Emerging Technologies for Detecting Antibiotic Resistance

The article titled “Detection of antimicrobial resistance via state-of-the-art technologies versus conventional methods” authored by Elbehiry, Marzouk, Abalkhail, Abdelsalam, Mostafa, Alasiri, Ibrahem, Ellethy, Almuzaini, Aljarallah, Abu-Okail, Marzook, Alhadyan, and Edrees, and published in Frontiers in Microbiology in 2025, offers a timely and insightful review of the evolving landscape of antimicrobial resistance (AMR) detection. The authors address AMR as one of the foremost global health challenges, significantly complicating the treatment of infectious diseases and contributing to increased morbidity and mortality rates worldwide. In 2019 alone, AMR was responsible for approximately 1.27 million deaths globally and contributed to an additional 4.95 million fatalities.

The core objective of this comprehensive review is to examine the advantages and disadvantages of both emerging technologies and traditional methods for detecting AMR. By understanding the strengths and limitations of these diverse technologies, the paper aims to empower stakeholders—including researchers, healthcare professionals, regulatory agencies, and financial managers—to make informed decisions aimed at preventing the emergence and dissemination of antibiotic-resistant strains, thereby ultimately increasing patient safety. The authors also aim to enhance the understanding of Antimicrobial Susceptibility Testing (AST) effectiveness and forecast promising future technologies.

Traditionally, the identification of AMR bacteria has relied on microbiological culture and susceptibility testing methods, such as disk diffusion and minimum inhibitory concentration (MIC) assays. While these conventional techniques are often inexpensive, easy to perform, and widely used in hospitals globally, they are frequently labor-intensive, time-consuming, and lack the requisite sensitivity for early detection of resistance. This delay in obtaining results can negatively impact patient management, with delayed antibiotic treatment being associated with higher mortality rates and longer hospital stays.

The paper emphasizes that recent advancements in molecular and genomic technologies have revolutionized the diagnosis of AMR. These innovative approaches offer increased sensitivity, reduced turnaround times, and the ability to identify genetic resistance mechanisms. The review categorizes and delves into various state-of-the-art technologies, including:

• Advanced automation techniques, such as Sensititre™ ARISTM 2X, Vitek 2 Compact System, Phoenix™ panel systems, and MicroScan WalkAway plus systems, which enhance the sensitivity of ASTs through optoelectronic systems, fiber optics, microfluidics, and pH- or redox-sensitive indicator dyes. These systems significantly reduce result times compared to traditional methods.
• Nucleic Acid Amplification Tests (NAATs), including isothermal amplification (e.g., LAMP), polymerase chain reaction (PCR), multiplex PCR, reverse transcriptase PCR (RT-PCR), and quantitative PCR (qPCR), are highlighted for their high accuracy, sensitivity, and ability to identify antibiotic resistance genes. While effective for tracking AMR infections, a key limitation is their inability to specify MICs or recommend specific antibiotics.
• Next-generation sequencing (NGS) technology, encompassing whole-genome sequencing (WGS) and metagenomics, is presented as a powerful tool for sequencing entire genomes, detecting mutations, and understanding complex resistance mechanisms, even in slow-growing or non-cultivable organisms. Despite its high cost and complexity, NGS is anticipated to replace standard cultivation methods in the future.
• Mass spectrometry (MALDI-TOF MS) is recognized for its rapid investigation capabilities, high productivity, and cost-effectiveness per sample run, bridging the gap between species identification and resistance evaluation. It can identify resistance mechanisms and biomarkers, providing results within 2–3 hours.
• Future techniques are also explored, such as Hybridization-based systems (Fluorescence In Situ Hybridization – FISH), effective for quantifying target microorganisms and detecting specific resistance determinants like mecA and vanA directly from raw samples. DNA microarray (DNA chip) techniques are also discussed for their ability to examine genomic AMR and identify multiple resistance genes simultaneously, offering a rapid and high-throughput method crucial for large-scale surveillance.
• Flow cytometry laser-based techniques are highlighted for their ability to assess a microorganism’s susceptibility, resistance, or intermediate status to antibiotics rapidly, often providing results in under 2 hours.
• Fourier transform infrared (FTIR) spectroscopy is presented as an innovative tool providing detailed chemical composition information, increasingly used to identify chemical changes linked to AMR in prokaryotic organisms. It offers speed, cost-effectiveness, and reliability, though its application as a point-of-care tool is hindered by instrument size and cost.
• Lab-on-a-chip technology and microfluidics offer rapid analysis, precise fluid control, cost-effectiveness, and minimal reagent use, with potential for early detection of antibiotic resistance during therapy.
• Lateral flow immunoassays (LFIAs) are highlighted for their speed, cost-effectiveness, and user-friendliness, particularly for rapidly screening specific resistance markers in gram-negative bacteria, such as beta-lactamases.
• Finally, CRISPR-Cas system antimicrobials are introduced as a novel strategy with potential for preventing and controlling AMR by targeting DNA sequences that carry resistance genes, offering high specificity and sensitivity in detection.

The article concludes that while many claims to detect resistance within hours, they often overlook time-consuming steps like culture isolation. The future of AMR detection will likely involve a combination of traditional and modern methods, facilitating quicker and more accurate diagnostics, improved treatment decisions, and enhanced surveillance. Continued research, investment in infrastructure, and supportive policies are crucial for the effective clinical application of these advancements in the global fight against antimicrobial resistance. The market for ASTs is projected to grow significantly, emphasizing the urgent need for rapid, accurate, and affordable tests to enable better-targeted medications and reduce AST turnaround times.

Reference: Elbehiry, A., Marzouk, E., Abalkhail, A., Abdelsalam, M. H., Mostafa, M. E. A., Alasiri, M., Ibrahem, M., Ellethy, A. T., Almuzaini, A., Aljarallah, S. N., Abu-Okail, A., Marzook, N., Alhadyan, S., & Edrees, H. M. (2025). Detection of antimicrobial resistance via state-of-the-art technologies versus conventional methods. Frontiers in Microbiology, 16, 1549044. https://doi.org/10.3389/fmicb.2025.1549044