Next-generation sequencing of microbial cell-free DNA for rapid noninvasive diagnosis of infectious diseases in immunocompromised hosts

Abstract

Background: Cell-free DNA (cfDNA) sequencing has emerged as an effective laboratory method for rapid and noninvasive diagnosis in prenatal screening testing, organ transplant rejection screening, and oncology liquid biopsies but clinical experience for use of this technology in diagnostic evaluation of infections in immunocompromised hosts is limited. Methods: We conducted an exploratory study using next-generation sequencing (NGS) for detection of microbial cfDNA in a cohort of ten immunocompromised patients with febrile neutropenia, pneumonia or intra-abdominal infection. Results: Pathogen identification by cfDNA NGS demonstrated positive agreement with conventional diagnostic laboratory methods in 7 (70%) cases, including patients with proven/probable invasive aspergillosis, Pneumocystis jirovecii pneumonia, Stenotrophomonas maltophilia bacteremia, Cytomegalovirus and Adenovirus viremia. NGS results were discordant in 3 (30%) cases including two patients with culture negative sepsis who had undergone hematopoietic stem cell transplant in whom cfDNA testing identified the potential etiological agent of sepsis; and one kidney transplant recipient with invasive aspergillosis who had received >6 months of antifungal therapy prior to NGS testing. Conclusion: These observations support the clinical utility of measurement of microbial cfDNA sequencing from peripheral blood for rapid noninvasive diagnosis of infections in immunocompromised hosts. Larger studies are needed.

Application of metagenomic next-generation sequencing in the diagnosis and treatment guidance of Pneumocystis jirovecii pneumonia in renal transplant recipients

“…What is more, mNGS is able to detect organisms in the setting of effective treatment, which was proved by our present study where Patient 2 and 5 had received 11 and 13 days of active therapy against PJ prior to the collection of BALF sample and the fourth blood sample for mNGS testing, respectively [ 12 ].…”

“…PJP has been confirmed in 4 cases by mNGS in peripheral blood rather than respiratory samples in only 2 previous studies [ 1 , 12 ]. Although PJ almost exclusively inhabits the human lungs, pieces of PJ could penetrate through respiratory infectious site and circulate into peripheral blood, especially in immune-suppressed patients; thus, blood PJ sequence reads can diagnose PJP [ 1 , 6 ].…”

“…In the present study, the mNGS analysis report could be obtained within 24–48 h starting from the samples received in the laboratory. To date, there have been several reports on successful use of mNGS to diagnose pulmonary infections involving PJ, with two of them reporting that mNGS is more sensitive than conventional methods (non-PCR based) [ 1 , 2 , 9 – 12 ]. The sensitivity (90%) and specificity (100%) of mNGS are consistent with the PCR test in our results.…”

“…Recently, metagenomic next-generation sequencing (mNGS), as an all-in-one diagnostic tool, has been successfully used for various infectious diseases, showing a higher detection rate of PJP compared to conventional methods [ 1 , 9 – 11 ]. Of note, 4 cases of PJP were reported to be confirmed by mNGS in peripheral blood rather than respiratory samples [ 1 , 12 ]. Although mNGS can diagnose PJP rapidly and noninvasively in immunocompromised patients, it was used to diagnose PJP only in 2 RTRs, awaiting further evaluation for its value [ 1 , 2 ].…”

Murine Typhus Infection in Pregnancy: Case Series and Literature Review

“…The confirmatory diagnosis was mainly based on serology and PCR amplification of rickettsial DNA. Recently, the use of microbial cell-free DNA in human plasma has become an attractive option for the diagnosis of MT, given the potential of higher sensitivity than conventional molecular diagnostic tests such as PCR [ 17 , 24 , 25 ]. However, this novel modality is not widely available as a standard diagnostic test.…”