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Immuno-Dipstick for Colletotrichum gloeosporioides Detection: Towards On-Farm Application. BIOSENSORS 2022; 12:bios12020049. [PMID: 35200310 PMCID: PMC8869205 DOI: 10.3390/bios12020049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/11/2022] [Accepted: 01/15/2022] [Indexed: 11/16/2022]
Abstract
Early and quick detection of pathogens are crucial for managing the spread of infections in the biomedical, biosafety, food, and agricultural fields. While molecular diagnostics can offer the specificity and reliability in acute infectious diseases, detection of pathogens is often slowed down by the current benchtop molecular diagnoses, which are time consuming, labor intensive, and lack the mobility for application at the point-of-need. In this work, we developed a complete on-farm use detection protocol for the plant-devastating anthracnose agent: Colletotrichum gloeosporioides. Our methods combined a simplified DNA extraction on paper that is compatible with loop-mediated isothermal amplification (LAMP), coupled with paper-based immunoassay lateral flow sensing. Our results offer simple, quick, easy, and a minimally instrumented toolkit for Colletotrichum gloeosporioides detection. This scalable and adaptable platform is a valuable alternative to traditional sensing systems towards on-the-go pathogen detection in food and agriculture, biomedical, and other fields.
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Qiu L, Zhang L, Horowitz GL, Turzhitsky V, Coughlan MF, Glyavina M, Khan U, Zakharov YN, Vitkin E, Itzkan I, Perelman LT. Rapid detection and identification of bacteria directly from whole blood with light scattering spectroscopy based biosensor. SENSORS AND ACTUATORS. B, CHEMICAL 2021; 346:130489. [PMID: 34483482 PMCID: PMC8415441 DOI: 10.1016/j.snb.2021.130489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial infections are one of the major causes of death worldwide. The identification of a bacterial species that is the source of an infection generally takes a long time, and often exceeds the treatment window for seriously ill patients. Many of these deaths are preventable if the bacterial species can be identified quickly. Here we present an optical spectroscopic method for rapid detection and identification of bacteria directly from whole blood using a light scattering spectroscopy technique. This technique was originally developed to detect pre-cancerous changes in epithelial tissues, characterize changes in tissue on the cellular scale, and characterize biological structures comparable to or smaller than a single wavelength. We demonstrate here that not only can an inexpensive light scattering spectroscopy-based biosensor rapidly detect and identify four bacteria species in the blood, responsible for the majority of death causing infections, but that species-level identification can potentially be made based on approximately one thousand bacterial cells per milliliter of blood. Observing entire colonies or performing susceptibility testing is therefore not required.
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Affiliation(s)
- Le Qiu
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Lei Zhang
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Gary L. Horowitz
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Tufts University, Boston, Massachusetts 02111 USA
| | - Vladimir Turzhitsky
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Mark F. Coughlan
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Maria Glyavina
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Umar Khan
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Yuri N. Zakharov
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Edward Vitkin
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Irving Itzkan
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Lev T. Perelman
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
- Biological and Biomedical Sciences Program, Harvard University, Boston, Massachusetts 02115 USA
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3
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Chen K, Malik AA, Sheng YJ, Ahmed S, Sun C, Deng CL, Ojha SC. Clinical Utility of Molecular Tests for Guiding Therapeutic Decisions in Bloodstream Staphylococcal Infections: A Meta-Analysis. Front Pediatr 2021; 9:713447. [PMID: 34422731 PMCID: PMC8374148 DOI: 10.3389/fped.2021.713447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 07/12/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Treatment of bloodstream staphylococcal infections (BSI) necessitates the prompt initiation of appropriate antimicrobial agents and the rapid de-escalation of excessive broad-spectrum coverage to reduce the risk of mortality. We, therefore, aimed to demonstrate the diagnostic accuracy of nucleic acid amplification tests (NAAT) for the identification of methicillin-resistant S. aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) in clinically suspected patients. Methods: Until November 23, 2020, databases including PubMed, Scopus, Embase, and Web of Science were scanned for eligible studies. A bivariate random-effects model was used for meta-analysis of the 33 included studies obtained from 1606 citations, and pooled summary estimates with 95% confidence intervals (CI) were generated. Results: Twenty-three studies (n = 8,547) assessed NAAT accuracy for MSSA detection, while three studies (n = 479) evaluated MRSA detection in adults. The pooled NAAT sensitivity and specificity for MRSA in adults was higher [sensitivity: 0.83 (95% CI 0.59-0.96), specificity: 0.99 (95% CI 0.98-1.0)] as compared to MSSA [sensitivity: 0.76 (95% CI 0.69-0.82), specificity: 0.98 (95% CI 0.98-0.99)]. Similarly, eight studies (n = 4,089) investigating MSSA in pediatric population reported higher NAAT accuracy [sensitivity: 0.89 (95% CI 0.76-0.96), specificity: 0.98 (95% CI 0.97-0.98)] compared to adults. Among NAA tests, SeptiFast (real-time PCR, commercial) was frequently applied, and its diagnostic accuracy corresponded well to the overall summary estimates. A meta-regression and subgroup analysis of study design, sample condition, and patient selection method could not explain the heterogeneity (P > 0.05) in the diagnostic efficiency. Conclusions: NAAT could be applied as the preferred initial tests for timely diagnosis and BSI management.
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Affiliation(s)
- Ke Chen
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Luzhou, China
| | - Aijaz Ahmad Malik
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Yun-Jian Sheng
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Luzhou, China
| | - Sarfraz Ahmed
- Department of Basic Sciences, University of Veterinary and Animal Sciences Lahore, Narowal, Pakistan
| | - Changfeng Sun
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Luzhou, China
| | - Cun-Liang Deng
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Luzhou, China
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4
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Abafogi AT, Kim J, Lee J, Mohammed MO, van Noort D, Park S. 3D-Printed Modular Microfluidic Device Enabling Preconcentrating Bacteria and Purifying Bacterial DNA in Blood for Improving the Sensitivity of Molecular Diagnostics. SENSORS 2020; 20:s20041202. [PMID: 32098268 PMCID: PMC7070462 DOI: 10.3390/s20041202] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/19/2020] [Accepted: 02/20/2020] [Indexed: 01/22/2023]
Abstract
Molecular diagnostics for sepsis is still a challenge due to the presence of compounds that interfere with gene amplification and bacteria at concentrations lower than the limit of detection (LOD). Here, we report on the development of a 3D printed modular microfluidic device (3DpmμFD) that preconcentrates bacteria of interest in whole blood and purifies their genomic DNA (gDNA). It is composed of a W-shaped microchannel and a conical microchamber. Bacteria of interest are magnetically captured from blood in the device with antibody conjugated magnetic nanoparticles (Ab-MNPs) at 5 mL/min in the W-shaped microchannel, while purified gDNA of the preconcentrated bacteria is obtained with magnetic silica beads (MSBs) at 2 mL/min in the conical microchamber. The conical microchamber was designed to be connected to the microchannel after the capturing process using a 3D-printed rotary valve to minimize the exposure of the MSBs to interfering compounds in blood. The pretreatment process of spiked blood (2.5 mL) can be effectively completed within about 50 min. With the 3DpmμFD, the LOD for the target microorganism Escherichia coli O157:H7 measured by both polymerase chain reaction (PCR) with electrophoresis and quantitative PCR was 10 colony forming unit (CFU) per mL of whole blood. The results suggest that our method lowers the LOD of molecular diagnostics for pathogens in blood by providing bacterial gDNA at high purity and concentration.
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Affiliation(s)
- Abdurhaman Teyib Abafogi
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea; (A.T.A.); (J.K.); (J.L.)
| | - Jaewon Kim
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea; (A.T.A.); (J.K.); (J.L.)
| | - Jinyeop Lee
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea; (A.T.A.); (J.K.); (J.L.)
| | - Merem Omer Mohammed
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon 16419, Korea;
| | - Danny van Noort
- Division of Biotechnology, IFM, Linkoping University, 58183 Linkoping, Sweden;
- Chair of Micro Process Engineering and Technology (COMPETE), University of Ljubljana, 1000 Ljubljana, Slovenia
- Centro de Investigación en Bioingeniería -BIO, Universidad de Ingenieria y Tecnologia—UTEC, Barranco 15036, Peru
| | - Sungsu Park
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea; (A.T.A.); (J.K.); (J.L.)
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon 16419, Korea;
- Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Korea
- Correspondence: ; Tel.: +82-31-290-7431; Fax: +82-31-290-5889
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Sinha M, Jupe J, Mack H, Coleman TP, Lawrence SM, Fraley SI. Emerging Technologies for Molecular Diagnosis of Sepsis. Clin Microbiol Rev 2018; 31:e00089-17. [PMID: 29490932 PMCID: PMC5967692 DOI: 10.1128/cmr.00089-17] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Rapid and accurate profiling of infection-causing pathogens remains a significant challenge in modern health care. Despite advances in molecular diagnostic techniques, blood culture analysis remains the gold standard for diagnosing sepsis. However, this method is too slow and cumbersome to significantly influence the initial management of patients. The swift initiation of precise and targeted antibiotic therapies depends on the ability of a sepsis diagnostic test to capture clinically relevant organisms along with antimicrobial resistance within 1 to 3 h. The administration of appropriate, narrow-spectrum antibiotics demands that such a test be extremely sensitive with a high negative predictive value. In addition, it should utilize small sample volumes and detect polymicrobial infections and contaminants. All of this must be accomplished with a platform that is easily integrated into the clinical workflow. In this review, we outline the limitations of routine blood culture testing and discuss how emerging sepsis technologies are converging on the characteristics of the ideal sepsis diagnostic test. We include seven molecular technologies that have been validated on clinical blood specimens or mock samples using human blood. In addition, we discuss advances in machine learning technologies that use electronic medical record data to provide contextual evaluation support for clinical decision-making.
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Affiliation(s)
- Mridu Sinha
- Bioengineering Department, University of California, San Diego, San Diego, California, USA
| | - Julietta Jupe
- Donald Danforth Plant Science Center, Saint Louis, Missouri, USA
| | - Hannah Mack
- Bioengineering Department, University of California, San Diego, San Diego, California, USA
| | - Todd P Coleman
- Bioengineering Department, University of California, San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California, San Diego, San Diego, California, USA
| | - Shelley M Lawrence
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, University of California, San Diego, San Diego, California, USA
- Rady Children's Hospital of San Diego, San Diego, California, USA
- Clinical Translational Research Institute, University of California, San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California, San Diego, San Diego, California, USA
| | - Stephanie I Fraley
- Bioengineering Department, University of California, San Diego, San Diego, California, USA
- Clinical Translational Research Institute, University of California, San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California, San Diego, San Diego, California, USA
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6
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Stevenson M, Pandor A, Martyn-St James M, Rafia R, Uttley L, Stevens J, Sanderson J, Wong R, Perkins GD, McMullan R, Dark P. Sepsis: the LightCycler SeptiFast Test MGRADE®, SepsiTest™ and IRIDICA BAC BSI assay for rapidly identifying bloodstream bacteria and fungi - a systematic review and economic evaluation. Health Technol Assess 2018; 20:1-246. [PMID: 27355222 DOI: 10.3310/hta20460] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Sepsis can lead to multiple organ failure and death. Timely and appropriate treatment can reduce in-hospital mortality and morbidity. OBJECTIVES To determine the clinical effectiveness and cost-effectiveness of three tests [LightCycler SeptiFast Test MGRADE(®) (Roche Diagnostics, Risch-Rotkreuz, Switzerland); SepsiTest(TM) (Molzym Molecular Diagnostics, Bremen, Germany); and the IRIDICA BAC BSI assay (Abbott Diagnostics, Lake Forest, IL, USA)] for the rapid identification of bloodstream bacteria and fungi in patients with suspected sepsis compared with standard practice (blood culture with or without matrix-absorbed laser desorption/ionisation time-of-flight mass spectrometry). DATA SOURCES Thirteen electronic databases (including MEDLINE, EMBASE and The Cochrane Library) were searched from January 2006 to May 2015 and supplemented by hand-searching relevant articles. REVIEW METHODS A systematic review and meta-analysis of effectiveness studies were conducted. A review of published economic analyses was undertaken and a de novo health economic model was constructed. A decision tree was used to estimate the costs and quality-adjusted life-years (QALYs) associated with each test; all other parameters were estimated from published sources. The model was populated with evidence from the systematic review or individual studies, if this was considered more appropriate (base case 1). In a secondary analysis, estimates (based on experience and opinion) from seven clinicians regarding the benefits of earlier test results were sought (base case 2). A NHS and Personal Social Services perspective was taken, and costs and benefits were discounted at 3.5% per annum. Scenario analyses were used to assess uncertainty. RESULTS For the review of diagnostic test accuracy, 62 studies of varying methodological quality were included. A meta-analysis of 54 studies comparing SeptiFast with blood culture found that SeptiFast had an estimated summary specificity of 0.86 [95% credible interval (CrI) 0.84 to 0.89] and sensitivity of 0.65 (95% CrI 0.60 to 0.71). Four studies comparing SepsiTest with blood culture found that SepsiTest had an estimated summary specificity of 0.86 (95% CrI 0.78 to 0.92) and sensitivity of 0.48 (95% CrI 0.21 to 0.74), and four studies comparing IRIDICA with blood culture found that IRIDICA had an estimated summary specificity of 0.84 (95% CrI 0.71 to 0.92) and sensitivity of 0.81 (95% CrI 0.69 to 0.90). Owing to the deficiencies in study quality for all interventions, diagnostic accuracy data should be treated with caution. No randomised clinical trial evidence was identified that indicated that any of the tests significantly improved key patient outcomes, such as mortality or duration in an intensive care unit or hospital. Base case 1 estimated that none of the three tests provided a benefit to patients compared with standard practice and thus all tests were dominated. In contrast, in base case 2 it was estimated that all cost per QALY-gained values were below £20,000; the IRIDICA BAC BSI assay had the highest estimated incremental net benefit, but results from base case 2 should be treated with caution as these are not evidence based. LIMITATIONS Robust data to accurately assess the clinical effectiveness and cost-effectiveness of the interventions are currently unavailable. CONCLUSIONS The clinical effectiveness and cost-effectiveness of the interventions cannot be reliably determined with the current evidence base. Appropriate studies, which allow information from the tests to be implemented in clinical practice, are required. STUDY REGISTRATION This study is registered as PROSPERO CRD42015016724. FUNDING The National Institute for Health Research Health Technology Assessment programme.
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Affiliation(s)
- Matt Stevenson
- School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Abdullah Pandor
- School of Health and Related Research, University of Sheffield, Sheffield, UK
| | | | - Rachid Rafia
- School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Lesley Uttley
- School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - John Stevens
- School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Jean Sanderson
- School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Ruth Wong
- School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Gavin D Perkins
- Warwick Clinical Trials Unit, University of Warwick, Coventry, UK.,Heart of England NHS Foundation Trust, Coventry, UK
| | - Ronan McMullan
- Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK.,Belfast Health and Social Care Trust, The Royal Hospitals, Belfast, UK
| | - Paul Dark
- Institute of Inflammation and Repair, University of Manchester, Manchester, UK.,Salford Royal NHS Foundation Trust, Salford, UK
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7
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Warhurst G, Dunn G, Chadwick P, Blackwood B, McAuley D, Perkins GD, McMullan R, Gates S, Bentley A, Young D, Carlson GL, Dark P. Rapid detection of health-care-associated bloodstream infection in critical care using multipathogen real-time polymerase chain reaction technology: a diagnostic accuracy study and systematic review. Health Technol Assess 2016; 19:1-142. [PMID: 25961752 DOI: 10.3310/hta19350] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND There is growing interest in the potential utility of real-time polymerase chain reaction (PCR) in diagnosing bloodstream infection by detecting pathogen deoxyribonucleic acid (DNA) in blood samples within a few hours. SeptiFast (Roche Diagnostics GmBH, Mannheim, Germany) is a multipathogen probe-based system targeting ribosomal DNA sequences of bacteria and fungi. It detects and identifies the commonest pathogens causing bloodstream infection. As background to this study, we report a systematic review of Phase III diagnostic accuracy studies of SeptiFast, which reveals uncertainty about its likely clinical utility based on widespread evidence of deficiencies in study design and reporting with a high risk of bias. OBJECTIVE Determine the accuracy of SeptiFast real-time PCR for the detection of health-care-associated bloodstream infection, against standard microbiological culture. DESIGN Prospective multicentre Phase III clinical diagnostic accuracy study using the standards for the reporting of diagnostic accuracy studies criteria. SETTING Critical care departments within NHS hospitals in the north-west of England. PARTICIPANTS Adult patients requiring blood culture (BC) when developing new signs of systemic inflammation. MAIN OUTCOME MEASURES SeptiFast real-time PCR results at species/genus level compared with microbiological culture in association with independent adjudication of infection. Metrics of diagnostic accuracy were derived including sensitivity, specificity, likelihood ratios and predictive values, with their 95% confidence intervals (CIs). Latent class analysis was used to explore the diagnostic performance of culture as a reference standard. RESULTS Of 1006 new patient episodes of systemic inflammation in 853 patients, 922 (92%) met the inclusion criteria and provided sufficient information for analysis. Index test assay failure occurred on 69 (7%) occasions. Adult patients had been exposed to a median of 8 days (interquartile range 4-16 days) of hospital care, had high levels of organ support activities and recent antibiotic exposure. SeptiFast real-time PCR, when compared with culture-proven bloodstream infection at species/genus level, had better specificity (85.8%, 95% CI 83.3% to 88.1%) than sensitivity (50%, 95% CI 39.1% to 60.8%). When compared with pooled diagnostic metrics derived from our systematic review, our clinical study revealed lower test accuracy of SeptiFast real-time PCR, mainly as a result of low diagnostic sensitivity. There was a low prevalence of BC-proven pathogens in these patients (9.2%, 95% CI 7.4% to 11.2%) such that the post-test probabilities of both a positive (26.3%, 95% CI 19.8% to 33.7%) and a negative SeptiFast test (5.6%, 95% CI 4.1% to 7.4%) indicate the potential limitations of this technology in the diagnosis of bloodstream infection. However, latent class analysis indicates that BC has a low sensitivity, questioning its relevance as a reference test in this setting. Using this analysis approach, the sensitivity of the SeptiFast test was low but also appeared significantly better than BC. Blood samples identified as positive by either culture or SeptiFast real-time PCR were associated with a high probability (> 95%) of infection, indicating higher diagnostic rule-in utility than was apparent using conventional analyses of diagnostic accuracy. CONCLUSION SeptiFast real-time PCR on blood samples may have rapid rule-in utility for the diagnosis of health-care-associated bloodstream infection but the lack of sensitivity is a significant limiting factor. Innovations aimed at improved diagnostic sensitivity of real-time PCR in this setting are urgently required. Future work recommendations include technology developments to improve the efficiency of pathogen DNA extraction and the capacity to detect a much broader range of pathogens and drug resistance genes and the application of new statistical approaches able to more reliably assess test performance in situation where the reference standard (e.g. blood culture in the setting of high antimicrobial use) is prone to error. STUDY REGISTRATION The systematic review is registered as PROSPERO CRD42011001289. FUNDING The National Institute for Health Research Health Technology Assessment programme. Professor Daniel McAuley and Professor Gavin D Perkins contributed to the systematic review through their funded roles as codirectors of the Intensive Care Foundation (UK).
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Affiliation(s)
- Geoffrey Warhurst
- Infection, Injury and Inflammation Research Group, Salford Royal NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Salford, UK
| | - Graham Dunn
- Centre for Biostatistics, Institute of Population Health, Faculty of Medical and Human Sciences, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Salford, UK
| | - Paul Chadwick
- Microbiology Department, Salford Royal NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Salford, UK
| | - Bronagh Blackwood
- Centre for Infection and Immunity, Queen's University Belfast, Belfast, UK
| | - Daniel McAuley
- Centre for Infection and Immunity, Queen's University Belfast, Belfast, UK
| | - Gavin D Perkins
- Clinical Trials Unit, Medical School, Warwick University, Coventry, UK
| | - Ronan McMullan
- Medical Microbiology, Royal Victoria Hospital, Belfast, UK
| | - Simon Gates
- Clinical Trials Unit, Medical School, Warwick University, Coventry, UK
| | - Andrew Bentley
- Institue of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Salford, UK
| | - Duncan Young
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, Oxford, UK
| | - Gordon L Carlson
- Infection, Injury and Inflammation Research Group, Salford Royal NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Salford, UK
| | - Paul Dark
- Infection, Injury and Inflammation Research Group, Salford Royal NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Salford, UK
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8
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Tafelski S, Nachtigall I, Adam T, Bereswill S, Faust J, Tamarkin A, Trefzer T, Deja M, Idelevich EA, Wernecke KD, Becker K, Spies C. Randomized controlled clinical trial evaluating multiplex polymerase chain reaction for pathogen identification and therapy adaptation in critical care patients with pulmonary or abdominal sepsis. J Int Med Res 2015; 43:364-77. [PMID: 25911587 DOI: 10.1177/0300060514561135] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 10/29/2014] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVE To determine whether a multiplex polymerase chain reaction (PCR)-based test could reduce the time required for initial pathogen identification in patients in an intensive care unit (ICU) setting. METHODS This double-blind, parallel-group randomized controlled trial** enrolled adults with suspected pulmonary or abdominal sepsis caused by an unknown pathogen. Both the intervention and control groups underwent the standard blood culture (BC) testing, but additional pathogen identification, based on the results of a LightCycler® SeptiFast PCR test, were provided in the intervention group. RESULTS The study enrolled 37 patients in the control group and 41 in the intervention group. Baseline clinical and demographic characteristics were similar in both groups. The PCR-based test identified a pathogen in 10 out of 41 (24.4%) patients in the intervention group, with a mean duration from sampling to providing the information to the ICU of 15.9 h. In the control group, BC results were available after a significantly longer period (38.1 h). CONCLUSION The LightCycler® SeptiFast PCR test demonstrated a significant reduction in the time required for initial pathogen identification, compared with standard BC.
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Affiliation(s)
- Sascha Tafelski
- Department of Anaesthesiology and Intensive Care Medicine, Charité-Universitaetsmedizin Berlin, Berlin, Germany
| | - Irit Nachtigall
- Department of Anaesthesiology and Intensive Care Medicine, Charité-Universitaetsmedizin Berlin, Berlin, Germany
| | - Thomas Adam
- Institute for Microbiology and Hygiene Berlin, Charité-Universitaetsmedizin Berlin, Berlin, Germany
| | - Stefan Bereswill
- Institute for Microbiology and Hygiene Berlin, Charité-Universitaetsmedizin Berlin, Berlin, Germany
| | - Jana Faust
- Department of Anaesthesiology and Intensive Care Medicine, Charité-Universitaetsmedizin Berlin, Berlin, Germany
| | - Andrey Tamarkin
- Department of Anaesthesiology and Intensive Care Medicine, Charité-Universitaetsmedizin Berlin, Berlin, Germany
| | - Tanja Trefzer
- Department of Anaesthesiology and Intensive Care Medicine, Charité-Universitaetsmedizin Berlin, Berlin, Germany
| | - Maria Deja
- Department of Anaesthesiology and Intensive Care Medicine, Charité-Universitaetsmedizin Berlin, Berlin, Germany
| | - Evgeny A Idelevich
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Klaus-Dieter Wernecke
- Institute of Medical Biometry, Charité-Universitaetsmedizin Berlin, Berlin, Germany SOSTANA GmbH, Berlin, Germany
| | - Karsten Becker
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Claudia Spies
- Department of Anaesthesiology and Intensive Care Medicine, Charité-Universitaetsmedizin Berlin, Berlin, Germany
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9
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Dark P, Blackwood B, Gates S, McAuley D, Perkins GD, McMullan R, Wilson C, Graham D, Timms K, Warhurst G. Accuracy of LightCycler(®) SeptiFast for the detection and identification of pathogens in the blood of patients with suspected sepsis: a systematic review and meta-analysis. Intensive Care Med 2014; 41:21-33. [PMID: 25416643 DOI: 10.1007/s00134-014-3553-8] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 11/07/2014] [Indexed: 01/10/2023]
Abstract
PURPOSE There is an urgent need to develop diagnostic tests to improve the detection of pathogens causing life-threatening infection (sepsis). SeptiFast is a CE-marked multi-pathogen real-time PCR system capable of detecting DNA sequences of bacteria and fungi present in blood samples within a few hours. We report here a systematic review and meta-analysis of diagnostic accuracy studies of SeptiFast in the setting of suspected sepsis. METHODS A comprehensive search strategy was developed to identify studies that compared SeptiFast with blood culture in suspected sepsis. Methodological quality was assessed using QUADAS. Heterogeneity of studies was investigated using a coupled forest plot of sensitivity and specificity and a scatter plot in receiver operator characteristic space. Bivariate model method was used to estimate summary sensitivity and specificity. RESULTS From 41 phase III diagnostic accuracy studies, summary sensitivity and specificity for SeptiFast compared with blood culture were 0.68 (95 % CI 0.63-0.73) and 0.86 (95 % CI 0.84-0.89) respectively. Study quality was judged to be variable with important deficiencies overall in design and reporting that could impact on derived diagnostic accuracy metrics. CONCLUSIONS SeptiFast appears to have higher specificity than sensitivity, but deficiencies in study quality are likely to render this body of work unreliable. Based on the evidence presented here, it remains difficult to make firm recommendations about the likely clinical utility of SeptiFast in the setting of suspected sepsis.
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Affiliation(s)
- Paul Dark
- Infection, Injury and Inflammation Research Group, Biomedical Facility, Clinical Sciences, Manchester Academic Health Sciences Centre, Salford Royal NHS Foundation Trust, Salford, Greater Manchester, M6 8HD, UK,
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Leli C, Cardaccia A, Ferranti M, Cesarini A, D'Alò F, Ferri C, Cenci E, Mencacci A. Procalcitonin better than C-reactive protein, erythrocyte sedimentation rate, and white blood cell count in predicting DNAemia in patients with sepsis. ACTA ACUST UNITED AC 2014; 46:745-52. [PMID: 25195647 DOI: 10.3109/00365548.2014.936493] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
BACKGROUND Procalcitonin (PCT) levels can be used to predict bacteremia and DNAemia in patients with sepsis. In this study, the diagnostic accuracy of PCT in predicting blood culture (BC) results and DNAemia, as detected by real-time PCR (RT-PCR), was compared with that of other markers of inflammation commonly evaluated in patients with suspected sepsis, such as C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), and white blood cell (WBC) count. METHODS A total of 571 patients for whom BC, blood RT-PCR, PCT, CRP, ESR, and WBC count were requested for laboratory diagnosis of sepsis were included in the study. Receiver operating characteristic curve analysis was performed to compare the ability of the above biomarkers to predict BC and blood RT-PCR results. RESULTS A total of 108 pathogens were identified by BC (79 pathogens, 14.5% positive rate) and/or RT-PCR (90 pathogens, 16.5% positive rate), after exclusion of 26 contaminated samples. The PCT areas under the curve (AUCs) in predicting BC (0.843; 95% CI 0.796-0.890; p < 0.0001) and RT-PCR (0.916; 95% CI 0.888-0.945; p < 0.0001) results were significantly greater than AUCs found for CRP, ESR, and WBC count. CONCLUSIONS PCT showed a better diagnostic accuracy than CRP, ESR, and WBC count in predicting DNAemia and bacteremia in patients with suspected sepsis.
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Affiliation(s)
- Christian Leli
- From the Microbiology Section, Department of Experimental Medicine, University of Perugia, Santa Maria della Misericordia Hospital , Perugia , Italy
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Enzymatic treatment of specimens before DNA extraction directly influences molecular detection of infectious agents. PLoS One 2014; 9:e94886. [PMID: 24936792 PMCID: PMC4061000 DOI: 10.1371/journal.pone.0094886] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/20/2014] [Indexed: 12/31/2022] Open
Abstract
INTRODUCTION Biological samples, pharmaceuticals or food contain proteins, lipids, polymers, ammoniums and macromolecules that alter the detection of infectious agents by DNA amplification techniques (PCR). Moreover the targeted DNA has to be released from the complex cell walls and the compact nucleoprotein matrixes and cleared from potential inhibitors. The goal of the present work was to assess the efficiency of enzymatic pretreatments on infectious agents to make DNA available for further extraction and amplification. METHODS Staphylococcus epidermidis, Streptococcus mitis, Propionibacterium acnes, Escherichia coli, Pseudomonas aeruginosa, Candida albicans, Aspergillus niger and Fusarium solani were mixed with an internal control virus and treated with: 1) proteinase K; 2) lyticase and 3) lyticase followed by proteinase K. DNAs was manually extracted using the QIAmp DNA Mini kit or the MagNA Pure Compact automate. DNA extraction yields and the inhibitors were assessed with a phocid Herpesvirus. Bacterial detection was performed using TaqMan real-time PCR and yeasts and filamentous Fungi with HRM (real-time PCR followed by high-resolution melting analysis). RESULTS Viral DNA was released, extracted and detected using manual and automatic methods without pre enzymatic treatments. Either the manual or the automatic DNA extraction systems did not meet the sensitivity expectations if enzymatic treatments were not performed before: lyticase for Fungi and Proteinase K for Bacteria. The addition of lyticase and proteinase K did not improve results. For Fungi the detection after lyticase was higher than for Proteinase K, for which melting analysis did not allow fungal specification. DISCUSSION Columns and magnetic beads allowed collecting DNA and separate PCR inhibitors. Detection rates cannot be related to DNA-avidity of beads or to elution but to the lack of proteolysis.
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Chang SS, Hsieh WH, Liu TS, Lee SH, Wang CH, Chou HC, Yeo YH, Tseng CP, Lee CC. Multiplex PCR system for rapid detection of pathogens in patients with presumed sepsis - a systemic review and meta-analysis. PLoS One 2013; 8:e62323. [PMID: 23734173 PMCID: PMC3667030 DOI: 10.1371/journal.pone.0062323] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 03/13/2013] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Blood culture is viewed as the golden standard for the diagnosis of sepsis but suffers from low sensitivity and long turnaround time. LightCycler SeptiFast (LC-SF) is a real-time multiplex polymerase chain reaction test able to detect 25 common pathogens responsible for bloodstream infections within hours. We aim to assess the accuracy of LC-SF by systematically reviewing the published studies. METHOD Related literature on Medline, Embase, and Cochrane databases was searched up to October 2012 for studies utilizing LC-SF to diagnose suspected sepsis and that provided sufficient data to construct two-by-two tables. RESULTS A total of 34 studies enrolling 6012 patients of suspected sepsis were included. The overall sensitivity and specificity for LC-SF to detect bacteremia or fungemia was 0·75 (95% CI: 0·65-0·83) and 0·92 (95%CI:0·90-0·95), respectively. LC-SF had a high positive likelihood ratio (10·10) and a moderate negative likelihood ratio (0·27). Specifically, LC-SF had a sensitivity of 0·80 (95%CI: 0·70-0·88) and a specificity of 0·95(95%CI: 0·93-0·97) for the bacteremia outcome, and a sensitivity of 0·61 (95%CI: 0·48-0·72) and a specificity of 0·99 (95%CI: 0·99-0·99) for the fungemia outcome. High heterogeneity was found in the bacteremia outcome subgroup but not in the fungemia outcome subgroup. CONCLUSION LC-SF is of high rule-in value for early detection of septic patients. In a population with low pretest probability, LC-SF test can still provide valuable information for ruling out bacteremia or fungemia.
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Affiliation(s)
- Shy-Shin Chang
- Department of Family Medicine, Chang Gung Memorial Hospital, Taoyuan, and Chang Gung University College of Medicine, Taoyuan, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wen-Han Hsieh
- Department of Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Ting-Shou Liu
- Department of Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Si-Huei Lee
- Department of Rehabilitation and Physical Medicine, Taipei Veteran General Hospital, Taipei, Taiwan
- Department of Rehabilitation and Physical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chih-Hung Wang
- Department of Emergency Medicine, National Taiwan University Hospital, Yunlin Branch, Douliou, Taiwan
| | - Hao-Chang Chou
- Department of Emergency Medicine, National Taiwan University Hospital, Yunlin Branch, Douliou, Taiwan
| | - Yee Hui Yeo
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Ching-Ping Tseng
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Tao-Yuan, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan
| | - Chien-Chang Lee
- Department of Emergency Medicine, National Taiwan University Hospital, Yunlin Branch, Douliou, Taiwan
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
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Schreiber J, Nierhaus A, Braune SA, de Heer G, Kluge S. Comparison of three different commercial PCR assays for the detection of pathogens in critically ill sepsis patients. Med Klin Intensivmed Notfmed 2013; 108:311-8. [PMID: 23516029 DOI: 10.1007/s00063-013-0227-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 01/16/2013] [Accepted: 02/03/2013] [Indexed: 12/31/2022]
Abstract
INTRODUCTION The high mortality rate associated with sepsis necessitates a timely identification of the causative organism in order to optimize antimicrobial therapy. PCR assays are increasingly being used for this purpose. The aim of this study was to compare three commercially available PCR systems for the diagnosis of systemic infections. PATIENTS AND METHODS In a prospective observational study, a broad-range (SepsiTest®; Molzym, Bremen, Germany) and two multiplex PCR assays (VYOO®; SIRS-Lab, Jena, Germany and LightCycler® SeptiFast; Roche, Mannheim, Germany) were compared to blood cultures with respect to the clinical course of 50 critically ill patients with sepsis, severe sepsis or septic shock. RESULTS Pathogens were detected by PCR in 12 % (SepsiTest®), 10 % (VYOO®) and 14 % (LightCycler® SeptiFast) of samples and in 26 % by blood culture. Negative results were obtained using all four methods in 32 samples (64 %) and 3 (6 %) samples were positive in all tests. Upon consideration of additional diagnostic findings and the clinical course, eight (16 %) of the positive blood culture results were deemed clinically relevant. All three PCR assays could also identify the causative organism (or a specific gene thereof) in three of these eight positive blood cultures, whereas for five of the eight, all three PCR assays were negative. In one patient with a negative blood culture, the SepsiTest®, VYOO® and LightCycler® SeptiFast assays were positive for Streptococcus species. The PCR assays appeared to be less susceptible than blood cultures to false-positive results arising from contamination with coagulase-negative staphylococcal organisms. CONCLUSION There was some variability between the three PCR assays tested and the corresponding blood cultures with regards to the type of pathogen detected. The three PCR assays appeared to be less susceptible to false-positive results than blood cultures.
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Affiliation(s)
- J Schreiber
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany.
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Abstract
Sepsis is among the most common causes of death in hospitals. It arises from the host response to infection. Currently, diagnosis relies on nonspecific physiological criteria and culture-based pathogen detection. This results in diagnostic uncertainty, therapeutic delays, the mis- and overuse of antibiotics, and the failure to identify patients who might benefit from immunomodulatory therapies. There is a need for new sepsis biomarkers that can aid in therapeutic decision making and add information about screening, diagnosis, risk stratification, and monitoring of the response to therapy. The host response involves hundreds of mediators and single molecules, many of which have been proposed as biomarkers. It is, however, unlikely that one single biomarker is able to satisfy all the needs and expectations for sepsis research and management. Among biomarkers that are measurable by assays approved for clinical use, procalcitonin (PCT) has shown some usefulness as an infection marker and for antibiotic stewardship. Other possible new approaches consist of molecular strategies to improve pathogen detection and molecular diagnostics and prognostics based on transcriptomic, proteomic, or metabolic profiling. Novel approaches to sepsis promise to transform sepsis from a physiologic syndrome into a group of distinct biochemical disorders and help in the development of better diagnostic tools and effective adjunctive sepsis therapies.
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Mencacci A, Leli C, Cardaccia A, Meucci M, Moretti A, D'Alò F, Farinelli S, Pagliochini R, Barcaccia M, Bistoni F. Procalcitonin predicts real-time PCR results in blood samples from patients with suspected sepsis. PLoS One 2012; 7:e53279. [PMID: 23300907 PMCID: PMC3531374 DOI: 10.1371/journal.pone.0053279] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 11/27/2012] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Early diagnosis and rapid bacterial identification are of primary importance for outcome of septic patients. SeptiFast® (SF) real-time PCR assay is of potential utility in the etiological diagnosis of sepsis, but it cannot replace blood culture (BC) for routine use in clinical laboratory. Procalcitonin (PCT) is a marker of sepsis and can predict bacteremia in septic patients. The aim of the present study was to investigate whether PCT serum levels could predict SF results, and could help screening febrile patients in which a SF assay can improve the etiological diagnosis of sepsis. METHODS From 1009 febrile patients with suspected sepsis, 1009 samples for BC, SF real-time PCR, and PCT determination were obtained simultaneously, and results were compared and statistically analysed. Receiver operating characteristic (ROC) curves were generated to determine the area under the curve and to identify which cut-off of PCT value produced the best sensitivity to detect SF results. RESULTS Mean PCT values of sera drawn simultaneously with samples SF positive (35.42 ± 61.03 ng/ml) or BC positive (23.14 ± 51.56 ng/ml) for a pathogen were statistically higher than those drawn simultaneously with SF negative (0.84 ± 1.67 ng/ml) or BC negative (2.79 ± 16.64 ng/ml) samples (p<0.0001). For SF, ROC analysis showed an area under the curve of 0.927 (95% confidence interval: 0.899-0.955, p<0.0001). The PCT cut-off value of 0.37 ng/ml showed a negative predictive value of 99%, reducing the number of SF assays of 53.9%, still identifying the 96.4% of the pathogens. CONCLUSION PCT can be used in febrile patients with suspected sepsis to predict SF positive or negative results. A cut-off value of 0.37 ng/ml can be considered for optimal sensitivity, so that, in the routine laboratory activity, SF assay should not be used for diagnosis of sepsis in an unselected patient population with a PCT value <0.37 ng/ml.
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Affiliation(s)
- Antonella Mencacci
- Microbiology Section, Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy.
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Bissonnette L, Bergeron MG. Multiparametric technologies for the diagnosis of syndromic infections. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.clinmicnews.2012.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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New strategy for rapid diagnosis and characterization of fungal infections: the example of corneal scrapings. PLoS One 2012; 7:e37660. [PMID: 22768289 PMCID: PMC3388096 DOI: 10.1371/journal.pone.0037660] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 04/23/2012] [Indexed: 11/19/2022] Open
Abstract
Purpose The prognosis of people infected with Fungi especially immunocompromised depends on rapid and accurate diagnosis to capitalize on time administration of specific treatments. However, cultures produce false negative results and nucleic-acid amplification techniques require complex post-amplification procedures to differentiate relevant fungal types. The objective of this work was to develop a new diagnostic strategy based on real-time polymerase-chain reaction high-resolution melting analysis (PCR-HRM) that a) detects yeasts and filamentous Fungi, b) differentiates yeasts from filamentous Fungi, and c) discriminates among relevant species of yeasts. Methods PCR-HRM detection limits and specificity were assessed with a) isolated strains; b) human blood samples experimentally infected with Fungi; c) blood experimentally infected with other infectious agents; d) corneal scrapings from patients with suspected fungal keratitis (culture positive and negative) and e) scrapings from patients with suspected bacterial, viral or Acanthamoeba infections. The DNAs were extracted and mixed with primers diluted in the MeltDoctor® HRM Master Mix in 2 tubes, the first for yeasts, containing the forward primer CandUn (5'CATGCCTGTTTGAGCGTC) and the reverse primer FungUn (5'TCCTCCGCTT ATTGATATGCT) and the second for filamentous Fungi, containing the forward primer FilamUn (5'TGCCTGTCCGAGCGTCAT) and FungUn. Molecular probes were not necessary. The yields of DNA extraction and the PCR inhibitors were systematically monitored. Results PCR-HRM detected 0.1 Colony Forming Units (CFU)/µl of yeasts and filamentous Fungi, differentiated filamentous Fungi from yeasts and discriminated among relevant species of yeasts. PCR-HRM performances were higher than haemoculture and sensitivity and specificity was 100% for culture positive samples, detecting and characterizing Fungi in 7 out 10 culture negative suspected fungal keratitis. Conclusions PCR-HRM appears as a new, sensitive, specific and inexpensive test that detects Fungi and differentiates filamentous Fungi from yeasts. It allows direct fungal detection from clinical samples and experimentally infected blood in less than 2.30 h after DNA extraction.
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Diagnostic performance of a multiple real-time PCR assay in patients with suspected sepsis hospitalized in an internal medicine ward. J Clin Microbiol 2012; 50:1285-8. [PMID: 22322348 DOI: 10.1128/jcm.06793-11] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Early identification of causative pathogen in sepsis patients is pivotal to improve clinical outcome. SeptiFast (SF), a commercially available system for molecular diagnosis of sepsis based on PCR, has been mostly used in patients hospitalized in hematology and intensive care units. We evaluated the diagnostic accuracy and clinical usefulness of SF, compared to blood culture (BC), in 391 patients with suspected sepsis, hospitalized in a department of internal medicine. A causative pathogen was identified in 85 patients (22%). Sixty pathogens were detected by SF and 57 by BC. No significant differences were found between the two methods in the rates of pathogen detection (P = 0.74), even after excluding 9 pathogens which were isolated by BC and were not included in the SF master list (P = 0.096). The combination of SF and BC significantly improved the diagnostic yield in comparison to BC alone (P < 0.001). Compared to BC, SF showed a significantly lower contamination rate (0 versus 19 cases; P < 0.001) with a higher specificity for pathogen identification (1.00, 95% confidence interval [CI] of 0.99 to 1.00, versus 0.94, 95% CI of 0.90 to 0.96; P = 0.005) and a higher positive predictive value (1.00, 95% CI of 1.00 to 0.92%, versus 0.75, 95% CI of 0.63 to 0.83; P = 0.005). In the subgroup of patients (n = 191) who had been receiving antibiotic treatment for ≥24 h, SF identified more pathogens (16 versus 6; P = 0.049) compared to BC. These results suggest that, in patients with suspected sepsis, hospitalized in an internal medicine ward, SF could be a highly valuable adjunct to conventional BC, particularly in patients under antibiotic treatment.
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