In the Journals

Next-generation sequencing assay demonstrates high sensitivity

Photo of William Muller
William J. Muller

A commercially available next-generation sequencing, or NGS, plasma assay demonstrated high sensitivity in both immunocompromised and non-immunocompromised children with one or more bacterial, viral or fungal infection compared with conventional diagnostic testing in a single-center study published in Open Forum Infectious Diseases.

William J. Muller, MD, PhD, associate professor of pediatrics at the Northwestern University Feinberg School of Medicine and attending physician at the Ann & Robert H. Lurie Children’s Hospital of Chicago, told Infectious Diseases in Children that this test is offered by several companies. However, cost may be a barrier to its use.

“One of the bigger drawbacks to NGS testing is cost, which is one reason our institution primarily uses the test in patients we suspect of having difficult-do-diagnose infections, including fungal infections or unusual bacterial infections,” he said. “Another drawback is that the test does not currently allow determination of antimicrobial susceptibility, so if the local microbiology lab does not recover the organism, we need to treat that empirically.”

The researchers retrospectively examined data from patients whose plasma was sent for NGS testing to identify infectious pathogens. All orders were sent between December 2016 and August 2018 to a Clinical Laboratory Improvement Amendments-certified lab.

Infectious disease specialists ordered 94% of the NGS testing of plasma, and an infectious disease consultant was involved in interpreting the results of all cases.

During the study period, 100 tests were ordered for 79 patients, of which 76% were immunocompromised. Clinicians most often ordered testing because of concern for a fungal or atypical infection (55%), followed by acute fever/sepsis (22%), prolonged/recurrent fever (18%), recurrent lymphadenopathy (4%) and evaluation to discontinue antifungals (1%). The lab produced NGS test results within 48 hours of receiving samples for 86% of cases.

According to Muller and colleagues, 37 tests identified one organism included in the assay, 15 tests identified two organisms, five tests identified three organisms and 14 tests identified four or more organisms.

More than half of the tests (n = 52) identified at least one bacterium, 25 identified at least one virus and18 tests identified at least one fungus, according to the researchers. They considered 80% of the positive NGS tests clinically relevant.

The sensitivity for NGS was 92% for clinically relevant infections vs. 77% for conventional microbiological testing (P < .01), the researchers noted. The specificity of the test was 64% for NGS and 89% for conventional microbiological testing (P < .01). When the test was used for immunocompromised patients, the sensitivity and specificity of the assay was 93% and 59%, respectively. Conventional testing had a lower sensitivity (76%) but a higher specificity (92%; P < .01).

Upon examination of the clinical sites of infection, NGS most commonly identified bloodstream and respiratory tract infections. It also identified skin, bone, internal hardware, UTI and cerebrospinal fluid infections.

“Personally, I would not say that NGS testing should be used more than it currently is in comparison with conventional testing,” Muller said. “Conventional microbiologic testing is sufficient for the majority of infections we diagnose and can provide susceptibility information that NGS testing does not currently allow.”– by Katherine Bortz

Disclosures: The authors report no relevant financial disclosures.

Photo of William Muller
William J. Muller

A commercially available next-generation sequencing, or NGS, plasma assay demonstrated high sensitivity in both immunocompromised and non-immunocompromised children with one or more bacterial, viral or fungal infection compared with conventional diagnostic testing in a single-center study published in Open Forum Infectious Diseases.

William J. Muller, MD, PhD, associate professor of pediatrics at the Northwestern University Feinberg School of Medicine and attending physician at the Ann & Robert H. Lurie Children’s Hospital of Chicago, told Infectious Diseases in Children that this test is offered by several companies. However, cost may be a barrier to its use.

“One of the bigger drawbacks to NGS testing is cost, which is one reason our institution primarily uses the test in patients we suspect of having difficult-do-diagnose infections, including fungal infections or unusual bacterial infections,” he said. “Another drawback is that the test does not currently allow determination of antimicrobial susceptibility, so if the local microbiology lab does not recover the organism, we need to treat that empirically.”

The researchers retrospectively examined data from patients whose plasma was sent for NGS testing to identify infectious pathogens. All orders were sent between December 2016 and August 2018 to a Clinical Laboratory Improvement Amendments-certified lab.

Infectious disease specialists ordered 94% of the NGS testing of plasma, and an infectious disease consultant was involved in interpreting the results of all cases.

During the study period, 100 tests were ordered for 79 patients, of which 76% were immunocompromised. Clinicians most often ordered testing because of concern for a fungal or atypical infection (55%), followed by acute fever/sepsis (22%), prolonged/recurrent fever (18%), recurrent lymphadenopathy (4%) and evaluation to discontinue antifungals (1%). The lab produced NGS test results within 48 hours of receiving samples for 86% of cases.

According to Muller and colleagues, 37 tests identified one organism included in the assay, 15 tests identified two organisms, five tests identified three organisms and 14 tests identified four or more organisms.

More than half of the tests (n = 52) identified at least one bacterium, 25 identified at least one virus and18 tests identified at least one fungus, according to the researchers. They considered 80% of the positive NGS tests clinically relevant.

The sensitivity for NGS was 92% for clinically relevant infections vs. 77% for conventional microbiological testing (P < .01), the researchers noted. The specificity of the test was 64% for NGS and 89% for conventional microbiological testing (P < .01). When the test was used for immunocompromised patients, the sensitivity and specificity of the assay was 93% and 59%, respectively. Conventional testing had a lower sensitivity (76%) but a higher specificity (92%; P < .01).

Upon examination of the clinical sites of infection, NGS most commonly identified bloodstream and respiratory tract infections. It also identified skin, bone, internal hardware, UTI and cerebrospinal fluid infections.

“Personally, I would not say that NGS testing should be used more than it currently is in comparison with conventional testing,” Muller said. “Conventional microbiologic testing is sufficient for the majority of infections we diagnose and can provide susceptibility information that NGS testing does not currently allow.”– by Katherine Bortz

Disclosures: The authors report no relevant financial disclosures.