Next-Generation Sequencing (NGS) Shows Promising Potential for Fast Detection of Pathogens

An accurate diagnosis is necessary for effective treatment. To identify the bacterium, virus, fungus, or other pathogens responsible for an infection, doctors have traditionally used different methods, including culturing patient samples on various media, reviewing countless medical records, and analyzing clinical data using complex mathematical algorithms. The hunt is frequently slow and tedious, and the methods utilized may not be wide enough to identify specific disease pathogens. Microbiological procedures for bronchoalveolar lavage (BAL) fluid specimens, for example, are extensive. However, these approaches are time-consuming and may miss fastidious organisms, rare and atypical infections, or pathogens rendered inactive by antibiotic therapy.

Multi-Drug Resistant Bacteria. Image Courtesy of Dr Graham Beards

According to a recent study by Johns Hopkins Medicine experts, next-generation sequencing (NGS) could be one promising option. NGS allows clinicians to sequence several strands of DNA present in patient samples and utilizes that information to quickly and accurately identify a single infection from among hundreds of candidates.

Improved searching abilities is the way of the future

NGS procedures use simultaneous and parallel approaches to amplify and sequence high volumes of genetic material, with possible pathogens detected by bioinformatic screening of the results against databases.

The novel Respiratory Pathogen Infectious Diseases/Antimicrobial Resistance Panel (RPIP) NGS system compares to a previously studied NGS system and standard of care (SOC) diagnostic procedures for samples collected by bronchoalveolar lavage.

According to the researchers, their investigation is one of the first to compare NGS and SOC diagnoses for respiratory infections.

The scientists first assessed the diagnostic capability of metagenomic NGS. A previously established workflow procedure in which all DNA extracted from a bronchoalveolar lavage is sequenced, including genetic material unique to the patient and the pathogen of interest. By removing the host DNA, clinicians can focus their search on the remaining genetic information in the hopes of finding the microbial read and, ultimately, determining the source of the patient’s disease. Secondly, the researchers used the RPIP system to test a different NGS approach called focused NGS. As with metagenomic NGS, they sequenced everything in the patient respiratory sample in this approach, but a new addition was capture probes to improve the searching ability. The researchers discovered that the efficiency of metagenomic and targeted NGS differed depending on the type of organism sought. Both NGS approaches successfully identified viruses, with the herpes virus being the most easily recognized. The results for bacteria and mycobacteria (including the organism causing tuberculosis) neared the level of SOC diagnostics. There was a reduction compared to SOC as the number of species decreased—even with capture probes in targeted NGS. Neither NGS approaches reliably found fungus.

Clinical significance

Assays based on next-generation sequencing (NGS) technology offer the potential to improve diagnostic testing by expanding detection, decreasing the time to detection for specific bacteria, and allowing the detection of previously undetected or treated diseases. Using NGS assays could directly impact patient care outcomes, such as optimal antibiotic administration and a shorter period of mechanical ventilation. Some or all diagnostic techniques for pathogen detection and characterization may be consolidated into a single assay using NGS technologies.

Conclusion

Based on their findings, the researchers believe that metagenomic and focused NGS workflows can be used in conjunction with, but not as a replacement for, SOC diagnostic approaches. They predict that with further improvement, NGS systems will one day become the gold standard for respiratory pathogen diagnosis.