1
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Dave R, Banerjee D. Bacteriophage therapy- a refurbished age-old potential strategy to treat antibiotic and multidrug resistant bacterial infections in future. Braz J Microbiol 2024:10.1007/s42770-024-01434-7. [PMID: 38951476 DOI: 10.1007/s42770-024-01434-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/20/2024] [Indexed: 07/03/2024] Open
Abstract
The worldwide prevalence of antimicrobial resistance coupled with the unavailability of newer antibiotics, has brought the sharp focus back among the scientific community, towards the discovery of novel alternative therapeutics to tackle the menace. Consequently, in the current post-antibiotic era, 'Bacteriophage Therapy' has emerged as one of the most promising option to address this problem. Bacteriophages, actually discovered long back, has shown greater potential to kill various bacterial pathogens, including the resistant clinical ones. Some of the other advantages for the use of bacteriophage therapy to treat infectious diseases include, wider availability of these microorganisms in nature, host-specific action, absence of any significant side-effects in humans and most often also exhibiting a broader anti-bacterial potential. In the recent times, the potential of phage therapy has been demonstrated in various treatments, clinical trials and infection models across the globe, where even antibiotics have completely failed. To address the global threat of AMR, WHO and UN have jointly illustrated "One Health" approach, recently extending the context to bacteriophage therapy. Many pharmaceutical companies have also recently started employing bacteriophages for developing different kinds of formulations for catering to medical and other industries. It has even shown great effect as combinatorial therapy along with antibiotics, to treat or manage various critical antibiotic resistant clinical infections. This continuously expanding potential of the bacteriophages holds great promise in the future, in the fight against the rising threat of AMR globally.
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Affiliation(s)
- Rajal Dave
- Department of Microbiology, Faculty of Science, Atmiya University, "Yogidham Gurukul", Kalawad Road, Rajkot, 360005, Gujarat, India
| | - Debashis Banerjee
- Dept. Of Biotechnology, Faculty of Science, Atmiya University, "Yogidham Gurukul", Kalawad Road, Rajkot, 360005, Gujarat, India.
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2
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Munier C, Dupieux C, Kolenda C, Ranc AG, Dauwalder O, Bes M, Vandenesch F, Tristan A, Laurent F. Sensitivity of the PBP2a SA Culture Colony Test on shortly incubated subcultures of methicillin-resistant staphylococci from positive blood cultures. Diagn Microbiol Infect Dis 2023; 106:115917. [PMID: 36907018 DOI: 10.1016/j.diagmicrobio.2023.115917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 01/04/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
The sensitivity of an immunochromatographic assay for detecting methicillin resistance (PBP2a SA Culture Colony Test, Alere-Abbott) on shortly incubated subcultures of staphylococci in blood cultures was evaluated. The assay is highly sensitive for the detection of methicillin-resistant Staphylococcus aureus after 4 hour-subculture but requires 6 hour-incubation for methicillin-resistant coagulase-negative staphylococci.
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Affiliation(s)
- Clément Munier
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Céline Dupieux
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, Ecole Normale Supérieure de Lyon, Lyon, France.
| | - Camille Kolenda
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Anne-Gaelle Ranc
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Olivier Dauwalder
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Michèle Bes
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, Ecole Normale Supérieure de Lyon, Lyon, France
| | - François Vandenesch
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Anne Tristan
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Frédéric Laurent
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, Ecole Normale Supérieure de Lyon, Lyon, France
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3
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Brown M, Hall A, Zahn H, Eisenberg M, Erickson S. Bacteriophage-Based Detection of Staphylococcus aureus in Human Serum. Viruses 2022; 14:v14081748. [PMID: 36016370 PMCID: PMC9416288 DOI: 10.3390/v14081748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/09/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Bacteriophages have been investigated for clinical utility, both as diagnostic tools and as therapeutic interventions. In order to be applied successfully, a detailed understanding of the influence of the human matrix on the interaction between bacteriophage and the host bacterium is required. In this study, a cocktail of luciferase bacteriophage reporters was assessed for functionality in a matrix containing human serum and spiked with Staphylococcus aureus. The inhibition of signal and loss of sensitivity was evident with minimal amounts of serum. This phenotype was independent of bacterial growth and bacteriophage viability. Serum-mediated loss of signal was common, albeit not universal, among S. aureus strains. Immunoglobulin G was identified as an inhibitory component and partial inhibition was observed with both the f(ab’)2 and Fc region. A modified bacteriophage cocktail containing recombinant protein A was developed, which substantially improved signal without the need for additional sample purification. This study highlights the importance of assessing bacteriophage activity in relevant host matrices. Furthermore, it identifies an effective solution, recombinant protein A, for promoting bacteriophage-based detection of S. aureus in matrices containing human serum.
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Affiliation(s)
- Matthew Brown
- Laboratory Corporation of America Holdings, Burlington, NC 27215, USA
| | - Alex Hall
- Laboratory Corporation of America Holdings, Burlington, NC 27215, USA
| | - Henriett Zahn
- Laboratory Corporation of America Holdings, New Brighton, MN 55112, USA
| | - Marcia Eisenberg
- Laboratory Corporation of America Holdings, Burlington, NC 27215, USA
| | - Stephen Erickson
- Laboratory Corporation of America Holdings, New Brighton, MN 55112, USA
- Correspondence:
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4
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Costa SP, Nogueira CL, Cunha AP, Lisac A, Carvalho CM. Potential of bacteriophage proteins as recognition molecules for pathogen detection. Crit Rev Biotechnol 2022:1-18. [PMID: 35848817 DOI: 10.1080/07388551.2022.2071671] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Bacterial pathogens are leading causes of infections with high mortality worldwide having a great impact on healthcare systems and the food industry. Gold standard methods for bacterial detection mainly rely on culture-based technologies and biochemical tests which are laborious and time-consuming. Regardless of several developments in existing methods, the goal of achieving high sensitivity and specificity, as well as a low detection limit, remains unaccomplished. In past years, various biorecognition elements, such as antibodies, enzymes, aptamers, or nucleic acids, have been widely used, being crucial for the pathogens detection in different complex matrices. However, these molecules are usually associated with high detection limits, demand laborious and costly production, and usually present cross-reactivity. (Bacterio)phage-encoded proteins, especially the receptor binding proteins (RBPs) and cell-wall binding domains (CBDs) of endolysins, are responsible for the phage binding to the bacterial surface receptors in different stages of the phage lytic cycle. Due to their remarkable properties, such as high specificity, sensitivity, stability, and ability to be easily engineered, they are appointed as excellent candidates to replace conventional recognition molecules, thereby contributing to the improvement of the detection methods. Moreover, they offer several possibilities of application in a variety of detection systems, such as magnetic, optical, and electrochemical. Herein we provide a review of phage-derived bacterial binding proteins, namely the RBPs and CBDs, with the prospect to be employed as recognition elements for bacteria. Moreover, we summarize and discuss the various existing methods based on these proteins for the detection of nosocomial and foodborne pathogens.
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Affiliation(s)
- Susana P Costa
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,International Iberian Nanotechnology Laboratory, Braga, Portugal.,Instituto de Engenharia de Sistemas e Computadores-Microsistemas e Nanotecnologias (INESC MN), IN-Institute of Nanoscience and Nanotechnolnology, Lisbon, Portugal
| | - Catarina L Nogueira
- International Iberian Nanotechnology Laboratory, Braga, Portugal.,Instituto de Engenharia de Sistemas e Computadores-Microsistemas e Nanotecnologias (INESC MN), IN-Institute of Nanoscience and Nanotechnolnology, Lisbon, Portugal
| | - Alexandra P Cunha
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Ana Lisac
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Carla M Carvalho
- International Iberian Nanotechnology Laboratory, Braga, Portugal
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5
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Costa SP, Carvalho CM. Burden of bacterial bloodstream infections and recent advances for diagnosis. Pathog Dis 2022; 80:6631550. [PMID: 35790126 DOI: 10.1093/femspd/ftac027] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/07/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
Bloodstream infections (BSIs) and subsequent organ dysfunction (sepsis and septic shock) are conditions that rank among the top reasons for human mortality and have a great impact on healthcare systems. Their treatment mainly relies on the administration of broad-spectrum antimicrobials since the standard blood culture-based diagnostic methods remain time-consuming for the pathogen's identification. Consequently, the routine use of these antibiotics may lead to downstream antimicrobial resistance and failure in treatment outcomes. Recently, significant advances have been made in improving several methodologies for the identification of pathogens directly in whole blood especially regarding specificity and time to detection. Nevertheless, for the widespread implementation of these novel methods in healthcare facilities, further improvements are still needed concerning the sensitivity and cost-effectiveness to allow a faster and more appropriate antimicrobial therapy. This review is focused on the problem of BSIs and sepsis addressing several aspects like their origin, challenges, and causative agents. Also, it highlights current and emerging diagnostics technologies, discussing their strengths and weaknesses.
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Affiliation(s)
- Susana P Costa
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.,International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal.,Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias (INESC MN) and IN - Institute of Nanoscience and Nanotechnology, Rua Alves Redol, 9 1000-029 Lisbon, Portugal
| | - Carla M Carvalho
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
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6
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Li Z, Lu W, Jia S, Yuan H, Gao LH. Design and Application of Conjugated Polymer Nanomaterials for Detection and Inactivation of Pathogenic Microbes. ACS APPLIED BIO MATERIALS 2020; 4:370-386. [DOI: 10.1021/acsabm.0c01395] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Zelin Li
- Department of Chemistry, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, P. R. China
| | - Wen Lu
- Department of Chemistry, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, P. R. China
| | - Shaochuan Jia
- Department of Chemistry, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, P. R. China
| | - Huanxiang Yuan
- Department of Chemistry, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, P. R. China
| | - Li-Hua Gao
- Department of Chemistry, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, P. R. China
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7
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Reporter Phage-Based Detection of Bacterial Pathogens: Design Guidelines and Recent Developments. Viruses 2020; 12:v12090944. [PMID: 32858938 PMCID: PMC7552063 DOI: 10.3390/v12090944] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/10/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
Fast and reliable detection of bacterial pathogens in clinical samples, contaminated food products, and water supplies can drastically improve clinical outcomes and reduce the socio-economic impact of disease. As natural predators of bacteria, bacteriophages (phages) have evolved to bind their hosts with unparalleled specificity and to rapidly deliver and replicate their viral genome. Not surprisingly, phages and phage-encoded proteins have been used to develop a vast repertoire of diagnostic assays, many of which outperform conventional culture-based and molecular detection methods. While intact phages or phage-encoded affinity proteins can be used to capture bacteria, most phage-inspired detection systems harness viral genome delivery and amplification: to this end, suitable phages are genetically reprogrammed to deliver heterologous reporter genes, whose activity is typically detected through enzymatic substrate conversion to indicate the presence of a viable host cell. Infection with such engineered reporter phages typically leads to a rapid burst of reporter protein production that enables highly sensitive detection. In this review, we highlight recent advances in infection-based detection methods, present guidelines for reporter phage construction, outline technical aspects of reporter phage engineering, and discuss some of the advantages and pitfalls of phage-based pathogen detection. Recent improvements in reporter phage construction and engineering further substantiate the potential of these highly evolved nanomachines as rapid and inexpensive detection systems to replace or complement traditional diagnostic approaches.
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8
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Development and Evaluation of a Sensitive Bacteriophage-Based MRSA Diagnostic Screen. Viruses 2020; 12:v12060631. [PMID: 32545159 PMCID: PMC7354448 DOI: 10.3390/v12060631] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/27/2022] Open
Abstract
Engineered luciferase reporter bacteriophages provide specific, sensitive, rapid and low-cost detection of target bacteria and address growing diagnostic needs in multiple industries. Detection of methicillin-resistant Staphylococcus aureus (MRSA) nasal colonization and antibiotic susceptibility play a critical supportive role in preventing hospital-acquired infections and facilitating antibiotic stewardship. We describe the development and evaluation of a novel phage-based MRSA diagnostic screen for nasal swab specimens. The screen utilizes two luciferase reporter phages capable of recognizing genetically-diverse Staphylococcus aureus. The beta-lactam antibiotic cefoxitin is included to differentiate between resistant (MRSA) and susceptible organisms. The screen positively identified 97.7% of 390 clinical MRSA isolates at low bacterial concentrations. At higher inoculums, 93.5% of 123 clinical non-MRSA Staphylococcus aureus yielded appropriate negative results. Although cross-reactivity of the phage cocktail was observed with other staphylococcal and bacillus species, these false positives were absent under selective conditions. MRSA remained detectable in the presence of 38 distinct competing species and was accurately identified in 100% of 40 spiked nasal specimens. Thus, this six-hour screen sensitively detected MRSA both in vitro and in human nasal matrix.
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9
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Phage-Mediated Molecular Detection (PMMD): A Novel Rapid Method for Phage-Specific Bacterial Detection. Viruses 2020; 12:v12040435. [PMID: 32290520 PMCID: PMC7232155 DOI: 10.3390/v12040435] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/06/2020] [Accepted: 04/10/2020] [Indexed: 01/08/2023] Open
Abstract
Bacterial infections pose a challenge to human health and burden the health care system, especially with the spread of antibiotic-resistant populations. To provide effective treatment and improved prognosis, effective diagnostic methods are of great importance. Here we present phage-mediated molecular detection (PMMD) as a novel molecular method for the detection and assessment of bacterial antibiotic resistance. This technique consists of a brief incubation, of approximately ten minutes, of the biological sample with a natural bacteriophage (phage) targeting the bacteria of interest. This is followed by total RNA extraction and RT-PCR. We applied this approach to Staphylococcus aureus (SA), a major causative agent of human bacterial infections. PMMD demonstrated a high sensitivity, rapid implementation, and specificity dependent on the phage host range. Moreover, due to the dependence of the signal on the physiological state of the bacteria, PMMD can discriminate methicillin-sensitive from methicillin-resistant SA (MSSA vs. MRSA). Finally, we extended this method to the detection and antibiotic sensitivity determination of other bacteria by proving PMMD efficacy for Bacillus anthracis.
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10
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Costa SP, Dias NM, Melo LDR, Azeredo J, Santos SB, Carvalho CM. A novel flow cytometry assay based on bacteriophage-derived proteins for Staphylococcus detection in blood. Sci Rep 2020; 10:6260. [PMID: 32277078 PMCID: PMC7148305 DOI: 10.1038/s41598-020-62533-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/06/2019] [Indexed: 02/08/2023] Open
Abstract
Bloodstream infections (BSIs) are considered a major cause of death worldwide. Staphylococcus spp. are one of the most BSIs prevalent bacteria, classified as high priority due to the increasing multidrug resistant strains. Thus, a fast, specific and sensitive method for detection of these pathogens is of extreme importance. In this study, we have designed a novel assay for detection of Staphylococcus in blood culture samples, which combines the advantages of a phage endolysin cell wall binding domain (CBD) as a specific probe with the accuracy and high-throughput of flow cytometry techniques. In order to select the biorecognition molecule, three different truncations of the C-terminus of Staphylococcus phage endolysin E-LM12, namely the amidase (AMI), SH3 and amidase+SH3 (AMI_SH3) were cloned fused with a green fluorescent protein. From these, a higher binding efficiency to Staphylococcus cells was observed for AMI_SH3, indicating that the amidase domain possibly contributes to a more efficient binding of the SH3 domain. The novel phage endolysin-based flow cytometry assay provided highly reliable and specific detection of 1-5 CFU of Staphylococcus in 10 mL of spiked blood, after 16 hours of enrichment culture. Overall, the method developed herein presents advantages over the standard BSIs diagnostic methods, potentially contributing to an early and effective treatment of BSIs.
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Affiliation(s)
- Susana P Costa
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- International Iberian Nanotechnology Laboratory (INL), Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Nicolina M Dias
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Luís D R Melo
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Sílvio B Santos
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Carla M Carvalho
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- International Iberian Nanotechnology Laboratory (INL), Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal.
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11
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Tominaga T, Ishii M. Detection of microorganisms with lateral flow test strips. METHODS IN MICROBIOLOGY 2020. [DOI: 10.1016/bs.mim.2019.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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12
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Maugeri G, Lychko I, Sobral R, Roque ACA. Identification and Antibiotic-Susceptibility Profiling of Infectious Bacterial Agents: A Review of Current and Future Trends. Biotechnol J 2019; 14:e1700750. [PMID: 30024110 PMCID: PMC6330097 DOI: 10.1002/biot.201700750] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/06/2018] [Indexed: 12/16/2022]
Abstract
Antimicrobial resistance is one of the most worrying threats to humankind with extremely high healthcare costs associated. The current technologies used in clinical microbiology to identify the bacterial agent and profile antimicrobial susceptibility are time-consuming and frequently expensive. As a result, physicians prescribe empirical antimicrobial therapies. This scenario is often the cause of therapeutic failures, causing higher mortality rates and healthcare costs, as well as the emergence and spread of antibiotic resistant bacteria. As such, new technologies for rapid identification of the pathogen and antimicrobial susceptibility testing are needed. This review summarizes the current technologies, and the promising emerging and future alternatives for the identification and profiling of antimicrobial resistance bacterial agents, which are expected to revolutionize the field of clinical diagnostics.
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Affiliation(s)
- Gaetano Maugeri
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Iana Lychko
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Rita Sobral
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Ana C A Roque
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
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13
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She RC, Bender JM. Advances in Rapid Molecular Blood Culture Diagnostics: Healthcare Impact, Laboratory Implications, and Multiplex Technologies. J Appl Lab Med 2018; 3:617-630. [PMID: 31639730 DOI: 10.1373/jalm.2018.027409] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 09/28/2018] [Indexed: 01/11/2023]
Abstract
BACKGROUND For far too long, the diagnosis of bloodstream infections has relied on time-consuming blood cultures coupled with traditional organism identification and susceptibility testing. Technologies to define the culprit in bloodstream infections have gained sophistication in recent years, notably by application of molecular methods. CONTENT In this review, we summarize the tests available to clinical laboratories for molecular rapid identification and resistance marker detection in blood culture bottles that have flagged positive. We explore the cost-benefit ratio of such assays, covering aspects that include performance characteristics, effect on patient care, and relevance to antibiotic stewardship initiatives. SUMMARY Rapid blood culture diagnostics represent an advance in the care of patients with bloodstream infections, particularly those infected with resistant organisms. These diagnostics are relatively easy to implement and appear to have a positive cost-benefit balance, particularly when fully incorporated into a hospital's antimicrobial stewardship program.
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Affiliation(s)
- Rosemary C She
- Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, CA;
| | - Jeffrey M Bender
- Division of Infectious Diseases of the Department of Pediatrics, Keck School of Medicine of the University of Southern California, Los Angeles, CA
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14
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Lee AS, de Lencastre H, Garau J, Kluytmans J, Malhotra-Kumar S, Peschel A, Harbarth S. Methicillin-resistant Staphylococcus aureus. Nat Rev Dis Primers 2018; 4:18033. [PMID: 29849094 DOI: 10.1038/nrdp.2018.33] [Citation(s) in RCA: 725] [Impact Index Per Article: 120.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Since the 1960s, methicillin-resistant Staphylococcus aureus (MRSA) has emerged, disseminated globally and become a leading cause of bacterial infections in both health-care and community settings. However, there is marked geographical variation in MRSA burden owing to several factors, including differences in local infection control practices and pathogen-specific characteristics of the circulating clones. Different MRSA clones have resulted from the independent acquisition of staphylococcal cassette chromosome mec (SCCmec), which contains genes encoding proteins that render the bacterium resistant to most β-lactam antibiotics (such as methicillin), by several S. aureus clones. The success of MRSA is a consequence of the extensive arsenal of virulence factors produced by S. aureus combined with β-lactam resistance and, for most clones, resistance to other antibiotic classes. Clinical manifestations of MRSA range from asymptomatic colonization of the nasal mucosa to mild skin and soft tissue infections to fulminant invasive disease with high mortality. Although treatment options for MRSA are limited, several new antimicrobials are under development. An understanding of colonization dynamics, routes of transmission, risk factors for progression to infection and conditions that promote the emergence of resistance will enable optimization of strategies to effectively control MRSA. Vaccine candidates are also under development and could become an effective prevention measure.
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Affiliation(s)
- Andie S Lee
- Departments of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia.,Faculty of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Hermínia de Lencastre
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY, USA.,Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Javier Garau
- Department of Medicine, Hospital Universitari Mutua de Terrassa, Barcelona, Spain
| | - Jan Kluytmans
- Department of Infection Control, Amphia Hospital, Breda, Netherlands.,Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Universiteit Antwerpen, Wilrijk, Belgium
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology Department, University of Tübingen, Tübingen, Germany.,German Center for Infection Research, Partner Site Tübingen, Tübingen, Germany
| | - Stephan Harbarth
- Infection Control Programme, University of Geneva Hospitals and Faculty of Medicine, WHO Collaborating Center, Geneva, Switzerland
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15
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Wei TY, Cheng CM. Synthetic Biology-Based Point-of-Care Diagnostics for Infectious Disease. Cell Chem Biol 2017; 23:1056-1066. [PMID: 27662252 DOI: 10.1016/j.chembiol.2016.07.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 06/15/2016] [Accepted: 07/08/2016] [Indexed: 02/09/2023]
Abstract
Infectious diseases outpace all other causes of death in low-income countries, posing global health risks, laying stress on healthcare systems and societies, and taking an avoidable human toll. One solution to this crisis is early diagnosis of infectious disease, which represents a powerful way to optimize treatment, increase patient survival rate, and decrease healthcare costs. However, conventional early diagnosis methods take a long time to generate results, lack accuracy, and are known to seriously underperform with regard to fungal and viral infections. Synthetic biology offers a fast and highly accurate alternative to conventional infectious disease diagnosis. In this review, we outline obstacles to infectious disease diagnostics and discuss two emerging alternatives: synthetic viral diagnostic systems and biosensors. We argue that these synthetic biology-based approaches may overcome diagnostic obstacles in infectious disease and improve health outcomes.
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Affiliation(s)
- Ting-Yen Wei
- Interdisciplinary Program of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Chao-Min Cheng
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan.
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16
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Li Y, Yang X, Zhao W. Emerging Microtechnologies and Automated Systems for Rapid Bacterial Identification and Antibiotic Susceptibility Testing. SLAS Technol 2017; 22:585-608. [PMID: 28850804 DOI: 10.1177/2472630317727519] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Rapid bacterial identification (ID) and antibiotic susceptibility testing (AST) are in great demand due to the rise of drug-resistant bacteria. Conventional culture-based AST methods suffer from a long turnaround time. By necessity, physicians often have to treat patients empirically with antibiotics, which has led to an inappropriate use of antibiotics, an elevated mortality rate and healthcare costs, and antibiotic resistance. Recent advances in miniaturization and automation provide promising solutions for rapid bacterial ID/AST profiling, which will potentially make a significant impact in the clinical management of infectious diseases and antibiotic stewardship in the coming years. In this review, we summarize and analyze representative emerging micro- and nanotechnologies, as well as automated systems for bacterial ID/AST, including both phenotypic (e.g., microfluidic-based bacterial culture, and digital imaging of single cells) and molecular (e.g., multiplex PCR, hybridization probes, nanoparticles, synthetic biology tools, mass spectrometry, and sequencing technologies) methods. We also discuss representative point-of-care (POC) systems that integrate sample processing, fluid handling, and detection for rapid bacterial ID/AST. Finally, we highlight major remaining challenges and discuss potential future endeavors toward improving clinical outcomes with rapid bacterial ID/AST technologies.
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Affiliation(s)
- Yiyan Li
- 1 Sue and Bill Gross Stem Cell Research Center, University of California-Irvine, Irvine, CA, USA.,7 Department of Physics and Engineering, Fort Lewis College, Durango, Colorado, USA
| | | | - Weian Zhao
- 1 Sue and Bill Gross Stem Cell Research Center, University of California-Irvine, Irvine, CA, USA.,6 Department of Biological Chemistry, University of California-Irvine, Irvine, CA, USA
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17
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Highly Sensitive Bacteriophage-Based Detection of Brucella abortus in Mixed Culture and Spiked Blood. Viruses 2017; 9:v9060144. [PMID: 28604602 PMCID: PMC5490821 DOI: 10.3390/v9060144] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 05/25/2017] [Accepted: 06/06/2017] [Indexed: 01/18/2023] Open
Abstract
For decades, bacteriophages (phages) have been used for Brucella species identification in the diagnosis and epidemiology of brucellosis. Traditional Brucella phage typing is a multi-day procedure including the isolation of a pure culture, a step that can take up to three weeks. In this study, we focused on the use of brucellaphages for sensitive detection of the pathogen in clinical and other complex samples, and developed an indirect method of Brucella detection using real-time quantitative PCR monitoring of brucellaphage DNA amplification via replication on live Brucella cells. This assay allowed the detection of single bacteria (down to 1 colony-forming unit per milliliter) within 72 h without DNA extraction and purification steps. The technique was equally efficient with Brucella abortus pure culture and with mixed cultures of B. abortus and α-proteobacterial near neighbors that can be misidentified as Brucella spp., Ochrobactrum anthropi and Afipia felis. The addition of a simple short sample preparation step enabled the indirect phage-based detection of B. abortus in spiked blood, with the same high sensitivity. This indirect phage-based detection assay enables the rapid and sensitive detection of live B. abortus in mixed cultures and in blood samples, and can potentially be applied for detection in other clinical samples and other complex sample types.
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18
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Göçeri E. Fully automated liver segmentation using Sobolev gradient-based level set evolution. INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING 2016; 32:e02765. [PMID: 26728097 DOI: 10.1002/cnm.2765] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 09/23/2015] [Accepted: 12/25/2015] [Indexed: 06/05/2023]
Abstract
Quantitative analysis and precise measurements on the liver have vital importance for pre-evaluation of surgical operations and require high accuracy in liver segmentation from all slices in a data set. However, automated liver segmentation from medical image data sets is more challenging than segmentation of any other organ due to various reasons such as vascular structures in the liver, high variability of liver shapes, similar intensity values, and unclear edges between liver and its adjacent organs. In this study, a variational level set-based segmentation approach is proposed to be efficient in terms of processing time and accuracy. The efficiency of this method is achieved by (1) automated initialization of a large initial contour, (2) using an adaptive signed pressure force function, and also (3) evolution of the level set with Sobolev gradient. Experimental results show that the proposed fully automated segmentation technique avoids local minima and stops evolution of the active contour at desired liver boundaries with high speed and accuracy. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Evgin Göçeri
- Department of Computer Engineering, Akdeniz University, 07058, Antalya, Turkey.
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19
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Emonet S, Charles PG, Harbarth S, Stewardson AJ, Renzi G, Uckay I, Cherkaoui A, Rougemont M, Schrenzel J. Rapid molecular determination of methicillin resistance in staphylococcal bacteraemia improves early targeted antibiotic prescribing: a randomized clinical trial. Clin Microbiol Infect 2016; 22:946.e9-946.e15. [PMID: 27475737 DOI: 10.1016/j.cmi.2016.07.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/09/2016] [Accepted: 07/16/2016] [Indexed: 11/16/2022]
Abstract
Empiric therapy of methicillin-susceptible Staphylococcus aureus (MSSA) infections with vancomycin is associated with poorer outcome than targeted therapy with β-lactams. Our objective was to evaluate whether rapid determination of methicillin resistance shortens the time from Gram stain to targeted antimicrobial therapy in staphylococcal bacteraemia, thereby reducing vancomycin overuse. This was a single-centre open parallel RCT. Gram-positive cocci in clusters in positive blood culture underwent real-time PCR for rapid species and methicillin resistance determination parallel to conventional microbiology. Patients were randomized 1:1 so that clinicians would be informed of PCR results (intervention group) or not (control group). Eighty-nine patients (intervention 48, control 41) were analysed. MRSA was identified in seven patients, MSSA in 46, and CoNS in 36. PCR results were highly concordant (87/89) with standard microbiology. Median time (hours) from Gram stain to transmission of methicillin-susceptibility was 3.9 (2.8-4.3) vs. 25.4 (24.4-26-7) in intervention vs. control groups (p <0.001). Median time (hours) from Gram stain to targeted treatment was similar for 'all staphylococci' [6 (3.8-10) vs. 8 (1-36) p 0.13] but shorter in the intervention group when considering S. aureus only [5 (3-7) vs. 25.5 (3.8-54) p <0.001]. When standard susceptibility testing was complete, 41/48 (85.4%) patients in the intervention group were already receiving targeted therapy compared with 23/41 (56.1%) in the control group (p 0.004). There was no significant effect on clinical outcomes. Rapid determination of methicillin resistance in staphylococcal bacteraemia is accurate and reduces significantly the time to targeted antibiotic therapy in the subgroup of S. aureus, thereby avoiding unnecessary exposure to vancomycin.
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Affiliation(s)
- S Emonet
- Division of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland; Bacteriology Laboratory, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland.
| | - P G Charles
- Departments of Infectious Diseases and General Medicine, Austin Health, Heidelberg, Australia
| | - S Harbarth
- Division of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - A J Stewardson
- Departments of Infectious Diseases and General Medicine, Austin Health, Heidelberg, Australia
| | - G Renzi
- Bacteriology Laboratory, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - I Uckay
- Division of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - A Cherkaoui
- Bacteriology Laboratory, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - M Rougemont
- Division of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - J Schrenzel
- Division of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland; Bacteriology Laboratory, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland; Genomic Research Laboratory, Division of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
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20
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Saichek NR, Cox CR, Kim S, Harrington PB, Stambach NR, Voorhees KJ. Strain-level Staphylococcus differentiation by CeO2-metal oxide laser ionization mass spectrometry fatty acid profiling. BMC Microbiol 2016; 16:72. [PMID: 27107714 PMCID: PMC4842276 DOI: 10.1186/s12866-016-0658-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 03/02/2016] [Indexed: 11/10/2022] Open
Abstract
Background The Staphylococcus genus is composed of 44 species, with S. aureus being the most pathogenic. Isolates of S. aureus are generally susceptible to β-lactam antibiotics, but extensive use of this class of drugs has led to increasing emergence of resistant strains. Increased occurrence of coagulase-negative staphylococci as well as S. aureus infections, some with resistance to multiple classes of antibiotics, has driven the necessity for innovative options for treatment and infection control. Despite these increasing needs, current methods still only possess species-level capabilities and require secondary testing to determine antibiotic resistance. This study describes the use of metal oxide laser ionization mass spectrometry fatty acid (FA) profiling as a rapid, simultaneous Staphylococcus identification and antibiotic resistance determination method. Results Principal component analysis was used to classify 50 Staphyloccocus isolates. Leave-one-spectrum-out cross-validation indicated 100 % correct assignment at the species and strain level. Fuzzy rule building expert system classification and self-optimizing partial least squares discriminant analysis, with more rigorous evaluations, also consistently achieved greater than 94 and 84 % accuracy, respectively. Preliminary analysis differentiating MRSA from MSSA demonstrated the feasibility of simultaneous determination of strain identification and antibiotic resistance. Conclusion The utility of CeO2-MOLI MS FA profiling coupled with multivariate statistical analysis for performing strain-level differentiation of various Staphylococcus species proved to be a fast and reliable tool for identification. The simultaneous strain-level detection and antibiotic resistance determination achieved with this method should greatly improve outcomes and reduce clinical costs for therapeutic management and infection control.
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Affiliation(s)
- Nicholas R Saichek
- Department of Chemistry, Colorado School of Mines, Golden, CO, 80401, USA
| | - Christopher R Cox
- Department of Chemistry, Colorado School of Mines, Golden, CO, 80401, USA
| | - Seungki Kim
- Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 136-791, Republic of Korea
| | - Peter B Harrington
- Center for Intelligent Chemical Instrumentation, Department of Chemistry, Clippinger Laboratories, Ohio University, Athens, OH, 45701, USA
| | | | - Kent J Voorhees
- Department of Chemistry, Colorado School of Mines, Golden, CO, 80401, USA.
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21
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Bradley P, Gordon NC, Walker TM, Dunn L, Heys S, Huang B, Earle S, Pankhurst LJ, Anson L, de Cesare M, Piazza P, Votintseva AA, Golubchik T, Wilson DJ, Wyllie DH, Diel R, Niemann S, Feuerriegel S, Kohl TA, Ismail N, Omar SV, Smith EG, Buck D, McVean G, Walker AS, Peto TEA, Crook DW, Iqbal Z. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat Commun 2015; 6:10063. [PMID: 26686880 PMCID: PMC4703848 DOI: 10.1038/ncomms10063] [Citation(s) in RCA: 366] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 10/28/2015] [Indexed: 01/14/2023] Open
Abstract
The rise of antibiotic-resistant bacteria has led to an urgent need for rapid detection of drug resistance in clinical samples, and improvements in global surveillance. Here we show how de Bruijn graph representation of bacterial diversity can be used to identify species and resistance profiles of clinical isolates. We implement this method for Staphylococcus aureus and Mycobacterium tuberculosis in a software package ('Mykrobe predictor') that takes raw sequence data as input, and generates a clinician-friendly report within 3 minutes on a laptop. For S. aureus, the error rates of our method are comparable to gold-standard phenotypic methods, with sensitivity/specificity of 99.1%/99.6% across 12 antibiotics (using an independent validation set, n=470). For M. tuberculosis, our method predicts resistance with sensitivity/specificity of 82.6%/98.5% (independent validation set, n=1,609); sensitivity is lower here, probably because of limited understanding of the underlying genetic mechanisms. We give evidence that minor alleles improve detection of extremely drug-resistant strains, and demonstrate feasibility of the use of emerging single-molecule nanopore sequencing techniques for these purposes.
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Affiliation(s)
- Phelim Bradley
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - N Claire Gordon
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 1NF, UK
| | - Timothy M Walker
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 1NF, UK
| | - Laura Dunn
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 1NF, UK
| | - Simon Heys
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Bill Huang
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Sarah Earle
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 1NF, UK
| | - Louise J Pankhurst
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 1NF, UK
| | - Luke Anson
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 1NF, UK
| | | | - Paolo Piazza
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | - Tanya Golubchik
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 1NF, UK
| | - Daniel J Wilson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.,Nuffield Department of Medicine, University of Oxford, Oxford OX1 1NF, UK
| | - David H Wyllie
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 1NF, UK
| | - Roland Diel
- Institute for Epidemiology, University Medical Hospital Schleswig-Holstein, Niemannsweg 11, 24105 Kiel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Centre Borstel, Parkallee 1, 23845 Borstel, Germany.,German Centre for Infection Research, Partner Site Borstel, Parkallee 1, 23845 Borstel, Germany
| | - Silke Feuerriegel
- Molecular and Experimental Mycobacteriology, Research Centre Borstel, Parkallee 1, 23845 Borstel, Germany.,German Centre for Infection Research, Partner Site Borstel, Parkallee 1, 23845 Borstel, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Centre Borstel, Parkallee 1, 23845 Borstel, Germany
| | - Nazir Ismail
- Centre for Tuberculosis, National Institute for Communicable Diseases, Private Bag X4 Sandringham, Johannesburg 2131, South Africa.,Department of Medical Microbiology, University of Pretoria, PO Box 667, Pretoria 0001, South Africa
| | - Shaheed V Omar
- Centre for Tuberculosis, National Institute for Communicable Diseases, Private Bag X4 Sandringham, Johannesburg 2131, South Africa
| | - E Grace Smith
- Regional Centre for Mycobacteriology, PHE Public Health Laboratory Birmingham. Heartlands Hospital, Bordesley Green East, Birmingham B9 5SS, UK
| | - David Buck
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 1NF, UK.,Biomedical Research Centre, NIHR (National Institutes of Health Research) Oxford Biomedical Research Centre, Oxford OX3 7LE, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 1NF, UK.,Biomedical Research Centre, NIHR (National Institutes of Health Research) Oxford Biomedical Research Centre, Oxford OX3 7LE, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 1NF, UK.,Biomedical Research Centre, NIHR (National Institutes of Health Research) Oxford Biomedical Research Centre, Oxford OX3 7LE, UK.,National Infection Service, Public Health England, Wellington House, 133-155 Waterloo Road, London SE1 8UG, UK
| | - Zamin Iqbal
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
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22
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Stambach NR, Carr SA, Cox CR, Voorhees KJ. Rapid Detection of Listeria by Bacteriophage Amplification and SERS-Lateral Flow Immunochromatography. Viruses 2015; 7:6631-41. [PMID: 26694448 PMCID: PMC4690885 DOI: 10.3390/v7122962] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 11/02/2015] [Accepted: 12/10/2015] [Indexed: 11/16/2022] Open
Abstract
A rapid Listeria detection method was developed utilizing A511 bacteriophage amplification combined with surface-enhanced Raman spectroscopy (SERS) and lateral flow immunochromatography (LFI). Anti-A511 antibodies were covalently linked to SERS nanoparticles and printed onto nitrocellulose membranes. Antibody-conjugated SERS nanoparticles were used as quantifiable reporters. In the presence of A511, phage-SERS nanoparticle complexes were arrested and concentrated as a visible test line, which was interrogated quantitatively by Raman spectroscopy. An increase in SERS intensity correlated to an increase in captured phage-reporter complexes. SERS limit of detection was 6 × 10(6) pfu·mL(-1), offering detection below that obtainable by the naked eye (LOD 6 × 10(7) pfu·mL(-1)). Phage amplification experiments were carried out at a multiplicity of infection (MOI) of 0.1 with 4 different starting phage concentrations monitored over time using SERS-LFI and validated by spot titer assay. Detection of L. monocytogenes concentrations of 1 × 10(7) colony forming units (cfu)·mL(-1), 5 × 10(6) cfu·mL(-1), 5 × 10(5) cfu·mL(-1) and 5 × 10(4) cfu·mL(-1) was achieved in 2, 2, 6, and 8 h, respectively. Similar experiments were conducted at a constant starting phage concentration (5 × 10(5) pfu·mL(-1)) with MOIs of 1, 2.5, and 5 and were detected in 2, 4, and 5 h, respectively.
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Affiliation(s)
- Nicholas R Stambach
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA.
| | - Stephanie A Carr
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA.
| | - Christopher R Cox
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA.
| | - Kent J Voorhees
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA.
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23
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Dong T, Zhao X. Rapid identification and susceptibility testing of uropathogenic microbes via immunosorbent ATP-bioluminescence assay on a microfluidic simulator for antibiotic therapy. Anal Chem 2015; 87:2410-8. [PMID: 25584656 DOI: 10.1021/ac504428t] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The incorporation of pathogen identification with antimicrobial susceptibility testing (AST) was implemented on a concept microfluidic simulator, which is well suited for personalizing antibiotic treatment of urinary tract infections (UTIs). The microfluidic device employs a fiberglass membrane sandwiched between two polypropylene components, with capture antibodies immobilized on the membrane. The chambers in the microfluidic device share the same geometric distribution as the wells in a standard 384-well microplate, resulting in compatibility with common microplate readers. Thirteen types of common uropathogenic microbes were selected as the analytes in this study. The microbes can be specifically captured by various capture antibodies and then quantified via an ATP bioluminescence assay (ATP-BLA) either directly or after a variety of follow-up tests, including urine culture, antibiotic treatment, and personalized antibiotic therapy simulation. Owing to the design of the microfluidic device, as well as the antibody specificity and the ATP-BLA sensitivity, the simulator was proven to be able to identify UTI pathogen species in artificial urine samples within 20 min and to reliably and simultaneously verify the antiseptic effects of eight antibiotic drugs within 3-6 h. The measurement range of the device spreads from 1 × 10(3) to 1 × 10(5) cells/mL in urine samples. We envision that the medical simulator might be broadly employed in UTI treatment and could serve as a model for the diagnosis and treatment of other diseases.
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Affiliation(s)
- Tao Dong
- Institute of Applied Micro-Nano Science and Technology, Chongqing Engineering Laboratory for Detection, Control and Integrated System, Chongqing Technology and Business University , Nan'an District, Chongqing 400067, China
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24
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Heffernan DS, Fox ED. Advancing technologies for the diagnosis and management of infections. Surg Clin North Am 2014; 94:1163-74. [PMID: 25440117 DOI: 10.1016/j.suc.2014.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Infections remain a significant problem among surgical patients. Technological advances, especially in the arena of nano-technology, have markedly improved the ability to detect, prevent and treat surgical infections. No longer limited to culture-based methods of pathogen detection or standard antimicrobial therapies, options for management of surgical infections are rapidly expanding. Such advances are critical in this era of rapidly developing resistant and virulent strains of organisms. Further, our understanding of the host pathogen interaction grows exponentially with the development of computer-based modeling, aiding in expediting research endeavors.
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Affiliation(s)
- Daithi S Heffernan
- Division of Trauma and Surgical Critical Care, Department of Surgery, Alpert Medical School Brown University, Rhode Island Hospital, 435 APC Building, 593 Eddy Street, Providence, RI 02903, USA.
| | - Elizabeth D Fox
- Department of Surgery, Alpert Medical School Brown University, Rhode Island Hospital, 429 APC Building, 593 Eddy Street, Providence, RI 02903, USA
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25
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Göçeri E, Gürcan MN, Dicle O. Fully automated liver segmentation from SPIR image series. Comput Biol Med 2014; 53:265-78. [PMID: 25192606 DOI: 10.1016/j.compbiomed.2014.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/04/2014] [Accepted: 08/10/2014] [Indexed: 10/24/2022]
Abstract
Accurate liver segmentation is an important component of surgery planning for liver transplantation, which enables patients with liver disease a chance to survive. Spectral pre-saturation inversion recovery (SPIR) image sequences are useful for liver vessel segmentation because vascular structures in the liver are clearly visible in these sequences. Although level-set based segmentation techniques are frequently used in liver segmentation due to their flexibility to adapt to different problems by incorporating prior knowledge, the need to initialize the contours on each slice is a common drawback of such techniques. In this paper, we present a fully automated variational level set approach for liver segmentation from SPIR image sequences. Our approach is designed to be efficient while achieving high accuracy. The efficiency is achieved by (1) automatically defining an initial contour for each slice, and (2) automatically computing weight values of each term in the applied energy functional at each iteration during evolution. Automated detection and exclusion of spurious structures (e.g. cysts and other bright white regions on the skin) in the pre-processing stage increases the accuracy and robustness. We also present a novel approach to reduce computational cost by employing binary regularization of level set function. A signed pressure force function controls the evolution of the active contour. The method was applied to ten data sets. In each image, the performance of the algorithm was measured using the receiver operating characteristics method in terms of accuracy, sensitivity and specificity. The accuracy of the proposed method was 96%. Quantitative analyses of results indicate that the proposed method can accurately, efficiently and consistently segment liver images.
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Affiliation(s)
- Evgin Göçeri
- Department of Computer Engineering, Pamukkale University, Denizli, Turkey.
| | - Metin N Gürcan
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Oğuz Dicle
- Department of Radiology, Faculty of Medicine, Dokuz Eylul University, Narlıdere, Izmir, Turkey
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26
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Bacteriophage-based latex agglutination test for rapid identification of Staphylococcus aureus. J Clin Microbiol 2014; 52:3394-8. [PMID: 25031449 DOI: 10.1128/jcm.01432-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid diagnosis is essential for the management of Staphylococcus aureus infections. A host recognition protein from S. aureus bacteriophage phiSLT was recombinantly produced and used to coat streptavidin latex beads to develop a latex agglutination test (LAT). The diagnostic accuracy of this bacteriophage-based test was compared with that of a conventional LAT, Pastorex Staph-Plus, by investigating a clinical collection of 86 S. aureus isolates and 128 coagulase-negative staphylococci (CoNS) from deep tissue infections. All of the clinical S. aureus isolates were correctly identified by the bacteriophage-based test. While most of the CoNS were correctly identified as non-S. aureus isolates, 7.9% of the CoNS caused agglutination. Thus, the sensitivity of the bacteriophage-based LAT for identification of S. aureus among clinical isolates was 100%, its specificity was 92.1%, its positive predictive value (PPV) was 89.6%, and its negative predictive value (NPV) was 100%. The sensitivity, specificity, PPV, and NPV of the Pastorex LAT for the identification of S. aureus were 100%, 99.2%, 98.9%, and 100%, respectively. Among the additionally tested 35 S. aureus and 91 non-S. aureus staphylococcal reference and type strains, 1 isolate was false negative by each system; 13 and 8 isolates were false positive by the bacteriophage-based and Pastorex LATs, respectively. The ability of the phiSLT protein to detect S. aureus was dependent on the presence of wall teichoic acid (WTA) and corresponded to the production of ribitol phosphate WTA, which is found in most S. aureus clones but only a small minority of CoNS. Bacteriophage-based LAT identification is a promising strategy for rapid pathogen identification. Finding more specific bacteriophage proteins would increase the specificity of this novel diagnostic approach.
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27
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Tjhung KF, Burnham S, Anany H, Griffiths MW, Derda R. Rapid enumeration of phage in monodisperse emulsions. Anal Chem 2014; 86:5642-8. [PMID: 24892245 DOI: 10.1021/ac500244g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Phage-based detection assays have been developed for the detection of viable bacteria for applications in clinical diagnosis, monitoring of water quality, and food safety. The majority of these assays deliver a positive readout in the form of newly generated progeny phages by the bacterial host of interest. Progeny phages are often visualized as plaques, or holes, in a lawn of bacteria on an agar-filled Petri dish; however, this rate-limiting step requires up to 12 h of incubation time. We have previously described an amplification of bacteriophages M13 inside droplets of media suspended in perfluorinated oil; a single phage M13 in a droplet yields 10(7) copies in 3-4 h. Here, we describe that encapsulation of reporter phages, both lytic T4-LacZ and nonlytic M13, in monodisperse droplets can also be used for rapid enumeration of phage. Compartmentalization in droplets accelerated the development of the signal from the reporter enzyme; counting of "positive" droplets yields accurate enumeration of phage particles ranging from 10(2) to 10(6) pfu/mL. For enumeration of T4-LacZ phage, the fluorescent signal appeared in as little as 90 min. Unlike bulk assays, quantification in emulsion is robust and insensitive to fluctuations in environmental conditions (e.g., temperature). Power-free emulsification using gravity-driven flow in the absence of syringe pumps and portable fluorescence imaging solutions makes this technology promising for use at the point of care in low-resource environments. This droplet-based phage enumeration method could accelerate and simplify point-of-care detection of the pathogens for which reporter bacteriophages have been developed.
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Affiliation(s)
- Katrina F Tjhung
- Department of Chemistry, University of Alberta , Edmonton, AB T6G 2G2, Canada
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Valencia-Shelton F, Loeffelholz M. Nonculture techniques for the detection of bacteremia and fungemia. Future Microbiol 2014; 9:543-59. [DOI: 10.2217/fmb.14.8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
ABSTRACT: Bacteremia and fungemia account for a substantial proportion of all cases of severe sepsis. Antibiotic resistance is a contributing factor in many hospital-acquired infection deaths. Traditional phenotypic methods for the identification of bacteria and yeasts from positive blood cultures and determining antimicrobial susceptibility require 48–72 h, delaying optimal therapy and negatively impacting patient outcomes. Molecular methods, including nonamplified DNA probe panels and peptide nucleic acid probes, and nucleic acid amplification methods such as PCR, proteomic methods (matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry) and direct biochemical tests provide more rapid identification of bacteria and fungi, and in some cases antimicrobial resistance markers, from positive blood cultures, as well as directly from whole blood. These methods vary in the breadth of organisms that they detect, and equally important, their ease of use. This article examines the principles, performance and practicality of the various rapid, nonculture techniques for the detection of bacteremia and fungemia.
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Affiliation(s)
- Frances Valencia-Shelton
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
- Current affiliation: Strong Memorial Hospital, University of Rochester, Rochester, NY, USA
| | - Michael Loeffelholz
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
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Molecular identification of staphylococcal bacteraemia. THE LANCET. INFECTIOUS DISEASES 2014; 14:94-6. [PMID: 24457164 DOI: 10.1016/s1473-3099(13)70364-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Sorokulova I, Olsen E, Vodyanoy V. Bacteriophage biosensors for antibiotic-resistant bacteria. Expert Rev Med Devices 2014; 11:175-86. [DOI: 10.1586/17434440.2014.882767] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Kong H, Tong L, Zhang W, Fu Y, Li X. Combined use of the BinaxNOW Staphylococcus aureus test with the Clearview PBP2a assay for the early detection of methicillin-resistant S. aureus from positive blood cultures. Diagn Microbiol Infect Dis 2013; 78:226-8. [PMID: 24360266 DOI: 10.1016/j.diagmicrobio.2013.11.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/12/2013] [Accepted: 11/16/2013] [Indexed: 10/26/2022]
Abstract
The use of combination 2 novel immunochromatographic assays for same-day detection of methicillin-resistant Staphylococcus aureus (MRSA) from positive blood cultures was evaluated. Compared to the standard culture methods, the BinaxNOW® S. aureus test demonstrated 98.7% sensitivity and 100% specificity in correctly identifying S. aureus. The sensitivity and specificity of the Clearview® PBP2a assay in differentiating MRSA from methicillin-susceptible S. aureus were 97.1% and 100%.
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Affiliation(s)
- Haishen Kong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang, PR China
| | - Ling Tong
- Center of Clinical Laboratory, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Weili Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang, PR China
| | - Yajie Fu
- Center of Clinical Laboratory, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Xuefen Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang, PR China; Center of Clinical Laboratory, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China.
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Biographical feature: Melvin P. Weinstein, M.D. J Clin Microbiol 2013; 51:2476-8. [PMID: 23740724 DOI: 10.1128/jcm.01354-13] [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] Open
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