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Samuel L. Direct-from-Blood Detection of Pathogens: a Review of Technology and Challenges. J Clin Microbiol 2023; 61:e0023121. [PMID: 37222587 PMCID: PMC10358183 DOI: 10.1128/jcm.00231-21] [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: 05/25/2023] Open
Abstract
Blood cultures have been the staple of clinical microbiology laboratories for well over half a century, but gaps remain in our ability to identify the causative agent in patients presenting with signs and symptoms of sepsis. Molecular technologies have revolutionized the clinical microbiology laboratory in many areas but have yet to present a viable alternative to blood cultures. There has been a recent surge of interest in utilizing novel approaches to address this challenge. In this minireview, I discuss whether molecular tools will finally give us the answers we need and the practical challenges of incorporating them into the diagnostic algorithm.
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Affiliation(s)
- Linoj Samuel
- Division of Clinical Microbiology, Department of Pathology and Laboratory Medicine, Henry Ford Health, Detroit, Michigan, USA
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2
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A culture-free biphasic approach for sensitive and rapid detection of pathogens in dried whole-blood matrix. Proc Natl Acad Sci U S A 2022; 119:e2209607119. [PMID: 36161889 DOI: 10.1073/pnas.2209607119] [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: 11/18/2022] Open
Abstract
Blood stream infections (BSIs) cause high mortality, and their rapid detection remains a significant diagnostic challenge. Timely and informed administration of antibiotics can significantly improve patient outcomes. However, blood culture, which takes up to 5 d for a negative result, followed by PCR remains the gold standard in diagnosing BSI. Here, we introduce a new approach to blood-based diagnostics where large blood volumes can be rapidly dried, resulting in inactivation of the inhibitory components in blood. Further thermal treatments then generate a physical microscale and nanoscale fluidic network inside the dried matrix to allow access to target nucleic acid. The amplification enzymes and primers initiate the reaction within the dried blood matrix through these networks, precluding any need for conventional nucleic acid purification. High heme background is confined to the solid phase, while amplicons are enriched in the clear supernatant (liquid phase), giving fluorescence change comparable to purified DNA reactions. We demonstrate single-molecule sensitivity using a loop-mediated isothermal amplification reaction in our platform and detect a broad spectrum of pathogens, including gram-positive methicillin-resistant and methicillin-susceptible Staphylococcus aureus bacteria, gram-negative Escherichia coli bacteria, and Candida albicans (fungus) from whole blood with a limit of detection (LOD) of 1.2 colony-forming units (CFU)/mL from 0.8 to 1 mL of starting blood volume. We validated our assay using 63 clinical samples (100% sensitivity and specificity) and significantly reduced sample-to-result time from over 20 h to <2.5 h. The reduction in instrumentation complexity and costs compared to blood culture and alternate molecular diagnostic platforms can have broad applications in healthcare systems in developed world and resource-limited settings.
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3
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Wilson-Nieuwenhuis J, El-Mohtadi M, Edwards K, Whitehead K, Dempsey-Hibbert N. Factors Involved in the onset of infection following bacterially contaminated platelet transfusions. Platelets 2021; 32:909-918. [PMID: 32762589 DOI: 10.1080/09537104.2020.1803253] [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: 10/23/2022]
Abstract
Transfusion of platelet concentrates (PCs) is associated with several adverse patient reactions, the most common of which are febrile non-hemolytic transfusion reactions (FNHTRs) and transfusion-associated bacterial-infection/transfusion-associated sepsis (T-ABI/TA-S). Diagnosis of T-ABI/T-AS requires a positive blood culture (BC) result from the transfusion recipient and also a positive identification of bacterial contamination within a test aliquot of the transfused PC. In a significant number of cases, clinical symptoms post-transfusion are reported by the clinician, yet the BCs from the patient and/or PC are negative. The topic of 'missed bacterial detection' has therefore been the focus of several primary research studies and review articles, suggesting that biofilm formation in the blood bag and the presence of viable but non-culturable (VBNC) pathogens are the major causes of this missed detection. However, platelets are emerging as key players in early host responses to infection and as such, the aforementioned biofilm formation could elicit 'platelet priming', which could lead to significant immunological reactions in the host, in the absence of planktonic bacteria in the host bloodstream. This review reflects on what is known about missed detection and relates this to the emerging understanding of the effect of bacterial contamination on the platelets themselves and the significant role played by platelets in exacerbation of an immune response to infection within the transfusion setting.
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Affiliation(s)
| | - Mohamed El-Mohtadi
- Centre for Bioscience, Manchester Metropolitan University, Manchester, UK
| | - Kurtis Edwards
- Centre for Bioscience, Manchester Metropolitan University, Manchester, UK
| | - Kathryn Whitehead
- Centre for Bioscience, Manchester Metropolitan University, Manchester, UK
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4
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Jyoti A, Kumar S, Kumar Srivastava V, Kaushik S, Govind Singh S. Neonatal sepsis at point of care. Clin Chim Acta 2021; 521:45-58. [PMID: 34153274 DOI: 10.1016/j.cca.2021.06.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/14/2021] [Accepted: 06/14/2021] [Indexed: 01/03/2023]
Abstract
Sepsis, which includes infection followed by inflammation, is one of the leading causes of death among neonates worldwide. The major attribute of this disease process is dysregulated host response to infection leading to organ dysfunction and potentially death. A comprehensive understanding of the host response as well as the pathogen itself are important factors contributing to outcome. Early diagnosis is paramount, as it leads to accurate assessment and improved clinical management. Accordingly, a number of diagnostic platforms have been introduced to assess the presence of blood stream pathogens in septic neonates. Unfortunately, current point-of-care (POC) methods rely on a single parameter/biomarker and thus lack a comprehensive evaluation. The emerging field of biosensing has, however, resulted in the development of a wide range of analytical devices that may be useful at POC. This review discusses currently available methods to screen the inflammatory process in neonatal sepsis. We describe POC sensor-based methods for single platform multi-analyte detection and highlight the latest advances in this evolving technology. Finally, we critically evaluate the applicability of these POC devices clinically for early diagnosis of sepsis in neonates.
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Affiliation(s)
- Anupam Jyoti
- Amity Institute of Biotechnology, Amity University, Jaipur, Rajasthan 303002, India; Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh, 173229, India.
| | - Sanni Kumar
- Department of Electrical Engineering, Indian Institute of Technology, Hyderabad, Telangana 502285, India.
| | | | - Sanket Kaushik
- Amity Institute of Biotechnology, Amity University, Jaipur, Rajasthan 303002, India.
| | - Shiv Govind Singh
- Department of Electrical Engineering, Indian Institute of Technology, Hyderabad, Telangana 502285, India.
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5
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Carvalho-Pereira J, Fernandes F, Araújo R, Springer J, Loeffler J, Buitrago MJ, Pais C, Sampaio P. Multiplex PCR Based Strategy for Detection of Fungal Pathogen DNA in Patients with Suspected Invasive Fungal Infections. J Fungi (Basel) 2020; 6:E308. [PMID: 33238439 PMCID: PMC7712097 DOI: 10.3390/jof6040308] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/15/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
A new and easy polymerase chain reaction (PCR) multiplex strategy, for the identification of the most common fungal species involved in invasive fungal infections (IFI) was developed in this work. Two panels with species-specific markers were designed, the Candida Panel for the identification of Candida species, and the Filamentous Fungi Panel for the identification of Aspergillus species and Rhizopusarrhizus. The method allowed the correct identification of all targeted pathogens using extracted DNA or by colony PCR, showed no cross-reactivity with nontargeted species and allowed identification of different species in mixed infections. Sensitivity reached 10 to 1 pg of DNA and was suitable for clinical samples from sterile sites, with a sensitivity of 89% and specificity of 100%. Overall, the study showed that the new method is suitable for the identification of the ten most important fungal species involved in IFI, not only from positive blood cultures but also from clinical samples from sterile sites. The method provides a unique characteristic, of seeing the peak in the specific region of the panel with the correct fluorescence dye, that aids the ruling out of unspecific amplifications. Furthermore, the panels can be further customized, selecting markers for different species and/or resistance genes.
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Affiliation(s)
- Joana Carvalho-Pereira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710 Braga, Portugal; (J.C.-P.); (F.F.); (C.P.)
| | - Filipa Fernandes
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710 Braga, Portugal; (J.C.-P.); (F.F.); (C.P.)
| | - Ricardo Araújo
- Department Medical Biotechnology, Health Sciences, Flinders University, Adelaide 5042, Australia;
| | - Jan Springer
- Department of Internal Medicine II, University Hospital of Würzburg, 97080 Würzburg, Germany; (J.S.); (J.L.)
| | - Juergen Loeffler
- Department of Internal Medicine II, University Hospital of Würzburg, 97080 Würzburg, Germany; (J.S.); (J.L.)
| | - María José Buitrago
- Mycology Reference Laboratory, National Centre of Microbiology, Instituto de Salud Carlos III, 28220 Madrid, Spain;
| | - Célia Pais
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710 Braga, Portugal; (J.C.-P.); (F.F.); (C.P.)
| | - Paula Sampaio
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710 Braga, Portugal; (J.C.-P.); (F.F.); (C.P.)
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6
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D'Onofrio V, Salimans L, Bedenić B, Cartuyvels R, Barišić I, Gyssens IC. The Clinical Impact of Rapid Molecular Microbiological Diagnostics for Pathogen and Resistance Gene Identification in Patients With Sepsis: A Systematic Review. Open Forum Infect Dis 2020; 7:ofaa352. [PMID: 33033730 PMCID: PMC7528559 DOI: 10.1093/ofid/ofaa352] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
Fast microbiological diagnostics (MDx) are needed to ensure early targeted antimicrobial treatment in sepsis. This systematic review focuses on the impact on antimicrobial management and patient outcomes of MDx for pathogen and resistance gene identification compared with blood cultures. PubMed was searched for clinical studies using either whole blood directly or after short-term incubation. Twenty-five articles were retrieved describing the outcomes of 8 different MDx. Three interventional studies showed a significant increase in appropriateness of antimicrobial therapy and a nonsignificant change in time to appropriate therapy. Impact on mortality was conflicting. Length of stay was significantly lower in 2 studies. A significant decrease in antimicrobial cost was demonstrated in 6 studies. The limitations of this systematic review include the low number and observed heterogeneity of clinical studies. In conclusion, potential benefits of MDx regarding antimicrobial management and some patient outcomes were reported. More rigorous intervention studies are needed focusing on the direct benefits for patients.
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Affiliation(s)
- Valentino D'Onofrio
- Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium.,Department of Infectious Diseases and Immunity, Jessa Hospital, Hasselt, Belgium.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lene Salimans
- Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium
| | - Branka Bedenić
- Department of Microbiology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Ivan Barišić
- Molecular diagnostics, Austrian Institute of Technology, Vienna, Austria
| | - Inge C Gyssens
- Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
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7
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Cesewski E, Johnson BN. Electrochemical biosensors for pathogen detection. Biosens Bioelectron 2020; 159:112214. [PMID: 32364936 PMCID: PMC7152911 DOI: 10.1016/j.bios.2020.112214] [Citation(s) in RCA: 335] [Impact Index Per Article: 83.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 12/19/2022]
Abstract
Recent advances in electrochemical biosensors for pathogen detection are reviewed. Electrochemical biosensors for pathogen detection are broadly reviewed in terms of transduction elements, biorecognition elements, electrochemical techniques, and biosensor performance. Transduction elements are discussed in terms of electrode material and form factor. Biorecognition elements for pathogen detection, including antibodies, aptamers, and imprinted polymers, are discussed in terms of availability, production, and immobilization approach. Emerging areas of electrochemical biosensor design are reviewed, including electrode modification and transducer integration. Measurement formats for pathogen detection are classified in terms of sample preparation and secondary binding steps. Applications of electrochemical biosensors for the detection of pathogens in food and water safety, medical diagnostics, environmental monitoring, and bio-threat applications are highlighted. Future directions and challenges of electrochemical biosensors for pathogen detection are discussed, including wearable and conformal biosensors, detection of plant pathogens, multiplexed detection, reusable biosensors for process monitoring applications, and low-cost, disposable biosensors.
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Affiliation(s)
- Ellen Cesewski
- Department of Industrial and Systems Engineering, Virginia Tech, Blacksburg, VA, 24061, USA; Department of Materials Science and Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Blake N Johnson
- Department of Industrial and Systems Engineering, Virginia Tech, Blacksburg, VA, 24061, USA; Department of Materials Science and Engineering, Virginia Tech, Blacksburg, VA, 24061, USA; Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA.
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8
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Lamy B, Sundqvist M, Idelevich EA. Bloodstream infections – Standard and progress in pathogen diagnostics. Clin Microbiol Infect 2020; 26:142-150. [DOI: 10.1016/j.cmi.2019.11.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/11/2019] [Accepted: 11/12/2019] [Indexed: 12/17/2022]
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Trung NT, Thau NS, Bang MH, Song LH. PCR-based Sepsis@Quick test is superior in comparison with blood culture for identification of sepsis-causative pathogens. Sci Rep 2019; 9:13663. [PMID: 31541157 PMCID: PMC6754458 DOI: 10.1038/s41598-019-50150-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 09/05/2019] [Indexed: 12/17/2022] Open
Abstract
Sepsis is an acute, often fatal syndrome that requires early diagnosis and proper treatment. Blood culture (BC) is the gold standard for the identification of pathogens, however it has marked limitations, including that it is time-consuming (delaying treatment) and can only detect microbes that readily grow under culture conditions. Alternatively, non-culture-based methodologies like polymerase chain reaction (PCR) are faster but also have limitations; e.g., the reaction is often inhibited by the abundance of human DNA and thus can only detect limited known target pathogens. In our previous publication, we have demonstrated a proof-of-concept of a simple pre-analytical tool to remove human DNA from patients’ blood specimens, hence allowing downstream PCRs to detect rare bacterial genetic materials. In the current study, we reported a better performance of a novel prototype diagnosis kit named Sepsis@Quick that combines human DNA removal step with real-time PCRs compared to blood-culture for identifying sepsis causative bacteria. Our data showed that Sepsis@Quick is superior to blood culture in which the novel diagnostic kit could identify more pathogens and even polymicrobial infection, faster and less influenced by the empirical administration of broad spectrum antibiotic therapy (single administration or combination of cephalosporin III and fluoroquinolon). Additionally, for the first time, we demonstrated that positive results achieved by Sepsis@Quick are significantly associated with a reduction of sepsis-related mortality.
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Affiliation(s)
- Ngo Tat Trung
- Vietnamese-German Center for Medical Research (VG-CARE), 108 Military Central Hospital, Hà Nội, Vietnam. .,Centre for Genetic Consultation and Cancer Screening, 108 Military Central Hospital, Hà Nội, Vietnam. .,Department of Molecular Biology, 108 Military Central Hospital, Hà Nội, Vietnam.
| | - Nguyen Sy Thau
- Vietnamese-German Center for Medical Research (VG-CARE), 108 Military Central Hospital, Hà Nội, Vietnam.,Faculty of Tropical and Infectious Diseases, 108 Military Central Hospital, Hà Nội, Vietnam
| | - Mai Hong Bang
- Vietnamese-German Center for Medical Research (VG-CARE), 108 Military Central Hospital, Hà Nội, Vietnam
| | - Le Huu Song
- Vietnamese-German Center for Medical Research (VG-CARE), 108 Military Central Hospital, Hà Nội, Vietnam. .,Faculty of Tropical and Infectious Diseases, 108 Military Central Hospital, Hà Nội, Vietnam.
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10
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Idelevich EA, Reischl U, Becker K. New Microbiological Techniques in the Diagnosis of Bloodstream Infections. DEUTSCHES ARZTEBLATT INTERNATIONAL 2019; 115:822-832. [PMID: 30678752 DOI: 10.3238/arztebl.2018.0822] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/04/2017] [Accepted: 10/12/2018] [Indexed: 01/12/2023]
Abstract
BACKGROUND When a bloodstream infection is suspected, the preliminary and definitive results of culture-based microbiological testing arrive too late to have any influence on the initial choice of empirical antibiotic treatment. METHODS This review is based on pertinent publications retrieved by a selective search of the literature and on the authors' clinical and scientific experience. RESULTS A number of technical advances now enable more rapid microbiological diagnosis of bloodstream infections. DNA- based techniques for the direct detection of pathogenic organisms in whole blood have not yet become established in routine use because of various limitations. On the other hand, matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become available for routine use in clinical laboratories and has markedly shortened the time to diagnosis after blood samples that have been cultured in automated blood-culture systems turn positive. Further developments of this technique now enable it to be used directly for blood cultures that have been flagged positive, as well as for subcultures that have been incubated for only a short time on a solid nutrient medium. The microbial biomass of the subculture can also be used in parallel for more rapid susceptibility testing with conventional methods, or, in future, with MALDI-TOF MS. CONCLUSION The potential of all of these new techniques will only be realizable in practice if they are optimally embedded in the diagnostic process and if sufficient attention is paid to pre-analytical issues, particularly storage and transport times.
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Zhang Y, Hu A, Andini N, Yang S. A 'culture' shift: Application of molecular techniques for diagnosing polymicrobial infections. Biotechnol Adv 2019; 37:476-490. [PMID: 30797092 PMCID: PMC6447436 DOI: 10.1016/j.biotechadv.2019.02.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/04/2019] [Accepted: 02/19/2019] [Indexed: 12/11/2022]
Abstract
With the advancement of microbiological discovery, it is evident that many infections, particularly bloodstream infections, are polymicrobial in nature. Consequently, new challenges have emerged in identifying the numerous etiologic organisms in an accurate and timely manner using the current diagnostic standard. Various molecular diagnostic methods have been utilized as an effort to provide a fast and reliable identification in lieu or parallel to the conventional culture-based methods. These technologies are mostly based on nucleic acid, proteins, or physical properties of the pathogens with differing advantages and limitations. This review evaluates the different molecular methods and technologies currently available to diagnose polymicrobial infections, which will help determine the most appropriate option for future diagnosis.
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Affiliation(s)
- Yi Zhang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore.
| | - Anne Hu
- Emergency Medicine, Stanford University, Stanford, California 94305, USA
| | - Nadya Andini
- Emergency Medicine, Stanford University, Stanford, California 94305, USA
| | - Samuel Yang
- Emergency Medicine, Stanford University, Stanford, California 94305, USA.
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12
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Noh CS, Kim SS, Park SY, Moon HS, Hong Y, Ryu JS. Comparison of Two PCR Assays for Trichomonas vaginalis. THE KOREAN JOURNAL OF PARASITOLOGY 2019; 57:27-31. [PMID: 30840796 PMCID: PMC6409213 DOI: 10.3347/kjp.2019.57.1.27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/31/2019] [Indexed: 11/23/2022]
Abstract
PCR is known to be the most sensitive method for diagnosing Trichomonas vaginalis infections. This study aimed to compare the sensitivity of a PCR assay for trichomoniasis (HY-PCR) developed in Hanyang University with the use of a Seeplex Ace Detection Kit®, using urine collected from four Korean men with prostatic disease. Overall, HY-PCR was more sensitive than the Seeplex Kit. The use of Chelex 100 is recommended for DNA isolation in order to increase the sensitivity of the PCR test.
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Affiliation(s)
- Chang-Suk Noh
- Department of Internal Medicine, Hallym University Hangang Sacred Heart Hospital, Seoul 07247, Korea
| | - Sang-Su Kim
- Department of Environmental Biology and Medical Parasitology, Hanyang University College of Medicine, Seoul 04763, Korea.,Department of Biomedical Science, Hanyang University Graduate School of Biomedical Science and Engineering, Hanyang University College of Medicine, Seoul 04763, Korea
| | - Sung-Yul Park
- Department of Urology, Hanyang University College of Medicine, Seoul 04763, Korea
| | - Hong-Sang Moon
- Department of Urology, Hanyang University College of Medicine, Seoul 04763, Korea
| | - Yeonchul Hong
- Department of Parasitology and Tropical Medicine, Kyungpook National University School of Medicine, Daegu 41944, Korea
| | - Jae-Sook Ryu
- Department of Environmental Biology and Medical Parasitology, Hanyang University College of Medicine, Seoul 04763, Korea.,Department of Biomedical Science, Hanyang University Graduate School of Biomedical Science and Engineering, Hanyang University College of Medicine, Seoul 04763, Korea
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13
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Substantial diagnostic impact of blood culture independent molecular methods in bloodstream infections: Superior performance of PCR/ESI-MS. Sci Rep 2018; 8:16024. [PMID: 30375435 PMCID: PMC6207717 DOI: 10.1038/s41598-018-34298-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 09/28/2018] [Indexed: 02/06/2023] Open
Abstract
This study analyzed the performance of different molecular technologies along with blood culture (BC) in the diagnosis of bloodstream infections (BSI) in patients from internal medicine wards - including intensive care units (ICUs) - and the emergency room. Patients with systemic inflammatory response syndrome were prospectively included. BCs and EDTA whole blood were obtained simultaneously. The latter was analyzed by PCR combined with electrospray ionization mass spectrometry (PCR/ESI-MS; IRIDICA BAC BSI assay, Abbott) and by SeptiFast (Roche). Cases were classified as BSI according to adapted European Centre for Disease Prevention and Control criteria. Out of 462 analyzed episodes, 193 with valid test results fulfilled the inclusion criteria and were further evaluated. Sixty-nine (35.8%) were classified as BSI. PCR/ESI-MS showed a significantly better overall performance than BC (p = 0.004) or SeptiFast (p = 0.034). Only in patients from the ICU the performance of SeptiFast was comparable to that of PCR/ESI-MS. Mainly due to the negative effect of antimicrobial pre-treatment on BC results, the cumulative performance of each of the molecular tests with BC was significantly higher than that of BC alone (p < 0.001). SeptiFast and in particular the broad-range pathogen detection system PCR/ESI-MS proved to be an essential addition to BC-based diagnostics in BSI.
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14
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Viana JD, Ferreira SC, Matana SR, Rossi F, Patel P, Garson JA, Rocha V, Tedder R, Mendrone-Júnior A, Levi JE. Detection of bacterial contamination in platelet concentrates from Brazilian donors by molecular amplification of the ribosomal 16S gene. Transfus Med 2018; 28:420-426. [PMID: 30304760 DOI: 10.1111/tme.12561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 08/09/2018] [Accepted: 09/12/2018] [Indexed: 11/30/2022]
Abstract
OBJECTIVE The aim of our work was to establish a semi-automated high-throughput DNA amplification method for the universal screening of bacteria in platelet concentrates (PCs). BACKGROUND Among cases of transfusion transmission of infectious agents, bacterial contamination ranks first in the number of events, morbidity and mortality. Transmission occurs mainly by transfused PCs. Automated culture is adopted by some blood banks for screening of bacterial contamination, but this procedure is expensive and has a relatively long turnaround time. METHODS PCs were spiked with suspensions of five different bacterial species in a final concentration of 1 and 10 colony-forming units (CFU) per millilitre. After incubation, the presence of bacteria was investigated by real-time polymerase chain reaction (PCR) and by the Enhanced Bacterial Detection System (eBDS, Pall) assay as a reference method. Real-time PCR amplification was performed with a set of universal primers and probes targeting the 16S rRNA gene. Co-amplification of human mitochondrial DNA served as an internal control. RESULTS Using the real-time PCR method, it was possible to detect the presence of all bacterial species tested with an initial concentration of 10 CFU mL-1 24 h after contamination, except for Staphylococcus hominis. The PCR assay also detected, at 24 h, the presence of Serratia marcescens and Enterobacter cloacae with an initial concentration of 1 CFU mL-1 . CONCLUSIONS The real-time PCR assay may be a reliable alternative to conventional culture methods in the screening of bacterial contamination of PCs, enabling bacterial detection even with a low initial concentration of microorganisms.
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Affiliation(s)
- J D Viana
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil
| | - S C Ferreira
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil
| | - S R Matana
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil
| | - F Rossi
- Departamento de Microbiologia do Laboratório Central, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - P Patel
- Microbiology Services, NHS Blood and Transplant, London, UK
| | - J A Garson
- Microbiology Services, NHS Blood and Transplant, London, UK.,Division of Infection and Immunity, University College London, London, UK
| | - V Rocha
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil
| | - R Tedder
- Microbiology Services, NHS Blood and Transplant, London, UK.,Division of Infection and Immunity, University College London, London, UK
| | | | - J E Levi
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil
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15
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T2Candida ® to guide antifungal and lengh of treatment of candidemia in a pediatric multivisceral transplant recipient. Med Mycol Case Rep 2018; 21:66-68. [PMID: 30094130 PMCID: PMC6076387 DOI: 10.1016/j.mmcr.2018.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 05/25/2018] [Indexed: 11/24/2022] Open
Abstract
A case of 1-year- old male multivisceral transplant recipient with candidemia diagnosed by the T2Candida® test is presented. Optimal management of the candidemia complemented the treatment of the global clinical episode. Duration of treatment might be established much more precisely with the T2Candida® test than with blood cultures. T2Candida® anticipated blood culture in the candidemia diagnosis. Appropriate antifungal treatment was established when T2Candida® result was reported. Length of candidemia treatment was established based on T2Candida® results.
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16
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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: 177] [Impact Index Per Article: 29.5] [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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17
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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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18
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Tang YW, Stratton CW. Interpretation and Relevance of Advanced Technique Results. ADVANCED TECHNIQUES IN DIAGNOSTIC MICROBIOLOGY 2018. [PMCID: PMC7120226 DOI: 10.1007/978-3-319-95111-9_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Advanced techniques in the field of diagnostic microbiology have made amazing progress over the past 25 years due largely to a technological revolution in the molecular aspects of microbiology [1, 2]. In particular, rapid molecular methods for nucleic acid amplification and characterization combined with automation in the clinical microbiology laboratory as well as user-friendly software and robust laboratory informatics systems have significantly broadened the diagnostic capabilities of modern clinical microbiology laboratories. Molecular methods such as nucleic acid amplification tests (NAATs) rapidly are being developed and introduced in the clinical laboratory setting [3, 4]. Indeed, every section of the clinical microbiology laboratory, including bacteriology, mycology, mycobacteriology, parasitology, and virology, has benefited from these advanced techniques. Because of the rapid development and adaptation of these molecular techniques, the interpretation and relevance of the results produced by such molecular methods continues to lag behind. The purpose of this chapter is to review, update, and discuss the interpretation and relevance of results produced by these advanced molecular techniques.
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Affiliation(s)
- Yi-Wei Tang
- Departments of Laboratory Medicine and Internal Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Charles W. Stratton
- Department of Pathology, Microbiology and Immunology and Medicine, Vanderbilt University Medical Center, Nashville, TN USA
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19
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Straub J, Paula H, Mayr M, Kasper D, Assadian O, Berger A, Rittenschober-Böhm J. Diagnostic accuracy of the ROCHE Septifast PCR system for the rapid detection of blood pathogens in neonatal sepsis-A prospective clinical trial. PLoS One 2017; 12:e0187688. [PMID: 29117261 PMCID: PMC5678863 DOI: 10.1371/journal.pone.0187688] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/24/2017] [Indexed: 12/03/2022] Open
Abstract
Introduction Diagnosis of neonatal sepsis remains a major challenge in neonatology. Most molecular-based methods are not customized for neonatal requirements. The aim of the present study was to assess the diagnostic accuracy of a modified multiplex PCR protocol for the detection of neonatal sepsis using small blood volumes. Methods 212 episodes of suspected neonatal late onset sepsis were analyzed prospectively using the Roche SeptiFast® MGRADE PCR with a modified DNA extraction protocol and software-handling tool. Results were compared to blood culture, laboratory biomarkers and clinical signs of sepsis. Results Of 212 episodes, 85 (40.1%) were categorized as “not infected”. Among these episodes, 1 was false positive by blood culture (1.2%) and 23 were false positive by PCR (27.1%). Of 51 (24.1%) episodes diagnosed as “culture proven sepsis”, the same pathogen was detected by blood culture and PCR in 39 episodes (76.5%). In 8 episodes, more pathogens were detected by PCR compared to blood culture, and in 4 episodes the pathogen detected by blood culture was not found by PCR. One of these episodes was caused by Bacillus cereus, a pathogen not included in the PCR panel. In 76/212 (35.8%) episodes, clinical sepsis was diagnosed. Among these, PCR yielded positive results in 39.5% of episodes (30/76 episodes). For culture-positive sepsis, PCR showed a sensitivity of 90.2% (95%CI 86.2–94.2%) and a specificity of 72.9% (95%CI 67.0–79.0%). Conclusion The Roche SeptiFast® MGRADE PCR using a modified DNA extraction protocol showed acceptable results for rapid detection of neonatal sepsis in addition to conventional blood culture. The benefit of rapid pathogen detection has to be balanced against the considerable risk of contamination, loss of information on antibiotic sensitivity pattern and increased costs.
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Affiliation(s)
- Julia Straub
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Medical University Vienna, Vienna, Austria
| | - Helga Paula
- Department of Hospital Epidemiology and Infection Control, Medical University Vienna, Vienna, Austria
| | - Michaela Mayr
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Medical University Vienna, Vienna, Austria
| | - David Kasper
- Department of Pediatrics and Adolescent Medicine, Research Core Unit of Pediatric Biochemistry and Analytics, Medical University Vienna, Vienna, Austria
| | - Ojan Assadian
- Department of Hospital Epidemiology and Infection Control, Medical University Vienna, Vienna, Austria
| | - Angelika Berger
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Medical University Vienna, Vienna, Austria
| | - Judith Rittenschober-Böhm
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Medical University Vienna, Vienna, Austria
- * E-mail:
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20
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Korber F, Zeller I, Grünstäudl M, Willinger B, Apfalter P, Hirschl AM, Makristathis A. SeptiFast versus blood culture in clinical routine - A report on 3 years experience. Wien Klin Wochenschr 2017; 129:427-434. [PMID: 28243751 PMCID: PMC5486735 DOI: 10.1007/s00508-017-1181-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 02/08/2017] [Indexed: 12/28/2022]
Abstract
BACKGROUND In recent years a multiplex real-time PCR (SeptiFast) has been introduced, allowing detection of 25 common blood pathogens considerably faster than conventional blood culture. METHODS SeptiFast was applied routinely in addition to blood culture in cases of critically ill patients with fever and other signs of severe systemic infections. In this study data of 470 episodes were retrospectively analysed to assess the impact of various parameters, such as clinical indications, assigning ward and antimicrobial treatment on test outcome using a multivariate logistic model. RESULTS After exclusion of microorganisms classified as contaminants, the concordance between SeptiFast and blood culture was 85.5%. SeptiFast detected 98 out of 120, while blood culture merely found 63 out of 120 potential pathogens. In comparison to blood culture, SeptiFast showed considerably higher positivity rates in sepsis, pneumonia and febrile immunosuppression and a lower rate in endocarditis. The highest positivity and concordance between tests was shown in patients from the emergency room (P = 0.007). CONCLUSIONS The results obtained in this study are similar to those from prospective settings confirming the robustness of the SeptiFast assay in routine use. Our data suggest that SeptiFast is a valuable add-on to blood culture and may increase the diagnostic efficiency of a microbiological laboratory.
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Affiliation(s)
- Florian Korber
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.,Praxis Dr. med. Norbert Haßfurther, Launsbach, Germany
| | - Iris Zeller
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Michaela Grünstäudl
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Birgit Willinger
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Petra Apfalter
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.,Krankenhaus der Elisabethinen Linz, Linz, Austria
| | - Alexander M Hirschl
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Athanasios Makristathis
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.
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21
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Safarkar R, Mehrabadi JF, Noormohammadi Z, Mirnejad R. Development a rapid and accurate multiplex real time PCR method for the detection Chlamydia trachomatis and Mycoplasma hominis. J Clin Lab Anal 2017; 31. [PMID: 28238212 DOI: 10.1002/jcla.22126] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 11/29/2016] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Sexually transmitted diseases easily spread among sexually active people and often have no symptoms. Rapid and accurate method for detecting these infections are necessary in early stages. The traditional detection methods of them are difficult and time-consuming. METHODS In this study, multiplex real time PCR was optimized for rapid identification of Chlamydia trachomatis and Mycoplasma hominis in a single tube and was performed with our designed primers. The sensitivity test was carried out to designed primers with diluted genomic DNA. To defined the specificity, non STD bacteria were used as DNA template. RESULTS This study indicated that the developed multiplex real time PCR can be an effective alternative procedure to the conventional methods for rapid and accurate identification of C Chlamydia trachomatis and Mycoplasma hominis. Multiplex real-time PCR Results of them were checked with melting curves. The sensitivity of our designed primer by multiplex real time PCR for Chlamydia trachomatis and Mycoplasma hominis were 4.78×1010 and 8.35×1010 , respectively, Which the primers did not amplify any product from a non-STD species. CONCLUSIONS Multiplex real time PCR by our new primers and analysis of melting curves were successfully usable for rapid and accurate detection of Chlamydia trachomatis and Mycoplasma hominis. This assay instead of traditional culture method, has considerable potential to be rapid, accurate and highly sensitive molecular diagnostic tool for simultaneous and direct detection.
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Affiliation(s)
- Roya Safarkar
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Zahra Noormohammadi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Reza Mirnejad
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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22
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23
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Tröger B, Härtel C, Buer J, Dördelmann M, Felderhoff-Müser U, Höhn T, Hepping N, Hillebrand G, Kribs A, Marissen J, Olbertz D, Rath PM, Schmidtke S, Siegel J, Herting E, Göpel W, Steinmann J, Stein A. Clinical Relevance of Pathogens Detected by Multiplex PCR in Blood of Very-Low-Birth Weight Infants with Suspected Sepsis - Multicentre Study of the German Neonatal Network. PLoS One 2016; 11:e0159821. [PMID: 27472282 PMCID: PMC4966931 DOI: 10.1371/journal.pone.0159821] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 07/09/2016] [Indexed: 11/18/2022] Open
Abstract
Introduction In the German Neonatal Network (GNN) 10% of very-low-birth weight infants (VLBWI) suffer from blood-culture confirmed sepsis, while 30% of VLBWI develop clinical sepsis. Diagnosis of sepsis is a difficult task leading to potential over-treatment with antibiotics. This study aims to investigate whether the results of blood multiplex-PCR (SeptiFast®) for common sepsis pathogens are relevant for clinical decision making when sepsis is suspected in VLBWI. Methods We performed a prospective, multi-centre study within the GNN including 133 VLBWI with 214 episodes of suspected late onset sepsis (LOS). In patients with suspected sepsis a multiplex-PCR (LightCycler SeptiFast MGRADE-test®) was performed from 100 μl EDTA blood in addition to center-specific laboratory biomarkers. The attending neonatologist documented whether the PCR-result, which was available after 24 to 48 hrs, had an impact on the choice of antibiotic drugs and duration of therapy. Results PCR was positive in 110/214 episodes (51%) and blood culture (BC) was positive in 55 episodes (26%). Both methods yielded predominantly coagulase-negative staphylococci (CoNS) followed by Escherichia coli and Staphylococcus aureus. In 214 BC—PCR paired samples concordant results were documented in 126 episodes (59%; n = 32 were concordant pathogen positive results, n = 94 were negative in both methods). In 65 episodes (30%) we found positive PCR results but negative BCs, with CoNS being identified in 43 (66%) of these samples. Multiplex-PCR results influenced clinical decision making in 30% of episodes, specifically in 18% for the choice of antimicrobial therapy and in 22% for the duration of antimicrobial therapy. Conclusions Multiplex-PCR results had a moderate impact on clinical management in about one third of LOS-episodes. The main advantage of multiplex-PCR was the rapid detection of pathogens from micro-volume blood samples. In VLBWI limitations include risk of contamination, lack of resistance testing and high costs. The high rate of positive PCR results in episodes of negative BC might lead to overtreatment of infants which is associated with risk of mortality, antibiotic resistance, fungal sepsis and NEC.
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Affiliation(s)
- Birte Tröger
- Department of Pediatrics at the University of Lübeck, Lübeck, Germany
- * E-mail:
| | - Christoph Härtel
- Department of Pediatrics at the University of Lübeck, Lübeck, Germany
| | - Jan Buer
- Institute of Medical Microbiology, University of Duisburg-Essen, Essen, Germany
| | - Michael Dördelmann
- Department of Pediatrics at Diakonissen Hospital Flensburg, Flensburg, Germany
| | - Ursula Felderhoff-Müser
- Department of Pediatrics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Thomas Höhn
- Department of Pediatrics at the University of Düsseldorf, Düsseldorf, Germany
| | - Nico Hepping
- Department of Pediatrics at St. Marien Hospital Bonn, Bonn, Germany
| | - Georg Hillebrand
- Department of Pediatrics at Hospital of Itzehoe, Itzehoe, Germany
| | - Angela Kribs
- Department of Pediatrics at the University of Cologne, Cologne, Germany
| | - Janina Marissen
- Department of Pediatrics at the University of Lübeck, Lübeck, Germany
| | - Dirk Olbertz
- Neonatology Unit at Südstadt Hospital Rostock, Rostock, Germany
| | - Peter-Michael Rath
- Institute of Medical Microbiology, University of Duisburg-Essen, Essen, Germany
| | - Susanne Schmidtke
- Neonatology Unit at Asclepios Hospital Hamburg-Barmbek, Hamburg, Germany
| | - Jens Siegel
- Neonatology Unit at the Children´s Hospital Hannover Auf der Bult, Hannover, Germany
| | - Egbert Herting
- Department of Pediatrics at the University of Lübeck, Lübeck, Germany
| | - Wolfgang Göpel
- Department of Pediatrics at the University of Lübeck, Lübeck, Germany
| | - Joerg Steinmann
- Institute of Medical Microbiology, University of Duisburg-Essen, Essen, Germany
| | - Anja Stein
- Department of Pediatrics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
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24
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Cartwright M, Rottman M, Shapiro NI, Seiler B, Lombardo P, Gamini N, Tomolonis J, Watters AL, Waterhouse A, Leslie D, Bolgen D, Graveline A, Kang JH, Didar T, Dimitrakakis N, Cartwright D, Super M, Ingber DE. A Broad-Spectrum Infection Diagnostic that Detects Pathogen-Associated Molecular Patterns (PAMPs) in Whole Blood. EBioMedicine 2016; 9:217-227. [PMID: 27333027 PMCID: PMC4972566 DOI: 10.1016/j.ebiom.2016.06.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 01/01/2023] Open
Abstract
Background Blood cultures, and molecular diagnostic tests that directly detect pathogen DNA in blood, fail to detect bloodstream infections in most infected patients. Thus, there is a need for a rapid test that can diagnose the presence of infection to triage patients, guide therapy, and decrease the incidence of sepsis. Methods An Enzyme-Linked Lectin-Sorbent Assay (ELLecSA) that uses magnetic microbeads coated with an engineered version of the human opsonin, Mannose Binding Lectin, containing the Fc immunoglobulin domain linked to its carbohydrate recognition domain (FcMBL) was developed to quantify pathogen-associated molecular patterns (PAMPs) in whole blood. This assay was tested in rats and pigs to explore whether it can detect infections and monitor disease progression, and in prospectively enrolled, emergency room patients with suspected sepsis. These results were also compared with data obtained from non-infected patients with or without traumatic injuries. Results The FcMBL ELLecSA was able to detect PAMPS present on, or released by, 85% of clinical isolates representing 47 of 55 different pathogen species, including the most common causes of sepsis. The PAMP assay rapidly (< 1 h) detected the presence of active infection in animals, even when blood cultures were negative and bacteriocidal antibiotics were administered. In patients with suspected sepsis, the FcMBL ELLecSA detected infection in 55 of 67 patients with high sensitivity (> 81%), specificity (> 89%), and diagnostic accuracy of 0·87. It also distinguished infection from trauma-related inflammation in the same patient cohorts with a higher specificity than the clinical sepsis biomarker, C-reactive Protein. Conclusion The FcMBL ELLecSA-based PAMP assay offers a rapid, simple, sensitive and specific method for diagnosing infections, even when blood cultures are negative and antibiotic therapy has been initiated. It may help to triage patients with suspected systemic infections, and serve as a companion diagnostic to guide administration of emerging dialysis-like sepsis therapies. The FcMBL ELLecSA-based PAMP assay offers a rapid, simple, sensitive and specific method for diagnosing infections. The FcMBL ELLecSA distinguished infection from trauma-related inflammation. It can detect infection even when blood cultures are negative and antibiotic therapy has been initiated.
Current diagnostics of sepsis using blood cultures and molecular diagnostic tests fail to detect bloodstream infections in most infected patients, whereas the inflammatory biomarkers of infection that have a higher sensitivity of detection, lack specificity in distinguishing infection from trauma-related inflammation. Therefore we have leveraged a broad-spectrum pathogen binding opsonin and developed a rapid test to directly diagnose the presence of infection in the blood to triage patients and guide antibiotic therapy.
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Affiliation(s)
- Mark Cartwright
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, United States
| | - Martin Rottman
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, United States; Hôpitaux Universitaires Paris Ile de France Ouest (AP-HP), UMR INSERM U1173-UFR SSSV Université de Versailles St Quentin en Yvelines, Montigny, France
| | - Nathan I Shapiro
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, United States
| | - Benjamin Seiler
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, United States
| | - Patrick Lombardo
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, United States
| | - Nazita Gamini
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, United States
| | - Julie Tomolonis
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, United States
| | - Alexander L Watters
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, United States
| | - Anna Waterhouse
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, United States
| | - Dan Leslie
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, United States
| | - Dana Bolgen
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, United States
| | - Amanda Graveline
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, United States
| | - Joo H Kang
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, United States
| | - Tohid Didar
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, United States
| | - Nikolaos Dimitrakakis
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, United States
| | - David Cartwright
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, United States
| | - Michael Super
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, United States
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, United States; Vascular Biology Program, Boston Children's Hospital and Harvard Medical School, Boston, MA, United States; Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, MA, United States.
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25
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Scerbo MH, Kaplan HB, Dua A, Litwin DB, Ambrose CG, Moore LJ, Murray COLCK, Wade CE, Holcomb JB. Beyond Blood Culture and Gram Stain Analysis: A Review of Molecular Techniques for the Early Detection of Bacteremia in Surgical Patients. Surg Infect (Larchmt) 2016; 17:294-302. [PMID: 26918696 PMCID: PMC5118953 DOI: 10.1089/sur.2015.099] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Sepsis from bacteremia occurs in 250,000 cases annually in the United States, has a mortality rate as high as 60%, and is associated with a poorer prognosis than localized infection. Because of these high figures, empiric antibiotic administration for patients with systemic inflammatory response syndrome (SIRS) and suspected infection is the second most common indication for antibiotic administration in intensive care units (ICU)s. However, overuse of empiric antibiotics contributes to the development of opportunistic infections, antibiotic resistance, and the increase in multi-drug-resistant bacterial strains. The current method of diagnosing and ruling out bacteremia is via blood culture (BC) and Gram stain (GS) analysis. METHODS Conventional and molecular methods for diagnosing bacteremia were reviewed and compared. The clinical implications, use, and current clinical trials of polymerase chain reaction (PCR)-based methods to detect bacterial pathogens in the blood stream were detailed. RESULTS BC/GS has several disadvantages. These include: some bacteria do not grow in culture media; others do not GS appropriately; and cultures can require up to 5 d to guide or discontinue antibiotic treatment. PCR-based methods can be potentially applied to detect rapidly, accurately, and directly microbes in human blood samples. CONCLUSIONS Compared with the conventional BC/GS, particular advantages to molecular methods (specifically, PCR-based methods) include faster results, leading to possible improved antibiotic stewardship when bacteremia is not present.
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Affiliation(s)
- Michelle H. Scerbo
- The Center for Translational Injury Research (CeTIR), Department of Surgery, University of Texas Health Science Center, Houston, Texas
| | - Heidi B. Kaplan
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas
| | - Anahita Dua
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Douglas B. Litwin
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas
| | - Catherine G. Ambrose
- Department of Orthopedic Surgery, University of Texas Health Science Center, Houston, Texas
| | - Laura J. Moore
- The Center for Translational Injury Research (CeTIR), Department of Surgery, University of Texas Health Science Center, Houston, Texas
| | - COL Clinton K. Murray
- Department of Medicine, Infectious Disease Service, Brooke Army Medical Center, Fort Sam Houston, Texas
| | - Charles E. Wade
- The Center for Translational Injury Research (CeTIR), Department of Surgery, University of Texas Health Science Center, Houston, Texas
| | - John B. Holcomb
- The Center for Translational Injury Research (CeTIR), Department of Surgery, University of Texas Health Science Center, Houston, Texas
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Syndrome Evaluation System (SES) versus Blood Culture (BACTEC) in the Diagnosis and Management of Neonatal Sepsis--A Randomized Controlled Trial. Indian J Pediatr 2016; 83:370-9. [PMID: 26732807 DOI: 10.1007/s12098-015-1956-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 11/06/2015] [Indexed: 10/22/2022]
Abstract
OBJECTIVE To compare the clinical outcome of a multiplex polymerase chain reaction (PCR) based molecular diagnostic method -- Syndrome Evaluation System (SES) directed treatment strategy vs. standard of care (blood culture) directed treatment strategy for neonatal sepsis. METHODS This randomized controlled trial (RCT) included 385 neonates with sepsis who were randomized into two groups -- SES and control (BACTEC). Both tests were performed for all the neonates. However, in the SES group, the results of SES test were revealed to the treating clinicians, while in the control group, SES results were withheld. Two ml of blood was drawn from each baby. One aliquot was sent for blood culture, whereas the remaining aliquot was sent for SES. Babies were then administered empirical IV antibiotics and given supportive care. Further antibiotic changes, if required were done in SES and control groups based on their respective reports. The microbiological profile, immediate outcome, duration of hospital stay, number of antibiotics used and readmission within a month in both groups were compared. RESULTS SES was better than BACTEC in identifying the causative organism in both the groups (68 % vs. 18 % in SES group and 72 % vs. 18 % in control group). SES had 100 % concordance with blood culture by BACTEC. Detection of bacteria and fungi were four and ten-fold higher respectively with SES when compared to BACTEC culture. Microbiological diagnosis was rapid with SES compared to BACTEC (7 h vs. 72 h). Treatment based on SES resulted in significantly less mortality (3 % vs. 18 %). Readmission rate, duration of hospital stay and change in antibiotics were also significantly less in SES group. CONCLUSIONS This new molecular based diagnostic system (SES) helps in rapid and accurate diagnosis of neonatal sepsis and reduces mortality and morbidity in affected neonates.
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Ratzinger F, Tsirkinidou I, Haslacher H, Perkmann T, Schmetterer KG, Mitteregger D, Makristathis A, Burgmann H. Evaluation of the Septifast MGrade Test on Standard Care Wards--A Cohort Study. PLoS One 2016; 11:e0151108. [PMID: 26986826 PMCID: PMC4795709 DOI: 10.1371/journal.pone.0151108] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 02/22/2016] [Indexed: 12/22/2022] Open
Abstract
Background The immediate need for appropriate antimicrobial therapy in septic patients requires the detection of the causative pathogen in a timely and reliable manner. In this study, the real-time PCR Septifast MGrade test was evaluated in adult patients meeting the systemic inflammatory response syndrome (SIRS) criteria that were treated at standard care wards. Methods Patients with clinical suspected infection, drawn blood cultures (BC), the Septifast MGrade test (SF) and sepsis biomarkers were prospectively screened for fulfillment of SIRS criteria and evaluated using the criteria of the European Centre of Disease Control (ECDC) for infection point prevalence studies. Results In total, 220 patients with SIRS were prospectively enrolled, including 56 patients with detection of bacteria in the blood (incidence: 25.5%). BC analysis resulted in 75.0% sensitivity (95% confidence interval, CI: 61.6%– 85.6%) with 97.6% specificity (CI: 93.9%– 99.3%) for detecting bacteria in the blood. In comparison to BC, SF presented with 80.4% sensitivity (CI: 67.6%– 89.8%) and with 97.6% specificity (CI: 93.9%– 99.3%). BC and SF analysis yielded comparable ROC-AUCs (0.86, 0.89), which did not differ significantly (p = 0.558). A trend of a shorter time-to-positivity of BC analysis was not seen in bacteremic patients with a positive SF test than those with a negative test result. Sepsis biomarkers, including PCT, IL-6 or CRP, did not help to explain discordant test results for BC and SF. Conclusion Since negative results do not exclude bacteremia, the Septifast MGrade test is not suited to replacing BC, but it is a valuable tool with which to complement BC for faster detection of pathogens.
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Affiliation(s)
- Franz Ratzinger
- Department of Laboratory Medicine, Division of Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Vienna, Austria
| | - Irene Tsirkinidou
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Helmuth Haslacher
- Department of Laboratory Medicine, Division of Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Vienna, Austria
| | - Thomas Perkmann
- Department of Laboratory Medicine, Division of Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Vienna, Austria
| | - Klaus G. Schmetterer
- Department of Laboratory Medicine, Division of Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Vienna, Austria
| | - Dieter Mitteregger
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | - Athanasios Makristathis
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | - Heinz Burgmann
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
- * E-mail:
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Schuler F, Trotter M, Zengerle R, von Stetten F. Monochrome Multiplexing in Polymerase Chain Reaction by Photobleaching of Fluorogenic Hydrolysis Probes. Anal Chem 2016; 88:2590-5. [DOI: 10.1021/acs.analchem.5b02960] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Friedrich Schuler
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Laboratory
for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Martin Trotter
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Roland Zengerle
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Laboratory
for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- BIOSS-Centre
for Biological Signalling Studies, University of Freiburg, 79110 Freiburg, Germany
| | - Felix von Stetten
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Laboratory
for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
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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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Evaluation of the FilmArray Blood Culture Identification Panel: Results of a Multicenter Controlled Trial. J Clin Microbiol 2016; 54:687-98. [PMID: 26739158 PMCID: PMC4767991 DOI: 10.1128/jcm.01679-15] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 12/28/2015] [Indexed: 12/16/2022] Open
Abstract
Sepsis is a major cause of morbidity, mortality, and increased medical expense. Rapid diagnosis improves outcomes and reduces costs. The FilmArray blood culture identification panel (BioFire Diagnostics LLC, Salt Lake City, UT), a highly multiplexed PCR assay, can identify 24 etiologic agents of sepsis (8 Gram-positive, 11 Gram-negative, and 5 yeast species) and three antimicrobial resistance genes (mecA, vanA/B, and blaKPC) from positive blood culture bottles. It provides results in about 1 h with 2 min for assay setup. We present the results of an eight-center trial comparing the sensitivity and specificity of the panel with those of the laboratories' standard phenotypic identification techniques, as well as with molecular methods used to distinguish Acinetobacter baumannii from other members of the A. calcoaceticus-A. baumannii complex and to detect antimicrobial resistance genes. Testing included 2,207 positive aerobic blood culture samples, 1,568 clinical and 639 seeded. Samples were tested fresh or were frozen for later testing within 8 h after the bottles were flagged as positive by an automated blood culture system. At least one organism was detected by the panel in 1,382 (88.1%) of the positive clinical specimens. The others contained primarily off-panel organisms. The panel reported multiple organisms in 81 (5.86%) positive clinical specimens. The unresolved blood culture identification sensitivity for all target detections exceeded 96%, except for Klebsiella oxytoca (92.2%), which achieved 98.3% sensitivity after resolution of an unavoidable phenotypic error. The sensitivity and specificity for vanA/B and blaKPC were 100%; those for mecA were 98.4 and 98.3%, respectively.
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Fukumoto H, Sato Y, Hasegawa H, Saeki H, Katano H. Development of a new real-time PCR system for simultaneous detection of bacteria and fungi in pathological samples. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:15479-15488. [PMID: 26823918 PMCID: PMC4713704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/20/2015] [Indexed: 06/05/2023]
Abstract
A novel system for simultaneous detection of pathogenic bacteria and fungi in pathological samples was developed using a real-time polymerase chain reaction (PCR) system. This system, designated the "multi-microbial real-time PCR", has the potential to simultaneously detect 68 bacterial and 9 fungal species in a 96-well plate format. All probe-primer sets were designed to produce amplicons smaller than 210 bp using formalin-fixed paraffin-embedded samples as input. The specificity and sensitivity of each probe-primer set were tested against DNA extracted from pure cultures of specific pathogens. The multi-microbial real-time PCR system revealed profiles of microorganism infection in lung samples collected at autopsy from 10 patients with acquired immunodeficiency syndrome. Staphylococcus aureus was the most common microbe detected (n=8), but with low copy numbers. High copy numbers of Pseudomonas aeruginosa were detected in the lung samples with abscess (n=6). Enterococcus faecium (n=6), Elizabethkingia meningoseptica (n=4), and Candida albicans (n=4) were also frequently detected. In addition, a latent infection of Mycobacterium tuberculosis was detected in one case of pneumonia. In conclusion, this multi-microbial real-time PCR system can be useful for detecting bacteria and fungi in pathological specimens from patients with uncertain diagnoses.
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Affiliation(s)
- Hitomi Fukumoto
- Department of Pathology, National Institute of Infectious Diseases1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
- Department of Dermatology, Nippon Medical School1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8603, Japan
| | - Yuko Sato
- Department of Pathology, National Institute of Infectious Diseases1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Hideki Hasegawa
- Department of Pathology, National Institute of Infectious Diseases1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Hidehisa Saeki
- Department of Dermatology, Nippon Medical School1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8603, Japan
| | - Harutaka Katano
- Department of Pathology, National Institute of Infectious Diseases1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
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Sircar M, Ranjan P, Gupta R, Jha OK, Gupta A, Kaur R, Chavhan N, Singh M, Singh SK. Impact of bronchoalveolar lavage multiplex polymerase chain reaction on microbiological yield and therapeutic decisions in severe pneumonia in intensive care unit. J Crit Care 2015; 31:227-32. [PMID: 26611381 DOI: 10.1016/j.jcrc.2015.10.012] [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: 05/21/2015] [Revised: 09/23/2015] [Accepted: 10/11/2015] [Indexed: 12/12/2022]
Abstract
PURPOSE The purpose of the study is to evaluate the impact of adding bronchoalveolar lavage multiplex polymerase chain reaction (M-PCR) to conventional cultures (CC) on microbiological yield and therapeutic decisions in adult intensive care unit patients with pneumonia and severe sepsis or septic shock. MATERIAL AND METHODS In this retrospective case-control study, bronchoalveolar lavage cultures were taken for control (58 patients, 58 admissions) and study arms (57 patients, 58 admissions). Bronchoalveolar lavage M-PCR was sent simultaneously for the latter. RESULTS A total of 267 microorganisms were identified (M-PCR alone, 211; CC alone, 15; both, 41) in the study arm vs 64 in controls. Concordance between M-PCR and culture was complete in 32 (55.17%), partial in 4 (6.9%), and discordant in 22 (37.93%) including 17 with positive M-PCR but negative CC. Time to antibiotic therapy modification was significantly less (P < .001) in M-PCR group compared to controls (32.40 ± 14.41 vs 41.74 ± 45.61 hours). There was no significant difference in index episode resolution (48.3% vs 50%; P = 1), intensive care unit mortality (57.4% vs 51.2%; P = .67), and hospital mortality (59.6% vs 61.5%; P = 1) in study and control arms, respectively, despite more septic shock patients in the study arm (89.7% vs 75.9%; P = .05). CONCLUSION Bronchoalveolar lavage M-PCR with culture leads to higher microbiological yield and earlier modification of antibiotics compared to conventional culture.
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Affiliation(s)
- Mrinal Sircar
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, Noida, Uttar Pradesh, India.
| | - Prashant Ranjan
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, Noida, Uttar Pradesh, India.
| | - Rajesh Gupta
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, Noida, Uttar Pradesh, India.
| | - Onkar Kumar Jha
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, Noida, Uttar Pradesh, India
| | - Amit Gupta
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, Noida, Uttar Pradesh, India.
| | | | - Neela Chavhan
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, Noida, Uttar Pradesh, India.
| | - Mukta Singh
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, Noida, Uttar Pradesh, India.
| | - Sujeet Kumar Singh
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, Noida, Uttar Pradesh, India.
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Wang HY, Kim J, Kim S, Park SD, Kim HY, Choi HK, Uh Y, Lee H. Performance of PCR-REBA assay for screening and identifying pathogens directly in whole blood of patients with suspected sepsis. J Appl Microbiol 2015; 119:1433-42. [PMID: 26299262 DOI: 10.1111/jam.12941] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/23/2015] [Accepted: 08/11/2015] [Indexed: 12/01/2022]
Abstract
AIMS Rapid and accurate identification of a broad range of bacterial and fungal pathogens is the key to successful management of patients with bloodstream infections (BSIs). The aim of this study was to evaluate the diagnostic performance of PCR-REBA Sepsis-ID test for the detection of BSIs pathogens. METHODS AND RESULTS EDTA anticoagulated blood for REBA Sepsis-ID assay and blood culture samples from 882 patients with suspected sepsis were simultaneously collected from January 2014 to December 2014. Of 115 patients with positive blood culture, 64 (55·7%) were Gram-positive bacteria, 35 (30·4%) were Gram-negative bacteria, 1 (0·9%) was Candida albicans and 15 (13·0%) were polymicrobial infections. The concordance rate of blood culture system and PCR-REBA Sepsis ID test was 83·0% (95% confidence interval (CI), 79·8-84·8, P < 0·0001). Compared to blood culture, the diagnosis of bacterial proven pathogens by PCR-REBA revealed 81·0% (95% CI, 73·4-86·8, P < 0·0001) sensitivity, 83·4% (95% CI, 80·0-85·4, P < 0·0001) specificity, 80·9% positive and 95·8% negative predictive values respectively. In 10 cases with PCR-REBA positive but blood culture negative, the levels of C-reactive protein were significantly elevated 18·5 mg dl(-1) (SD ± 13·7, 95% CI 1·8-41·9) and six cases has been proven to have pathogen by bacterial 16S rRNA sequencing. Although the sensitivity for pathogen identification was not significantly different between PCR-REBA and blood culture (P = 0·5), the combination of the two methods resulted in a significantly increased rate of pathogen detection (P = 0·002). The results of this study suggested that PCR-REBA may be helpful when added to blood culture in the diagnosis and management of sepsis. CONCLUSIONS PCR-REBA Sepsis-ID test is a useful tool for the rapid identification of pathogenic isolates in whole blood to ensure adequate treatment for the causative agents of BSIs. SIGNIFICANCE AND IMPACT OF THE STUDY Although the cost of molecular diagnostic assays is higher than the cost of conventional methods, clinical and economic cost-benefit analysis is still needed. PCR-REBA may provide essential information for accelerating therapeutic decisions to ensure effective treatment with antibiotics in the acute phase of pathogen infection.
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Affiliation(s)
- H-Y Wang
- Wonju Eco Environmental Technology Center, M&D, Inc., Wonju, Korea
| | - J Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - S Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - S D Park
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - H Y Kim
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - H K Choi
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Y Uh
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - H Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
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Abstract
Background: Prediction of the species of pathogen among patients with sepsis within hours would be helpful in accelerating proper treatment. As a potential method of shortening the time to identification, this study considered the usefulness of measuring procalcitonin (PCT) to predict blood culture (BC) results. Methods: The authors retrospectively analyzed the data of patients with a diagnosis of sepsis in their hospital from December 2012 to December 2013. The authors analyzed all diagnostic episodes consisting of BC and PCT concentration. The diagnostic performance of PCT to predict gram-negative bacteremia was tested using a receiver operative characteristic curve. Logistic regression was constructed using the presence of gram-negative bacteria as the dependent variable. Results: A total of 262 diagnostic episodes met the inclusion criteria. According to BC classifications, a significantly higher value of PCT was observed in bloodstream infections caused by gram-negative bacteria (26.7 ng/mL, 0.09–188.3) than that in bloodstream infections caused by gram-positive bacteria (0.84 ng/mL, 0.05–18.79) or Candida spp. (1.12 ng/mL, 0.07–49.68). A cutoff value of ≥3.39 ng/mL for PCT showed a sensitivity of 80%, a specificity of 71%, a positive predictive value of 35%, a negative predictive value of 91% and an area under the curve of 0.73 for gram-negative bacteremia identification by BC. Among the 122 diagnostic episodes with positive BC results, a cutoff value of ≥6.47 ng/mL for PCT yielded a sensitivity of 74%, a specificity of 81%, a positive predictive value of 82%, a negative predictive value of 75% and an area under the curve of 0.81 for gram-negative bacteremia identification. Conclusions: PCT may represent a useful tool for differentiating gram-positive from gram-negative bloodstream infection with a significantly higher PCT level indicating gram-negative bacteremia.
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Quiles MG, Menezes LC, Bauab KDC, Gumpl EK, Rocchetti TT, Palomo FS, Carlesse F, Pignatari ACC. Diagnosis of bacteremia in pediatric oncologic patients by in-house real-time PCR. BMC Infect Dis 2015. [PMID: 26201513 PMCID: PMC4512024 DOI: 10.1186/s12879-015-1033-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background Infections are the major cause of morbidity and mortality in children with cancer. Gaining a favorable prognosis for these patients depends on selecting the appropriate therapy, which in turn depends on rapid and accurate microbiological diagnosis. This study employed real-time PCR (qPCR) to identify the main pathogens causing bloodstream infection (BSI) in patients treated at the Pediatric Oncology Institute IOP-GRAACC-UNIFESP-Brazil. Antimicrobial resistance genes were also investigated using this methodology. Methods A total of 248 samples from BACTEC® blood culture bottles and 99 whole-blood samples collected in tubes containing EDTA K2 Gel were isolated from 137 patients. All samples were screened by specific Gram probes for multiplex qPCR. Seventeen sequences were evaluated using gender-specific TaqMan probes and the resistance genes blaSHV, blaTEM, blaCTX, blaKPC, blaIMP, blaSPM, blaVIM, vanA, vanB and mecA were detected using the SYBR Green method. Results Positive qPCR results were obtained in 112 of the blood culture bottles (112/124), and 90 % agreement was observed between phenotypic and molecular microbial detection methods. For bacterial and fungal identification, the performance test showed: sensitivity 87 %; specificity 91 %; NPV 90 %; PPV 89 % and accuracy of 89 % when compared with the phenotypic method. The mecA gene was detected in 37 samples, extended-spectrum β-lactamases were detected in six samples and metallo-β-lactamase coding genes in four samples, with 60 % concordance between the two methods. The qPCR on whole blood detected eight samples possessing the mecA gene and one sample harboring the vanB gene. The blaKPC, blaVIM, blaIMP and blaSHV genes were not detected in this study. Conclusion Real-time PCR is a useful tool in the early identification of pathogens and antimicrobial resistance genes from bloodstream infections of pediatric oncologic patients.
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Affiliation(s)
- Milene Gonçalves Quiles
- Special Laboratory of Clinical Microbiology (LEMC), Federal University of São Paulo/UNIFESP, São Paulo, Brazil.
| | - Liana Carballo Menezes
- Special Laboratory of Clinical Microbiology (LEMC), Federal University of São Paulo/UNIFESP, São Paulo, Brazil.
| | - Karen de Castro Bauab
- Special Laboratory of Clinical Microbiology (LEMC), Federal University of São Paulo/UNIFESP, São Paulo, Brazil.
| | - Elke Kreuscher Gumpl
- Special Laboratory of Clinical Microbiology (LEMC), Federal University of São Paulo/UNIFESP, São Paulo, Brazil.
| | - Talita Trevizani Rocchetti
- Special Laboratory of Clinical Microbiology (LEMC), Federal University of São Paulo/UNIFESP, São Paulo, Brazil.
| | - Flavia Silva Palomo
- Special Laboratory of Clinical Microbiology (LEMC), Federal University of São Paulo/UNIFESP, São Paulo, Brazil.
| | - Fabianne Carlesse
- Institute of Pediatric Oncology IOP-GRAACC, Federal University of São Paulo, São Paulo, Brazil.
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Yamaguchi A, Matsuda K, Sueki A, Taira C, Uehara M, Saito Y, Honda T. Development of a rapid and sensitive one-step reverse transcription-nested polymerase chain reaction in a single tube using the droplet-polymerase chain reaction machine. Clin Chim Acta 2015; 448:150-4. [PMID: 26148723 DOI: 10.1016/j.cca.2015.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/02/2015] [Indexed: 11/25/2022]
Abstract
BACKGROUND Reverse transcription (RT)-nested polymerase chain reaction (PCR) is a time-consuming procedure because it has several handling steps and is associated with the risk of cross-contamination during each step. Therefore, a rapid and sensitive one-step RT-nested PCR was developed that could be performed in a single tube using a droplet-PCR machine. METHODS The K562 BCR-ABL mRNA-positive cell line as well as bone marrow aspirates from 5 patients with chronic myelogenous leukemia (CML) and 5 controls without CML were used. We evaluated one-step RT-nested PCR using the droplet-PCR machine. RESULTS One-step RT-nested PCR performed in a single tube using the droplet-PCR machine enabled the detection of BCR-ABL mRNA within 40min, which was 10(3)-fold superior to conventional RT nested PCR using three steps in separate tubes. The sensitivity of the one-step RT-nested PCR was 0.001%, with sample reactivity comparable to that of the conventional assay. CONCLUSIONS One-step RT-nested PCR was developed using the droplet-PCR machine, which enabled all reactions to be performed in a single tube accurately and rapidly and with high sensitivity. This one-step RT-nested PCR may be applicable to a wide spectrum of genetic tests in clinical laboratories.
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Affiliation(s)
- Akemi Yamaguchi
- Graduate School of Science and Technology, Shinshu University, Nagano, Japan; Core Technology Development Center, Seiko Epson Corporation, Suwa, Japan
| | - Kazuyuki Matsuda
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan.
| | - Akane Sueki
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan
| | - Chiaki Taira
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan
| | - Masayuki Uehara
- Core Technology Development Center, Seiko Epson Corporation, Suwa, Japan
| | - Yasunori Saito
- Institute of Engineering, Academic Assembly, Shinshu University, Nagano, Japan
| | - Takayuki Honda
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Japan
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Unanticipated Multiplex PCR-Based Identification of Polymicrobial Blood Culture Resulting in Earlier Isolation, Determination of Susceptibilities, and Optimization of Clinical Care. J Clin Microbiol 2015; 53:2371-3. [PMID: 25878349 DOI: 10.1128/jcm.00058-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/10/2015] [Indexed: 01/20/2023] Open
Abstract
We describe a case of polymicrobial bloodstream infection with six organisms identified by multiplex PCR that was initially thought to be a monomicrobial infection. Early recognition of specific Gram-positive, Gram-negative, and fungal organisms and resistance elements allowed significantly more rapid optimization of therapy.
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Mwaigwisya S, Assiri RAM, O'Grady J. Emerging commercial molecular tests for the diagnosis of bloodstream infection. Expert Rev Mol Diagn 2015; 15:681-92. [PMID: 25866124 DOI: 10.1586/14737159.2015.1029459] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Bloodstream infection (BSI) by microorganisms can lead to sepsis. This condition has a high mortality rate, which rises significantly with delays in initiation of appropriate antimicrobial treatment. Current culture methods for diagnosing BSI have long turnaround times and poor clinical sensitivity. While clinicians wait for culture diagnosis, patients are treated empirically, which can result in inappropriate treatment, undesirable side effects and contribute to drug resistance development. Molecular diagnostics assays that target pathogen DNA can identify pathogens and resistance markers within hours. Early diagnosis improves antibiotic stewardship and is associated with favorable clinical outcomes. Nonetheless, limitations of current molecular diagnostic methods are substantial. This article reviews recent commercially available molecular methods that use pathogen DNA to diagnose BSI, either by testing positive blood cultures or directly testing patient blood. We critically assess these tests and their application in clinical microbiology. A view of future directions in BSI diagnosis is also provided.
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Bartsch MS, Edwards HS, Lee D, Moseley CE, Tew KE, Renzi RF, Van de Vreugde JL, Kim H, Knight DL, Sinha A, Branda SS, Patel KD. The rotary zone thermal cycler: a low-power system enabling automated rapid PCR. PLoS One 2015; 10:e0118182. [PMID: 25826708 PMCID: PMC4380418 DOI: 10.1371/journal.pone.0118182] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 01/09/2015] [Indexed: 12/17/2022] Open
Abstract
Advances in molecular biology, microfluidics, and laboratory automation continue to expand the accessibility and applicability of these methods beyond the confines of conventional, centralized laboratory facilities and into point of use roles in clinical, military, forensic, and field-deployed applications. As a result, there is a growing need to adapt the unit operations of molecular biology (e.g., aliquoting, centrifuging, mixing, and thermal cycling) to compact, portable, low-power, and automation-ready formats. Here we present one such adaptation, the rotary zone thermal cycler (RZTC), a novel wheel-based device capable of cycling up to four different fixed-temperature blocks into contact with a stationary 4-microliter capillary-bound sample to realize 1-3 second transitions with steady state heater power of less than 10 W. We demonstrate the utility of the RZTC for DNA amplification as part of a highly integrated rotary zone PCR (rzPCR) system that uses low-volume valves and syringe-based fluid handling to automate sample loading and unloading, thermal cycling, and between-run cleaning functionalities in a compact, modular form factor. In addition to characterizing the performance of the RZTC and the efficacy of different online cleaning protocols, we present preliminary results for rapid single-plex PCR, multiplex short tandem repeat (STR) amplification, and second strand cDNA synthesis.
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Affiliation(s)
- Michael S. Bartsch
- Sandia National Laboratories, Livermore, CA, United States of America
- * E-mail:
| | | | - Daniel Lee
- Sandia National Laboratories, Livermore, CA, United States of America
| | | | - Karen E. Tew
- Sandia National Laboratories, Livermore, CA, United States of America
| | - Ronald F. Renzi
- Sandia National Laboratories, Livermore, CA, United States of America
| | | | - Hanyoup Kim
- Sandia National Laboratories, Livermore, CA, United States of America
| | | | - Anupama Sinha
- Sandia National Laboratories, Livermore, CA, United States of America
| | - Steven S. Branda
- Sandia National Laboratories, Livermore, CA, United States of America
| | - Kamlesh D. Patel
- Sandia National Laboratories, Livermore, CA, United States of America
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40
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Molecular Diagnosis in Fungal Infection Control. CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2015. [DOI: 10.1007/s40506-015-0040-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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41
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Vendemiato AVR, von Nowakonski A, Marson FADL, Levy CE. Microbiological characteristics of sepsis in a University hospital. BMC Infect Dis 2015; 15:58. [PMID: 25887416 PMCID: PMC4334605 DOI: 10.1186/s12879-015-0798-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 02/03/2015] [Indexed: 12/29/2022] Open
Abstract
Background Microbiological characteristics of sepsis and antimicrobial resistance are well studied, although in State University of Campinas, no data has been published yet. Methods The main agents related to sepsis and antimicrobial resistance were analyzed. The blood culture records requested from 4,793 hospitalized patients were analyzed. The samples were processed using the Bact/Alert® system for agent identification and antimicrobial susceptibility. Results A total of 1,017 patients met the inclusion criteria for a sepsis diagnosis, with 2,309 samples tested (2.27 samples/patient). There were 489 positive samples (21% positive) isolated from 337 patients (33.13%), but more rigorous criteria excluding potential contaminants resulted in analysis being restricted to 266 patients (315 agents). The prevalent microorganisms were coagulase negative Staphylococcus (CNS) (15.87%), Escherichia coli (13.0%), Staphylococcus aureus (11.7%), Klebsiella pneumoniae (9.8%), Enterobacter sp (9.5%), Acinetobacter baumannii (9.2%), Pseudomonas aeruginosa (5.7%) and Candida sp (5.1%). Examining antimicrobial resistance in the agents revealed that 51% of the S. aureus isolates were methicillin-resistant S. aureus (MRSA) and 80% of the CNS isolates were oxacillin-resistant. For A. baumannii, the ideal profile drugs were ampicillin sulbactam and piperacillin/tazobactam, and for P. aeruginosa, they were piperacillin/tazobactam and ceftazidime. Enterobacteria showed on average 32.5% and 35.7% resistance to beta-lactams and ciprofloxacin, respectively. When all Gram-negative bacteria were considered, the resistance to beta-lactams rose to 40.5%, and the resistance to ciprofloxacin rose to 42.3%. Conclusions Eighty percent of the agents identified in blood cultures from patients with sepsis belonged to a group of eight different agents. For empirical treatment, carbapenems and vancomycin unfortunately still remain the best therapeutic choice, except for A. baumannii and P. aeruginosa, for which piperacillin/tazobactan is the best option.
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Affiliation(s)
| | - Angela von Nowakonski
- Clinical Microbiology Laboratory, Clinical Hospital, State University of Campinas, Campinas, SP, Brazil.
| | - Fernando Augusto de Lima Marson
- Department of Medical Genetics and Department of Pediatrics, Faculty of Medical Sciences - State University of Campinas, Campinas, SP, Brazil. .,Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo 126, "Zeferino Vaz", Barão Geraldo, Campinas, São Paulo, CEP 13083-887, Brazil.
| | - Carlos Emilio Levy
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo 126, "Zeferino Vaz", Barão Geraldo, Campinas, São Paulo, CEP 13083-887, Brazil.
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Ma F, Rehman A, Liu H, Zhang J, Zhu S, Zeng X. Glycosylation of Quinone-Fused Polythiophene for Reagentless and Label-Free Detection of E. coli. Anal Chem 2015; 87:1560-8. [DOI: 10.1021/ac502712q] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Fen Ma
- Department
of Chemistry, Oakland University, Rochester, Michigan 48309, United States
| | - Abdul Rehman
- Department
of Chemistry, Oakland University, Rochester, Michigan 48309, United States
| | - Haiying Liu
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Jingtuo Zhang
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Shilei Zhu
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Xiangqun Zeng
- Department
of Chemistry, Oakland University, Rochester, Michigan 48309, United States
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Impact of multiplex PCR on antimicrobial treatment in febrile neutropenia: a randomized controlled study. Med Microbiol Immunol 2015; 204:585-92. [PMID: 25573349 DOI: 10.1007/s00430-014-0385-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/30/2014] [Indexed: 10/24/2022]
Abstract
Multiplex PCR (mPCR) directly from blood has been suggested as a promising method for rapid identification of pathogens causing sepsis. This study aimed to investigate whether mPCR has any impact on antimicrobial treatment. Hematological patients with febrile neutropenia were randomized into two groups. In the study group, mPCR was performed as an addition to standard diagnostics, and PCR finding was immediately communicated to the clinicians, thus being available for decision making. In the control group, clinicians were not aware of PCR result. PCR samples were collected simultaneously with clinically indicated blood culture specimens from peripheral vein and/or central venous catheter at fever onset and once again if fever persisted up to 72 h. Overall, 74 patients of the study group and 76 patients of the control group were enrolled and 253 samples collected. Therapy was changed to targeted antimicrobial therapy (AMT) in 12 patients (16.2%) in the study group and in 12 patients (15.8%) in the control group. For patients with changes, the median time to change to the targeted AMT was 21.4 h in the study group and 47.5 h in the control group (p = 0.018). In the study group, 57.1% (8/14) of changes to targeted AMT was due to PCR finding. PCR led to AMT change in 9.5% (7/74) of study group patients, i.e., in 33.3% (7/21) of patients who had positive PCR finding. There were no significant differences in patient outcomes (secondary endpoints). In conclusion, PCR method accelerates change to the targeted AMT in febrile neutropenic patients.
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44
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Wong CL, Dinish U, Olivo M. Recent advances in SPR and SERS for sensitive translational medical diagnostics. ACTA ACUST UNITED AC 2015. [DOI: 10.1515/plm-2014-0009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractPersonalized medicine is revolutionizing modern health care. The aim of personalized diagnostics is to provide rapid, portable and simple tests that will reduce diagnosis time. They enable rapid analysis performed near the patient and provide specific details of the patient’s condition so that a personalized treatment can be made. This review focuses on the recent advances in optical diagnostic techniques based on surface plasmon resonance (SPR) and surface-enhanced Raman scattering spectroscopy (SERS) for translational medical diagnostics. In the first part, recent developments in SPR biosensors for infectious disease diagnosis are presented including the first two-dimensional multiplex influenza SPR biosensor for H1N1 (influenza A) and H3N2 (seasonal influenza) detection. In the second part, advances in SERS, which is another ultra-sensitive optical diagnostic technique for various cancer detection applications in pre-clinical and clinical settings, are reviewed.
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Burillo A, Bouza E. Use of rapid diagnostic techniques in ICU patients with infections. BMC Infect Dis 2014; 14:593. [PMID: 25430913 PMCID: PMC4247221 DOI: 10.1186/s12879-014-0593-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 10/28/2014] [Indexed: 12/12/2022] Open
Abstract
Background Infection is a common complication seen in ICU patients. Given the correlation between infection and mortality in these patients, a rapid etiological diagnosis and the determination of antimicrobial resistance markers are of paramount importance, especially in view of today's globally spread of multi drug resistance microorganisms. This paper reviews some of the rapid diagnostic techniques available for ICU patients with infections. Methods A narrative review of recent peer-reviewed literature (published between 1995 and 2014) was performed using as the search terms: Intensive care medicine, Microbiological techniques, Clinical laboratory techniques, Diagnosis, and Rapid diagnosis, with no language restrictions. Results The most developed microbiology fields for a rapid diagnosis of infection in critically ill patients are those related to the diagnosis of bloodstream infection, pneumonia -both ventilator associated and non-ventilator associated-, urinary tract infection, skin and soft tissue infections, viral infections and tuberculosis. Conclusions New developments in the field of microbiology have served to shorten turnaround times and optimize the treatment of many types of infection. Although there are still some unresolved limitations of the use of molecular techniques for a rapid diagnosis of infection in the ICU patient, this approach holds much promise for the future.
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Affiliation(s)
| | - Emilio Bouza
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Doctor Esquerdo 46, Madrid, 28007, Spain.
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47
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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: 70] [Impact Index Per Article: 7.0] [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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Vitrat V, Hautefeuille S, Janssen C, Bougon D, Sirodot M, Pagani L. Optimizing antimicrobial therapy in critically ill patients. Infect Drug Resist 2014; 7:261-71. [PMID: 25349478 PMCID: PMC4208492 DOI: 10.2147/idr.s44357] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Critically ill patients with infection in the intensive care unit (ICU) would certainly benefit from timely bacterial identification and effective antimicrobial treatment. Diagnostic techniques have clearly improved in the last years and allow earlier identification of bacterial strains in some cases, but these techniques are still quite expensive and not readily available in all institutions. Moreover, the ever increasing rates of resistance to antimicrobials, especially in Gram-negative pathogens, are threatening the outcome for such patients because of the lack of effective medical treatment; ICU physicians are therefore resorting to combination therapies to overcome resistance, with the direct consequence of promoting further resistance. A more appropriate use of available antimicrobials in the ICU should be pursued, and adjustments in doses and dosing through pharmacokinetics and pharmacodynamics have recently shown promising results in improving outcomes and reducing antimicrobial resistance. The aim of multidisciplinary antimicrobial stewardship programs is to improve antimicrobial prescription, and in this review we analyze the available experiences of such programs carried out in ICUs, with emphasis on results, challenges, and pitfalls. Any effective intervention aimed at improving antibiotic usage in ICUs must be brought about at the present time; otherwise, we will face the challenge of intractable infections in critically ill patients in the near future.
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Affiliation(s)
- Virginie Vitrat
- Antimicrobial Stewardship Program, Infectious Diseases Unit, Annecy, France
| | - Serge Hautefeuille
- Intensive Care Unit, Annecy-Genevois Hospital Center (CHANGE), Annecy, France
| | - Cécile Janssen
- Antimicrobial Stewardship Program, Infectious Diseases Unit, Annecy, France
| | - David Bougon
- Intensive Care Unit, Annecy-Genevois Hospital Center (CHANGE), Annecy, France
| | - Michel Sirodot
- Intensive Care Unit, Annecy-Genevois Hospital Center (CHANGE), Annecy, France
| | - Leonardo Pagani
- Antimicrobial Stewardship Program, Infectious Diseases Unit, Annecy, France ; Infectious Diseases Unit, Bolzano Central Hospital, Bolzano, Italy
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Loonen AJM, Wolffs PFG, Bruggeman CA, van den Brule AJC. Developments for improved diagnosis of bacterial bloodstream infections. Eur J Clin Microbiol Infect Dis 2014; 33:1687-702. [PMID: 24848132 DOI: 10.1007/s10096-014-2153-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 04/30/2014] [Indexed: 12/26/2022]
Abstract
Bloodstream infections (BSIs) are associated with high mortality and increased healthcare costs. Optimal management of BSI depends on several factors including recognition of the disease, laboratory tests and treatment. Rapid and accurate identification of the etiologic agent is crucial to be able to initiate pathogen specific antibiotic therapy and decrease mortality rates. Furthermore, appropriate treatment might slow down the emergence of antibiotic resistant strains. Culture-based methods are still considered to be the "gold standard" for the detection and identification of pathogens causing BSI. Positive blood cultures are used for Gram-staining. Subsequently, positive blood culture material is subcultured on solid media, and (semi-automated) biochemical testing is performed for species identification. Finally, a complete antibiotic susceptibility profile can be provided based on cultured colonies, which allows the start of pathogen-tailored antibiotic therapy. This conventional workflow is extremely time-consuming and can take up to several days. Furthermore, fastidious and slow-growing microorganisms, as well as antibiotic pre-treated samples can lead to false-negative results. The main aim of this review is to present different strategies to improve the conventional laboratory diagnostic steps for BSI. These approaches include protein-based (MALDI-TOF mass spectrometry) and nucleic acid-based (polymerase chain reaction [PCR]) identification from subculture, blood cultures, and whole blood to decrease time to results. Pathogen enrichment and DNA isolation methods, to enable optimal pathogen DNA recovery from whole blood, are described. In addition, the use of biomarkers as patient pre-selection tools for molecular assays are discussed.
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Affiliation(s)
- A J M Loonen
- Laboratory for Molecular Diagnostics, Department of Medical Microbiology and Pathology, Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
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50
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Caliendo AM, Gilbert DN, Ginocchio CC, Hanson KE, May L, Quinn TC, Tenover FC, Alland D, Blaschke AJ, Bonomo RA, Carroll KC, Ferraro MJ, Hirschhorn LR, Joseph WP, Karchmer T, MacIntyre AT, Reller LB, Jackson AF. Better tests, better care: improved diagnostics for infectious diseases. Clin Infect Dis 2014; 57 Suppl 3:S139-70. [PMID: 24200831 PMCID: PMC3820169 DOI: 10.1093/cid/cit578] [Citation(s) in RCA: 411] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In this IDSA policy paper, we review the current diagnostic landscape, including unmet needs and emerging technologies, and assess the challenges to the development and clinical integration of improved tests. To fulfill the promise of emerging diagnostics, IDSA presents recommendations that address a host of identified barriers. Achieving these goals will require the engagement and coordination of a number of stakeholders, including Congress, funding and regulatory bodies, public health agencies, the diagnostics industry, healthcare systems, professional societies, and individual clinicians.
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Affiliation(s)
- Angela M Caliendo
- Department of Medicine, Alpert Medical School of Brown University, Providence, Rhode Island
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