How bacteria develop antibiotic resistance and what science is doing about it

According to a recent study, superbugs could kill up to 40 million people by 2050.¹ The World Health Organization has identified antimicrobial resistance (AMR) as one of the most serious global public health threats.

Image Credit: Norgen Biotek Corp.

Several factors contribute to the emergence and spread of AMR, the most significant of which is the misuse and overuse of antibiotics in clinical settings.

How does antimicrobial resistance occur?

The mechanism of antimicrobial resistance is well studied and is generally divided into two categories.

Intrinsic resistance

The first way AMR develops is through intrinsic resistance, which refers to a microorganism’s natural ability to withstand antibiotics. "For example, an antibiotic that affects the wall-building mechanism of the bacteria, such as penicillin, cannot affect bacteria that do not have a cell wall."¹⁰

Acquired resistance

The second mechanism is acquired resistance, which occurs when antibiotic-susceptible bacteria gain the ability to resist the effects of an antibiotic, allowing them to survive and multiply under selective pressure.

Acquired resistance can result from either modification to existing genetic material (gene mutation) or the acquisition of new genetic material from another source (horizontal gene transfer).

These acquired resistance genes may enable bacteria to degrade or chemically modify antibiotics, rendering them ineffective. Bacteria may also produce or upregulate efflux pumps, which actively transport antibiotics out of the cell, preventing the drug from reaching its intracellular target.

They may also modify the drug’s target site or develop an alternative metabolic pathway that bypasses the action of the drug.²

Gene mutation and selection

When exposed to antibiotics, approximately one out of every 10⁸-10⁹ bacteria develops resistance due to spontaneous mutation. For instance, E. coli, when exposed to high quantities of streptomycin, develops resistance at a rate of about 10⁹.

Mutation is a rare event, but due to the rapid growth rate of bacteria, it does not take long for resistance to develop within a population.³

Horizontal gene transfer

Horizontal gene transfer (HGT) is the exchange of genetic information between organisms that are more or less closely related. Bacteria can acquire resistance by obtaining additional genetic material from resistant organisms.

HGT can occur across strains of the same species or between different bacterial species. There are three main pathways for HGT:

Image Credit: Norgen Biotek Corp.

• Transformation: Bacteria absorb extracellular, bare DNA from their surroundings. This DNA is typically found in the external environment because of another bacteria's death and lysis.
• Conjugation: Conjugation refers to the direct transfer of DNA between cells. During conjugation, a gram-negative bacterium often transfers plasmid-containing resistance genes to a neighboring bacterium via an extended protein structure known as a pilus. Gram-positive bacteria, on the other hand, typically initiate conjugation by producing sex pheromones, which promote clumping of donor and recipient cells, facilitating DNA exchange.
• Transduction: Transduction refers to bacteriophage-mediated DNA transfer. Bacteriophages are viruses that infect bacterial cells and replicate within them. After replicating, these viruses assemble and may occasionally incorporate a fragment of the host bacterium’s DNA. When such a bacteriophage infects a new bacterial cell, the bacterial DNA can be integrated into the new host's genome. Many scientists use bacteriophages to transfer new genetic elements into different host cells.⁴

Norgen Biotek provides various kits for isolating high-quality bacterial DNA and RNA (both gram-positive and gram-negative) from a wide range of sample types, including stool, cell culture, sand, urine, plasma, tissue, and more.

Image Credit: Norgen Biotek Corp.

The role of biofilm in antimicrobial resistance

Pathogens can also create a protective barrier around themselves, making treatment more difficult. This is referred to as a biofilm. A biofilm forms when bacteria cling to a surface and combine to form an extracellular polysaccharide (EPS) matrix, which has a glue-like consistency.

The microorganisms in the biofilm can continue to reproduce and even join other biofilm colonies. This complex structure has been shown to significantly increase antibiotic resistance.

Bacteria that live in a biofilm can exhibit a 10 to 1000-fold increase in resistance compared to bacteria that do not exist in a biofilm.⁵

Image Credit: Norgen Biotek Corp.

Mechanisms of antimicrobial resistance

In any battle, the side that best understands its opponent has the advantage. Similarly, the more we understand about antibiotic-resistant microorganisms, the more effectively we can treat them.

Understanding the mechanisms of resistance is critical to developing new antibiotics to combat these pathogens. Various bacteria exhibit resistance, each using unique strategies.

Efflux pumps

One of the primary mechanisms of antibiotic resistance in gram-negative bacteria is the use of efflux pumps. These protein pumps are designed to remove hazardous compounds (such as antibiotics) from within the bacterial cell.⁶

They reduce the intracellular concentration of antibiotics, limiting their potency and ability to target essential cellular functions.

Enzymatic inactivation

β-lactams, known as penicillins, are among the most widely used antimicrobials. They contain a four-membered β-lactam ring. Bacteria have developed multiple resistance mechanisms against these drugs.

The most common method involves β-lactamase enzymes, which hydrolyze the β-lactam rings, rendering the antibiotics ineffective.

Despite the development of β-lactamase inhibitors such as clavulanic acid and avibactam, newer and more resilient bacterial strains, like carbapenem-resistant Enterobacteriaceae (CRE), pose significant challenges.⁷

Target site modification

Bacteria also use other mechanisms to resist β-lactams. Gram-positive bacteria, for example, may modify the shape or number of penicillin-binding proteins (PBPs), reducing or entirely preventing antibiotic binding to the target.⁷ PBPs are bacterial cell membrane proteins involved in the formation of peptidoglycans (PG).⁸

Gram-negative bacteria are intrinsically resistant to drugs such as vancomycin, a glycopeptide that inhibits cell wall synthesis, and daptomycin, a lipopeptide that depolarizes the cell membrane.

Some bacteria can develop resistance to glycopeptides by altering the structure of PG precursors, reducing glycopeptide binding.

In other cases, gene mutations change the charge of the cell membrane, preventing calcium from binding, a step required for daptomycin activity. This reduces daptomycin's binding ability and its capacity to depolarize the cell membrane.⁷

Discovery of new AMR mechanisms

There are likely many undiscovered resistance mechanisms. The mechanisms of AMR are studied using a combination of molecular, microbiological, and bioinformatic techniques.

Researchers employ various approaches to discover, classify, and understand how bacteria develop and transmit resistance. Clinical bacterial isolates are collected from humans, animals, and the environment to track changes in resistance.

Phenotypic testing, such as standard antibiotic susceptibility tests (for example, disk diffusion and broth microdilution), can be used to detect resistant organisms.

Researchers may also use genotypic analysis, including molecular approaches such as PCR and whole-genome sequencing, to screen for known resistance genes and mutations.⁹

The most common molecular method used by clinical laboratories to study the mechanisms behind observed phenotypic resistance is PCR-based testing, including conventional PCR, real-time PCR, and qRT-PCR.

This strategy involves amplifying and sequencing genes known to be involved in resistance. The sequences are then compared to those of the wild-type strain to identify potential mutations.

qRT-PCR can also be used to analyze and compare the expression levels of resistance genes between mutant strains with resistant phenotypes and wild-type strains.⁹

Functional genomics can help identify new antibiotic-resistance genes that encode enzymes based on their function. This approach involves extracting DNA fragments and creating a specific library of homogenous size. The library is then cloned into an expression vector, which is screened based on the antibiotic being studied.

The development of genomic approaches that enable the study of diverse microbial communities without the need for cultivation has been critical in identifying novel resistance pathways. Moreover, cultivating harmful bacteria poses major risks to the scientists handling them and requires specialized equipment and strict safety protocols.

Modern sequencing technologies offer significant potential in addressing the growing problem of antibiotic resistance. Metagenomic sequencing, in particular, has uncovered a vast reservoir of antibiotic resistance genes within the complex microbial communities found in the gastrointestinal systems of humans and animals, as well as in natural environments such as surface water and soil.

This has been made possible by the rapid decrease in sequencing costs, which has led to the identification of an increasing number of resistance genes.

Integrating genetic analysis with continuously updated databases is a powerful and expanding strategy. It enables access to large volumes of information and enhances our ability to investigate antibiotic resistance while offering deeper insights into bacterial behavior.¹⁰

The role of gene sequencing in AMR

The prediction of new antimicrobial resistance through genome sequencing can be accelerated by prior knowledge of all variables that contribute to phenotypic resistance, such as inactivating enzymes, porin mutations, influx system alterations, binding site mutations, gene inactivation, and promoter mutations.

Sequence-based identification of known resistance markers covers only a small portion of the resistance spectrum, whereas transcriptome analysis may provide a more comprehensive phenotypic profile.

Bacterial expression patterns can differ significantly in the presence or absence of antibiotics, offering the potential to detect resistance at the RNA level in response to environmental stressors.¹¹

Transcriptome analysis is a promising alternative to genome sequencing for resistance gene identification.

High-throughput RNA sequencing (RNA-Seq) is a cutting-edge technology that uses deep sequencing techniques to analyze an RNA population converted into a library of complementary DNA (cDNA) fragments. These sequences are then bioinformatically assembled to reconstruct the entire transcriptome and accurately measure gene expression levels.¹²

The study of RNA offers a feasible alternative for exploring the genetic factors driving antibiotic resistance. For example, recent research on colistin (a polymyxin antibiotic used to treat infections caused by susceptible gram-negative bacteria) has combined genome sequencing with transcriptional profiling via RNA-Seq.

This approach led to the identification of crr genes, previously reported as uncharacterized histidine kinases, as additional regulators of colistin resistance. These discoveries expand the range of genes implicated in colistin resistance and highlight the many ways bacteria may respond to antimicrobial peptides.¹³

The future of antibiotic resistance

Pathogens continually evolve, finding new ways to become stronger and evade our treatments. As they become more resistant, the challenge of infection control intensifies.

But there is hope! Innovative research is paving the way for discoveries that may shift the balance back in our favor. Scientists are developing new approaches to combat disease and protect global health by staying one step ahead of these clever microorganisms.

That’s why Norgen is here to support you every step of the way.

Image Credit: Norgen Biotek Corp.

Phage therapy

Phage therapy offers a promising alternative to antibiotics in the fight against AMR. Bacteriophages, commonly known as phages, are viruses that infect bacteria and replicate within them, causing cell lysis and, ultimately, bacterial death.

Unlike traditional antibiotics, phages specifically target and destroy bacteria, offering a precise method of treatment that preserves beneficial microbes. Due to its targeted action, phage therapy is a valuable strategy for managing multidrug-resistant infections, where conventional treatments often fail.

To advance phage therapy research, reliable technologies for isolating and studying bacteriophages are essential. Norgen Biotek’s Phage DNA Isolation Kit simplifies this process by providing a fast and efficient method for isolating high-quality phage DNA.

Phage therapy research highlights

Researchers at Bu-Ali Sina University studied a new lytic bacteriophage isolated from poultry slaughterhouse wastewater to evaluate its potential as an antibiotic alternative.

They tested Escherichia phage VaT-2019a isolate PE17 and a novel phage, Escherichia phage AG-MK-2022 Basu. The host range, environmental stability, genetic makeup, and bactericidal activity against 100 MDR-APEC bacteria were investigated.

Based on the morphology of Escherichia phage AG-MK-2022 Basu, the research team identified its family as Myoviridae. More importantly, they analyzed the phage genome using Norgen’s Phage DNA Isolation Kit and found that it lacks antibiotic resistance genes, mobile genetic elements, and E. coli virulence-associated genes.

They also tested the phage’s stability and found it to be stable at temperatures ranging from 4 °C to 80 °C, pH levels between 4 and 10, and NaCl concentrations ranging from 1 % to 13 %. These findings support the potential of Escherichia phage AG-MK-2022 Basu as a safe biocontrol agent.

The team stated that it “may safely be used as a biocontrol agent” but cautioned that "more work, such as whole genome sequencing of the isolated phage, is necessary to achieve more information regarding its safe use".¹⁴

AMR is a clear threat to global health, and the rise of superbugs is increasingly concerning. The misuse and overuse of antibiotics, combined with natural microbial evolution, have created a problem that requires urgent attention.

Innovative solutions like phage therapy offer hope, demonstrating that advanced research and cutting-edge technologies can help us outpace resistant infections. Norgen Biotek is committed to supporting researchers in this effort by providing reliable tools like the Phage DNA Isolation Kit, helping to drive progress in the fight against AMR.

The future of global health depends on staying ahead of these emerging threats. Through investment in research, responsible antibiotic use, and continued technological innovation, we can combat antimicrobial resistance.

References and further reading

1. Naghavi, M., et al. (2024). Global Burden of Bacterial Antimicrobial Resistance 1990–2021: a Systematic Analysis with Forecasts to 2050. The Lancet, (online) 404(10459), pp.1199–1226. https://doi.org/10.1016/s0140-6736(24)01867-1.
2. Tenover, F.C. (2006). Mechanisms of Antimicrobial Resistance in Bacteria. The American Journal of Medicine, 119(6), pp.S3–S10. https://doi.org/10.1016/j.amjmed.2006.03.011.
3. Bacterial Resistance to Antibiotics (page 3) Antibiotic Method of resistance. (n.d.). Available at: https://www.mifami.org/eLibrary/Bacterial%20Resistance%20to%20Antibiotics.pdf.
4. Michaelis, C. and Grohmann, E. (2023). Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms. Antibiotics, 12(2), p.328. https://doi.org/10.3390/antibiotics12020328.
5. Prinzi, A. and Rohde, R. (2023). The Role of Bacterial Biofilms in Antimicrobial Resistance. (online) ASM. Available at: https://asm.org/Articles/2023/March/The-Role-of-Bacterial-Biofilms-in-Antimicrobial-Re.
6. Soto, S.M. (2013). Role of efflux pumps in the antibiotic resistance of bacteria embedded in a biofilm. Virulence, 4(3), pp.223–229. https://doi.org/10.4161/viru.23724.
7. Reygaert, W.C. (2018). An overview of the antimicrobial resistance mechanisms of bacteria. AIMS Microbiology, (online) 4(3), pp.482–501. https://doi.org/10.3934/microbiol.2018.3.482.
8. Sharifzadeh, S., et al. (2020). Chemical tools for selective activity profiling of bacterial penicillin-binding proteins. Methods in enzymology, (online) 638, pp.27–55. https://doi.org/10.1016/bs.mie.2020.02.015.
9. Hamel, M., Rolain, J.-M. and Baron, S.A. (2021). The History of Colistin Resistance Mechanisms in Bacteria: Progress and Challenges. Microorganisms, 9(2), p.442. https://doi.org/10.3390/microorganisms9020442.
10. Crofts, T.S., Gasparrini, A.J. and Dantas, G. (2017). Next-generation approaches to understand and combat the antibiotic resistome. Nature Reviews Microbiology, (online) 15(7), pp.422–434. https://doi.org/10.1038/nrmicro.2017.28.
11. Barczak, A.K., et al. (2012). RNA signatures allow rapid identification of pathogens and antibiotic susceptibilities. Proceedings of the National Academy of Sciences of the United States of America, (online) 109(16), pp.6217–6222. https://doi.org/10.1073/pnas.1119540109.
12. Guigo, R. and de Hoon, M. (2018). Recent advances in functional genome analysis. F1000Research, 7, p.1968. https://doi.org/10.12688/f1000research.15274.1.
13. Wright, M.S., et al. (2014). Genomic and Transcriptomic Analyses of Colistin-Resistant Clinical Isolates of Klebsiella pneumoniae Reveal Multiple Pathways of Resistance. Antimicrobial Agents and Chemotherapy, 59(1), pp.536–543. https://doi.org/10.1128/aac.04037-14.
14. Karami, M., et al. (2024). In vitro evaluation of two novel Escherichia bacteriophages against multiple drug resistant avian pathogenic Escherichia coli. BMC infectious diseases, (online) 24(1), p.497. https://doi.org/10.1186/s12879-024-09402-0.

About Norgen Biotek Corp.

Norgen Biotek: Advancing science with best-in-class, scientist-backed innovations

Norgen Biotek is a fully integrated biotechnology company that focuses on providing complete workflows for molecular biology sample preparation and analysis. With a diverse portfolio of over 600 products, the company delivers high-performance, user-friendly, and cost-effective solutions.

Scientifically driven, industry trusted

Norgen kits cover a broad range of applications from collection and preservation to isolation and purification. Our expert R&D team continuously develops cutting-edge technologies that set new industry standards for RNA, DNA, protein, and exosomal isolation, ensuring superior yield, purity, and integrity from even the most challenging sample types.

Unparalleled performance

At the heart of Norgen’s success is its patented Silicon Carbide (SiC) Technology. This proprietary resin exhibits uniform binding affinity for all RNA species, regardless of molecular weight or GC content. This ensures the full diversity of small and microRNA are captured while eliminating the need for phenol extraction. This innovative technology sets Norgen kits apart from others, positioning them as leaders in RNA purification.

Comprehensive solutions for any challenge

Norgen is committed to providing high-quality kits capable of processing a wide range of sample types, from ultra-low input samples such as liquid biopsies to highly impure samples like stool or soil. Our sample collection and preservation devices for stool and saliva simplify handling by rendering samples non-infectious by preventing microbial growth and inactivating viruses, while our blood and urine preservation solutions ensure the stability of highly vulnerable cell-free nucleic acids.

To meet varying research demands, we offer multiple isolation methods including, but not limited to high-throughput and automation-ready magnetic bead-based formats. Additionally, our multiple-analyte kits enable the simultaneous purification of RNA, DNA, and proteins, maximizing data extraction from a single sample.

Norgen offers an extensive variety of TaqMan qPCR kits designed for molecular diagnostic use, including lyophilized kits for easy shipping. Library preparation kits for both DNA and RNA samples are also available to support genomic applications. Norgen recently released their EXTRAClean technology, an innovative solution that minimizes background noise while providing high-purity RNA, significantly enhancing NGS performance.

Why choose Norgen?

• Scientist-Driven Innovation – Developed by leading experts in molecular biology
• Proven Quality & Reliability – ISO 9001 and ISO 13485 certified, indicating a commitment to selling high-quality products
• Global Presence – We ship to over 150 countries and have a network of 60+ distributors
• Award Winning – Norgen Biotek Corp. was honored with the 2021 Innovative Leaders Award, and recognized as the 2024 Rapid Star Award Winner in the PCR category.
• Innovative Products – Hold more than thirty issued and pending patents for products presenting solutions for all research & clinical applications

Driven by a mission to accelerate scientific discoveries, Norgen Biotek actively supports researchers by providing educational resources, technical workshops, and application notes. Their NorBlog serves as a hub for the latest scientific discoveries, protocol optimizations, and industry trends.

Explore Norgen Biotek’s innovative solutions today and take your research to the next level.

Sponsored Content Policy: News-Medical.net publishes articles and related content that may be derived from sources where we have existing commercial relationships, provided such content adds value to the core editorial ethos of News-Medical.Net which is to educate and inform site visitors interested in medical research, science, medical devices and treatments.