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Drevinek P, Hollweck R, Lorenz MG, Lustig M, Bjarnsholt T. Direct 16S/18S rRNA Gene PCR Followed by Sanger Sequencing as a Clinical Diagnostic Tool for Detection of Bacterial and Fungal Infections: a Systematic Review and Meta-Analysis. J Clin Microbiol 2023; 61:e0033823. [PMID: 37367430 PMCID: PMC10575125 DOI: 10.1128/jcm.00338-23] [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: 06/28/2023] Open
Abstract
rRNA gene Sanger sequencing is being used for the identification of cultured pathogens. A new diagnostic approach is sequencing of uncultured samples by using the commercial DNA extraction and sequencing platform SepsiTest (ST). The goal was to analyze the clinical performance of ST with a focus on nongrowing pathogens and the impact on antibiotic therapy. A literature search used PubMed/Medline, Cochrane, Science Direct, and Google Scholar. Eligibility followed PRISMA-P criteria. Quality and risk of bias were assessed drawing on QUADAS-2 (quality assessment of diagnostic accuracy studies, revised) criteria. Meta-analyses were performed regarding accuracy metrics compared to standard references and the added value of ST in terms of extra found pathogens. We identified 25 studies on sepsis, infectious endocarditis, bacterial meningitis, joint infections, pyomyositis, and various diseases from routine diagnosis. Patients with suspected infections of purportedly sterile body sites originated from various hospital wards. The overall sensitivity (79%; 95% confidence interval [CI], 73 to 84%) and specificity (83%; 95% CI, 72 to 90%) were accompanied by large effect sizes. ST-related positivity was 32% (95% CI, 30 to 34%), which was significantly higher than the culture positivity (20%; 95% CI, 18 to 22%). The overall added value of ST was 14% (95% CI, 10 to 20%) for all samples. With 130 relevant taxa, ST uncovered high microbial richness. Four studies demonstrated changes of antibiotic treatment at 12% (95% CI, 9 to 15%) of all patients upon availability of ST results. ST appears to be an approach for the diagnosis of nongrowing pathogens. The potential clinical role of this agnostic molecular diagnostic tool is discussed regarding changes of antibiotic treatment in cases where culture stays negative.
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Affiliation(s)
- Pavel Drevinek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | | | | | | | - Thomas Bjarnsholt
- Department of Clinical Microbiology, Centre for Diagnostics, Rigshospitalet, Copenhagen, Denmark
- Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
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Lin KP, Yeh TK, Chuang YC, Wang LA, Fu YC, Liu PY. Blood Culture Negative Endocarditis: A Review of Laboratory Diagnostic Approaches. Int J Gen Med 2023; 16:317-327. [PMID: 36718144 PMCID: PMC9884005 DOI: 10.2147/ijgm.s393329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023] Open
Abstract
Infective endocarditis is a potentially fatal condition, and identifying the pathogen is crucial to optimizing antibiotic treatment. While a blood culture takes time and may yield negative results, it remains the gold standard for diagnosis, blood culture-negative endocarditis, which accounts for up to 20% of infective endocarditis cases, poses a clinical challenge with increasing mortality. To better understand the etiology of blood culture-negative infective endocarditis, we reviewed non-culture-based strategies and compared the results. Serology tests work best in limited pathogens, such as Coxiella burnetii and Bartonella infections. Most of the pathogens identified by broad-range PCR tests are Streptococcus spp, Staphylococcus spp and Propionibacterium spp. adding specific real-time PCR assays to the systematic PCR testing of patients with blood culture-negative endocarditis will increase the efficiency of diagnosis. Recently, metagenomic next-generation sequencing has also shown promising results.
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Affiliation(s)
- Kuan-Pei Lin
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Ting-Kuang Yeh
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan,Genomic Center for Infectious Diseases, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yu-Chuan Chuang
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Li-An Wang
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yun-Ching Fu
- Children’s Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan,Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan,Correspondence: Yun-Ching Fu; Po-Yu Liu, Taichung Veterans General Hospital, No. 1650, Section 4, Taiwan Blvd, Xitun District, Taichung City, 40705, Taiwan, Tel +886-4-2359-2525 ext.3110, Fax +886-4-2359-5046, Email ;
| | - Po-Yu Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan,Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan,Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan,Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
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Chen K, Malik AA, Sheng YJ, Ahmed S, Sun C, Deng CL, Ojha SC. Clinical Utility of Molecular Tests for Guiding Therapeutic Decisions in Bloodstream Staphylococcal Infections: A Meta-Analysis. Front Pediatr 2021; 9:713447. [PMID: 34422731 PMCID: PMC8374148 DOI: 10.3389/fped.2021.713447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 07/12/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Treatment of bloodstream staphylococcal infections (BSI) necessitates the prompt initiation of appropriate antimicrobial agents and the rapid de-escalation of excessive broad-spectrum coverage to reduce the risk of mortality. We, therefore, aimed to demonstrate the diagnostic accuracy of nucleic acid amplification tests (NAAT) for the identification of methicillin-resistant S. aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) in clinically suspected patients. Methods: Until November 23, 2020, databases including PubMed, Scopus, Embase, and Web of Science were scanned for eligible studies. A bivariate random-effects model was used for meta-analysis of the 33 included studies obtained from 1606 citations, and pooled summary estimates with 95% confidence intervals (CI) were generated. Results: Twenty-three studies (n = 8,547) assessed NAAT accuracy for MSSA detection, while three studies (n = 479) evaluated MRSA detection in adults. The pooled NAAT sensitivity and specificity for MRSA in adults was higher [sensitivity: 0.83 (95% CI 0.59-0.96), specificity: 0.99 (95% CI 0.98-1.0)] as compared to MSSA [sensitivity: 0.76 (95% CI 0.69-0.82), specificity: 0.98 (95% CI 0.98-0.99)]. Similarly, eight studies (n = 4,089) investigating MSSA in pediatric population reported higher NAAT accuracy [sensitivity: 0.89 (95% CI 0.76-0.96), specificity: 0.98 (95% CI 0.97-0.98)] compared to adults. Among NAA tests, SeptiFast (real-time PCR, commercial) was frequently applied, and its diagnostic accuracy corresponded well to the overall summary estimates. A meta-regression and subgroup analysis of study design, sample condition, and patient selection method could not explain the heterogeneity (P > 0.05) in the diagnostic efficiency. Conclusions: NAAT could be applied as the preferred initial tests for timely diagnosis and BSI management.
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Affiliation(s)
- Ke Chen
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Luzhou, China
| | - Aijaz Ahmad Malik
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Yun-Jian Sheng
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Luzhou, China
| | - Sarfraz Ahmed
- Department of Basic Sciences, University of Veterinary and Animal Sciences Lahore, Narowal, Pakistan
| | - Changfeng Sun
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Luzhou, China
| | - Cun-Liang Deng
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Luzhou, China
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Singhal C, Bruno JG, Kaushal A, Sharma TK. Recent Advances and a Roadmap to Aptamer-Based Sensors for Bloodstream Infections. ACS APPLIED BIO MATERIALS 2021; 4:3962-3984. [PMID: 35006817 DOI: 10.1021/acsabm.0c01358] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The present review is intended to describe bloodstream infections (BSIs), the major pathogens responsible for BSIs, conventional tests and their limitations, commercially available methods used, and the aptamer and nanomaterials-based approaches developed so far for the detection of BSIs. The advantages associated with aptamers and the aptamer-based sensors, the comparison between the aptamers and the antibodies, and the various types of aptasensors developed so far for the detection of bloodstream infections have been described in detail in the present review. Also, the future outlook and roadmap toward aptamer-based sensors and the challenges associated with the aptamer development have also been concluded in this review.
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Affiliation(s)
- Chaitali Singhal
- Aptamer Technology and Diagnostic Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana 121001, India
| | - John G Bruno
- Nanohmics, Inc., Austin, Texas 78741, United States
| | - Ankur Kaushal
- Centre of Nanotechnology, Amity University, Manesar, Gurugram, Haryana 122413, India
| | - Tarun K Sharma
- Aptamer Technology and Diagnostic Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana 121001, India
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Maheshwarappa HM, Guru P, Mundre RS, Lawrence N, Majumder S, Sigamani A, Anupama CN, Adak S. Validation of an Isothermal Amplification Platform for Microbial Identification and Antimicrobial Resistance Detection in Blood: A Prospective Study. Indian J Crit Care Med 2021; 25:299-304. [PMID: 33790511 PMCID: PMC7991769 DOI: 10.5005/jp-journals-10071-23761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Background: Recent advances in nucleic acid amplification technique (NAAT)-based identification of pathogens in blood stream infections (BSI) have revolutionized molecular diagnostics in comparison to traditional clinical microbiology practice of blood culture. Rapid pathogen detection with point-of-care diagnostic-applicable platform is prerequisite for efficient patient management. The aim of the study is to evaluate an in-house developed, lyophilized OmiX-AMP pathogen test for the detection of top six BSI-causing bacteria along with two major antimicrobial resistance (AMR) markers of carbapenem and compare it to the traditional blood culture-based detection. Materials and methods: One hundred forty-three patients admitted to the Medical Intensive Care Unit, Narayana Hrudayalaya, Bangalore, with either suspected or proven sepsis, of either gender, of age ≥18 years were enrolled for the study. Pathogen DNA extracted from blood culture sample using OmiX pReP method was amplified at isothermal conditions and analyzed in real time using OmiX Analysis software. Results: Among the processed 143 samples, 54 were true negative, 83 were true positive, 3 were false negative, and 2 were false positive as analyzed by OmiX READ software. Gram-negative bacteria (91.3%) and gram-positive bacteria (75%) were detected with 100% specificity and 95.6% sensitivity along with the AMR marker pattern with a turnaround time of 4 hours from sample collection to results. Conclusion: OmiX-AMP pathogen test detected pathogens with 96.5% concordance in comparison to traditional blood culture. Henceforth, OmiX-AMP pathogen test could be used as a readily deployable diagnostic kit even in low-resource settings. How to cite this article: Maheshwarappa HM, Guru P, Mundre RS, Lawrence N, Majumder S, Sigamani A, et al. Validation of an Isothermal Amplification Platform for Microbial Identification and Antimicrobial Resistance Detection in Blood: A Prospective Study. Indian J Crit Care Med 2021;25(3):299–304.
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Affiliation(s)
- Harish M Maheshwarappa
- Department of Intensive Care Medicine, Narayana Hrudayalaya, Bangalore, Karnataka, India
| | - Prasadini Guru
- Department of Laboratory Medicine, Microbiology and Serology, Narayana Hrudayalaya, Bangalore, Karnataka, India
| | | | - Nima Lawrence
- OmiX Research and Diagnostics Laboratories, Bangalore, Karnataka, India
| | - Snehali Majumder
- Department of Clinical Research, Narayana Hrudayalaya, Bangalore, Karnataka, India
| | - Alben Sigamani
- Department of Clinical Research, Narayana Hrudayalaya, Bangalore, Karnataka, India
| | - C N Anupama
- OmiX Research and Diagnostics Laboratories, Bangalore, Karnataka, India
| | - Sudeshna Adak
- OmiX Research and Diagnostics Laboratories, Bangalore, Karnataka, India
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Rub DM, Dhudasia MB, Healy T, Mukhopadhyay S. Role of microbiological tests and biomarkers in antibiotic stewardship. Semin Perinatol 2020; 44:151328. [PMID: 33158600 DOI: 10.1016/j.semperi.2020.151328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Laboratory tests are critical in the detection and timely treatment of infection. Two categories of tests are commonly used in neonatal sepsis management: those that identify the pathogen and those that detect host response to a potential pathogen. Decision-making around antibiotic choice is related to the performance of tests that directly identify pathogens. Advances in these tests hold the key to progress in antibiotic stewardship. Tests measuring host response, on the other hand, are an indirect marker of potential infection. While an important measure of the patient's clinical state, in the absence of pathogen detection these tests cannot confirm the appropriateness of antibiotic selection. The overall impact these tests then have on antibiotic utilization depends the test's specificity for bacterial infection, clinical scenario where it is being used and the decision-rule it is being integrated into for use. In this review we discuss common and emerging laboratory tests available for assisting management of neonatal infection and specifically focus on the role they play in optimizing antibiotic utilization.
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Affiliation(s)
- David M Rub
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Miren B Dhudasia
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Pediatric Clinical Effectiveness, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Tracy Healy
- Pennsylvania Hospital, University of Pennsylvania, Philadelphia, PA, USA
| | - Sagori Mukhopadhyay
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Pediatric Clinical Effectiveness, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Pennsylvania Hospital, University of Pennsylvania, Philadelphia, PA, USA.
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7
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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: 187] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Rapid and accurate profiling of infection-causing pathogens remains a significant challenge in modern health care. Despite advances in molecular diagnostic techniques, blood culture analysis remains the gold standard for diagnosing sepsis. However, this method is too slow and cumbersome to significantly influence the initial management of patients. The swift initiation of precise and targeted antibiotic therapies depends on the ability of a sepsis diagnostic test to capture clinically relevant organisms along with antimicrobial resistance within 1 to 3 h. The administration of appropriate, narrow-spectrum antibiotics demands that such a test be extremely sensitive with a high negative predictive value. In addition, it should utilize small sample volumes and detect polymicrobial infections and contaminants. All of this must be accomplished with a platform that is easily integrated into the clinical workflow. In this review, we outline the limitations of routine blood culture testing and discuss how emerging sepsis technologies are converging on the characteristics of the ideal sepsis diagnostic test. We include seven molecular technologies that have been validated on clinical blood specimens or mock samples using human blood. In addition, we discuss advances in machine learning technologies that use electronic medical record data to provide contextual evaluation support for clinical decision-making.
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Affiliation(s)
- Mridu Sinha
- Bioengineering Department, University of California, San Diego, San Diego, California, USA
| | - Julietta Jupe
- Donald Danforth Plant Science Center, Saint Louis, Missouri, USA
| | - Hannah Mack
- Bioengineering Department, University of California, San Diego, San Diego, California, USA
| | - Todd P Coleman
- Bioengineering Department, University of California, San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California, San Diego, San Diego, California, USA
| | - Shelley M Lawrence
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, University of California, San Diego, San Diego, California, USA
- Rady Children's Hospital of San Diego, San Diego, California, USA
- Clinical Translational Research Institute, University of California, San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California, San Diego, San Diego, California, USA
| | - Stephanie I Fraley
- Bioengineering Department, University of California, San Diego, San Diego, California, USA
- Clinical Translational Research Institute, University of California, San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California, San Diego, San Diego, California, USA
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8
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Molecular and Mass Spectrometry Detection and Identification of Causative Agents of Bloodstream Infections. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Opota O, Jaton K, Greub G. Microbial diagnosis of bloodstream infection: towards molecular diagnosis directly from blood. Clin Microbiol Infect 2015; 21:323-31. [PMID: 25686695 DOI: 10.1016/j.cmi.2015.02.005] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 02/01/2015] [Accepted: 02/04/2015] [Indexed: 11/19/2022]
Abstract
When a bloodstream infection (BSI) is suspected, most of the laboratory results-biochemical and haematologic-are available within the first hours after hospital admission of the patient. This is not the case for diagnostic microbiology, which generally takes a longer time because blood culture, which is to date the reference standard for the documentation of the BSI microbial agents, relies on bacterial or fungal growth. The microbial diagnosis of BSI directly from blood has been proposed to speed the determination of the etiological agent but was limited by the very low number of circulating microbes during these paucibacterial infections. Thanks to recent advances in molecular biology, including the improvement of nucleic acid extraction and amplification, several PCR-based methods for the diagnosis of BSI directly from whole blood have emerged. In the present review, we discuss the advantages and limitations of these new molecular approaches, which at best complement the culture-based diagnosis of BSI.
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Affiliation(s)
- O Opota
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - K Jaton
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - G Greub
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland; Infectious Diseases Service, University of Lausanne and University Hospital Center, Lausanne, Switzerland.
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