Microbial Cell-Free DNA Identifies Etiology of Bloodstream Infections, Persists Longer Than Conventional Blood Cultures, and its Duration of Detection is Associated with Metastatic Infection in Patients with Staphylococcus aureus and Gram-Negative Bacteremia

2021 ◽  
Author(s):  
Emily M Eichenberger ◽  
Christiaan R de Vries ◽  
Felicia Ruffin ◽  
Batu Sharma-Kuinkel ◽  
Lawrence Park ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Blood Culture ◽  
Bloodstream Infection ◽  
Blood Cultures ◽  
Microbial Cell ◽  
Cell Free Dna ◽  
Gram Negative ◽  
Free Dna ◽  
Metastatic Infection ◽  
Gram Negative Bacteremia

Abstract Background Microbial cell-free DNA (mcfDNA) sequencing of plasma can identify presence of a pathogen in a host. This study evaluated the duration of pathogen detection by mcfDNA sequencing vs. conventional blood culture in patients with bacteremia. Methods Blood samples from patients with culture-confirmed bloodstream infection were collected within 24 hours of the index positive blood culture and 48 to 72 hours thereafter. mcfDNA was extracted from plasma and next-generation sequencing (NGS) applied. Reads were aligned against a curated pathogen database. Statistical significance was defined with Bonferroni adjustment for multiple comparisons (p < 0.0033). Results A total of 175 patients with Staphylococcus aureus bacteremia (SAB; n=66), Gram-negative bacteremia (GNB; n=74), or non-infected controls (n=35) were enrolled. The overall sensitivity of mcfDNA sequencing compared to index blood culture was 89.3% (125/140) and the specificity was 74.3%. Among patients with bacteremia, pathogen specific mcfDNA remained detectable for significantly longer than conventional blood cultures (median 15 days vs. 2 days; p<0.0001). Each additional day of mcfDNA detection significantly increased the odds of metastatic infection (Odds Ratio [OR]: 2.89; 95% Confidence Interval [CI]: 1.53-5.46; p=0.0011). Conclusions Pathogen mcfDNA identified the bacterial etiology of bloodstream infection for a significantly longer interval than conventional cultures, and its duration of detection was associated with increased risk for metastatic infection. mcfDNA could play a role in the diagnosis of partially treated endovascular infections.

scholarly journals 156. Direct Detection and Quantification of Bacterial Cell-free DNA in Patients with Infective Endocarditis (IE) Using the Karius Plasma Next Generation Sequencing (NGS) Test

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S12-S12 ◽  
Author(s):  
Pratik Shah ◽  
Felicia Ruffin ◽  
Hon Seng ◽  
Desiree Hollemon ◽  
Laura Winn ◽  
...  
Keyword(s):  
Blood Culture ◽  
Blood Cultures ◽  
Molecular Diagnostic ◽  
Plasma Samples ◽  
Cell Free Dna ◽  
Cardiac Devices ◽  
Free Dna ◽  
Wide Range ◽  
Pathogen Dna ◽  
Culture Negative

Abstract Background The variable clinical presentation of IE requires a diagnostic tool that accurately detects a wide range of organisms, including in culture-negative (CN) scenarios. A sensitive molecular diagnostic assay that quantitates pathogen DNA could be a useful tool to diagnose IE and evaluate response to antimicrobial therapy. Methods We prospectively enrolled 30 hospitalized adult patients evaluated for acute IE classified using the Duke Criteria. Residual plasma samples within 24 hours and/or fresh whole blood within 48–72 hours of enrollment blood culture were collected. Additional samples were collected every 2–3 days for up to 7 time points until discharge. Samples were shipped to the Karius laboratory (Redwood City, California) for testing. Cell-free DNA was extracted and NGS was performed. Human sequences were removed and remaining sequences were aligned to a curated pathogen database of over 1,000 organisms. Organisms present above a predefined statistical threshold were reported. Quantity of DNA for each reported pathogen was expressed as molecules per microliter. Results Of 29 patients eligible for analysis, 18 had prosthetic valves and 7 had implanted cardiac devices. Twenty-four patients had Definite IE. Twenty patients had positive blood cultures (including S. aureus, S. epidermidis, E. faecalis, S. agalactiae, Pantoea ananatis, S. sanguinis, C. albicans); NGS identified the same organism isolated in all 20 patients as well as E. cloacae complex, and E. faecalis in 2 of 4 CN Definite IE patients. For 1 CN patient with Possible IE, NGS identified E. coli. NGS and BC were negative for 4 patients with Rejected IE. NGS identified the IE etiology in patients pretreated with antibiotics up to 20 days prior to sample collection. Pathogen DNA signal was often observed in both initial and repeat plasma samples, while repeat blood cultures remained negative. Conclusion This novel, cell-free pathogen quantitative NGS plasma assay accurately identified causative organisms in patients with IE, even when blood cultures were negative due to pretreatment with antibiotics. Pathogen DNA, detected in plasma longer than blood culture, is a promising biomarker to aid in the diagnosis and monitoring of IE, particularly culture-negative IE. Disclosures P. Shah, Karius Inc.: Collaborator and Research Contractor, Salary. F. Ruffin, Karius Inc.: Collaborator and Research Contractor, Salary. H. Seng, Karius Inc.: Employee, Salary. D. Hollemon, Karius Inc.: Employee, Salary. L. Winn, Karius Inc.: Collaborator and Research Contractor, Salary. C. Drennan, Karius Inc.: Collaborator and Research Contractor, Salary. K. L. Chan, Karius Inc.: Employee, Salary. H. Quach, Karius Inc.: Employee, Salary. T. Blauwkamp, Karius Inc.: Employee, Salary. G. Meshulam-Simon, Karius Inc.: Employee, Salary. D. Hong, Karius Inc.: Employee, Salary. V. G. Fowler Jr., Merck, Cerexa/Actavis, Pfizer, Advanced Liquid Logis, NIH, MedImmune, Basilea, Karius, Contrafect, Regneron, Genentech, Affinergy, Locus, Medical Surface, Inc., Achaogen, Astellas, Arsanis, Bayer, Cubist, Debiopharm, Durata, Grifols, Medicines Co, Novartis: Collaborator, Consultant and Scientific Advisor, Consulting fee, Research grant and Research support.

scholarly journals Different characteristics of bloodstream infection during venoarterial and venovenous extracorporeal membrane oxygenation in adult patients

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hyoung Soo Kim ◽  
Sunghoon Park ◽  
Ho Hyun Ko ◽  
Sang Ook Ha ◽  
Sun Hee Lee ◽  
...  
Keyword(s):  
Blood Culture ◽  
Extracorporeal Membrane Oxygenation ◽  
Bloodstream Infection ◽  
Clinical Characteristics ◽  
Gram Positive ◽  
Gram Negative ◽  
Membrane Oxygenation ◽  
Gram Negative Bacteremia ◽  
Va Ecmo ◽  
Vv Ecmo

AbstractCurrently, there is scarcity of data on whether differences exist in clinical characteristics and outcomes of bloodstream infection (BSI) between venoarterial (VA) and venovenous (VV) extracorporeal membrane oxygenation (ECMO) and whether they differ between Candida BSI and bacteremia in adult ECMO patients. We retrospectively reviewed data of patients who required ECMO for > 48 h and had BSIs while receiving ECMO between January 2015 and June 2020. Cases with a positive blood culture result within 24 h of ECMO implantation were excluded. We identified 94 (from 64 of 194 patients) and 38 (from 17 of 56 patients) BSI episodes under VA and VV ECMO, respectively. Fifty nine BSIs of VA ECMO (59/94, 62.8%) occurred in the first 2 weeks after ECMO implantation, whereas 24 BSIs of VV ECMO (24/38, 63.2%) occurred after 3 weeks of ECMO implantation. Gram-negative bacteremia (39/59, 66.1%) and gram-positive bacteremia (10/24, 41.7%) were the most commonly identified BSI types in the first 2 weeks after VA ECMO implantation and after 3 weeks of VV implantation, respectively. Timing of Candida BSI was early (6/11, 54.5% during the first 2 weeks) in VA ECMO and late (6/9, 66.7% after 3 weeks of initiation) in VV ECMO. Compared with bacteremia, Candida BSI showed no differences in clinical characteristics and outcomes during VA and VV ECMO, except the significant association with prior exposure to carbapenem in VA ECMO (vs. gram-negative bacteremia [P = 0.006], vs. gram-positive bacteremia [P = 0.03]). Our results suggest that ECMO modes may affect BSI clinical features and timing. In particular, Candida BSI occurrence during the early course of VA ECMO is not uncommon, especially in patients with prior carbapenem exposure; however, it usually occurs during the prolonged course of VV ECMO. Consequently, routine blood culture surveillance and empiric antifungal therapy might be warranted in targeted populations of adult ECMO patients, regardless of levels of inflammatory markers and severity scores.

scholarly journals 1039. Surveillance Blood Cultures Associated With Decreased Mortality in Gram-Negative Bacteremia

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S310-S311
Author(s):  
Stacey A Maskarinec ◽  
David Van Duin ◽  
Felicia Ruffin ◽  
Vance G Fowler Jr ◽  
Joshua T Thaden
Keyword(s):  
Blood Culture ◽  
Hospital Mortality ◽  
Positive Blood Culture ◽  
Blood Cultures ◽  
Statistical Testing ◽  
Chi Square ◽  
Gram Negative ◽  
Staphylococcus Aureus Bacteremia ◽  
Gram Negative Bacteremia ◽  
Persistent Bacteremia

Abstract Background Prior studies have suggested that surveillance blood cultures (SBCs) may not be indicated in the setting of Gram-negative bacteremia (GNB). However, it is unclear how particular microbial species influence the need for SBCs in GNB. Methods We conducted a prospective cohort study of inpatients at Duke with Staphylococcus aureus bacteremia (SAB) and GNB from 2002–2015. Patients who died <24 hours from the first positive blood culture were excluded. Patients provided written informed consent. SBCs were defined as a blood culture drawn from 24 hours to 7 days from initial positive blood culture. Persistent bacteremia was defined as a positive SBC with the same organism. Statistical testing included Fishers exact and chi-square tests. Results There were 2856 episodes of bacteremia over the study period (SAB: 1,147 [40%]; GNB: 1,709 [60%]). SBCs were drawn in 87% (1,003/1,147) of SAB patients and 64% (1,097/1,709) of GNB patients. SBC rates varied by GNB species (P < 0.001), being more commonly drawn for those patients with Pseudomonas bacteremia (128/159 [80%]) than those with Escherichia bacteremia (377/592 [62%]). In GNB, acquisition of SBCs, regardless of positivity, was associated with decreased in-hospital mortality (177/1,173 [15%] vs. 109/536 [20%]; P = 0.008). The in-hospital mortality benefit associated with SBCs varied with GNB species, including Pseudomonas (30/128 [23%] vs. 14/31 [45%]; P = 0.02) and Escherichia (33/377 [9%] vs. 37/215 [17%]; P = 0.003). In-hospital mortality in those with SAB was also lower when SBCs were drawn (143/1003 [14%] vs. 46/144 [32%]; P = 0.0001) (figure). In GNB, positive SBCs, relative to negative SBCs, was associated with increased in-hospital mortality (44/217 [20%] vs. 133/956 [14%]; P = 0.02). Persistent bacteremia occurred in 49% (494/1003) of SAB patients and 20% (217/1097) of GNB patients with SBCs. Persistent bacteremia risk differed by GNB species (P = 0.004), and was highest among those with Stenotrophomonas maltophilia (9/19 [47%]) or Serratia (24/76 [31%]). Conclusion Acquisition of SBCs in patients with GNB was associated with decreased mortality, and this was driven in part by species-specific differences. Disclosures D. Van Duin, achaogen: Scientific Advisor, Consulting fee. shionogi: Scientific Advisor, Consulting fee. Allergan: Scientific Advisor, Consulting fee. Astellas: Scientific Advisor, Consulting fee. Neumedicine: Scientific Advisor, Consulting fee. Roche: Scientific Advisor, Consulting fee. T2 Biosystems: Scientific Advisor, Consulting fee. V. G. Fowler Jr., Merck, Cerexa/Actavis, Pfizer, Advanced Liquid Logis, NIH, MedImmune, Basilea, Karius, Contrafect, Regneron, Genentech, Affinergy, Locus, Medical Surface, Inc., Achaogen, Astellas, Arsanis, Bayer, Cubist, Debiopharm, Durata, Grifols, Medicines Co, Novartis: Collaborator, Consultant and Scientific Advisor, Consulting fee, Research grant and Research support.

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 Plasma Microbial Cell-Free DNA Sequencing Technology for the Diagnosis of Sepsis in the ICU

2021 ◽  
Vol 8 ◽  
Author(s):  
Lili Wang ◽  
Wenzheng Guo ◽  
Hui Shen ◽  
Jian Guo ◽  
Donghua Wen ◽  
...  
Keyword(s):  
Blood Culture ◽  
Central Nervous System Infection ◽  
The Body ◽  
Microbial Cell ◽  
Sepsis Group ◽  
Acid Extraction ◽  
Sequencing Analysis ◽  
Cell Free Dna ◽  
Free Dna ◽  
Significant Difference

Sepsis is a common life-threatening disease in the intensive care unit (ICU) that is usually treated empirically without pathogen identification. As a non-invasive and high-throughput technology, plasma microbial cell-free DNA (mcfDNA) sequencing can detect unknown pathogens independent of previous clinical or laboratory information. In this study, a total of 199 cases suspected of bloodstream infection (BSI) from January 2020 to June 2020 were collected, and potential pathogens were detected by simultaneous blood culture and plasma mcfDNA sequencing. Other clinical microbiological assays were performed within 7 days of plasma mcfDNA sequencing, including smear, culture of samples taken from relevant infected sites, and β-D-glucan/galactomannan (BDG/GM) tests, among others. The diagnoses were classified as sepsis [94 (47.2%)], non-sepsis [87 (43.7%)], and non-infectious disease [18 (9.0%)]. The sensitivity and specificity of plasma mcfDNA sequencing for diagnosing sepsis were 68.1 and 63.2%, respectively, which were significantly better than those of blood culture, especially for the common bacteria that cause hospital-acquired infection, namely, Acinetobacter baumannii (p < 0.01) and Klebsiella pneumoniae (p < 0.01), and DNA viruses (plasma mcfDNA sequencing only, p < 0.01). However, there was no significant difference in the rate of positivity between plasma mcfDNA sequencing and blood culture for antibiotic-non-exposed cases (43.6 vs. 30.9%, p = 0.17). In the non-sepsis group, 44.8% of cases (13/29) detected only by plasma mcfDNA sequencing showed infections in other parts of the body, such as lower respiratory infection (LRI), intra-abdominal infection (IAI) and central nervous system infection (CNSI). For some common pathogens (not including anaerobes), turnaround time (TAT) 3 (TAT from the initiation of blood sample processing by nucleic acid extraction to the completion of sequencing analysis) was longer than TAT1 (TAT from blood culture bottles in Virtuo to off Virtuo). With disease progression, significant dynamic changes in microbial species were clearly detected by plasma mcfDNA sequencing.

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 Impact of follow up blood cultures on outcomes of patients with community-onset gram-negative bloodstream infection

2021 ◽  
Vol 34 ◽  
pp. 100811
Author(s):  
Rajiv Amipara ◽  
Hana Rac Winders ◽  
Julie Ann Justo ◽  
P. Brandon Bookstaver ◽  
Joseph Kohn ◽  
...  
Keyword(s):  
Bloodstream Infection ◽  
Blood Cultures ◽  
Gram Negative ◽  
Community Onset

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)

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