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)

scholarly journals 663. Two (Plus) Birds, One Stone: The Rapid, Comprehensive, Non-invasive Detection of Co-Pathogens of Critical Importance Using A Plasma-based Microbial Cell-free DNA Next-generation Sequencing Test

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S433-S434
Author(s):  
Matthew Smollin ◽  
Martin S Lindner ◽  
Nicholas R Degner ◽  
Ricardo Castillo-Galvan ◽  
Jose Alexander ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Rapid Identification ◽  
Microbial Cell ◽  
Next Generation ◽  
Critical Importance ◽  
Cell Free Dna ◽  
Non Invasive ◽  
Free Dna ◽  
Aspergillus Sp ◽  
Generation Sequencing

Abstract Background Immunocompromised (IC) patients are at risk for infections by a spectrum of invasive pathogens. The overlap in presentation makes it challenging to differentiate among infectious etiologies and critical co-infections (CI) may remain undiagnosed. Open-ended, comprehensive assessment of infection through microbial cell-free DNA (mcfDNA) next-generation sequencing (NGS) of plasma offers the potential for the rapid identification of multiple co-infecting pathogens of critical importance (CI-POCI) with one test. Methods Karius TestTM (KT) results from patients who underwent clinical testing from December 2016 to April 2021 were reviewed for detections of two or more CI-POCI including parasites, fungi (Pneumocystis jirovecii, Trichosporon sp, endemic mycoses, Aspergillus sp., Mucorales, Non-Aspergillus/Non-Mucorales molds), mycobacteria, Legionella sp., Nocardia sp. and Listeria. KT, developed and validated in Karius’ CLIA certified/CAP accredited lab, detects mcfDNA from plasma. McfDNA is extracted, NGS performed, human sequences removed and remaining sequences aligned to a curated pathogen database of > 1500 organisms. Organisms present above a statistical threshold are reported and quantified. For > 85% of tests the time to result reporting is the next day from sample receipt. Results KT detected CI of two or more POCI in 59 samples (75% adults, 25% children). The most common partnering co-pathogens of critical importance were Aspergillus sp (38), Mucorales (17) and PJP (14); the most common combinations were two or more distinct Aspergillus sp (14) followed by an Aspergillus sp and a Mucorales (12). There were 17 samples with the detection of three or more CI-POCI (29%). Figure 1. Chord Plot of Co-infections with Pathogens of Critical Importance The outer circle sections represent Karius Test detections belonging to different taxonomic groups. The length of each circle section is proportional to the total number of detections of a taxon belonging to that group. The chords connecting a pair of circle sections are proportional to the number of times two taxa from those groups were observed together, weighted by the total number of taxa detected. Conclusion Plasma mcfDNA NGS offers a rapid, comprehensive non-invasive means of detecting CI-POCI in IC patients with one test. Although rare, co-infections with POCI can greatly increase mortality. The KT can provide important insights into pathogen-pathogen interactions in complex hosts and help optimize therapy. Disclosures Matthew Smollin, PharmD, Karius, Inc. (Employee) Martin S. Lindner, PhD, Karius, Inc. (Consultant) Nicholas R. Degner, MD, MPH, MS, Karius Inc. (Employee, Shareholder) Ricardo Castillo-Galvan, MD MPH, Karius Inc. (Consultant) Jose Alexander, MD, D(ABMM), FCCM, CIC, SM, MB(ASCP), BCMAS, Karius (Employee) Ann Macintyre, DO, Karius, Inc. (Employee) Bradley Perkins, MD, Karius, Inc. (Employee) Asim A. Ahmed, MD, Karius, Inc. (Employee) Aparna Arun, MD, Karius (Employee)

scholarly journals 1177. Rapid, Non-invasive Detection of Invasive Mucormycosis Caused by Syncephalastrum monosporum Using Next-Generation Sequencing of Circulating Microbial Cell-free DNA in Plasma

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S613-S614
Author(s):  
Melissa Sanacore ◽  
Melhem M Solh ◽  
H Kent Holland ◽  
Asad Bashey ◽  
Samuel Webster ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Microbial Cell ◽  
Ct Scans ◽  
Cell Transplant ◽  
Next Generation ◽  
Cell Free Dna ◽  
Non Invasive ◽  
Free Dna ◽  
Serial Ct ◽  
Generation Sequencing

Abstract Background Improving diagnostics have led to newly identified causes of invasive fungal infection (IFI) in immunocompromised hosts. Syncephalastrum spp. are Zygomycetes more commonly associated with skin infections and have only rarely been implicated as a cause of IFI(1). Next generation sequencing (NGS) for circulating microbial cell-free DNA (mcfDNA) in plasma offers a unique tool to diagnose rare causes of IFI (2,3). Methods Karius results were reviewed for Syncephalastrum detections with 2 identified at the same institution. McfDNA was extracted from plasma and NGS was performed by Karius, Inc. (Redwood City, California). Human sequences were removed and remaining sequences were aligned to a database of over 1,400 pathogens. Organisms present above a predefined statistical significance threshold were quantified in DNA molecules per microliter (MPM). Chart review was performed for clinical correlation. Results A 66 y/o male one month out of induction therapy for acute myeloblastic leukemia (AML) developed pneumonia. Although BAL was negative for mold and despite empiric antifungals, plasma NGS for mcfDNA showed S. monosporum at 562 MPM; the reference range is 0 MPM. Amphotericin was added to empiric posaconazole. The patient was discharged 10 days later and serial CT scans showed improvement. Repeat NGS mcfDNA 11 days later was negative. He underwent stem cell transplant (SCT) 4 months later. In a second case, a 66 y/o female with acute prolymphocytic leukemia was admitted for fever with neutropenia. A CT chest showed new multifocal, bilateral, nodular opacities. Despite negative BAL fungal culture and pretreatment with fluconazole, plasma NGS mcfDNA revealed S. monosporum at 575 MPM. She was treated with micafungin, amphotericin, and posaconazole with clinical improvement. Repeat NGS mcfDNA 8 weeks later was negative. Serial CT scans showed improvement over 5 months. She proceeded to SCT. Conclusion Plasma-based NGS for mcfDNA enabled rapid, non-invasive detection of pulmonary mucormycosis caused by S. monosporum despite antifungal pretreatment and unrevealing invasive procedures in 2 patients with leukemia. The rapid identification of the specific etiology of IFI enabled targeted anti-fungal therapy and resumption of definitive oncological care including SCT. Table 1: Clinical Parameters Disclosures Christiaan R. de Vries, MD, PhD, Karius (Consultant, Independent Contractor)Stanford University (Employee)

scholarly journals 648. Rapid, Non-invasive Detection of Cryptic Tularemia Using a Plasma-Based Microbial Cell-Free DNA Next-Generation Sequencing Test

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S426-S426
Author(s):  
Salma Malik ◽  
Vishesh Paul ◽  
Thara Damodaran ◽  
Deepa Prabakhar ◽  
Amir Khan ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Francisella Tularensis ◽  
Clinical Manifestations ◽  
Microbial Cell ◽  
Microbiological Diagnosis ◽  
Next Generation ◽  
Cell Free Dna ◽  
Non Invasive ◽  
Free Dna ◽  
Generation Sequencing

Abstract Background Francisella tularensis causes severe infections and is a Category A potential bioterrorism agent but its microbiological diagnosis can be challenging. The diagnosis of tularemia is limited by non-specific protean clinical symptoms that overlap with other infectious syndromes, the fastidious nature of Francisella tularensis, along with insensitivity and poor specificity of serology. Rapid, non-invasive diagnosis of tularemia by microbial cell-free DNA (mcfDNA) next-generation sequencing (NGS) of plasma offers a means to overcome these limitations. Methods The Karius Test™ (KT) detects and quantifies mcfDNA in molecules/µL (MPM) from >1400 organisms in plasma (performed at the CLIA certified/CAP accredited Karius laboratory). KT detections of Francisella tularensis were compiled from three medical centers with clinical review by healthcare providers. Results KT detected Francisella tularensis in four patients. All were adult males in whom the diagnosis was unexpected. The most common symptoms were fever and chest pain. White blood cell count neutrophilic predominance and abnormal chest X-ray findings were found in three cases. A broad infectious disease work-up was performed with the initiation of broad spectrum empiric antibiotics in all cases. KT was the first test to identify Francisella tularensis as the microbiological diagnosis with a time to diagnosis of 2.25 days (avg) +/- 0.5 from sample collection (one day from sample receipt in all cases), enabling narrowed, targeted antibiotic treatment. Francisella tularensis mcfDNA concentration was 1772 MPM (avg) +/- 1914. KT was the only test to establish the diagnosis in two cases; tularemia serologies were confirmatory in two cases, one of which had confirmatory culture from lymph node biopsy. Three patients were diagnosed with the pneumonic form of the illness and one with a visceral glandular form. Possible epidemiological exposures were identified in all cases. Conclusion KT enabled rapid, non-invasive, plasma-based diagnosis of diverse clinical manifestations of invasive tularemia against a competing broad infectious and non-infectious differential diagnosis. Timely diagnosis enabled targeted narrowing of antibiotic therapy and successful treatment of pneumonic and glandular forms of the infection. Disclosures All Authors: No reported disclosures

scholarly journals 395. Rapid, Non-invasive Detection of Infection Using Plasma-based Next-Generation Sequencing for Microbial Cell-free DNA in Individuals Testing Negative for SARS-CoV-2 in a Pandemic Setting

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S266-S266
Author(s):  
William V La Via ◽  
Sudeb Dalai ◽  
Christiaan R de Vries ◽  
Ann Macintyre ◽  
Asim A Ahmed
Keyword(s):  
Next Generation Sequencing ◽  
Severe Pneumonia ◽  
Microbial Cell ◽  
Next Generation ◽  
Independent Contractor ◽  
Cell Free Dna ◽  
Non Invasive ◽  
Free Dna ◽  
Wide Range ◽  
Generation Sequencing

Abstract Background The clinical presentation of patients with severe COVID-19 infection can be protracted and deteriorate to ARDS and multi-organ dysfunction with prolonged fever. As such, there is clinical overlap with many infectious diseases especially those that cause pneumonia. Due to of the prevalence of COVID-19 illness amidst the pandemic, concerns about testing sensitivity and the attendant risk to health care personnel (HCP) delivering care, patients are frequently tested multiple times to ascertain that they are SARS-CoV-2 free. Often, alternative diagnoses are not considered because some diagnostic modalities—such as bronchoalveolar lavage (BAL)—pose an unacceptable risk to the patient and/or HCP. Methods We interrogated plasma for microbial cell-free DNA from 58 patients who were known to be SARS-CoV-2 negative. Clinical information is taken from information submitted with the test requisition or obtained at the time of result reporting from clinical consultations with the ordering provider. In each case, a plasma sample was analyzed with the Karius Test (KT) which is a CLIA certified/CAP-accredited next-generation sequencing (NGS) plasma test designed to detect and quantify circulating microbial cell-free DNA (mcfDNA), which can assist with the diagnosis of deep-seated infections. 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. The time to result is on average 24 hours from sample receipt. Results In a subset of 20 samples, we found a broad range of pathogens. Pneumocystis jirovecii was the most common. These detections were unexpected in the majority of these patients. (see Table) Broad range of Karius detected pathogens (including fastidious bacteria, mycobacteria, fungi and viruses) Conclusion Open-ended, plasma-based NGS for mcfDNA with the KT provides a rapid, non-invasive method to diagnose deep-seated infection like pneumonia. This broad-based test detected a wide range of pathogens – many unsuspected – in patients with severe pneumonia and other invasive infections during the COVID-19 pandemic. These detections highlight the utility of the tool; which allowed better management including de-escalation of SARS-CoV-2 testing and selection of appropriate antibiotic therapy for the unexpected diagnoses. Disclosures William V. La Via, MD, Karius (Employee) Sudeb Dalai, MD, Karius (Employee) Christiaan R. de Vries, MD, PhD, Karius (Consultant, Independent Contractor)Stanford University (Employee) Ann Macintyre, DO, Karius (Employee) Asim A. Ahmed, MD, Karius (Employee)

scholarly journals 710. Non-invasive Diagnosis of Whipple Endocarditis Using Next-Generation Sequencing for Microbial Cell-free DNA in Plasma

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S407-S407
Author(s):  
Christiaan R de Vries ◽  
Ann Macintyre ◽  
Brian Buggy
Keyword(s):  
Next Generation Sequencing ◽  
Microbial Cell ◽  
Next Generation ◽  
Independent Contractor ◽  
Cell Free Dna ◽  
Non Invasive ◽  
Free Dna ◽  
Whipple Disease ◽  
Culture Negative ◽  
Generation Sequencing

Abstract Background Tropheryma whipplei is a gram-positive bacillus that causes Whipple’s disease, a protean multisystemic syndrome classically characterized by arthralgias, chronic diarrhea, malabsorption, and weight loss. T. whipplei infection has a wide spectrum of clinical manifestations including pleuropulmonary disease, skin hyperpigmentation and cardiac infection. Endocarditis has been diagnosed in a small number of patients and may represent an atypical presentation of T. whipplei infection. Diagnosis can be challenging and has typically been accomplished with histopathology on resected valvular tissue or GI tract biopsy. Next-generation sequencing (NGS) of microbial cell-free DNA (mcfDNA) in plasma offers a rapid, non-invasive means of diagnosis of this rare cause of culture-negative endocarditis and challenging clinical entity. Methods McfDNA analysis was performed in a patient with culture negative endocarditis. McDNA was extracted from plasma and NGS was performed by Karius, Inc. (Redwood City, California). Human sequences were removed and remaining sequences were aligned to a curated database of over 1,400 pathogens. Organisms present above a predefined statistical significance threshold were reported and quantified in DNA molecules per microliter (MPM). Chart review was performed for clinical correlation. Results A 64 year-old male with history of valve replacement presented with significant deterioration of the mitral valve. An exhaustive infectious workup including blood cultures was negative. Karius testing detected T. whipplei at 766 MPM within two days of sample receipt. The normal range for T. whipplei is 0 MPM based on a cohort of 684 healthy individuals. Blood PCR for T. whipplei was confirmatory. Table 1: Clinical Parameters of Case Conclusion NGS for mcfDNA in plasma offers a rapid, non-invasive method for identifying T. whipplei and, to our knowledge, the first diagnosis of Whipple disease using NGS of plasma mcfDNA. Disclosures Christiaan R. de Vries, MD, PhD, Karius (Consultant, Independent Contractor)Stanford University (Employee) Ann Macintyre, DO, Karius (Employee)

scholarly journals 2139. Rickettsia typhi Detection in Clinical Infections by the Karius Test, a Plasma Microbial Cell-free DNA Next-Generation Sequencing Test

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S725-S725
Author(s):  
Fernando H Centeno ◽  
Asim A Ahmed ◽  
David K Hong ◽  
Sudeb Dalai ◽  
Laila Woc-Colburn
Keyword(s):  
Next Generation Sequencing ◽  
Medical Center ◽  
Severe Disease ◽  
Laboratory Data ◽  
Microbial Cell ◽  
Next Generation ◽  
Rickettsia Typhi ◽  
Cell Free Dna ◽  
Free Dna ◽  
Generation Sequencing

Abstract Background Rickettsia typhi typically causes a nonspecific syndrome characterized by fever, rash, and headache but can rarely progress to severe disease. R. typhi is transmitted by the rat flea and there has been an increased incidence in Houston, TX. Establishing the diagnosis can be challenging and is often made by serological studies. Prompt therapy with doxycycline is important especially in severe disease. Methods Karius Test results from the prior 2 years (Redwood City, CA) were reviewed for detections of R. typhi. The Karius Test 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 sequences are removed and remaining sequences are aligned to a curated pathogen database of >1,000 organisms. Organisms present above a statistical threshold are reported. Chart review was conducted on the cases of R. typhi identified by the Karius Test. Results The Karius Test detected R. typhi in 6 adult patients, 4 women and 2 men, from a medical center in Houston, TX. In 2 patients, R. typhi mcfDNA was present in the raw sequencing data but at an abundance below validated statistical thresholds. R. typhi mcfDNA was not found in negative controls run simultaneously with the samples. All patients presented with fever, 4 presented with headache, 3 presented with gastrointestinal symptoms, 3 developed rash, one presented with hypotension. Laboratory data were available for 5 patients. Four patients developed thrombocytopenia, 5 had anemia, 4 patients had WBC < 5, 4 had transaminase elevation and 3 developed hyponatremia. 3 out of 5 had R. typhi serologies sent; all 3 were positive (including two of the patients with R. typhi mcfDNA levels below threshold). In the two other patients the Karius test was the means of establishing the diagnosis. 3 out of 5 patients where data were available were treated with doxycyline. Conclusion The Karius test was able to detect R. typhi in a cluster of 6 patients in one medical center in Houston, TX. NGS for mcfDNA offers a rapid means of detecting R. typhi infection. Accurate, rapid diagnosis of R. typhi has important public health implications given its vector-borne mechanism of transmission. Disclosures All authors: No reported disclosures.

scholarly journals COMP-20. THE NON-INVASIVE DETECTION OF GLIOBLASTOMA-DERIVED CELL-FREE DNA IN PLASMA USING NEXT-GENERATION SEQUENCING AND AN UNTARGETED VARIANT SEARCH

2018 ◽  
Vol 20 (suppl_6) ◽  
pp. vi67-vi68
Author(s):  
Hunter Underhill ◽  
Sabine Hellwig ◽  
David Nix ◽  
Preetida Bhetariya ◽  
Carrie Fuertes ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Cell Free Dna ◽  
Non Invasive ◽  
Free Dna ◽  
Generation Sequencing
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