Going Beyond Phenotype Testing: The Advantages of Genomics-Based Antimicrobial Resistance Identification

Antimicrobial Resistance: A Threat to Global Health

What is antimicrobial resistance, and why is it one of the World Health Organization’s top ten global public health threats? Antimicrobial resistance (AMR) is when microbes, including bacteria, fungi, viruses and parasites, are no longer responsive to the drugs and treatments developed to target them. In short, the microbes have evolved (as commonly seen in viruses) or acquired resistance (like with horizontal gene transfer in bacteria).

Drug-resistant microbes pose a major health threat because of how challenging the resulting infections are to treat. When first-line antimicrobials fail, options for second or third-line drugs are slim and often have worse side effects. Even more alarming is the increasing incidence of multi drug-resistant microbes, which evade treatment by most or all known drugs. Examples include MRSA (a severe, drug-resistant strain of staph) and multi drug-resistant tuberculosis.

How Genomics Can Help

Surveilling and tracking the incidence of antimicrobial resistance and diagnosing afflicted patients accurately is a major epidemiological and public health challenge. However, advances in applying genomics to microbiology are helping to streamline AMR research. Rather than relying only on phenotype-based tests (e.g. plating bacteria and observing its response to different drugs), genomics-based tests have the potential to rapidly and accurately identify the exact mutations causing AMR in a given sample.

Applications of genomics to microbiology can be described as “behind” similar applications to human genomics, for a number of reasons. First, it has only recently become time and cost-effective enough to consider applying next generation sequencing technologies to studying the microbial world. Secondly, there is much more genetic diversity across the thousands of species of bacteria, viruses, fungi and other microbes compared to the relatively minimal amount of variation between humans. This makes piecing together microbial genomes to identify genetic variants involved in infectious disease a significant challenge. Innovations like long-read sequencing and an increasing focus on microbial genomics should help solve some of these current challenges.

Optimizing an AMR-Identification Pipeline: abritAMR

One of the most powerful existing tools in AMR genomics is part of the NCBI Pathogen Identification pipeline. The tool, AMRFinderPlus, is a bioinformatic tool for identifying AMR-related genes and variants in microbial genome sequences. In a recent paper in Nature Communications, Sherry et. al. built and validated a robust bioinformatics tool to further refine the output of the AMRFinderPlus tool to make reports that are easier to interpret and disseminate to clinicians and other decision-makers.

Their tool, called abritAMR, demonstrated 99.9% accuracy, 97.9% sensitivity and 100% specificity when compared to PCR, and will allow researchers in a variety of laboratories to implement an AMR genomics workflow. Genomics derives its power from scale, so the more researchers involved in searching for AMR-related genes and sequencing microbial genomes, the faster the promise of genomics can be realized in the microbial research space.

Outsourcing Bioinformatics Analysis: How Bridge Informatics Can Help

Many of our clients at Bridge Informatics are pursuing these kinds of research questions with sophisticated bioinformatics approaches like microbial sequencing analysis. From pipeline development and software engineering to deploying existing bioinformatics tools, Bridge Informatics can help you on every step of your research journey. 
As experts across data types from cutting-edge sequencing platforms, we can help you tackle the challenging computational tasks of storing, analyzing and interpreting genomic and transcriptomic data. Bridge Informatics’ bioinformaticians are trained bench biologists, so they understand the biological questions driving your computational analysis. Click here to schedule a free introductory call with a member of our team.

Jane Cook, Biochemist & Content Writer, Bridge Informatics

Jane Cook, leading Content Writer for Bridge Informatics, has written over 100 articles on the latest topics and trends for the bioinformatics community. Jane’s broad and deep interdisciplinary molecular biology experience spans developing biochemistry assays to genomics. Prior to joining Bridge, Jane held research assistant roles in biochemistry research labs across a variety of therapeutic areas. While obtaining her B.A. in Biochemistry from Trinity College in Dublin, Ireland, Jane also studied journalism at New York University’s Arthur L. Carter Journalism Institute. As a native Texan, she embraces any challenge that comes her way. Jane hails from Dallas but returns to Ireland any and every chance she gets. If you’re interested in reaching out, please email jennifer.martinez@old.bridgeinformatics.com or dan.ryder@old.bridgeinformatics.com.

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