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Park SY, Lindner MS, Brick K, Noll N, Ounit R, Noa LJ, Sabzwari R, Trible R, Sniffen JC, Roth P, Khan A, Rodriguez A, Sahra S, Davis MJ, Brar IS, Balasundaram G, Nolte FS, Blauwkamp TA, Perkins BA, Bercovici S. Detection of Mpox Virus Using Microbial Cell-Free DNA: The Potential of Pathogen-Agnostic Sequencing for Rapid Identification of Emerging Pathogens. J Infect Dis 2024; 229:S144-S155. [PMID: 37824825 DOI: 10.1093/infdis/jiad452] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND The 2022 global outbreak of Monkeypox virus (MPXV) highlighted challenges with polymerase chain reaction detection as divergent strains emerged and atypical presentations limited the applicability of swab sampling. Recommended testing in the United States requires a swab of lesions, which arise late in infection and may be unrecognized. We present MPXV detections using plasma microbial cell-free DNA (mcfDNA) sequencing. METHODS Fifteen plasma samples from 12 case-patients were characterized through mcfDNA sequencing. Assay performance was confirmed through in silico inclusivity and exclusivity assessments. MPXV isolates were genotyped using mcfDNA, and phylodynamic information was imputed using publicly available sequences. RESULTS MPXV mcfDNA was detected in 12 case-patients. Mpox was not suspected in 5, with 1 having documented resolution of mpox >6 months previously. Six had moderate to severe mpox, supported by high MPXV mcfDNA concentrations; 4 died. In 7 case-patients, mcfDNA sequencing detected coinfections. Genotyping by mcfDNA sequencing identified 22 MPXV mutations at 10 genomic loci in 9 case-patients. Consistent with variation observed in the 2022 outbreak, 21 of 22 variants were G > A/C > T. Phylogenetic analyses imputed isolates to sublineages arising at different time points and from different geographic locations. CONCLUSIONS We demonstrate the potential of plasma mcfDNA sequencing to detect, quantify, and, for acute infections with high sequencing coverage, subtype MPXV using a single noninvasive test. Sequencing plasma mcfDNA may augment existing mpox testing in vulnerable patient populations or in patients with atypical symptoms or unrecognized mpox. Strain type information may supplement disease surveillance and facilitate tracking emerging pathogens.
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Affiliation(s)
- Sarah Y Park
- Medical Affairs, Karius, Inc, Redwood City, California
| | | | - Kevin Brick
- Analytics, Karius, Inc., Redwood City, California
| | | | - Rachid Ounit
- Analytics, Karius, Inc., Redwood City, California
| | - Luis J Noa
- Infectious Disease Section, AdventHealth Orlando, Florida
| | - Rabeeya Sabzwari
- Infectious Diseases, Edward Hines Jr Veterans Affairs Hospital, Hines, Illinois
| | | | | | - Prerana Roth
- Infectious Diseases, Prisma Health-Upstate, Greenville, South Carolina
| | - Amir Khan
- Infectious Diseases, Carle Foundation Hospital, Urbana, Illinois
| | | | - Syeda Sahra
- Department of Infectious Diseases, Oklahoma University Medical Center, Oklahoma City
| | - Michael J Davis
- Department of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, MN
| | - Inderjeet S Brar
- Infectious Diseases, Baptist Memorial Health Care, Memphis, Tennessee
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Park SY, Chang EJ, Ledeboer N, Messacar K, Lindner MS, Venkatasubrahmanyam S, Wilber JC, Vaughn ML, Bercovici S, Perkins BA, Nolte FS. Plasma Microbial Cell-Free DNA Sequencing from over 15,000 Patients Identified a Broad Spectrum of Pathogens. J Clin Microbiol 2023; 61:e0185522. [PMID: 37439686 PMCID: PMC10446866 DOI: 10.1128/jcm.01855-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/23/2023] [Indexed: 07/14/2023] Open
Abstract
Microbial cell-free DNA (mcfDNA) sequencing is an emerging infectious disease diagnostic tool which enables unbiased pathogen detection and quantification from plasma. The Karius Test, a commercial mcfDNA sequencing assay developed by and available since 2017 from Karius, Inc. (Redwood City, CA), detects and quantifies mcfDNA as molecules/μL in plasma. The commercial sample data and results for all tests conducted from April 2018 through mid-September 2021 were evaluated for laboratory quality metrics, reported pathogens, and data from test requisition forms. A total of 18,690 reports were generated from 15,165 patients in a hospital setting among 39 states and the District of Columbia. The median time from sample receipt to reported result was 26 h (interquartile range [IQR] 25 to 28), and 96% of samples had valid test results. Almost two-thirds (65%) of patients were adults, and 29% at the time of diagnostic testing had ICD-10 codes representing a diverse array of clinical scenarios. There were 10,752 (58%) reports that yielded at least one taxon for a total of 22,792 detections spanning 701 unique microbial taxa. The 50 most common taxa detected included 36 bacteria, 9 viruses, and 5 fungi. Opportunistic fungi (374 Aspergillus spp., 258 Pneumocystis jirovecii, 196 Mucorales, and 33 dematiaceous fungi) comprised 861 (4%) of all detections. Additional diagnostically challenging pathogens (247 zoonotic and vector-borne pathogens, 144 Mycobacterium spp., 80 Legionella spp., 78 systemic dimorphic fungi, 69 Nocardia spp., and 57 protozoan parasites) comprised 675 (3%) of all detections. This is the largest reported cohort of patients tested using plasma mcfDNA sequencing and represents the first report of a clinical grade metagenomic test performed at scale. Data reveal new insights into the breadth and complexity of potential pathogens identified.
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Affiliation(s)
| | | | | | - Kevin Messacar
- University of Colorado, Children’s Hospital Colorado, Aurora, Colorado, USA
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3
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Smollin M, Lindner MS, Degner NR, Castillo-Galvan R, Alexander J, de Vries CR, Macintyre A, Perkins B, Ahmed AA, Arun A. 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. Open Forum Infect Dis 2021. [PMCID: PMC8644366 DOI: 10.1093/ofid/ofab466.860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
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)
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4
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Kalyatanda G, Rand K, Lindner MS, Hong DK, Sait Albayram M, Gregory J, Kresak J, Ibne KMA, Cope JR, Roy S, Gary JM, Reddy V, Ahmed AA. Rapid, Noninvasive Diagnosis of Balamuthia mandrillaris Encephalitis by a Plasma-Based Next-Generation Sequencing Test. Open Forum Infect Dis 2020; 7:ofaa189. [PMID: 32715017 PMCID: PMC7371414 DOI: 10.1093/ofid/ofaa189] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 05/26/2020] [Indexed: 12/19/2022] Open
Abstract
Granulomatous amoebic encephalitis (GAE) caused by Balamuthia mandrillaris is a rare subacute infection with exceptionally high mortality. Diagnosis is typically made by brain biopsy or at autopsy. Detection of Balamuthia mandrillaris cell-free DNA by next-generation sequencing of plasma enabled rapid, noninvasive diagnosis in a case of amoebic encephalitis.
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Affiliation(s)
- Gautam Kalyatanda
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Kenneth Rand
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA.,Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | | | | | - Mehmet Sait Albayram
- Department of Radiology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Jason Gregory
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Jesse Kresak
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Karim M Ali Ibne
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jennifer R Cope
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Shantanu Roy
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Joy M Gary
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Varalakshmi Reddy
- Department of Neurology, University of Florida College of Medicine, Gainesville, Florida, USA
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5
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Camargo JF, Ahmed AA, Lindner MS, Morris MI, Anjan S, Anderson AD, Prado CE, Dalai SC, Martinez OV, Komanduri KV. Next-generation sequencing of microbial cell-free DNA for rapid noninvasive diagnosis of infectious diseases in immunocompromised hosts. F1000Res 2019; 8:1194. [PMID: 31814964 PMCID: PMC6883395 DOI: 10.12688/f1000research.19766.3] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/19/2019] [Indexed: 12/23/2022] Open
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.
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Affiliation(s)
- Jose F. Camargo
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | | | - Michele I. Morris
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Shweta Anjan
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Anthony D. Anderson
- Department of Pharmacy, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL, 33136, USA
| | - Clara E. Prado
- Department of Microbiology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | - Octavio V. Martinez
- Department of Microbiology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Krishna V. Komanduri
- Division of Hematology Oncology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
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6
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Camargo JF, Ahmed AA, Lindner MS, Morris MI, Anjan S, Anderson AD, Prado CE, Dalai SC, Martinez OV, Komanduri KV. Next-generation sequencing of microbial cell-free DNA for rapid noninvasive diagnosis of infectious diseases in immunocompromised hosts. F1000Res 2019; 8:1194. [PMID: 31814964 PMCID: PMC6883395 DOI: 10.12688/f1000research.19766.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/12/2019] [Indexed: 03/28/2024] Open
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. Methods: Here we report our experience 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: Among five hematological malignancy patients, for whom a microbiological diagnosis was established, pathogen identification by cfDNA NGS demonstrated 100% positive agreement with conventional diagnostic laboratory methods. Further, cfDNA identified the etiological agent in two patients with culture negative sepsis who had undergone hematopoietic stem cell transplant. Conclusion: These data 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.
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Affiliation(s)
- Jose F. Camargo
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | | | - Michele I. Morris
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Shweta Anjan
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Anthony D. Anderson
- Department of Pharmacy, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL, 33136, USA
| | - Clara E. Prado
- Department of Microbiology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | - Octavio V. Martinez
- Department of Microbiology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Krishna V. Komanduri
- Division of Hematology Oncology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
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7
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Camargo JF, Ahmed AA, Lindner MS, Morris MI, Anjan S, Anderson AD, Prado CE, Dalai SC, Martinez OV, Komanduri KV. Next-generation sequencing of microbial cell-free DNA for rapid noninvasive diagnosis of infectious diseases in immunocompromised hosts. F1000Res 2019; 8:1194. [PMID: 31814964 PMCID: PMC6883395 DOI: 10.12688/f1000research.19766.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/03/2020] [Indexed: 11/12/2023] Open
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.
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Affiliation(s)
- Jose F. Camargo
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | | | - Michele I. Morris
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Shweta Anjan
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Anthony D. Anderson
- Department of Pharmacy, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL, 33136, USA
| | - Clara E. Prado
- Department of Microbiology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | - Octavio V. Martinez
- Department of Microbiology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Krishna V. Komanduri
- Division of Hematology Oncology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
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8
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Camargo JF, Ahmed AA, Lindner MS, Morris MI, Anjan S, Anderson AD, Prado CE, Dalai SC, Martinez OV, Komanduri KV. Next-generation sequencing of microbial cell-free DNA for rapid noninvasive diagnosis of infectious diseases in immunocompromised hosts. F1000Res 2019; 8:1194. [PMID: 31814964 PMCID: PMC6883395 DOI: 10.12688/f1000research.19766.4] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/03/2020] [Indexed: 12/14/2022] Open
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.
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Affiliation(s)
- Jose F Camargo
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | | | - Michele I Morris
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Shweta Anjan
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Anthony D Anderson
- Department of Pharmacy, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL, 33136, USA
| | - Clara E Prado
- Department of Microbiology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | - Octavio V Martinez
- Department of Microbiology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Krishna V Komanduri
- Division of Hematology Oncology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
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Tausch SH, Strauch B, Andrusch A, Loka TP, Lindner MS, Nitsche A, Renard BY. LiveKraken––real-time metagenomic classification of illumina data. Bioinformatics 2018; 34:3750-3752. [DOI: 10.1093/bioinformatics/bty433] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/30/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Simon H Tausch
- Bioinformatics Unit (MF1)
- Centre for Biological Threats and Special Pathogens (ZBS1), Robert Koch Institute, Berlin, Germany
| | | | - Andreas Andrusch
- Bioinformatics Unit (MF1)
- Centre for Biological Threats and Special Pathogens (ZBS1), Robert Koch Institute, Berlin, Germany
| | | | | | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens (ZBS1), Robert Koch Institute, Berlin, Germany
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10
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Lindner MS, Strauch B, Schulze JM, Tausch SH, Dabrowski PW, Nitsche A, Renard BY. HiLive: real-time mapping of illumina reads while sequencing. Bioinformatics 2017; 33:917-319. [PMID: 27794555 DOI: 10.1093/bioinformatics/btw659] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 10/19/2016] [Indexed: 11/13/2022] Open
Abstract
Motivation Next Generation Sequencing is increasingly used in time critical, clinical applications. While read mapping algorithms have always been optimized for speed, they follow a sequential paradigm and only start after finishing of the sequencing run and conversion of files. Since Illumina machines write intermediate output results, HiLive performs read mapping while still sequencing and thereby drastically reduces crucial overall sample analysis time, e.g. in precision medicine. Methods We present HiLive as a novel real time read mapper that implements a k-mer based alignment strategy. HiLive continuously reads intermediate BCL files produced by Illumina sequencers and then extends initial k-mer matches by increasingly produced data from the sequencer. Results We applied HiLive on real human transcriptome data to show that final read alignments are reported within few minutes after the end of a full Illumina HiSeq 1500 run, while already the necessary conversion to FASTQ files as the standard input to current read mapping methods takes roughly five times as long. Further, we show on simulated and real data that HiLive has comparable accuracy to recent read mappers. Availability and Implementation HiLive and its source code are freely available from https://gitlab.com/SimonHTausch/HiLive . Contact renardB@rki.de. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Martin S Lindner
- Research Group Bioinformatics (NG 4), Robert Koch Institute, Berlin, Germany
| | - Benjamin Strauch
- Research Group Bioinformatics (NG 4), Robert Koch Institute, Berlin, Germany
| | - Jakob M Schulze
- Research Group Bioinformatics (NG 4), Robert Koch Institute, Berlin, Germany
| | - Simon H Tausch
- Research Group Bioinformatics (NG 4), Robert Koch Institute, Berlin, Germany.,Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Piotr W Dabrowski
- Research Group Bioinformatics (NG 4), Robert Koch Institute, Berlin, Germany.,Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Bernhard Y Renard
- Research Group Bioinformatics (NG 4), Robert Koch Institute, Berlin, Germany
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Abstract
MOTIVATION Species identification and quantification are common tasks in metagenomics and pathogen detection studies. The most recent techniques are built on mapping the sequenced reads against a reference database (e.g. whole genomes, marker genes, proteins) followed by application-dependent analysis steps. Although these methods have been proven to be useful in many scenarios, there is still room for improvement in species and strain level detection, mainly for low abundant organisms. RESULTS We propose a new method: DUDes, a reference-based taxonomic profiler that introduces a novel top-down approach to analyze metagenomic Next-generation sequencing (NGS) samples. Rather than predicting an organism presence in the sample based only on relative abundances, DUDes first identifies possible candidates by comparing the strength of the read mapping in each node of the taxonomic tree in an iterative manner. Instead of using the lowest common ancestor we propose a new approach: the deepest uncommon descendent. We showed in experiments that DUDes works for single and multiple organisms and can identify low abundant taxonomic groups with high precision. AVAILABILITY AND IMPLEMENTATION DUDes is open source and it is available at http://sf.net/p/dudes SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. CONTACT renardB@rki.de.
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Affiliation(s)
- Vitor C Piro
- Research Group Bioinformatics (NG4), Robert Koch Institute, Nordufer 20, Berlin 13353, Germany CAPES Foundation, Ministry of Education of Brazil, Brasília - DF, 70040-020 Brazil
| | - Martin S Lindner
- Research Group Bioinformatics (NG4), Robert Koch Institute, Nordufer 20, Berlin 13353, Germany 4-Antibody AG, Hochberger Strasse 60C, Basel 4057, Switzerland
| | - Bernhard Y Renard
- Research Group Bioinformatics (NG4), Robert Koch Institute, Nordufer 20, Berlin 13353, Germany
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12
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Abstract
Microbial community profiling identifies and quantifies organisms in metagenomic sequencing data using either reference based or unsupervised approaches. However, current reference based profiling methods only report the presence and abundance of single reference genomes that are available in databases. Since only a small fraction of environmental genomes is represented in genomic databases, these approaches entail the risk of false identifications and often suggest a higher precision than justified by the data. Therefore, we developed MicrobeGPS, a novel metagenomic profiling approach that overcomes these limitations. MicrobeGPS is the first method that identifies microbiota in the sample and estimates their genomic distances to known reference genomes. With this strategy, MicrobeGPS identifies organisms down to the strain level and highlights possibly inaccurate identifications when the correct reference genome is missing. We demonstrate on three metagenomic datasets with different origin that our approach successfully avoids misleading interpretation of results and additionally provides more accurate results than current profiling methods. Our results indicate that MicrobeGPS can enable reference based taxonomic profiling of complex and less characterized microbial communities. MicrobeGPS is open source and available from https://sourceforge.net/projects/microbegps/ as source code and binary distribution for Windows and Linux operating systems.
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Affiliation(s)
- Martin S. Lindner
- Research Group Bioinformatics (NG4), Robert Koch Institute, Berlin, Germany
| | - Bernhard Y. Renard
- Research Group Bioinformatics (NG4), Robert Koch Institute, Berlin, Germany
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Penzlin A, Lindner MS, Doellinger J, Dabrowski PW, Nitsche A, Renard BY. Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics. ACTA ACUST UNITED AC 2014; 30:i149-56. [PMID: 24931978 PMCID: PMC4058918 DOI: 10.1093/bioinformatics/btu267] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
MOTIVATION Metaproteomic analysis allows studying the interplay of organisms or functional groups and has become increasingly popular also for diagnostic purposes. However, difficulties arise owing to the high sequence similarity between related organisms. Further, the state of conservation of proteins between species can be correlated with their expression level, which can lead to significant bias in results and interpretation. These challenges are similar but not identical to the challenges arising in the analysis of metagenomic samples and require specific solutions. RESULTS We introduce Pipasic (peptide intensity-weighted proteome abundance similarity correction) as a tool that corrects identification and spectral counting-based quantification results using peptide similarity estimation and expression level weighting within a non-negative lasso framework. Pipasic has distinct advantages over approaches only regarding unique peptides or aggregating results to the lowest common ancestor, as demonstrated on examples of viral diagnostics and an acid mine drainage dataset. AVAILABILITY AND IMPLEMENTATION Pipasic source code is freely available from https://sourceforge.net/projects/pipasic/. CONTACT RenardB@rki.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anke Penzlin
- Research Group Bioinformatics (NG4), Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Centre for Biological Threats and Special Pathogens 6 (ZBS 6) and Central Administration 4 (IT), Robert Koch Institute, 13353 Berlin, Germany
| | - Martin S Lindner
- Research Group Bioinformatics (NG4), Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Centre for Biological Threats and Special Pathogens 6 (ZBS 6) and Central Administration 4 (IT), Robert Koch Institute, 13353 Berlin, Germany
| | - Joerg Doellinger
- Research Group Bioinformatics (NG4), Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Centre for Biological Threats and Special Pathogens 6 (ZBS 6) and Central Administration 4 (IT), Robert Koch Institute, 13353 Berlin, GermanyResearch Group Bioinformatics (NG4), Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Centre for Biological Threats and Special Pathogens 6 (ZBS 6) and Central Administration 4 (IT), Robert Koch Institute, 13353 Berlin, Germany
| | - Piotr Wojtek Dabrowski
- Research Group Bioinformatics (NG4), Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Centre for Biological Threats and Special Pathogens 6 (ZBS 6) and Central Administration 4 (IT), Robert Koch Institute, 13353 Berlin, GermanyResearch Group Bioinformatics (NG4), Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Centre for Biological Threats and Special Pathogens 6 (ZBS 6) and Central Administration 4 (IT), Robert Koch Institute, 13353 Berlin, Germany
| | - Andreas Nitsche
- Research Group Bioinformatics (NG4), Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Centre for Biological Threats and Special Pathogens 6 (ZBS 6) and Central Administration 4 (IT), Robert Koch Institute, 13353 Berlin, Germany
| | - Bernhard Y Renard
- Research Group Bioinformatics (NG4), Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Centre for Biological Threats and Special Pathogens 6 (ZBS 6) and Central Administration 4 (IT), Robert Koch Institute, 13353 Berlin, Germany
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Abstract
MOTIVATION The reliable identification of genes is a major challenge in genome research, as further analysis depends on the correctness of this initial step. With high-throughput RNA-Seq data reflecting currently expressed genes, a particularly meaningful source of information has become commonly available for gene finding. However, practical application in automated gene identification is still not the standard case. A particular challenge in including RNA-Seq data is the difficult handling of ambiguously mapped reads. RESULTS We present GIIRA (Gene Identification Incorporating RNA-Seq data and Ambiguous reads), a novel prokaryotic and eukaryotic gene finder that is exclusively based on a RNA-Seq mapping and inherently includes ambiguously mapped reads. GIIRA extracts candidate regions supported by a sufficient number of mappings and reassigns ambiguous reads to their most likely origin using a maximum-flow approach. This avoids the exclusion of genes that are predominantly supported by ambiguous mappings. Evaluation on simulated and real data and comparison with existing methods incorporating RNA-Seq information highlight the accuracy of GIIRA in identifying the expressed genes. AVAILABILITY AND IMPLEMENTATION GIIRA is implemented in Java and is available from https://sourceforge.net/projects/giira/.
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Affiliation(s)
- Franziska Zickmann
- Research Group Bioinformatics (NG4), Robert Koch-Institute, Nordufer 20, 13353 Berlin, Germany
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Lindner MS, Kollock M, Zickmann F, Renard BY. Analyzing genome coverage profiles with applications to quality control in metagenomics. Bioinformatics 2013; 29:1260-7. [DOI: 10.1093/bioinformatics/btt147] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
One goal of sequencing-based metagenomic community analysis is the quantitative taxonomic assessment of microbial community compositions. In particular, relative quantification of taxons is of high relevance for metagenomic diagnostics or microbial community comparison. However, the majority of existing approaches quantify at low resolution (e.g. at phylum level), rely on the existence of special genes (e.g. 16S), or have severe problems discerning species with highly similar genome sequences. Yet, problems as metagenomic diagnostics require accurate quantification on species level. We developed Genome Abundance Similarity Correction (GASiC), a method to estimate true genome abundances via read alignment by considering reference genome similarities in a non-negative LASSO approach. We demonstrate GASiC’s superior performance over existing methods on simulated benchmark data as well as on real data. In addition, we present applications to datasets of both bacterial DNA and viral RNA source. We further discuss our approach as an alternative to PCR-based DNA quantification.
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Affiliation(s)
- Martin S Lindner
- Research Group Bioinformatics, NG4, Robert Koch-Institut, Nordufer 20, 13353 Berlin, Germany
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Voss B, Hanselmann M, Renard BY, Lindner MS, Köthe U, Kirchner M, Hamprecht FA. SIMA: simultaneous multiple alignment of LC/MS peak lists. ACTA ACUST UNITED AC 2011; 27:987-93. [PMID: 21296750 DOI: 10.1093/bioinformatics/btr051] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION Alignment of multiple liquid chromatography/mass spectrometry (LC/MS) experiments is a necessity today, which arises from the need for biological and technical repeats. Due to limits in sampling frequency and poor reproducibility of retention times, current LC systems suffer from missing observations and non-linear distortions of the retention times across runs. Existing approaches for peak correspondence estimation focus almost exclusively on solving the pairwise alignment problem, yielding straightforward but suboptimal results for multiple alignment problems. RESULTS We propose SIMA, a novel automated procedure for alignment of peak lists from multiple LC/MS runs. SIMA combines hierarchical pairwise correspondence estimation with simultaneous alignment and global retention time correction. It employs a tailored multidimensional kernel function and a procedure based on maximum likelihood estimation to find the retention time distortion function that best fits the observed data. SIMA does not require a dedicated reference spectrum, is robust with regard to outliers, needs only two intuitive parameters and naturally incorporates incomplete correspondence information. In a comparison with seven alternative methods on four different datasets, we show that SIMA yields competitive and superior performance on real-world data. AVAILABILITY A C++ implementation of the SIMA algorithm is available from http://hci.iwr.uni-heidelberg.de/MIP/Software.
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Affiliation(s)
- Björn Voss
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany
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Abstract
AIM Chronic radial epicondylitis (tennis elbow) is not a serious disease but patients may suffer greatly. If standard conservative and possibly operative treatment modalities have not been effective, patients need further therapy. First trials with injection of Botulinum toxin A (Btx A) have shown promising results. The purpose of the study was to clarify if a single injection of Btx A could be an efficient therapy for chronic radial epicondylitis. METHODS In this study 16 patients received injections into the forearm extensors. The site of injection was determined by local tenderness and pain provocation on finger and wrist extension. RESULTS A significant clinical improvement was already seen at 2 weeks following injection. The effect was noted up to the last follow-up at 2 years. Continuous and maximal pain during the last 48 h, as self-assessed on a visual analogue scale, was also significantly reduced. In a few cases a significant decrease of muscle strength was seen for the third finger two weeks after injection. It slowly returned thereafter. CONCLUSION A single injection of Btx A was effective as therapy for chronic tennis elbow. It can be carried out in an out-patient setting, and allows the patient to continue working.
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Affiliation(s)
- R Placzek
- Klinik und Poliklinik für Orthopädie, Universitätsklinikum Hamburg-Eppendorf.
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