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 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.

<p>Metagenomic Next-Generation Sequencing in Diagnosis of a Case of <em>Pneumocystis jirovecii</em> Pneumonia in a Kidney Transplant Recipient and Literature Review</p>

“…To date, there have been 5 reports on successful use of mNGS to diagnose pulmonary infections involving P. jirovecii (Table 2). [14][15][16][17][18] While the sample size is small (1 to 13 specimens each), these studies involve the use of different types of specimens (BALF, sputum, lung biopsy and blood) and different NGS platforms. The numbers of sequence reads for P. jirovecii are highly variable (2 to 303,572) among studies though all are less than the P. jirovecii reads identified from our case (1,665,693).…”

“…This method has been successfully used as a diagnostic tool for various infectious diseases including PCP. [14][15][16][17] Its application to diagnose PCP in renal transplant recipients has been attempted in one study, 18 and its value awaits further evaluation. Here we report a case of PCP diagnosed by mNGS following negative results in multiple conventional diagnostic tests.…”

Clinical Application of Metagenomic Next-Generation Sequencing in Patients with Hematologic Malignancies Suffering from Sepsis

“…A previous study by Grumaz et al revealed that the rate of positive mNGS results was constant over the different time points after sepsis developed, while the positivity of blood culture decreased at later time points [28]. Camargo et al indicated that cell-free DNA sequencing could still identify fungus such as P. jirovecii or Aspergillus species among patients receiving effective antifungal agents [29]. Another study by Miao et al also revealed that mNGS is less affected by prior antibiotic exposure, which showed opposite findings to our cohort.…”

Diagnosis of Pneumocystis jirovecii Pneumonia in Pediatric Patients in Serbia, Greece, and Romania. Current Status and Challenges for Collaboration

“…Less-expensive molecular assays for detection of P. jirovecii, such as loop-mediated isothermal amplification, is an alternative [37]. Recently, the next generation sequencing (NGS) and measurement of P. jirovecii-free DNA from peripheral blood showed promising results in immunocompromised hosts [38]. Molecular assays have increased detection rates of P. jirovecii, but the wide use of these methods is limited probably due to economic reasons, low incidence of PcP, and sometimes false positive results.…”