Bacterial culture and drug sensitivity testing have been the “gold standard” in clinical microbiology for more than 70 years. The drawbacks of this approach include the time to culture or grow the microbes, the reliance on secondary biochemical analysis, and the use of secondary drug sensitivity sub-cultures. Less than 2% of all bacterial species can be routinely cultivated; therefore, resulting in many false negative results. These facts create a need for a rapid microbial identification and antibiotic resistance assay that is affordable, accurate, and relevant. Over the last decade syndromic multiplex PCR panels have become increasingly common because of the rapid turn-around-time and affordability. Despite these advantages, these syndromic multiplex PCR panels exhibit a few limitations that include:
- 1. Limited number of detectable microbes that results in a high false negative rate.
- 2. A limited number of antimicrobial resistance genes are detectable.
- 3. Drug treatment confusion when there are two or more identified organisms alongside resistance.
A solution that addresses these limitations is DNA sequencing. Multiple studies, including clinical outcome studies, have been published in the last 5 years in nearly all major clinical specialty disciplines. These studies demonstrate the value and improved clinical outcome as a benefit of molecular and DNA sequencing-based diagnostics.
In 2013, Fry Laboratories was the first commercial laboratory worldwide to offer targeted bacterial (16S) DNA sequencing. This technology has resulted in numerous patents and peer-reviewed publications. This assay, based on a high-quality targeted amplicon approach, is accurate, cost effective, and sample agnostic (it can be used to test blood, urine, CSF, tissue, secretions, bone, and stool). This bacterial DNA sequencing assay is enrolled in both API and CAP proficiency testing programs and has maintained an excellent comparative results track record. A handful of other diagnostic laboratories offer DNA sequencing; however, these laboratories use a non-targeted or “shotgun” sequencing approach that suffers from inefficient sequencing and a more expensive price point. Lastly, this core technology has been independently evaluated by other institutions.