Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease

2019 ◽  
Vol 4 (4) ◽  
pp. 663-674 ◽  
Author(s):  
Timothy A. Blauwkamp ◽  
Simone Thair ◽  
Michael J. Rosen ◽  
Lily Blair ◽  
Martin S. Lindner ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Dna Sequencing ◽  
Microbial Cell ◽  
Clinical Validation ◽  
Cell Free Dna ◽  
Free Dna

scholarly journals 1097. Microbial Cell Free DNA Sequencing for Prediction of Culture-Negative Infection Events in Children with Cancer

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S578-S578
Author(s):  
Kathryn Goggin ◽  
Amanda griffen ◽  
Christina Kohler ◽  
Kim J Allison ◽  
Yuki Inaba ◽  
...  
Keyword(s):  
Febrile Neutropenia ◽  
Dna Sequencing ◽  
Bacterial Pathogen ◽  
Microbial Cell ◽  
Research Support ◽  
Convenience Sample ◽  
Cell Free Dna ◽  
Free Dna ◽  
Wide Range ◽  
Culture Negative

Abstract Background Culture-independent diagnostics may help diagnose or predict infection; microbial cell free DNA sequencing (mcfDNA-seq), can detect a wide range of pathogens directly from plasma. Immunocompromised children who develop febrile neutropenia (FN) without documented bloodstream infection (BSI) may have undiagnosed bacterial infection, but identification of this is difficult, and the proportion of such episodes is unknown, as is the relative contribution of non-bacterial etiologies. We analyzed mcfDNA-seq results in a convenience sample of FN cases without known etiology. Methods Participants were < 25 years of age and undergoing treatment for cancer. Remnant plasma was prospectively obtained and stored. Samples from Days 0 and -1 underwent mcfDNA-seq by Karius Inc., reported in molecules per microliter (MPM) of plasma. Samples from participants without impending or recent fever or infection were also tested. Results There were 8 episodes in 7 patients; 4 (50%) had a common bacterial pathogen identified by mcfDNA-seq on Day 0 (Table 1). In 2 (50%) of these cases, the same organism was also identified on Day -1, at a lower concentration. One fungal pathogen was identified prior to and at onset of FN. A common bacterial pathogen was identified in 3/64 (5%) control samples from the population. Culture-negative sepsis was the final diagnosis in one episode; Streptococcus mitis, an important cause of neutropenic sepsis, was found in Day 0 and Day -1 samples. In an episode where E. coli was identified by mcfDNA-seq, FN recurred after antibiotic discontinuation. Table 1. Quantitative mcfDNA-seq Results for Prediction & Diagnosis of Febrile Neutropenia Episodes Conclusion In this sample of culture-negative FN episodes in pediatric patients leukemia, mcfDNA-seq identified a bacterial pathogen in 50% of cases. The same organism was identifiable on the day prior to FN in 50% of cases, suggesting that predictive testing might be feasible. Disclosures Asim A. Ahmed, MD, Karius (Employee) Desiree D. Hollemon, MSN, MPH, Karius inc (Employee) Charles Gawad, MD PhD, Karius inc (Grant/Research Support) Joshua Wolf, MBBS, PhD, FRACP, Karius inc (Grant/Research Support)

scholarly journals Liquid biopsy for infectious diseases: a focus on microbial cell-free DNA sequencing

Theranostics ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 5501-5513
Author(s):  
Dongsheng Han ◽  
Rui Li ◽  
Jiping Shi ◽  
Ping Tan ◽  
Rui Zhang ◽  
...  
Keyword(s):  
Infectious Diseases ◽  
Dna Sequencing ◽  
Liquid Biopsy ◽  
Microbial Cell ◽  
Cell Free Dna ◽  
Free Dna

scholarly journals 666. Microbial Cell-Free DNA Sequencing for Evaluation of Response to Antibiotic Therapy in Patients with Relapsed or Refractory Leukemia

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S388-S388
Author(s):  
Joshua Wolf ◽  
Kathryn Goggin ◽  
Amanda griffen ◽  
Christina Kohler ◽  
Kim J Allison ◽  
...  
Keyword(s):  
Blood Culture ◽  
Antibiotic Therapy ◽  
Dna Sequencing ◽  
Microbial Cell ◽  
Response To Treatment ◽  
Research Support ◽  
Cell Free Dna ◽  
Free Dna ◽  
Slow Decay ◽  
Pathogen Dna

Abstract Background In patients with bloodstream infection (BSI), true eradication of infection takes longer than blood culture clearance. Therefore, optimal treatment duration, especially in immunocompromised hosts, is unknown. A sensitive test of microbiological response to treatment could improve care by indicating a time for safe antibiotic discontinuation. Microbial cell-free DNA sequencing (mcfDNA-seq) is a sensitive predictor of BSI, and we hypothesize that it might also be useful to measure response to treatment. Methods Eligible participants were < 25 years of age being treated for leukemia. Remnant plasma samples were collected as part of a prospective study (PREDSEQ), and underwent mcfDNA-seq by Karius Inc. in a CLIA/CAP-accredited laboratory. Pathogen DNA was reported in molecules per microliter (MPM). Testing was batched and blinded. Available samples from Day 1 through Day 7 after onset of bacterial BSI were included. We evaluated decay of the BSI pathogen DNA after initiation of effective antibiotic therapy, from the peak to last available sample, and compared episodes with slow (< 0.5 log10 MPM/day) vs. rapid DNA decay. Results There were 13 evaluable BSI episodes in 9 participants; 7 had slow DNA decay. Persistence of bacteremia or fever ≥1 day after initiation of effective antibiotics occurred in 9/13 episodes (7/7 slow decay and 2/6 rapid decay; P = 0.02). Slow decay persisted beyond resolution of bacteremia and fever in 3/7 of these cases. Figure 1. Pathogen DNA Concentration by mcfDNA-seq During Antibiotic Treatment of Bacteremia; Dashed line, blood culture positive; Red circle, last fever Conclusion In this small convenience sample of patients with leukemia, slow mcfDNA-seq DNA decay correlated with persistent fever or bacteremia. Post-BSI mcfDNA-seq monitoring should be investigated with the goal of decreasing inappropriate antibiotic therapy and preventing treatment failure. Disclosures Joshua Wolf, MBBS, PhD, FRACP, Karius inc (Grant/Research Support) Asim A. Ahmed, MD, Karius (Employee) Desiree D. Hollemon, MSN, MPH, Karius inc (Employee) Charles Gawad, MD PhD, Karius inc (Grant/Research Support)

scholarly journals #75: Microbial Cell-free DNA Sequencing for Prediction of Culture-Negative Infection Events in Children with Cancer

2021 ◽  
Vol 10 (Supplement_1) ◽  
pp. S8-S9
Author(s):  
K P Goggin ◽  
A Griffen ◽  
C Kohler ◽  
K J Allison ◽  
Y Inaba ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Pediatric Patients ◽  
Bacterial Pathogen ◽  
Antifungal Prophylaxis ◽  
Microbial Cell ◽  
Antibacterial Prophylaxis ◽  
Cell Free Dna ◽  
Free Dna ◽  
Culture Negative ◽  
Control Samples

Abstract Background New culture-independent diagnostics are being investigated for diagnosis and prediction of infection. One method is microbial cell-free DNA sequencing (mcfDNA-seq), which can detect a wide range of pathogens directly from plasma. Immunocompromised children who develop febrile neutropenia (FN) without documented bloodstream infection (BSI) may have an undiagnosed bacterial infection, but identification of this subset is difficult. The percentage of episodes of FN caused by bacterial pathogens that did not grow in culture is unknown, as is the relative contribution of other specific etiologies such as viruses, fungi, immunotherapies, and immune reconstitution or graft vs. host disease. The value of mcfDNA-seq in FN patients is also unknown. As part of a larger study evaluating the ability of mcfDNA-seq to predict BSI in a cohort of pediatric patients with relapsed or refractory leukemia, we analyzed mcfDNA-seq results in a sample of cases of FN for which the definitive etiology was unknown. Methods Eligible participants were <25 years of age and undergoing treatment for cancer. Remnant plasma from clinical testing was prospectively obtained and stored. Samples collected on the day of onset of FN (Day 0) and the day prior (Day –1) underwent mcfDNA-seq by Karius Inc. in a CLIA and CAP-accredited laboratory. Pathogen detection results were reported in molecules per microliter (MPM) of plasma. Negative control samples from study participants without impending or recent fever or infection were also obtained. Testing was batched and blinded, so results were not clinically available. Results mcfDNA-seq results were obtained from eight episodes of FN in seven patients. Five episodes occurred in participants awaiting engraftment after HCT and three were receiving chemotherapy only. All participants receiving chemotherapy were receiving antibacterial prophylaxis with vancomycin and ciprofloxacin, antifungal prophylaxis with micafungin or voriconazole, and PJP prophylaxis with TMP-SMX or pentamidine. No HCT recipients were receiving antibacterial prophylaxis, but all received PJP prophylaxis, antifungal prophylaxis or treatment, and antiviral prophylaxis or treatment. Of 8 FN episodes, 4 (50%) had a common bacterial pathogen identified by mcfDNA-seq on Day 0 (Table 1). In 2 (50%) of these cases, the same organism was also identified on Day –1, at a lower concentration. One fungal pathogen was identified prior to and at the onset of FN. A common bacterial pathogen was identified in 3/64 (5%) control samples from the study population. Culture-negative sepsis was the final diagnosis in one episode; in this case, Streptococcus mitis, an important cause of sepsis in neutropenic patients, was identified in both Day 0 and Day –1 samples. In another episode where E. coli was identified, antibiotics were discontinued after 48 hours, but the patient was re-admitted within 24 hours for recurrent FN. Conclusions In this sample of culture-negative FN episodes in pediatric patients with relapsed or refractory leukemia, mcfDNA-seq identified a common bacterial pathogen in 50% of cases. The same organism was identifiable on the day prior to FN in 50% of cases, suggesting that predictive testing might be feasible. More data regarding sensitivity and specificity of mcfDNA-seq to diagnose and predict FN are needed.

scholarly journals Evaluation of Plasma Microbial Cell-Free DNA Sequencing to Predict Bloodstream Infection in Pediatric Patients With Relapsed or Refractory Cancer

JAMA Oncology ◽  
2020 ◽  
Vol 6 (4) ◽  
pp. 552 ◽  
Author(s):  
Kathryn P. Goggin ◽  
Veronica Gonzalez-Pena ◽  
Yuki Inaba ◽  
Kim J. Allison ◽  
David K. Hong ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Bloodstream Infection ◽  
Pediatric Patients ◽  
Microbial Cell ◽  
Cell Free Dna ◽  
Free Dna

scholarly journals 670. Rapid, Non-invasive Detection of Invasive Mycoplasma hominis Infection using the Karius Test, A Next-Generation Sequencing Test for Microbial Cell-free DNA in Plasma

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S390-S390
Author(s):  
Priya Edward ◽  
William V La Via ◽  
Mehreen Arshad ◽  
Kiran Gajurel
Keyword(s):  
Next Generation Sequencing ◽  
Case Series ◽  
Mycoplasma Hominis ◽  
Microbial Cell ◽  
Next Generation ◽  
Cell Free Dna ◽  
Non Invasive ◽  
Free Dna ◽  
Hominis Infection ◽  
Generation Sequencing

Abstract Background Mycoplasma hominis is typically associated with genital infections in women and is a rare cause of musculoskeletal infections often in immunocompromised hosts. Diagnosis of invasive Mycoplasma hominis infections are difficult due to challenges in culturing these organisms. Molecular diagnostics require an index of suspicion which may not be present at the time of tissue sampling. Accurate, rapid diagnosis of Mycoplasma hominis infections are important for antibiotic management. Methods Two cases of invasive Mycoplasma hominis infections are presented in which the Karius test (KT) was used to make the diagnosis. The KT is a CLIA certified/CAP-accredited next-generation sequencing (NGS) plasma test that detects microbial cell-free DNA (mcfDNA). After mcfDNA is extracted and NGS performed, human reads are removed and remaining sequences are aligned to a curated database of > 1400 organisms. Organisms present above a statistical threshold are reported. Case review was performed for clinical correlation. Results A young woman with lupus nephritis status post renal transplant developed persistent fever with progressive multifocal culture-negative osteoarticular infection despite empiric ceftriaxone. An adolescent female presented with an ascending pelvic infection progressing to purulent polymicrobial peritonitis (see table) requiring surgical debridement and cefipime, metronidazole and micafungin therapy; her course was complicated by progressive peritonitis/abscesses. Karius testing detected high-levels of Mycoplasma hominis mcfDNA in both cases – at 3251 molecules/microliter (MPM) in the first case and 3914 MPM in the second case. The normal range of Mycoplasma hominis mcfDNA in a cohort of 684 normal adults is 0 MPM. The patients rapidly improved with atypical coverage with doxycycline and levofloxaxin. Clinical findings in 2 patients with M. hominis infection detected by the Karius Test Conclusion Open-ended, plasma-based NGS for mcfDNA provides a rapid, non-invasive method to diagnose invasive Mycoplasma hominis infection. This case series highlights the potential to diagnose infections caused by fastidious pathogens to better inform antimicrobial therapy and achieve favorable outcomes. Disclosures William V. La Via, MD, Karius (Employee)

Sequencing of Circulating Microbial Cell-Free DNA Can Identify Pathogens in Periprosthetic Joint Infections

2021 ◽  
Vol Publish Ahead of Print ◽  
Author(s):  
Adriana P. Echeverria ◽  
Ian S. Cohn ◽  
David C. Danko ◽  
Sara Shanaj ◽  
Lily Blair ◽  
...  
Keyword(s):  
Microbial Cell ◽  
Cell Free Dna ◽  
Joint Infections ◽  
Free Dna

Circulating microbial cell-free DNA is associated with inflammatory host-responses in severe pneumonia

Thorax ◽  
2021 ◽  
pp. thoraxjnl-2020-216013
Author(s):  
Haopu Yang ◽  
Ghady Haidar ◽  
Nameer S Al-Yousif ◽  
Haris Zia ◽  
Daniel Kotok ◽  
...  
Keyword(s):  
Large Scale ◽  
Inflammatory Responses ◽  
Severe Pneumonia ◽  
Systemic Circulation ◽  
Microbial Cell ◽  
Metagenomic Sequencing ◽  
Cell Free Dna ◽  
Free Dna ◽  
Culture Positive ◽  
Culture Negative

Host inflammatory responses predict worse outcome in severe pneumonia, yet little is known about what drives dysregulated inflammation. We performed metagenomic sequencing of microbial cell-free DNA (mcfDNA) in 83 mechanically ventilated patients (26 culture-positive, 41 culture-negative pneumonia, 16 uninfected controls). Culture-positive patients had higher levels of mcfDNA than those with culture-negative pneumonia and uninfected controls (p<0.005). Plasma levels of inflammatory biomarkers (fractalkine, procalcitonin, pentraxin-3 and suppression of tumorigenicity-2) were independently associated with mcfDNA levels (adjusted p<0.05) among all patients with pneumonia. Such host–microbe interactions in the systemic circulation of patients with severe pneumonia warrant further large-scale clinical and mechanistic investigations.

Sign in / Sign up

Export Citation Format

Share Document