobic and hydrophilic parts [13]. An initial scan of the proteome identified 2,603 peptide antibiotics. Only 55 of these were synthesised in the lab to verify the antimicrobial characteristics of the algorithm-derived peptides. When assessed against eight common pathogens (E. coli ATCC11775, Pseudomonas aeruginosa PAO1, P. aeruginosa PA14, Staphylococcus aureus ATCC12600, E. coli AIG221, E. coli AIG222, Klebsiella pneumoniae ATCC133883, Acinetobacter baumannii ATTC19606), 63.6% of the selected peptides displayed antibacterial capacity. Additionally, the encrypted peptides exhibited only minor effects on gut and skin microbes. This evidence suggests they may contribute to the equilibrium between the human body and its inhabitant microorganisms.
The study identified encrypted peptides as agents that do not readily select for bacterial resistance. The peptides damage the outer membrane of a chosen bacterium, a crucial permeability barrier. According to de la Fuente, damaging membrane permeation would require more energy and multiple generations to confer resistance in bacteria [13].
For antibiotic discovery, like many other branches of pharmaceutical science, animal testing for reactions is a crucial component. This study used mouse models to assess the activity of selected encrypted peptides. In one mouse experiment involving two of the most potent peptides, the number of bacteria present in skin infections was reduced by magnitudes of five to six. Another mouse experiment involved a combination of peptides for an infection in the leg. The result showed a reduction of bacteria by a magnitude of three. This experiment is outlined in Figure 3.
Figure 3: A schematic showing the timeline of the leg infection experiment [12].
The method of attack and the results of the mouse experiments** are among the many pieces of evidence that indicate the newly discovered peptides are promising candidates for sustainable antibiotics. However, more work will be required before antimicrobial peptides may be used by patients. The task of finding, developing, testing, and validating antibiotics is a lengthy process. Nonetheless, it is necessary if we wish to hold higher ground in this war. While our battle against bacteria will never cease, we can continue outwitting it.
Note
**To add to the large reduction of bacteria in infections, the mice did not lose weight under experimentation so we may believe that the treatments are safe.
Riya Balia - BSc, Biomedical Science
Riya is a second-year Biomedical Science student specialising in infection and immunity. Aside from her interest in all things immunology, she is passionate about space, art, and fresh fruit ice cream.