From Culture to Genomics: Diagnosing AMR in Livestock

Selecting the right antibiotic begins long before treatment is administered. As antimicrobial resistance (AMR) becomes increasingly common in livestock production, relying solely on empirical therapy may not always provide the desired clinical outcome. Diagnostic testing plays a critical role in identifying the causative pathogen, determining its susceptibility profile, and supporting evidence-based antimicrobial selection. By combining conventional laboratory methods with newer diagnostic technologies, veterinarians can make more informed treatment decisions while contributing to responsible antimicrobial use¹. 

Conventional Methods Remain the Foundation 

Several well-established laboratory techniques continue to serve as the backbone of AMR diagnosis. These include phenotypic methods, polymerase chain reaction (PCR)-based methods, isothermal amplification methods, and DNA microarrays¹. 

Among these, antimicrobial susceptibility testing (AST) remains one of the most widely used tools in veterinary practice. The process involves culturing a sample in the presence of different antimicrobial agents to evaluate whether the isolated pathogen is susceptible or resistant to specific antibiotics². 

Rather than identifying resistance alone, AST provides practical guidance on which antimicrobial agents are more likely to be effective against the organism causing disease. This information supports more targeted therapy instead of relying on broad-spectrum treatment whenever possible². 

Why Minimum Inhibitory Concentration Matters 

Once susceptibility testing has identified potential treatment options, determining the appropriate dosage becomes equally important. 

The Minimum Inhibitory Concentration (MIC) represents the lowest concentration of an antibiotic required to inhibit the growth of a specific microorganism³. When interpreted alongside culture results, MIC helps determine the degree of bacterial susceptibility or resistance to a particular antimicrobial agent. 

Culture combined with MIC testing provides valuable clinical information by helping veterinarians understand not only whether an antibiotic is likely to work, but also the concentration required to effectively inhibit bacterial growth³. 

Moving Beyond Conventional Diagnostics 

While conventional methods remain valuable, they may require longer turnaround times and involve multiple laboratory steps. Advances in diagnostic technology are expanding the options available for detecting antimicrobial resistance more rapidly and efficiently⁴. 

Several non-conventional diagnostic approaches are now available, including: 

• Genome sequencing 

• Metagenomics 

• Pyrosequencing 

• Whole genome sequencing 

• Combined short- and long-read whole genome sequencing 

• Nanopore sequencing 

• Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF) 

• Fourier Transform Infrared (FTIR) spectroscopy⁴ 

These technologies provide additional opportunities to detect resistance mechanisms while addressing several limitations associated with traditional diagnostic approaches. 

Emerging Technologies Improve Diagnostic Efficiency 

Microfluidic technologies represent another advancement in AMR diagnostics. These include spectroscopy-based, colorimetric-based, pH-based, multiplexing, and single-cell sequencing platforms⁴. 

Compared with conventional methods, these technologies offer several practical advantages. They can reduce diagnostic time while overcoming challenges such as limited sensitivity, extensive sample pretreatment, lack of automation, reduced portability, and difficulties in detecting microorganisms⁴. 

Although adoption may vary depending on laboratory availability and infrastructure, these innovations illustrate the continuing evolution of veterinary diagnostic capabilities. 

Making Diagnostic Results Work in Clinical Practice 

Laboratory reports provide valuable information, but their greatest benefit lies in how they guide treatment decisions. Culture, AST, and MIC results help veterinarians move from empirical antibiotic selection toward a more targeted approach that is aligned with the susceptibility profile of the infecting organism^2,3. 

Similarly, newer molecular and sequencing technologies expand the diagnostic toolbox by providing additional methods for identifying resistant organisms and improving the speed and precision of AMR detection⁴. 

Selecting appropriate diagnostic methods should therefore be viewed as an integral part of antimicrobial stewardship rather than simply a laboratory exercise. 

Practical Clinical Insights 

• Culture and antimicrobial susceptibility testing remain the primary methods for identifying effective antimicrobial options. 

• MIC testing complements culture by identifying the lowest antibiotic concentration required to inhibit bacterial growth. 

• Molecular and sequencing technologies broaden diagnostic capabilities and help address several limitations of conventional techniques. 

• Advances in microfluidic platforms have the potential to improve the speed, sensitivity, and efficiency of AMR diagnosis. 

As antimicrobial resistance continues to challenge livestock health, diagnostic testing is becoming increasingly central to everyday veterinary practice. Combining conventional culture-based methods with emerging genomic and molecular technologies enables veterinarians to make more informed antimicrobial choices, supporting effective treatment while promoting responsible antibiotic use.  

References 

1. Kaprou GD, Bergšpica I, Alexa EA, Alvarez-Ordonez A, Prieto M. Rapid methods for antimicrobial resistance diagnostics. Antibiotics. 2021 Feb 20;10(2):209. https://www.mdpi.com/2079-6382/10/2/209 

2. Bayot ML, Bragg BN. Antimicrobial susceptibility testing. InStatPearls [internet] 2024 May 27. StatPearls Publishing. https://www.ncbi.nlm.nih.gov/books/NBK539714/ 

3. Magréault S, Jauréguy F, Carbonnelle E, Zahar JR. When and how to use MIC in clinical practice?. Antibiotics. 2022 Dec 3;11(12):1748. https://www.mdpi.com/2079-6382/11/12/1748 

4. Kaprou GD, Bergšpica I, Alexa EA, Alvarez-Ordonez A, Prieto M. Rapid methods for antimicrobial resistance diagnostics. Antibiotics. 2021 Feb 20;10(2):209. https://www.mdpi.com/2079-6382/10/2/209