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Iyer V, Castro D, Malla B, Panda B, Rabson AR, Horowitz G, Heger N, Gupta K, Singer A, Norwitz ER. Culture-independent identification of bloodstream infections from whole blood: prospective evaluation in specimens of known infection status. J Clin Microbiol 2024; 62:e0149823. [PMID: 38315022 PMCID: PMC10935643 DOI: 10.1128/jcm.01498-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/19/2023] [Indexed: 02/07/2024] Open
Abstract
Sepsis caused by bloodstream infection (BSI) is a major healthcare burden and a leading cause of morbidity and mortality worldwide. Timely diagnosis is critical to optimize clinical outcome, as mortality rates rise every hour treatment is delayed. Blood culture remains the "gold standard" for diagnosis but is limited by its long turnaround time (1-7 days depending on the organism) and its potential to provide false-negative results due to interference by antimicrobial therapy or the presence of mixed (i.e., polymicrobial) infections. In this paper, we evaluated the performance of resistance and pathogen ID/BSI, a direct-from-specimen molecular assay. To reduce the false-positivity rate common with molecular methods, this assay isolates and detects genomic material only from viable microorganisms in the blood by incorporating a novel precursor step to selectively lyse host and non-viable microbial cells and remove cell-free genomic material prior to lysis and analysis of microbial cells. Here, we demonstrate that the assay is free of interference from host immune cells and common antimicrobial agents at elevated concentrations. We also demonstrate the accuracy of this technology in a prospective cohort pilot study of individuals with known sepsis/BSI status, including samples from both positive and negative individuals. IMPORTANCE Blood culture remains the "gold standard" for the diagnosis of sepsis/bloodstream infection (BSI) but has many limitations which may lead to a delay in appropriate and accurate treatment in patients. Molecular diagnostic methods have the potential for markedly improving the management of such patients through faster turnaround times and increased accuracy. But molecular diagnostic methods have not been widely adopted for the identification of BSIs. By incorporating a precursor step of selective lysis of host and non-viable microorganisms, our resistance and pathogen ID (RaPID)/BSI molecular assay addresses many limitations of blood culture and other molecular assay. The RaPID/BSI assay has an approximate turnaround time of 4 hours, thereby significantly reducing the time to appropriate and accurate diagnosis of causative microorganisms in such patients. The short turnaround time also allows for close to real-time tracking of pathogenic clearance of microorganisms from the blood of these patients or if a change of antimicrobial regimen is required. Thus, the RaPID/BSI molecular assay helps with optimization of antimicrobial stewardship; prompt and accurate diagnosis of sepsis/BSI could help target timely treatment and reduce mortality and morbidity in such patients.
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Affiliation(s)
- Vidya Iyer
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, Massachusetts, USA
- Department of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Division of Clinical Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Daniel Castro
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, Massachusetts, USA
| | - Bipin Malla
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, Massachusetts, USA
| | - Britta Panda
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, Massachusetts, USA
| | - Arthur R. Rabson
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, Massachusetts, USA
| | - Gary Horowitz
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, Massachusetts, USA
| | - Nicholas Heger
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, Massachusetts, USA
| | | | - Alon Singer
- HelixBind Inc., Boxborough, Massachusetts, USA
| | - Errol R. Norwitz
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, Massachusetts, USA
- Department of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Division of Clinical Research, Massachusetts General Hospital, Boston, Massachusetts, USA
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Sparks R, Balgahom R, Janto C, Polkinghorne A, Branley J. Evaluation of the BioFire Blood Culture Identification 2 panel and impact on patient management and antimicrobial stewardship. Pathology 2021; 53:889-895. [PMID: 34120744 DOI: 10.1016/j.pathol.2021.02.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 10/21/2022]
Abstract
Bloodstream infection survival is linked to timely administration of optimal antimicrobial therapy. Commercial multiplex polymerase chain reaction (PCR) assays, such as the BioFire Blood Culture Identification Panel (BCID) used for the rapid diagnosis of bloodstream infections, have significantly improved the turnaround time for optimisation of antimicrobial therapy. Reported concordance with culture-based methods and multiplex PCR analysis is high and only limited by (1) the range of targets available on the multiplex panel; and (2) the complexity of microorganisms present in the blood culture specimen. In this study, we evaluated the use of the BioFire Blood Culture Identification 2 panel (BCID2), including an expanded repertoire of targets for Gram-positive and Gram-negative bacteria, yeast and antimicrobial resistance genes compared to the BCID panel. The BCID2 panel identified microorganisms in 39/42 (92.9%) blood cultures where monomicrobial growth was detected; the three unidentified blood cultures contained organisms not included in the BCID2 panel. Polymicrobial blood culture analysis revealed a lower degree of concordance (28.6%); however, most disagreement was due to the culture-based identification of off-panel microorganisms of low clinical significance. Turnaround time, from blood culture collection to organism identification on the blood cultures correctly identified by BCID2, was 24.6 (±16.8) hours for the BCID2 panel versus 38.2 (±21.9) hours for conventional methods. Analysis of the theoretical impact of the BCID2 identification on clinical management found therapy would be altered in 45.1% (23/51) of patients. The BCID2 panel is anticipated to improve the diagnosis and antimicrobial management of patients with serious bloodstream infections.
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Affiliation(s)
- Rebecca Sparks
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Blue Mountains Pathology Service, Penrith, NSW, Australia
| | - Rifky Balgahom
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Blue Mountains Pathology Service, Penrith, NSW, Australia
| | - Catherine Janto
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Blue Mountains Pathology Service, Penrith, NSW, Australia
| | - Adam Polkinghorne
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Blue Mountains Pathology Service, Penrith, NSW, Australia; Nepean Clinical School, Faculty of Medicine and Health, University of Sydney, Kingswood, NSW, Australia
| | - James Branley
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Blue Mountains Pathology Service, Penrith, NSW, Australia; Nepean Clinical School, Faculty of Medicine and Health, University of Sydney, Kingswood, NSW, Australia.
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Tassinari M, Zannoli S, Farabegoli P, Pedna MF, Pierro A, Mastroianni A, Fontan R, Luongo L, Sarnataro G, Menegatti E, Caruso A, Sambri V. Rapid diagnosis of bloodstream infections in the critically ill: Evaluation of the broad-range PCR/ESI-MS technology. PLoS One 2018; 13:e0197436. [PMID: 29763469 PMCID: PMC5953471 DOI: 10.1371/journal.pone.0197436] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 05/02/2018] [Indexed: 12/30/2022] Open
Abstract
Bloodstream infection (BSI) and associated sepsis represent a major source of mortality in industrialized countries. Prompt treatment with targeted antibiotics affects both the financial impact and the clinical outcome of BSI: every hour gained in initiating the correct antimicrobial therapy significantly increases the probability of patient survival. However, the current standard-of-care, which depends on blood culture-based diagnosis, are often unable to provide such a fast response. Fast and sensitive molecular techniques for the detection of sepsis-related pathogens from primary blood samples are strongly needed. The aim of this study was to assess the usefulness of the IRIDICA BAC BSI Assay, a PCR/ESI-MS-based technology for the early diagnosis of bloodstream infections from primary blood samples in critical patients. This evaluation has been performed by comparison with the traditional culture-based methods. The study was performed on a total of 300 prospective whole blood specimens obtained from patients suspected of sepsis, admitted to enrolling ER units from The Greater Romagna Area. The overall concordance between the two techniques was of 86%, with a calculated sensitivity of 76% and an assay specificity of 90%. The clinical significance of discrepant results was evaluated reviewing the patients’ clinical records and the results of additional relevant microbiological tests. The data here obtained support the ability of the IRIDICA BAC BSI Assay to identify a broad range of bacteria directly from primary whole blood samples, within eight hours. This might allow a timely administration of a suitable treatment.
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Affiliation(s)
- Martina Tassinari
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Pievesestina, Italy
- * E-mail: (MT); (SZ)
| | - Silvia Zannoli
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Pievesestina, Italy
- * E-mail: (MT); (SZ)
| | - Patrizia Farabegoli
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Pievesestina, Italy
| | - Maria Federica Pedna
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Pievesestina, Italy
| | - Anna Pierro
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Pievesestina, Italy
| | | | | | | | | | | | | | - Vittorio Sambri
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Pievesestina, Italy
- DIMES, University of Bologna, Bologna, Italy
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Metzgar D, Frinder MW, Rothman RE, Peterson S, Carroll KC, Zhang SX, Avornu GD, Rounds MA, Carolan HE, Toleno DM, Moore D, Hall TA, Massire C, Richmond GS, Gutierrez JR, Sampath R, Ecker DJ, Blyn LB. The IRIDICA BAC BSI Assay: Rapid, Sensitive and Culture-Independent Identification of Bacteria and Candida in Blood. PLoS One 2016; 11:e0158186. [PMID: 27384540 PMCID: PMC4934770 DOI: 10.1371/journal.pone.0158186] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/10/2016] [Indexed: 12/12/2022] Open
Abstract
Bloodstream infection (BSI) and sepsis are rising in incidence throughout the developed world. The spread of multi-drug resistant organisms presents increasing challenges to treatment. Surviving BSI is dependent on rapid and accurate identification of causal organisms, and timely application of appropriate antibiotics. Current culture-based methods used to detect and identify agents of BSI are often too slow to impact early therapy and may fail to detect relevant organisms in many positive cases. Existing methods for direct molecular detection of microbial DNA in blood are limited in either sensitivity (likely the result of small sample volumes) or in breadth of coverage, often because the PCR primers and probes used target only a few specific pathogens. There is a clear unmet need for a sensitive molecular assay capable of identifying the diverse bacteria and yeast associated with BSI directly from uncultured whole blood samples. We have developed a method of extracting DNA from larger volumes of whole blood (5 ml per sample), amplifying multiple widely conserved bacterial and fungal genes using a mismatch- and background-tolerant PCR chemistry, and identifying hundreds of diverse organisms from the amplified fragments on the basis of species-specific genetic signatures using electrospray ionization mass spectrometry (PCR/ESI-MS). We describe the analytical characteristics of the IRIDICA BAC BSI Assay and compare its pre-clinical performance to current standard-of-care methods in a collection of prospectively collected blood specimens from patients with symptoms of sepsis. The assay generated matching results in 80% of culture-positive cases (86% when common contaminants were excluded from the analysis), and twice the total number of positive detections. The described method is capable of providing organism identifications directly from uncultured blood in less than 8 hours. Disclaimer: The IRIDICA BAC BSI Assay is not available in the United States.
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Affiliation(s)
- David Metzgar
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
- * E-mail:
| | - Mark W. Frinder
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Richard E. Rothman
- Department of Emergency Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Stephen Peterson
- Department of Emergency Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Karen C. Carroll
- The Johns Hopkins Hospital Clinical Microbiology Laboratory, Baltimore, Maryland, United States of America
| | - Sean X. Zhang
- The Johns Hopkins Hospital Clinical Microbiology Laboratory, Baltimore, Maryland, United States of America
| | - Gideon D. Avornu
- Department of Emergency Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Megan A. Rounds
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Heather E. Carolan
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Donna M. Toleno
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - David Moore
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Thomas A. Hall
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Christian Massire
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Gregory S. Richmond
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Jose R. Gutierrez
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Rangarajan Sampath
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - David J. Ecker
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Lawrence B. Blyn
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
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Walley KR, Thain KR, Russell JA, Reilly MP, Meyer NJ, Ferguson JF, Christie JD, Nakada TA, Fjell CD, Thair SA, Cirstea MS, Boyd JH. PCSK9 is a critical regulator of the innate immune response and septic shock outcome. Sci Transl Med 2015; 6:258ra143. [PMID: 25320235 DOI: 10.1126/scitranslmed.3008782] [Citation(s) in RCA: 257] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A decrease in the activity of proprotein convertase subtilisin/kexin type 9 (PCSK9) increases the amount of low-density lipoprotein (LDL) receptors on liver cells and, therefore, LDL clearance. The clearance of lipids from pathogens is related to endogenous lipid clearance; thus, PCSK9 may also regulate removal of pathogen lipids such as lipopolysaccharide (LPS). Compared to controls, Pcsk9 knockout mice displayed decreases in inflammatory cytokine production and in other physiological responses to LPS. In human liver cells, PCSK9 inhibited LPS uptake, a necessary step in systemic clearance and detoxification. Pharmacological inhibition of PCSK9 improved survival and inflammation in murine polymicrobial peritonitis. Human PCSK9 loss-of-function genetic variants were associated with improved survival in septic shock patients and a decrease in inflammatory cytokine response both in septic shock patients and in healthy volunteers after LPS administration. The PCSK9 effect was abrogated in LDL receptor (LDLR) knockout mice and in humans who are homozygous for an LDLR variant that is resistant to PCSK9. Together, our results show that reduced PCSK9 function is associated with increased pathogen lipid clearance via the LDLR, a decreased inflammatory response, and improved septic shock outcome.
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Affiliation(s)
- Keith R Walley
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver V6Z 1Y6, Canada.
| | - Katherine R Thain
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver V6Z 1Y6, Canada
| | - James A Russell
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver V6Z 1Y6, Canada
| | - Muredach P Reilly
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Nuala J Meyer
- Pulmonary, Allergy, and Critical Care Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA. Center for Translational Lung Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jane F Ferguson
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jason D Christie
- Pulmonary, Allergy, and Critical Care Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA. Center for Translational Lung Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA. Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Taka-aki Nakada
- Department of Emergency and Critical Care Medicine, Chiba University Graduate School of Medicine, Chiba 260-8677, Japan
| | - Chris D Fjell
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver V6Z 1Y6, Canada
| | - Simone A Thair
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver V6Z 1Y6, Canada
| | - Mihai S Cirstea
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver V6Z 1Y6, Canada
| | - John H Boyd
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver V6Z 1Y6, Canada
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Mearelli F, Orso D, Fiotti N, Altamura N, Breglia A, De Nardo M, Paoli I, Zanetti M, Casarsa C, Biolo G. Sepsis outside intensive care unit: the other side of the coin. Infection 2014; 43:1-11. [PMID: 25110153 DOI: 10.1007/s15010-014-0673-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 07/28/2014] [Indexed: 02/07/2023]
Abstract
INTRODUCTION A growing body of evidence points out that a large amount of patients with sepsis are admitted and treated in medical ward (MW). With most of the sepsis studies conducted in intensive care unit (ICU), these patients, older and with more comorbidities have received poor attention. Provided the differences between the two groups of patients, results of diagnostic and therapeutic trials from ICU should not be routinely transferred to MW, where sepsis seems to be at least as common as in ICU. METHODS We analyzed clinical trials on novel tools for an early diagnosis of sepsis published in the last two year adopting strict research criteria. Moreover we conducted a target review of the literature on non-invasive monitoring of severe sepsis and septic shock. RESULTS AND CONCLUSIONS The combination of innovative and non-invasive tools for sepsis rule in/out, as quick alternatives to blood cultures (gold standard) with bedside integrated ultrasonography could impact triage, diagnosis and prognosis of septic patients managed in MW, preventing ICU admissions, poor outcomes and costly complications, especially in elderly that are usually highly vulnerable to invasive procedures.
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Affiliation(s)
- F Mearelli
- Unit of Clinica Medica Generale e Terapia Medica, Surgical Health Sciences, Department of Medical, University of Trieste, Strada di Fiume Cattinara, Trieste, 447 34149, Italy,
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Lyle NH, Pena OM, Boyd JH, Hancock REW. Barriers to the effective treatment of sepsis: antimicrobial agents, sepsis definitions, and host-directed therapies. Ann N Y Acad Sci 2014; 1323:101-14. [PMID: 24797961 DOI: 10.1111/nyas.12444] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Sepsis is a complex clinical syndrome involving both infection and a deleterious host immune response. Antimicrobial agents are key elements of sepsis treatment, yet despite great strides in antimicrobial development in the last decades, sepsis continues to be associated with unacceptably high mortality (~30%). This is the result, on one hand, of the rise of antimicrobial resistant organisms and, on the other hand, of the dearth of effective host-directed immune therapies. A major obstacle to the development of good host-directed therapies is the lack of understanding of the host immune response. The problem is exacerbated by poor nonspecific clinical definitions of disease. Poor definitions have had a profound impact on sepsis research, from epidemiologic studies to the failed clinical trials of host-directed therapies. Therefore, better definitions must be developed to enable advancement in the field.
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Affiliation(s)
- Ngan H Lyle
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, British Columbia, Canada
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