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Study finds genetic method for identifying hundreds of disease agents promising

In the pursuit of accurate diagnoses for illnesses, doctors have traditionally used multiple methods — including culturing patient samples on a wide variety of media, reviewing countless medical records and analyzing clinical data using complex mathematical algorithms — to try to identify the bacterium, virus, fungus or other pathogen responsible for an infection. The hunt is often slow and laborious, and the processes used may not be broad enough in scope to find specific disease agents.

One solution may be next-generation sequencing (NGS), according to the findings of a recent study by Johns Hopkins Medicine researchers. NGS enables clinicians to simultaneously sequence multiple strands of DNA found in patient samples and use that analysis to rapidly and accurately identify a single pathogen — from among hundreds of suspects.

In a paper first posted online June 13, 2022, in the American Society for Microbiology’s Journal of Clinical Microbiology, the researchers compared the pathogen detecting ability of an NGS system — the Respiratory Pathogen Infectious Diseases/Antimicrobial Resistance Panel (RPIP) — with a previously studied NGS system and standard of care (SOC) diagnostic methods for samples obtained with bronchoalveolar lavage. This is where a bronchoscope is passed through the mouth or nose into the lungs, followed by a fluid wash that is collected for examination.

The researchers believe their study is among the first to compare NGS and SOC diagnostics for respiratory pathogens.

“We evaluated the two NGS diagnostic techniques, one of which was the RPIP, and found that in both cases, the ability of NGS to identify specific pathogens was nearly comparable to the battery of diagnostic tests clinicians have been using for decades,” says study senior author Patricia Simner, Ph.D., M.Sc., associate professor of pathology at the Johns Hopkins University School of Medicine. “Although this shows great promise for the RPIP and NGS diagnostics in general, we feel more work is needed to further refine the technology before NGS can be considered equal to or better than current SOC methods.”

In their study, Simner and her colleagues first evaluated the diagnostic ability of metagenomic NGS, a previously studied workflow process during which all DNA obtained from a bronchoalveolar lavage is sequenced — including genetic material unique to the patient (the “host read” or “human read”) and the sought-after pathogen (the “microbial read”). Removing the host DNA enable clinicians to concentrate their search on the remaining genetic material to hopefully find the microbial read and ultimately, identify the cause of the patient’s illness.

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