1
|
Marra AR, Lopes GOV, Pardo I, Hsieh MK, Kobayashi T, Marra PS, Marschall J, Pinho JRR, Amgarten DE, de Mello Malta F, Dos Santos NV, Edmond MB. Metagenomic next-generation sequencing in patients with fever of unknown origin: A comprehensive systematic literature review and meta-analysis. Diagn Microbiol Infect Dis 2024; 110:116465. [PMID: 39059148 DOI: 10.1016/j.diagmicrobio.2024.116465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/22/2024] [Accepted: 07/22/2024] [Indexed: 07/28/2024]
Abstract
Metagenomic Next-Generation Sequencing (mNGS) holds promise in diagnosing fever of unknown origin (FUO) by detecting diverse pathogens. We systematically reviewed the literature to evaluate mNGS's accuracy, clinical efficacy, and limitations in FUO diagnosis. Nine studies revealed mNGS's positivity rate ranging from 66.7% to 93.5% for bacterial bloodstream infections and systemic infections. Meta-analysis of three studies involving 857 patients, including 354 with FUO, showed a sensitivity of 0.91 (95% CI: 0.87-0.93) and specificity of 0.64 (95% CI: 0.58-0.70). Despite lower specificity, mNGS demonstrated a higher Diagnostic Odds Ratio (DOR) of 17.0 (95% CI: 4.5-63.4) compared to conventional microbiological tests (CMTs) at 4.7 (95% CI: 2.9-7.6). While mNGS offers high sensitivity but low specificity in identifying causative pathogens for FUO, its superior DOR suggests potential for more accurate diagnoses and targeted interventions. Further research is warranted to optimize its clinical application in FUO management.
Collapse
Affiliation(s)
- Alexandre R Marra
- Faculdade Israelita de Ciências da Saúde Albert Einstein, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil; Department of Internal Medicine, University of Iowa Carver College of Medicine, C51 GH - 200 Hawkins Drive, Iowa City, IA 52242, United States.
| | - Gabriel O V Lopes
- Faculdade Israelita de Ciências da Saúde Albert Einstein, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Isabele Pardo
- Faculdade Israelita de Ciências da Saúde Albert Einstein, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Mariana Kim Hsieh
- Program of Hospital Epidemiology, University of Iowa Hospitals and Clinics, Iowa City, Iowa, United States
| | - Takaaki Kobayashi
- Department of Internal Medicine, University of Iowa Carver College of Medicine, C51 GH - 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - Pedro S Marra
- University of California, San Francisco School of Medicine, San Francisco, CA, United States
| | - Jonas Marschall
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - João Renato Rebello Pinho
- Faculdade Israelita de Ciências da Saúde Albert Einstein, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil; LIM03/07, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil
| | - Deyvid Emanuel Amgarten
- Faculdade Israelita de Ciências da Saúde Albert Einstein, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Fernanda de Mello Malta
- Faculdade Israelita de Ciências da Saúde Albert Einstein, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Nathalia Villa Dos Santos
- Faculdade Israelita de Ciências da Saúde Albert Einstein, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Michael B Edmond
- Department of Medicine, West Virginia University School of Medicine, Morgantown, WV, United States
| |
Collapse
|
2
|
Liborio MP, Harris PNA, Ravi C, Irwin AD. Getting Up to Speed: Rapid Pathogen and Antimicrobial Resistance Diagnostics in Sepsis. Microorganisms 2024; 12:1824. [PMID: 39338498 PMCID: PMC11434042 DOI: 10.3390/microorganisms12091824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 08/26/2024] [Accepted: 08/27/2024] [Indexed: 09/30/2024] Open
Abstract
Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection. Time to receive effective therapy is a primary determinant of mortality in patients with sepsis. Blood culture is the reference standard for the microbiological diagnosis of bloodstream infections, despite its low sensitivity and prolonged time to receive a pathogen detection. In recent years, rapid tests for pathogen identification, antimicrobial susceptibility, and sepsis identification have emerged, both culture-based and culture-independent methods. This rapid narrative review presents currently commercially available approved diagnostic molecular technologies in bloodstream infections, including their clinical performance and impact on patient outcome, when available. Peer-reviewed publications relevant to the topic were searched through PubMed, and manufacturer websites of commercially available assays identified were also consulted as further sources of information. We have reviewed data about the following technologies for pathogen identification: fluorescence in situ hybridization with peptide nucleic acid probes (Accelerate PhenoTM), microarray-based assay (Verigene®), multiplex polymerase chain reaction (cobas® eplex, BioFire® FilmArray®, Molecular Mouse, Unyvero BCU SystemTM), matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (Rapid MBT Sepsityper®), T2 magnetic resonance (T2Bacteria Panel), and metagenomics-based assays (Karius©, DISQVER®, Day Zero Diagnostics). Technologies for antimicrobial susceptibility testing included the following: Alfed 60 ASTTM, VITEK® REVEALTM, dRASTTM, ASTar®, Fastinov®, QuickMIC®, ResistellTM, and LifeScale. Characteristics, microbiological performance, and issues of each method are described, as well as their clinical performance, when available.
Collapse
Affiliation(s)
- Mariana P. Liborio
- UQ Centre for Clinical Research, The University of Queensland, Herston, QLD 4029, Australia; (M.P.L.); (C.R.)
| | - Patrick N. A. Harris
- UQ Centre for Clinical Research, The University of Queensland, Herston, QLD 4029, Australia; (M.P.L.); (C.R.)
- Herston Infectious Disease Institute, Metro North, QLD Health, Herston, QLD 4029, Australia
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, QLD 4006, Australia
| | - Chitra Ravi
- UQ Centre for Clinical Research, The University of Queensland, Herston, QLD 4029, Australia; (M.P.L.); (C.R.)
| | - Adam D. Irwin
- UQ Centre for Clinical Research, The University of Queensland, Herston, QLD 4029, Australia; (M.P.L.); (C.R.)
- Infection Management and Prevention Service, Queensland Children’s Hospital, Brisbane, QLD 4101, Australia
| |
Collapse
|
3
|
Su LD, Chiu CY, Gaston D, Hogan CA, Miller S, Simon DW, Thakur KT, Yang S, Piantadosi A. Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Central Nervous System Infections: Advances and Challenges. Mol Diagn Ther 2024; 28:513-523. [PMID: 38992308 DOI: 10.1007/s40291-024-00727-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2024] [Indexed: 07/13/2024]
Abstract
Central nervous system (CNS) infections carry a substantial burden of morbidity and mortality worldwide, and accurate and timely diagnosis is required to optimize management. Metagenomic next-generation sequencing (mNGS) has proven to be a valuable tool in detecting pathogens in patients with suspected CNS infection. By sequencing microbial nucleic acids present in a patient's cerebrospinal fluid, brain tissue, or samples collected outside of the CNS, such as plasma, mNGS can detect a wide range of pathogens, including rare, unexpected, and/or fastidious organisms. Furthermore, its target-agnostic approach allows for the identification of both known and novel pathogens. This is particularly useful in cases where conventional diagnostic methods fail to provide an answer. In addition, mNGS can detect multiple microorganisms simultaneously, which is crucial in cases of mixed infections without a clear predominant pathogen. Overall, clinical mNGS testing can help expedite the diagnostic process for CNS infections, guide appropriate management decisions, and ultimately improve clinical outcomes. However, there are key challenges surrounding its use that need to be considered to fully leverage its clinical impact. For example, only a few specialized laboratories offer clinical mNGS due to the complexity of both the laboratory methods and analysis pipelines. Clinicians interpreting mNGS results must be aware of both false negatives-as mNGS is a direct detection modality and requires a sufficient amount of microbial nucleic acid to be present in the sample tested-and false positives-as mNGS detects environmental microbes and their nucleic acids, despite best practices to minimize contamination. Additionally, current costs and turnaround times limit broader implementation of clinical mNGS. Finally, there is uncertainty regarding the best practices for clinical utilization of mNGS, and further work is needed to define the optimal patient population(s), syndrome(s), and time of testing to implement clinical mNGS.
Collapse
Affiliation(s)
- LingHui David Su
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
| | - Charles Y Chiu
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Laboratory Medicine and Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - David Gaston
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Catherine A Hogan
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steve Miller
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Delve Bio, Inc., San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Dennis W Simon
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pediatric Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kiran T Thakur
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Neurology, Columbia University Irving Medical Center-New York Presbyterian Hospital, New York, NY, USA
| | - Shangxin Yang
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anne Piantadosi
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA.
- Department of Pathology and Laboratory Medicine, and Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 101 Woodruff Circle, Atlanta, GA, USA.
| |
Collapse
|
4
|
Christians FC, Akhund-Zade J, Jarman K, Venkatasubrahmanyam S, Noll N, Blauwkamp TA, Bercovici S, Zielinska A, Carr AL, Craney A, Pike M, Farrell JJ, Dadwal S, Wood JB, Matkovich E, McAdams S, Nolte FS. Analytical and clinical validation of direct detection of antimicrobial resistance markers by plasma microbial cell-free DNA sequencing. J Clin Microbiol 2024:e0042524. [PMID: 39194269 DOI: 10.1128/jcm.00425-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
Sequencing of plasma microbial cell-free DNA (mcfDNA) has gained increased acceptance as a valuable adjunct to standard-of-care testing for diagnosis of infections throughout the body. Here, we report the analytical and clinical validation of a novel application of mcfDNA sequencing, the non-invasive detection of seven common antimicrobial resistance (AMR) genetic markers in 18 important pathogens. The AMR markers include SCCmec, mecA, mecC, vanA, vanB, blaCTX-M, and blaKPC. The AMR markers were computationally linked to the pathogens detected. Analytical validation showed high reproducibility (100%), inclusivity (54 to 100%), and exclusivity (100%). Clinical accuracy was assessed with 114 unique plasma samples from patients at seven study sites with concordant culture results for target bacteria from a variety of specimen types and correlated with available phenotypic antimicrobial susceptibility test results and genotypic results. The positive percent agreement (PPA), negative percent agreement (NPA), and diagnostic yield (DY) were estimated for each AMR marker. DY was defined as the percentage of tests that yielded an actionable result of either detected or not detected. The results for the combination of SCCmec and mecA for staphylococci were PPA 19/20 (95.0%), NPA 21/22 (95.4%), DY 42/60 (70.0%); vanA for enterococci were PPA 3/3 (100%), NPA 2/2 (100%), DY 5/6 (83.3%); blaCTX-M for gram-negative bacilli were PPA 5/6 (83.3%), NPA 29/29 (100%), DY 35/49 (71.4%); and blaKPC for gram-negative bacilli were PPA 0/2 (0%), NPA: 23/23 (100%), DY 25/44 (56.8%). The addition of AMR capability to plasma mcfDNA sequencing should provide clinicians with an effective new culture-independent tool for optimization of therapy. IMPORTANCE This manuscript is ideally suited for the Innovative Diagnostic Methods sections as it reports the analytical and clinical validation of a novel application of plasma microbial cell-free DNA sequencing for direct detection of seven selected antimicrobial resistance markers in 18 target pathogens. Clearly, it has potential clinical utility in optimizing therapy and was incorporated into the Karius test workflow in September 2023. In addition, the workflow could readily be adapted to expand the number of target bacteria and antimicrobial resistance markers as needed.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Amy L Carr
- AdventHealth Orlando, Orlando, Florida, USA
| | | | - Matthew Pike
- Carle Foundation Hospital, Urbana, Illinois, USA
| | | | - Sanjeet Dadwal
- City of Hope National Medical Center, Duarte, California, USA
| | - James B Wood
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | | | | | | |
Collapse
|
5
|
Madut DB, Chemaly RF, Dadwal SS, Hill JA, Lee YJ, Haidar G, Luk A, Drelick A, Chin-Hong PV, Benamu E, Khawaja F, Nanayakkara D, Papanicolaou GA, Small CB, Fung M, Barron M, Davis T, McClain MT, Maziarz EK, Bedoya AD, Gilstrap DL, Todd JL, Barkauskas CE, Heldman MR, Bigelow R, Leimberger JD, Tsalik EL, Wolf O, Mughar M, Lau C, Noll N, Hollemon D, Duttagupta R, Lupu DS, Bercovici S, Perkins BA, Blauwkamp TA, Fowler VG, Holland TL, Bergin SP. Clinical Utility of Plasma Microbial Cell-Free DNA Sequencing Among Immunocompromised Patients With Pneumonia. Open Forum Infect Dis 2024; 11:ofae425. [PMID: 39091643 PMCID: PMC11292041 DOI: 10.1093/ofid/ofae425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
Background Plasma microbial cell-free DNA (mcfDNA) sequencing can establish the etiology of multiple infectious syndromes by identifying microbial DNA in plasma. However, data are needed to define the clinical scenarios where this tool offers the highest clinical benefit. Methods We conducted a prospective multicenter observational study that evaluated the impact of plasma mcfDNA sequencing compared with usual care testing among adults with hematologic malignancies. This is a secondary analysis of an expanded cohort that evaluated the clinical utility of plasma mcfDNA sequencing across prespecified and adjudicated outcomes. We examined the percentage of participants for whom plasma mcfDNA sequencing identified a probable cause of pneumonia or clinically relevant nonpneumonia infection. We then assessed potential changes in antimicrobial therapy based on plasma mcfDNA sequencing results and the potential for early mcfDNA testing to avoid bronchoscopy and its associated adverse events. Results Of 223 participants, at least 1 microbial detection by plasma mcfDNA sequencing was adjudicated as a probable cause of pneumonia in 57 (25.6%) and a clinically relevant nonpneumonia infection in 88 (39.5%). A probable cause of pneumonia was exclusively identified by plasma mcfDNA sequencing in 23 (10.3%) participants. Antimicrobial therapy would have changed for 41 (18.4%) participants had plasma mcfDNA results been available in real time. Among the 57 participants with a probable cause of pneumonia identified by plasma mcfDNA sequencing, bronchoscopy identified no additional probable cause of pneumonia in 52 (91.2%). Conclusions Plasma mcfDNA sequencing could improve management of both pneumonia and other concurrent infections in immunocompromised patients with suspected pneumonia.
Collapse
Affiliation(s)
- Deng B Madut
- Duke University School of Medicine, Durham, North Carolina, USA
| | - Roy F Chemaly
- The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Joshua A Hill
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
- University of Washington School of Medicine, Seattle, Washington, USA
| | - Yeon Joo Lee
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medicine, New York, New York, USA
| | - Ghady Haidar
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Alfred Luk
- Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Alexander Drelick
- Weill Cornell Medicine, New York, New York, USA
- New York-Presbyterian Hospital, New York, New York, USA
| | - Peter V Chin-Hong
- University of California San Francisco, San Francisco, California, USA
| | | | - Fareed Khawaja
- The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Genovefa A Papanicolaou
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medicine, New York, New York, USA
| | - Catherine Butkus Small
- Weill Cornell Medicine, New York, New York, USA
- New York-Presbyterian Hospital, New York, New York, USA
| | - Monica Fung
- University of California San Francisco, San Francisco, California, USA
| | | | - Thomas Davis
- Indiana University School of Medicine, Indianapolis Indiana, USA
| | - Micah T McClain
- Duke University School of Medicine, Durham, North Carolina, USA
- Duke Clinical Research Institute, Durham, North Carolina, USA
| | | | | | | | - Jamie L Todd
- Duke University School of Medicine, Durham, North Carolina, USA
- Duke Clinical Research Institute, Durham, North Carolina, USA
| | | | | | - Robert Bigelow
- Duke Clinical Research Institute, Durham, North Carolina, USA
| | | | - Ephraim L Tsalik
- Duke University School of Medicine, Durham, North Carolina, USA
- Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
- Danaher Diagnostics, Washington, DC, USA
| | - Olivia Wolf
- Duke Clinical Research Institute, Durham, North Carolina, USA
| | | | | | | | | | | | | | | | | | | | - Vance G Fowler
- Duke University School of Medicine, Durham, North Carolina, USA
- Duke Clinical Research Institute, Durham, North Carolina, USA
| | - Thomas L Holland
- Duke University School of Medicine, Durham, North Carolina, USA
- Duke Clinical Research Institute, Durham, North Carolina, USA
| | - Stephen P Bergin
- Duke University School of Medicine, Durham, North Carolina, USA
- Duke Clinical Research Institute, Durham, North Carolina, USA
| |
Collapse
|
6
|
Petri F, Mahmoud OK, Ranganath N, El Zein S, Abu Saleh O, Berbari EF, Fida M. Plasma Microbial Cell-free DNA Next-generation Sequencing Can Be a Useful Diagnostic Tool in Patients With Osteoarticular Infections. Open Forum Infect Dis 2024; 11:ofae328. [PMID: 38989532 PMCID: PMC11234144 DOI: 10.1093/ofid/ofae328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/15/2024] [Indexed: 07/12/2024] Open
Abstract
Background Recent advances in shotgun metagenomic sequencing (sMGS) for detecting microbial cell-free DNA (mcfDNA) in peripheral blood have shown promise across various patient populations. This study evaluates the application of sMGS for diagnosing osteoarticular infections (OAIs), a condition with significant diagnostic challenges. Methods We conducted a retrospective analysis on 73 patients suspected of OAIs at the Mayo Clinic from 2019 to 2023, incorporating mcfDNA sMGS (Karius test [KT]) into their diagnostic evaluation. We categorized the clinical impact of KT on OAI diagnoses and management into 4 distinct outcomes. (1) KT was able to confirm an established diagnosis, (2) KT supported noninfectious diseases diagnosis, (3) KT established an unsuspected diagnosis, (4) KT did not add relevant information. Results In our cohort, KT was performed in 73 patients. Among the infected individuals, KT yielded positive results in 22 of 43 (51.2%) cases. Of these 22 cases, 11 (50%) showed agreement with conventional diagnostic workup, whereas in 5 (22.7%) cases, the KT established an unsuspected diagnosis. Native vertebral osteomyelitis diagnosis (P < .001) or OAIs with concomitant presence of endocarditis or endovascular infection (P = .005) were statistically associated with a definite, probable, or possible diagnostic certainty of KT result. Conclusions In complex OAIs, KT enhanced diagnostic accuracy by 11.6%, proving especially beneficial in diagnosing native vertebral osteomyelitis and infections with concurrent endocarditis or endovascular complications. Our findings underscore the utility of KT in the diagnostic workflow for challenging OAI cases, potentially altering clinical management for a significant subset of patients.
Collapse
Affiliation(s)
- Francesco Petri
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, Minnesota, USA
- Department of Infectious Diseases, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Milan, Italy
| | - Omar K Mahmoud
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, Minnesota, USA
| | - Nischal Ranganath
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, Minnesota, USA
| | - Said El Zein
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, Minnesota, USA
| | - Omar Abu Saleh
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, Minnesota, USA
| | - Elie F Berbari
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, Minnesota, USA
| | - Madiha Fida
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
7
|
Olthoff M, Kobayashi T, Parsons MG, Ford B, Prasidthrathsint K, Non L, Salinas JL, Diekema DJ, Ince D. Impact of metagenomic next-generation sequencing on clinical decision-making at an academic medical center, a retrospective study, Iowa, 2020-2022. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2024; 4:e39. [PMID: 38562514 PMCID: PMC10983051 DOI: 10.1017/ash.2024.31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 04/04/2024]
Abstract
We assessed the impact of metagenomic next-generation sequencing (mNGS) on patient care using previously established criteria. Among 37 patients receiving mNGS testing, 16% showed results that had a positive clinical impact. While mNGS results may offer valuable supplementary information, results should be interpreted within the broader clinical context and evaluation.
Collapse
Affiliation(s)
- Michael Olthoff
- Department of Internal Medicine, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Takaaki Kobayashi
- Department of Internal Medicine, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
- Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Meredith G. Parsons
- Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Bradley Ford
- Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Kunatum Prasidthrathsint
- Department of Internal Medicine, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
- Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Lemuel Non
- Department of Internal Medicine, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Jorge L. Salinas
- Department of Internal Medicine, Stanford University, Stanford, CA, USA
| | - Daniel J. Diekema
- Department of Internal Medicine, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
- Department of Medicine, Maine Medical Center, Portland, ME, USA
| | - Dilek Ince
- Department of Internal Medicine, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| |
Collapse
|
8
|
Gaston DC, Chiang AD, Dee K, Dulek D, Banerjee R, Humphries RM. Diagnostic Stewardship for Next-Generation Sequencing Assays in Clinical Microbiology: An Appeal for Thoughtful Collaboration. Clin Lab Med 2024; 44:63-73. [PMID: 38280798 DOI: 10.1016/j.cll.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Abstract
Next-generation sequencing (NGS)-based assays are primarily available from reference laboratories for diagnostic use. These tests can provide helpful diagnostic data but also can be overused by ordering providers not fully understanding their limitations. At present, there are few best practice guidelines for use. NGS-based assays can carry a high cost to institutions and individual patients, requiring thoughtful use through application of diagnostic stewardship principles. This article provides an overview of diagnostic stewardship approaches as applied to these assays, focusing on principles of collaboration, differential diagnosis formation, and seeking the best patient, syndrome, sample, timing, and test for improved patient care.
Collapse
Affiliation(s)
- David C Gaston
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 1301 Medical Center Drive TVC 4519, Nashville, TN 37232, USA.
| | - Augusto Dulanto Chiang
- Division of Infectious Diseases, Vanderbilt University Medical Center, 1211 21st Avenue South, Suite 102A, Nashville, TN 37232, USA
| | - Kevin Dee
- Division of Infectious Diseases, Vanderbilt University Medical Center, 1211 21st Avenue South, Suite 102A, Nashville, TN 37232, USA
| | - Daniel Dulek
- Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, 1161 21st Avenue South, Medical Center North D7234, Nashville, TN 37232, USA
| | - Ritu Banerjee
- Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, 1161 21st Avenue, Medical Center North D7227, Nashville, TN 37232, USA
| | - Romney M Humphries
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 1301 Medical Center Drive TVC 4519, Nashville, TN 37232, USA
| |
Collapse
|
9
|
Rodino KG, Simner PJ. Status check: next-generation sequencing for infectious-disease diagnostics. J Clin Invest 2024; 134:e178003. [PMID: 38357923 PMCID: PMC10866643 DOI: 10.1172/jci178003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Next-generation sequencing (NGS) applications for the diagnostics of infectious diseases has demonstrated great potential with three distinct approaches: whole-genome sequencing (WGS), targeted NGS (tNGS), and metagenomic NGS (mNGS, also known as clinical metagenomics). These approaches provide several advantages over traditional microbiologic methods, though challenges still exist.
Collapse
Affiliation(s)
- Kyle G. Rodino
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Patricia J. Simner
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
10
|
Duster N, Ramchandar N, Foley J, Farnaes L, Coufal NG. Application of cell-free plasma next-generation sequencing technology in the diagnosis and management of pediatric meningitis. J Microbiol Methods 2024; 217-218:106887. [PMID: 38169204 DOI: 10.1016/j.mimet.2023.106887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/05/2024]
Abstract
This retrospective study evaluates the clinical utility of CFPNGS in the diagnosis and management of pediatric meningitis. CFPNGS identified a causative pathogen in 36% of 28 subjects, compared to 50% for diverse conventional testing (57% combined). CFPNGS may be considered as an adjunct to standard testing.
Collapse
Affiliation(s)
- Nicole Duster
- University of California San Diego, Department of Pediatrics, San Diego, CA, USA; Rady Children's Hospital, San Diego, CA, USA
| | - Nanda Ramchandar
- University of California San Diego, Department of Pediatrics, San Diego, CA, USA; Rady Children's Hospital, San Diego, CA, USA; Naval Medical Center San Diego, San Diego, CA, USA
| | | | - Lauge Farnaes
- University of California San Diego, Department of Pediatrics, San Diego, CA, USA; Rady Children's Hospital, San Diego, CA, USA
| | - Nicole G Coufal
- University of California San Diego, Department of Pediatrics, San Diego, CA, USA; Rady Children's Hospital, San Diego, CA, USA.
| |
Collapse
|
11
|
Xu CH, Chen X, Zhu GQ, Yi HM, Chen SL, Liu T, Yu YT, Zhang QH, Jiang EL, Feng SZ. Diagnostic performance and clinical impacts of metagenomic sequencing after allogeneic hematopoietic stem cell transplantation. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2024; 57:11-19. [PMID: 38065767 DOI: 10.1016/j.jmii.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 10/10/2023] [Accepted: 11/17/2023] [Indexed: 02/12/2024]
Abstract
BACKGROUND Metagenomic Next-Generation Sequencing (mNGS) is a rapid, non-culture-based, high-throughput technique for pathogen diagnosis. Despite its numerous advantages, only a few studies have investigated its use in patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT). METHODS We conducted a retrospective analysis of 404 mNGS tests performed on 264 patients after allo-HSCT. The tests were divided into three groups (Phase A, B, C) based on the time spent hospitalized post-transplantation, and we evaluated the analytical performance of mNGS in comparison with conventional microbiological tests (CMT), while also analyzing its clinical utility for clinical impacts. RESULTS Metagenomic sequencing demonstrated a significantly higher rate of positive microbiological findings as compared to CMT (334/404 (82.7 %) vs. 159/404 (39.4 %), respectively, P < 0.001). The detection rates by both mNGS and CMT varied across the three-phase (mNGS: A-60/89 (67.4 %), B-147/158 (93.0 %), C-125/157 (79.6 %), respectively, P < 0.001; CMT: A-21/89 (23.6 %), B-79/158 (50.0 %), C-59/157 (37.6 %), respectively, P < 0.001). The infection sites and types of pathogens were also different across the three phases. Compared to non-GVHD cases, mNGS detected more Aspergillus spp. and Mucorales in GVHD patients (Aspergillus: 12/102 (11.8 %) vs. 8/158 (5.1 %), respectively, P = 0.048; Mucorales: 6/102 (5.9 %) vs. 2/158 (1.3 %), respectively, P = 0.035). Forty-five (181/404) percent of mNGS tests yielded a positive impact on the clinical diagnosis, while 24.3 % (98/404) of tests benefited the patients in antimicrobial treatment. CONCLUSION mNGS is an indispensable diagnostic tool in identifying pathogens and optimizing antibiotic therapy for hematological patients receiving allo-HSCT.
Collapse
Affiliation(s)
- Chun-Hui Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China; Microbiology Laboratory, Tianjin Union Precision Medical Diagnostic Co., Ltd, Tianjin 301617, China
| | - Xin Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Guo-Qing Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Hui-Ming Yi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Shu-Lian Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Teng Liu
- Microbiology Laboratory, Tianjin Union Precision Medical Diagnostic Co., Ltd, Tianjin 301617, China
| | - Yue-Tian Yu
- Department of Critical Care Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiu-Hui Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Er-Lie Jiang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China.
| | - Si-Zhou Feng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China.
| |
Collapse
|
12
|
Overbeek R, Leitl CJ, Stoll SE, Wetsch WA, Kammerer T, Mathes A, Böttiger BW, Seifert H, Hart D, Dusse F. The Value of Next-Generation Sequencing in Diagnosis and Therapy of Critically Ill Patients with Suspected Bloodstream Infections: A Retrospective Cohort Study. J Clin Med 2024; 13:306. [PMID: 38256440 PMCID: PMC10816005 DOI: 10.3390/jcm13020306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 12/30/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Bloodstream infection (BSI), a frequent cause of severe sepsis, is a life-threatening complication in critically ill patients and still associated with a high mortality rate. Rapid pathogen identification from blood is crucial for an early diagnosis and the treatment of patients with suspected BSI. For this purpose, novel diagnostic tools on the base of genetic analysis have emerged for clinical application. The aim of this study was to assess the diagnostic value of additional next-generation sequencing (NGS) pathogen test for patients with suspected BSI in a surgical ICU and its potential impact on antimicrobial therapy. In this retrospective single-centre study, clinical data and results from blood culture (BC) and NGS pathogen diagnostics were analysed for ICU patients with suspected BSI. Consecutive changes in antimicrobial therapy and diagnostic procedures were evaluated. Results: 41 cases with simultaneous NGS and BC sampling were assessed. NGS showed a statistically non-significant higher positivity rate than BC (NGS: 58.5% (24/41 samples) vs. BC: 21.9% (9/41); p = 0.056). NGS detected eight different potentially relevant bacterial species, one fungus and six different viruses, whereas BC detected four different bacterial species and one fungus. NGS results affected antimicrobial treatment in 7.3% of cases. Conclusions: NGS-based diagnostics have the potential to offer a higher positivity rate than conventional culture-based methods in patients with suspected BSI. Regarding the high cost, their impact on anti-infective therapy is currently limited. Larger randomized prospective clinical multicentre studies are required to assess the clinical benefit of this novel diagnostic technology.
Collapse
Affiliation(s)
- Remco Overbeek
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Christoph J. Leitl
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Sandra E. Stoll
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Wolfgang A. Wetsch
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Tobias Kammerer
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Alexander Mathes
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Bernd W. Böttiger
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50935 Cologne, Germany
| | - Dominique Hart
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Fabian Dusse
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| |
Collapse
|
13
|
Vinh Dong H, Saleh T, Kaur I, Yang S. Elucidating the Clinical Interpretation and Impact of a Positive Plasma Cell-Free DNA Metagenomics Test Result-A Single Center Retrospective Study. J Appl Lab Med 2024; 9:14-27. [PMID: 38167775 DOI: 10.1093/jalm/jfad083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 09/18/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND The Karius Test (KT), a cell-free DNA metagenomic next-generation sequencing assay, has potential to improve diagnostic evaluation of infectious diseases. Published data describing clinical impact of positive KT results are limited. We attempt to elucidate the clinical interpretation and impact of positive KT results based on types and patterns of detected pathogens and patient characteristics. METHODS All positive KT results from a single institution in 2022 were screened. Patients with results that met predefined categories were included for review by a panel of 3 infectious diseases physicians and one clinical microbiologist. Predefined categories included reports with fungal, parasitic, notable bacterial, notable viral pathogens, or polybacterial results (≥3 bacteria). Polybacterial results were further classified into patterns of microbiome detected. Clinical impact and its correlation with result or patient characteristics were explored. RESULTS Ninety-two patients met the inclusion criteria, most were immunocompromised (73%). Positive KT results that met predefined categories had the following clinical impact: positive in 30.4%, negative in 2.2%, and none in 65.2%. Polybacterial results, especially interpreted as oral flora had lowest clinical impact (7.1% and 0.0%, respectively), while detection of parasites or notable bacterial pathogens had the highest clinical impact (100% and 77.8%, respectively). There was no correlation between patient characteristics and clinical impact. CONCLUSIONS Among a cohort of largely immunocompromised patients, we were able to demonstrate clinical impact of specific KT result types and patterns but did not find correlation between patient characteristics and clinical impact. Our results should be confirmed in future larger cohorts.
Collapse
Affiliation(s)
- Huan Vinh Dong
- Department of Pediatrics, Division of Pediatric Infectious Diseases, David Geffen School of Medicine, University of California Los Angles, Los Angeles, CA, United States
| | - Tawny Saleh
- Department of Pediatrics, Division of Pediatric Infectious Diseases, David Geffen School of Medicine, University of California Los Angles, Los Angeles, CA, United States
| | - Ishminder Kaur
- Department of Pediatrics, Division of Pediatric Infectious Diseases, David Geffen School of Medicine, University of California Los Angles, Los Angeles, CA, United States
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angles, Los Angeles, CA, United States
| |
Collapse
|
14
|
Feng S, Rao G, Wei X, Fu R, Hou M, Song Y, Xu C, Han P, Gong B, Chen X, Wang Y, Dong X, Jiang Z, Wang J. Clinical metagenomic sequencing of plasma microbial cell-free DNA for febrile neutropenia in patients with acute leukaemia. Clin Microbiol Infect 2024; 30:107-113. [PMID: 37271194 DOI: 10.1016/j.cmi.2023.05.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/28/2023] [Accepted: 05/30/2023] [Indexed: 06/06/2023]
Abstract
OBJECTIVES To evaluate the diagnostic performance and clinical impact of metagenomic next-generation sequencing (mNGS) of plasma microbial cell-free DNA (mcfDNA) in febrile neutropenia (FN). METHODS In a 1-year, multicentre, prospective study, we enrolled 442 adult patients with acute leukaemia with FN and investigated the usefulness of mNGS of plasma mcfDNA for identification of infectious pathogens. The results of mNGS were available to clinicians in real time. The performance of mNGS testing was evaluated in comparison with blood culture (BC) and a composite standard that incorporated standard microbiological testing and clinical adjudication. RESULTS In comparison with BC, the positive and negative agreements of mNGS were 81.91% (77 of 94) and 60.92% (212 of 348), respectively. By clinical adjudication, mNGS results were categorized by infectious diseases specialists as definite (n = 76), probable (n = 116), possible (n = 26), unlikely (n = 7), and false negative (n = 5). In 225 mNGS-positive cases, 81 patients (36%) underwent antimicrobials adjustment, resulting in positive impact on 79 patients and negative impact on two patients (antibiotics overuse). Further analysis indicated that mNGS was less affected by prior antibiotics exposure than BC. DISCUSSION Our results indicate that mNGS of plasma mcfDNA increased the detection of clinically significant pathogens and enabled early optimization of antimicrobial therapy in patients with acute leukaemia with FN.
Collapse
Affiliation(s)
- Sizhou Feng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Guanhua Rao
- Department of Medicine, Genskey Medical Technology Co, Ltd, Beijing, China
| | - Xudong Wei
- Department of Hematology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Rong Fu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Ming Hou
- Shandong Provincial Key Laboratory of Immunohematology, Department of Hematology, Qilu Hospital of Shandong University, Shandong University, Jinan, China
| | - Yongping Song
- Department of Hematology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Chunhui Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Peng Han
- Department of Medicine, Genskey Medical Technology Co, Ltd, Beijing, China
| | - Benfa Gong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Xin Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Yihao Wang
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaoyuan Dong
- Shandong Provincial Key Laboratory of Immunohematology, Department of Hematology, Qilu Hospital of Shandong University, Shandong University, Jinan, China
| | - Zhi Jiang
- Department of Medicine, Genskey Medical Technology Co, Ltd, Beijing, China
| | - Jianxiang Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.
| |
Collapse
|
15
|
Daher M, Iordanov R, Al Mohajer M, Sohail MR, Staggers KA, Hamdi AM. Clinical utility of metagenomic next-generation sequencing in fever of undetermined origin. Ther Adv Infect Dis 2024; 11:20499361241244969. [PMID: 38645300 PMCID: PMC11027448 DOI: 10.1177/20499361241244969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/18/2024] [Indexed: 04/23/2024] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) is a novel diagnostic tool increasingly used in the field of infectious diseases. Little guidance is available regarding its appropriate use in different patient populations and clinical syndromes. We aimed to review the clinical utility of mNGS in patients with a specific clinical syndrome and identify factors that may increase its utility. Methods We retrospectively reviewed charts of 72 non-immunocompromised adults hospitalized with the clinical syndrome of 'fever of undetermined origin' and underwent mNGS testing. Standardized criteria from a previously published study were used to determine the clinical impact of mNGS testing. We applied logistic regression to identify factors associated with a positive clinical impact. Results Of the 72 patients identified, 62.5% were males with a median age of 56. All patients had a fever at the time of evaluation. At least one organism was identified in 65.3% of cases; most commonly were Epstein-Barr virus (13.9%), cytomegalovirus (12.5%), and Rickettsia typhi (11.1%). Of those determined to have an infectious etiology of their febrile syndrome, 89.5% (n = 34/38) had a positive mNGS. Consistency between the organism(s) on mNGS and the clinically determined infectious etiology was 82.4%. mNGS had a positive clinical impact in 40.3% of cases, a negative impact in 2.8%, and no impact in 56.9% of cases. Besides age, we did not identify other factors associated with a higher likelihood of positive clinical impact. Conclusion In our review, mNGS had a positive clinical impact in a large proportion of adults with fever of undetermined origin, with minimal negative impact. However, mNGS results should be interpreted carefully given the high rate of detection of pathogens of unclear clinical significance. Randomized clinical trials are needed to assess the clinical utility of this novel diagnostic tool.
Collapse
Affiliation(s)
- Marilyne Daher
- Department of Internal Medicine, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Roumen Iordanov
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Mayar Al Mohajer
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Baylor St. Luke’s Medical Center, Houston, TX, USA
| | - M. Rizwan Sohail
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | | | | |
Collapse
|
16
|
Hogan CA, Miller S, Piantadosi A, Gaston DC, Simner PJ, Nash S, Babady NE. Which trial do we need? Plasma metagenomic next-generation sequencing to diagnose infections in patients with haematological malignancies and febrile neutropenia: proposal for a randomized-controlled trial. Clin Microbiol Infect 2023; 29:1474-1479. [PMID: 37244468 DOI: 10.1016/j.cmi.2023.05.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/18/2023] [Accepted: 05/20/2023] [Indexed: 05/29/2023]
Affiliation(s)
- Catherine A Hogan
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada; Department of Pathology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steve Miller
- Delve Bio, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Anne Piantadosi
- Emory University Department of Medicine, Division of Infectious Diseases, Atlanta, GA, USA; Emory University Department of Pathology and Laboratory Medicine, Atlanta, GA, USA
| | - David C Gaston
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Patricia J Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephen Nash
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Solna, Sweden
| | - N Esther Babady
- Department of Pathology and Laboratory Medicine, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Infectious Disease Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
17
|
Musher DM. Problems with etiologic diagnosis of community-acquired pneumonia using plasma microbial cell-free DNA sequencing. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2023; 3:e206. [PMID: 38028926 PMCID: PMC10654952 DOI: 10.1017/ash.2023.475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 12/01/2023]
Affiliation(s)
- Daniel M. Musher
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
18
|
Bell DT. Deciphering the potential of plasma cell-free metagenomic next-generation sequencing using the Karius test. Curr Opin Infect Dis 2023; 36:420-425. [PMID: 37493238 DOI: 10.1097/qco.0000000000000942] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
PURPOSE OF REVIEW Plasma cell-free metagenomic next-generation sequencing (cf-mNGS) is increasingly employed for the diagnosis of infection, but a consensus for optimal use has not been established. This minireview focuses on the commercially available Karius Test and is aimed at local leaders seeking to understand the complexities of cf-mNGS to make informed test utilization policies and better interpret results. RECENT FINDINGS Recent retrospective studies have reported how the Karius Test was applied at their institutions and identified areas of potential patient benefit. In addition, substantive studies have reported how this test performs in specific indications, particularly invasive fungal disease, endovascular infection and lower respiratory infection. SUMMARY Successfully integrating plasma cf-mNGS requires careful assessment of performance in the specific applications and patient populations in which it is used. Individual institutions must independently evaluate implementation strategies and determine where diagnostic yields outweigh the potential pitfalls.
Collapse
Affiliation(s)
- Drew T Bell
- Department of Laboratories, Seattle Children's Hospital, Seattle, Washington, USA
| |
Collapse
|
19
|
Weiss ZF, Pyden AD, Jhaveri TA, Kanjilal S. The diagnostic and clinical utility of microbial cell-free DNA sequencing in a real-world setting. Diagn Microbiol Infect Dis 2023; 107:116004. [PMID: 37467522 DOI: 10.1016/j.diagmicrobio.2023.116004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 04/13/2023] [Accepted: 06/07/2023] [Indexed: 07/21/2023]
Abstract
Microbial cell free DNA sequencing is increasingly used for diagnosis of infection but few studies describe its utility in real-world settings. We performed a single-center retrospective case series of microbial cell free DNA testing using the Karius assay from 29 patient samples to define the clinical reasoning and the impact of testing. Indications fell into 3 categories, identifying a causative pathogen in patients with an infectious syndrome and negative microbiologic workup (15/29, 52%), seeking another pathogen when organisms identified by traditional diagnostics failed to explain the clinical presentation (9/29, 31%) and to "rule out" infection in patients with nonspecific symptoms and negative microbiologic workup (5/29, 17%). Clinical impact was positive in 13/29 (45%) and all were for patients with high pretest probability for infection. Impact was negative in 3/29 (10%) cases. There was no impact in 15/29 (52%) cases. Further work is needed to define the optimal timing accounting for test performance, and patient characteristics.
Collapse
Affiliation(s)
- Zoe Freeman Weiss
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA; Division of Infectious Diseases and Geographic Medicine and Department of Anatomic and Clinical Pathology, Tufts University School of Medicine, Boston, MA, USA.
| | - Alexander D Pyden
- Department of Laboratory Medicine, Lahey Hospital and Medical Center, Burlington, MA, USA
| | - Tulip A Jhaveri
- Division of Infectious Diseases, University of Mississippi Medical Center, Jackson, MS, USA
| | - Sanjat Kanjilal
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA; Harvard Pilgrim Healthcare Institute & Harvard Medical School, Department of Population Medicine; Boston, MA, USA
| |
Collapse
|
20
|
Moufarrej MN, Bianchi DW, Shaw GM, Stevenson DK, Quake SR. Noninvasive Prenatal Testing Using Circulating DNA and RNA: Advances, Challenges, and Possibilities. Annu Rev Biomed Data Sci 2023; 6:397-418. [PMID: 37196360 PMCID: PMC10528197 DOI: 10.1146/annurev-biodatasci-020722-094144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Prenatal screening using sequencing of circulating cell-free DNA has transformed obstetric care over the past decade and significantly reduced the number of invasive diagnostic procedures like amniocentesis for genetic disorders. Nonetheless, emergency care remains the only option for complications like preeclampsia and preterm birth, two of the most prevalent obstetrical syndromes. Advances in noninvasive prenatal testing expand the scope of precision medicine in obstetric care. In this review, we discuss advances, challenges, and possibilities toward the goal of providing proactive, personalized prenatal care. The highlighted advances focus mainly on cell-free nucleic acids; however, we also review research that uses signals from metabolomics, proteomics, intact cells, and the microbiome. We discuss ethical challenges in providing care. Finally, we look to future possibilities, including redefining disease taxonomy and moving from biomarker correlation to biological causation.
Collapse
Affiliation(s)
| | - Diana W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development and Section on Prenatal Genomics and Fetal Therapy, Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gary M Shaw
- Department of Pediatrics and March of Dimes Prematurity Research Center at Stanford University, Stanford University School of Medicine, Stanford, California, USA
| | - David K Stevenson
- Department of Pediatrics and March of Dimes Prematurity Research Center at Stanford University, Stanford University School of Medicine, Stanford, California, USA
| | - Stephen R Quake
- Department of Bioengineering and Department of Applied Physics, Stanford University, Stanford, California, USA
- Chan Zuckerberg Initiative, Redwood City, California, USA
| |
Collapse
|
21
|
Linder KA, Miceli MH. Impact of Metagenomic Next-Generation Sequencing of Plasma Cell-free DNA Testing in the Management of Patients With Suspected Infectious Diseases. Open Forum Infect Dis 2023; 10:ofad385. [PMID: 37601730 PMCID: PMC10438880 DOI: 10.1093/ofid/ofad385] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 07/21/2023] [Indexed: 08/22/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) of cell-free DNA is an emerging modality for the diagnosis of infectious diseases, but studies on its clinical utility are limited. We conducted a retrospective single-center study including all patients who had plasma mNGS sent at the University of Michigan between 1 January 2021 and 25 July 2022. Test results were assessed for clinical impact. A total of 71 tests were sent on 69 patients; the mean ± SD age was 52 ± 19 years; and 35% of patients were immunocompromised. Forty-five (63%) mNGS test results were positive and 14 (31%) had clinical impact-from starting new antimicrobials (n = 7), discontinuing antimicrobials (n = 4), or changing antimicrobial duration (n = 2) or by affecting surgical decision making (n = 1). Twenty-six (37%) mNGS test results were negative and only 4 (15%) were impactful, leading to discontinuation of antimicrobials. Overall, just 25% of mNGS tests were clinically relevant. There was no significant difference in the proportion of tests that were clinically relevant between negative and positive results (P = .16) or if patients were immunocompromised (P = .57). Plasma mNGS was most frequently impactful (in 50% of patients) when included in the diagnostic workup of cardiovascular infection but less impactful in other clinical syndromes, including fever of unknown origin and pulmonary infection. Our findings underscore the need to further study this testing modality, particularly with prospective research including negative controls, before it is considered for widespread use.
Collapse
Affiliation(s)
- Kathleen A Linder
- Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Infectious Diseases Section, VA Ann Arbor Healthcare System, Ann Arbor, Michigan, USA
| | - Marisa H Miceli
- Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
22
|
Everhart J, Henshaw NG. Updates in Molecular Diagnostics in Solid Organ Transplantation Recipients. Infect Dis Clin North Am 2023:S0891-5520(23)00038-7. [PMID: 37244805 DOI: 10.1016/j.idc.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Advances in molecular diagnostics have the potential to improve patient care among solid organ transplant recipients by reducing time to pathogen identification and informing directed therapy. Although cultures remain the cornerstone of traditional microbiology, advanced molecular diagnostics, such as metagenomic next-generation sequencing (mNGS), may increase detection of pathogens. This is particularly true in the settings of prior antibiotic exposure, and when causative organisms are fastidious. mNGS also offers a hypothesis-free diagnostic method of testing. This is useful in situations whereby the differential is broad or when the infectious agent is unlikely to be detected by routine methods.
Collapse
Affiliation(s)
- James Everhart
- Duke University Medical Center, 2351 Erwin Road, Wadsworth Building, Room 0170, Durham, NC 27705, USA.
| | - Nancy G Henshaw
- Duke University Medical Center, 2351 Erwin Road, Wadsworth Building, Room 0170, Durham, NC 27705, USA
| |
Collapse
|
23
|
Onofrei VA, Adam CA, Marcu DTM, Crisan Dabija R, Ceasovschih A, Constantin M, Grigorescu ED, Petroaie AD, Mitu F. Infective Endocarditis during Pregnancy-Keep It Safe and Simple! MEDICINA (KAUNAS, LITHUANIA) 2023; 59:medicina59050939. [PMID: 37241171 DOI: 10.3390/medicina59050939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023]
Abstract
The diagnosis of infective endocarditis (IE) during pregnancy is accompanied by a poor prognosis for both mother and fetus in the absence of prompt management by multidisciplinary teams. We searched the electronic databases of PubMed, MEDLINE and EMBASE for clinical studies addressing the management of infective endocarditis during pregnancy, with the aim of realizing a literature review ranging from risk factors to diagnostic investigations to optimal therapeutic management for mother and fetus alike. The presence of previous cardiovascular pathologies such as rheumatic heart disease, congenital heart disease, prosthetic valves, hemodialysis, intravenous catheters or immunosuppression are the main risk factors predisposing patients to IE during pregnancy. The identification of modern risk factors such as intracardiac devices and intravenous drug administration as well as genetic diagnostic methods such as cell-free deoxyribonucleic acid (DNA) next-generation sequencing require that these cases be addressed in multidisciplinary teams. Guiding treatment to eradicate infection and protect the fetus simultaneously creates challenges for cardiologists and gynecologists alike.
Collapse
Affiliation(s)
- Viviana Aursulesei Onofrei
- Department of Medical Specialties I, II, III and Preventive Medicine and Interdisciplinary, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
- "St. Spiridon" Clinical Emergency Hospital, Independence Boulevard No. 1, 700111 Iasi, Romania
| | - Cristina Andreea Adam
- Department of Medical Specialties I, II, III and Preventive Medicine and Interdisciplinary, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
- Cardiovascular Rehabilitation Clinic, Clinical Rehabilitation Hospital, Pantelimon Halipa Street No. 14, 700661 Iasi, Romania
| | - Dragos Traian Marius Marcu
- Department of Medical Specialties I, II, III and Preventive Medicine and Interdisciplinary, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
- Clinical Hospital of Pneumophthisiology Iași, Doctor Iosif Cihac Street No. 30, 700115 Iasi, Romania
| | - Radu Crisan Dabija
- Department of Medical Specialties I, II, III and Preventive Medicine and Interdisciplinary, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
- Clinical Hospital of Pneumophthisiology Iași, Doctor Iosif Cihac Street No. 30, 700115 Iasi, Romania
| | - Alexandr Ceasovschih
- Department of Medical Specialties I, II, III and Preventive Medicine and Interdisciplinary, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
- "St. Spiridon" Clinical Emergency Hospital, Independence Boulevard No. 1, 700111 Iasi, Romania
| | - Mihai Constantin
- Department of Medical Specialties I, II, III and Preventive Medicine and Interdisciplinary, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
- "St. Spiridon" Clinical Emergency Hospital, Independence Boulevard No. 1, 700111 Iasi, Romania
| | - Elena-Daniela Grigorescu
- Department of Medical Specialties I, II, III and Preventive Medicine and Interdisciplinary, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
| | - Antoneta Dacia Petroaie
- Department of Medical Specialties I, II, III and Preventive Medicine and Interdisciplinary, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
| | - Florin Mitu
- Department of Medical Specialties I, II, III and Preventive Medicine and Interdisciplinary, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
- Cardiovascular Rehabilitation Clinic, Clinical Rehabilitation Hospital, Pantelimon Halipa Street No. 14, 700661 Iasi, Romania
- Academy of Medical Sciences, Ion C. Brătianu Boulevard No. 1, 030167 Bucharest, Romania
- Academy of Romanian Scientists, Professor Dr. Doc. Dimitrie Mangeron Boulevard No. 433, 700050 Iasi, Romania
| |
Collapse
|
24
|
Gaston DC. Clinical Metagenomics for Infectious Diseases: Progress toward Operational Value. J Clin Microbiol 2023; 61:e0126722. [PMID: 36728425 PMCID: PMC9945490 DOI: 10.1128/jcm.01267-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The field of clinical metagenomics for infectious disease diagnostics has advanced to combining questions of technical methodologies with best-use practices due to lowering barriers of implementation. This commentary identifies challenges facing further development of the field and proposes methods for advancement by highlighting a recent prospective pilot study evaluating a targeted metagenomic approach for infectious endocarditis. This commentary introduces the concept of operational value as a method for standardizing results generated by differing clinical metagenomic approaches. Operational value includes assessments of result quality, utility, and cost through incorporating methodological aspects of metagenomics as applied to various infectious syndromes, patient populations, and specimen types. Focus is placed on standardizing outcome-based metrics using an operational value matrix. As ambitions of clinical metagenomics are increasingly realized, new models of study design and collaboration could promote progress toward routine use and positive benefits for patients with infectious diseases.
Collapse
Affiliation(s)
- David C. Gaston
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| |
Collapse
|
25
|
Parrish NF, Gaston DC. Metagenomics in infectious disease diagnostics: Toward best-use practices to optimize actionable results. Transpl Infect Dis 2023; 25:e13959. [PMID: 36571492 DOI: 10.1111/tid.13959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 12/27/2022]
Affiliation(s)
- Nicholas F Parrish
- Section of Surgical Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,RIKEN Center for Integrative Medical Sciences, RIKEN Yokohama Institute, Yokohama, Japan
| | - David C Gaston
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| |
Collapse
|
26
|
Haddad SF, DeSimone DC, Chesdachai S, Gerberi DJ, Baddour LM. Utility of Metagenomic Next-Generation Sequencing in Infective Endocarditis: A Systematic Review. Antibiotics (Basel) 2022; 11:antibiotics11121798. [PMID: 36551455 PMCID: PMC9774888 DOI: 10.3390/antibiotics11121798] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Blood cultures have been the gold standard for identifying pathogens in infective endocarditis (IE). Blood culture-negative endocarditis (BCNE), however, occurs in 40% or more of IE cases with the bulk of them due to recent antibiotic exposure prior to obtaining blood cultures. Increasingly, molecular techniques are being used for pathogen identification in cases of BCNE and more recently has included metagenomic next-generation sequencing (mNGS). We therefore performed a literature search on August 31, 2022, that assessed the mNGS in IE and 13 publications were identified and included in a systematic review. Eight (61.5%) of them focused only on IE with mNGS performed on cardiac valve tissue in four studies, plasma in three studies and cardiac implantable electronic devices (CIED) in one study. Gram-positive cocci, including Staphylococcus aureus (n = 31, 8.9%), coagulase-negative staphylococci (n = 61, 17.6%), streptococci (n = 130, 37.5%), and Enterococcus faecalis (n = 23, 6.6%) were the predominant organisms identified by mNGS. Subsequent investigations are needed to further define the utility of mNGS in BCNE and its impact on patient outcomes. Despite some pitfalls, mNGS seems to be of value in pathogen identification in IE cases, particularly in those with BCNE. This study was registered and on the Open Science Framework platform.
Collapse
Affiliation(s)
- Sara F. Haddad
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA
- Correspondence: ; Tel.: +1-(507)-405-7588
| | - Daniel C. DeSimone
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Disease, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA
| | - Supavit Chesdachai
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA
| | - Danielle J. Gerberi
- Mayo Clinic Library Services, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA
| | - Larry M. Baddour
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA
- Department of Cardiovascular Disease, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN 55905, USA
| |
Collapse
|
27
|
Foong KS, Mabayoje M, AlMajali A. Clinical Impact of Noninvasive Plasma Microbial Cell-Free Deoxyribonucleic Acid Sequencing for the Diagnosis and Management of Pneumocystis jirovecii Pneumonia: A Single-Center Retrospective Study. Open Forum Infect Dis 2022; 9:ofac652. [PMID: 36578518 PMCID: PMC9793099 DOI: 10.1093/ofid/ofac652] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022] Open
Abstract
We present 23 cases of Pneumocystis jirovecii pneumonia (PCP) diagnosed with commercially available noninvasive plasma microbial cell-free deoxyribonucleic acid (mcfDNA) assay. Our findings suggest that plasma mcfDNA testing resulted in positive clinical impact for the diagnosis and treatment of PCP and coinfections in 82.6% of cases.
Collapse
Affiliation(s)
- Kap Sum Foong
- Correspondence: K. S. Foong, MD, Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, 800 Washington Street, Boston, MA 02111 ()
| | - Mojolaoluwa Mabayoje
- Department of Medicine, University of Illinois College of Medicine, Peoria, Illinois, USA
| | | |
Collapse
|
28
|
Chang SY, Santos CAQ. Could cell‐free DNA and host biomarkers assist in antimicrobial stewardship with organ transplant recipients? Transpl Infect Dis 2022; 24:e13971. [DOI: 10.1111/tid.13971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/26/2022] [Accepted: 09/16/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Sandy Y. Chang
- Division of Infectious Diseases Department of Medicine Loma Linda University Loma Linda California USA
| | - Carlos A. Q. Santos
- Division of Infectious Diseases Department of Internal Medicine Rush University Medical Center Chicago Illinois USA
| |
Collapse
|
29
|
Purushothaman S, Meola M, Egli A. Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics. Int J Mol Sci 2022; 23:9834. [PMID: 36077231 PMCID: PMC9456280 DOI: 10.3390/ijms23179834] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/21/2022] Open
Abstract
Whole genome sequencing (WGS) provides the highest resolution for genome-based species identification and can provide insight into the antimicrobial resistance and virulence potential of a single microbiological isolate during the diagnostic process. In contrast, metagenomic sequencing allows the analysis of DNA segments from multiple microorganisms within a community, either using an amplicon- or shotgun-based approach. However, WGS and shotgun metagenomic data are rarely combined, although such an approach may generate additive or synergistic information, critical for, e.g., patient management, infection control, and pathogen surveillance. To produce a combined workflow with actionable outputs, we need to understand the pre-to-post analytical process of both technologies. This will require specific databases storing interlinked sequencing and metadata, and also involves customized bioinformatic analytical pipelines. This review article will provide an overview of the critical steps and potential clinical application of combining WGS and metagenomics together for microbiological diagnosis.
Collapse
Affiliation(s)
- Srinithi Purushothaman
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
| | - Marco Meola
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
- Swiss Institute of Bioinformatics, University of Basel, 4031 Basel, Switzerland
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031 Basel, Switzerland
| |
Collapse
|