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Schumacher A, Vranken T, Malhotra A, Arts JJC, Habibovic P. In vitro antimicrobial susceptibility testing methods: agar dilution to 3D tissue-engineered models. Eur J Clin Microbiol Infect Dis 2018; 37:187-208. [PMID: 28871407 PMCID: PMC5780537 DOI: 10.1007/s10096-017-3089-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 07/20/2017] [Indexed: 12/22/2022]
Abstract
In the field of orthopaedic surgery, bacterial invasion of implants and the resulting periprosthetic infections are a common and unresolved problem. Antimicrobial susceptibility testing methods help to define the optimal treatment and identify antimicrobial resistance. This review discusses proven gold-standard techniques and recently developed models for antimicrobial susceptibility testing, while also providing a future outlook. Conventional, gold-standard methods, such as broth microdilution, are still widely applied in clinical settings. Although recently developed methods based on microfluidics and microdroplets have shown advantages over conventional methods in terms of testing speed, safety and the potential to provide a deeper insight into resistance mechanisms, extensive validation is required to translate this research to clinical practice. Recent optical and mechanical methods are complex and expensive and, therefore, not immediately clinically applicable. Novel osteoblast infection and tissue models best resemble infections in vivo. However, the integration of biomaterials into these models remains challenging and they require a long tissue culture, making their rapid clinical implementation unlikely. A method applicable for both clinical and research environments is difficult to realise. With a continuous increase in antimicrobial resistance, there is an urgent need for methods that analyse recurrent infections to identify the optimal treatment approaches. Graphical abstract Timeline of published and partly applied antimicrobial susceptibility testing methods, listed according to their underlying mechanism, complexity and application in research or clinics.
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Affiliation(s)
- A Schumacher
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, Room C3.577, 6229 ER, Maastricht, Netherlands.
- Science and Technology Faculty, University of Twente, Drienerlolaan 5, 7522 NB, Enschede, The Netherlands.
| | - T Vranken
- Department of Orthopaedic Surgery, CAPHRI Care and Public Health Research Institute, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - A Malhotra
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, Room C3.577, 6229 ER, Maastricht, Netherlands
| | - J J C Arts
- Department of Orthopaedic Surgery, CAPHRI Care and Public Health Research Institute, Maastricht University Medical Centre, Maastricht, The Netherlands
- Orthopaedic Biomechanics Group, Department of Biomedical Engineering, Eindhoven University of Technology (TU/e), Eindhoven, The Netherlands
| | - P Habibovic
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, Room C3.577, 6229 ER, Maastricht, Netherlands
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Abstract
Over half of the nearly two million healthcare-associated infections can be attributed to indwelling medical devices. In this review, we highlight the difficulty in diagnosing implantable device-related infection and how this leads to a likely underestimate of the prevalence. We then provide a length-scale conceptualization of device-related infection pathogenesis. Within this conceptualization we focus specifically on biofilm formation and the role of host immune and coagulation systems. Using this framework, we describe how current and developing preventative strategies target specific processes along the entire length-scale. In light of the significant time horizon for the development and translation of new preventative technologies, we also emphasize the need for parallel development of in situ treatment strategies. Specific examples of both preventative and treatment strategies and how they align with the length-scale conceptualization are described.
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103
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Chudejova K, Bohac M, Skalova A, Rotova V, Papagiannitsis CC, Hanzlickova J, Bergerova T, Hrabák J. Validation of a novel automatic deposition of bacteria and yeasts on MALDI target for MALDI-TOF MS-based identification using MALDI Colonyst robot. PLoS One 2017; 12:e0190038. [PMID: 29287094 PMCID: PMC5747426 DOI: 10.1371/journal.pone.0190038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 12/07/2017] [Indexed: 11/30/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) -based identification of bacteria and fungi significantly changed the diagnostic process in clinical microbiology. We describe here a novel technique for bacterial and yeast deposition on MALDI target using an automated workflow resulting in an increase of the microbes' score of MALDI identification. We also provide a comparison of four different sample preparation methods. In the first step of the study, 100 Gram-negative bacteria, 100 Gram-positive bacteria, 20 anaerobic bacteria and 20 yeasts were spotted on the MALDI target using manual deposition, semi-extraction, wet deposition onto 70% formic acid and by automatic deposition using MALDI Colonyst. The lowest scores were obtained by manual toothpick spotting which significantly differ from other methods. Identification score of semi-extraction, wet deposition and automatic wet deposition did not significantly differ using calculated relative standard deviation (RSD). Nevertheless, the best results with low error rate have been observed using MALDI Colonyst robot. The second step of validation included processing of 542 clinical isolates in routine microbiological laboratory by a toothpick direct spotting, on-plate formic acid extraction (for yeasts) and automatic deposition using MALDI Colonyst. Validation in routine laboratory process showed significantly higher identification scores obtained using automated process compared with standard manual deposition in all tested microbial groups (Gram-positive, Gram-negative, anaerobes, and yeasts). As shown by our data, automatic colony deposition on MALDI target results in an increase of MALDI-TOF MS identification scores and reproducibility.
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Affiliation(s)
- Katerina Chudejova
- Biomedical Center and Department of Microbiology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Plzen, Czech Republic
| | | | - Anna Skalova
- Biomedical Center and Department of Microbiology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Plzen, Czech Republic
- Department of Microbiology, University Hospital in Pilsen, Plzen, Czech Republic
| | - Veronika Rotova
- Biomedical Center and Department of Microbiology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Plzen, Czech Republic
| | - Costas C. Papagiannitsis
- Biomedical Center and Department of Microbiology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Plzen, Czech Republic
| | - Jana Hanzlickova
- Department of Microbiology, University Hospital in Pilsen, Plzen, Czech Republic
| | - Tamara Bergerova
- Biomedical Center and Department of Microbiology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Plzen, Czech Republic
- Department of Microbiology, University Hospital in Pilsen, Plzen, Czech Republic
| | - Jaroslav Hrabák
- Biomedical Center and Department of Microbiology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Plzen, Czech Republic
- Department of Microbiology, University Hospital in Pilsen, Plzen, Czech Republic
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104
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Carvalho WSP, Wei M, Ikpo N, Gao Y, Serpe MJ. Polymer-Based Technologies for Sensing Applications. Anal Chem 2017; 90:459-479. [DOI: 10.1021/acs.analchem.7b04751] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | - Menglian Wei
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Nduka Ikpo
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Yongfeng Gao
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Michael J. Serpe
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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105
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Cantón R, Gómez G. de la Pedrosa E. Impacto económico de los métodos de diagnóstico rápido en Microbiología Clínica: precio de la prueba o impacto clínico global. Enferm Infecc Microbiol Clin 2017; 35:659-666. [DOI: 10.1016/j.eimc.2017.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 09/13/2017] [Indexed: 12/19/2022]
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106
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Scherz V, Durussel C, Greub G. Internal quality assurance in diagnostic microbiology: A simple approach for insightful data. PLoS One 2017; 12:e0187263. [PMID: 29135992 PMCID: PMC5685576 DOI: 10.1371/journal.pone.0187263] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 10/17/2017] [Indexed: 11/18/2022] Open
Abstract
Given the importance of microbiology results on patient care, high quality standards are expected. Internal quality assurance (IQA) could mitigate the limitations of internal quality control, competency assessment and external quality assurance, adding a longitudinal insight, including pre- and post-analytical steps. Here, we implemented an IQA program in our clinical microbiology facilities with blind resubmission of routine samples during 22 months. One-hundred-and-twenty-one out of 123 (98.4%) serological analyses and 112 out of 122 (91.8%) molecular analyses were concordant. Among the discordances in molecular biology analyses, 6 results were low positive samples that turned out negative, likely due to stochastic repartition of nucleic acids. Moreover, one identified retranscription error led us to implement automated results transmission from the Applied Biosystems instruments to the laboratory information system (LIS). Regarding Gram stain microscopy, 560 out of 745 (75.2%) of compared parameters were concordant. As many as 67 out of 84 (79.8%) pairs of culture results were similar, including 16 sterile pairs, 27 having identical identification or description and semi-quantification and 24 only showing variations in semi-quantification with identical description or identification of colonies. Seventeen pairs had diverging identification or description of colonies. Culture was twice only done for one member of the pairs. Regarding antibiotic susceptibility testing, a major discrepancy was observed in 5 out of 48 results (10.4%). In conclusion, serological tests were highly reproducible. Molecular diagnosis also revealed to be robust except when the amounts of nucleic acids present in the sample were close to the limits of detection. Conventional microbiology was less robust with major discrepancies reaching 39.5% of the samples for microscopy. Similarly, culture and antibiotic susceptibility testing were prone to discrepancies. This work was ground for reconsidering multiples aspects of our practices and demonstrates the importance of IQA to complete the other quality management procedures.
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Affiliation(s)
- Valentin Scherz
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Christian Durussel
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
- * E-mail:
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107
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Heather CS, Maley M. Automated direct screening for resistance of Gram-negative blood cultures using the BD Kiestra WorkCell. Eur J Clin Microbiol Infect Dis 2017; 37:117-125. [PMID: 28971266 DOI: 10.1007/s10096-017-3109-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/14/2017] [Indexed: 10/18/2022]
Abstract
Early detection of resistance in sepsis due to Gram-negative organisms may lead to improved outcomes by reducing the time to effective antibiotic therapy. Traditional methods of resistance detection require incubation times of 18 to 48 h to detect resistance. We have utilised automated specimen processing, digital imaging and zone size measurements in conjunction with direct disc susceptibility testing to develop a method for the rapid screening of Gram-negative blood culture isolates for resistance. Positive clinical blood cultures with Gram-negative organisms were prospectively identified and additional resistant mock specimens were prepared. Broth was plated and antibiotic-impregnated discs (ampicillin, ceftriaxone, piperacillin-tazobactam, meropenem, ciprofloxacin, gentamicin) were added. Plates were incubated, digitally imaged and zone sizes were measured using the BD Kiestra WorkCell laboratory automation system. Minimum, clinically useful, incubation times and optimised zone size cut-offs for resistance detection were determined. We included 187 blood cultures in the study. At 5 h of incubation, > 90% of plates yielded interpretable results. Using optimised zone size cut-offs, the sensitivity for resistance detection ranged from 87 to 100%, while the specificity ranged from 84.7 to 100%. The sensitivity and specificity for piperacillin-tazobactam resistance detection was consistently worse than for the other agents. Automated direct disc susceptibility screening is a rapid and sensitive tool for resistance detection in Gram-negative isolates from blood cultures for most of the agents tested.
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Affiliation(s)
- C S Heather
- Department of Microbiology and Infectious Diseases, NSW Health Pathology South-Liverpool, Liverpool Hospital, Corner Goulburn and Forbes Street, Liverpool, NSW, Australia.
| | - M Maley
- Department of Microbiology and Infectious Diseases, NSW Health Pathology South-Liverpool, Liverpool Hospital, Corner Goulburn and Forbes Street, Liverpool, NSW, Australia
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El Houmami N, Bzdrenga J, Durand GA, Minodier P, Seligmann H, Prudent E, Bakour S, Bonacorsi S, Raoult D, Yagupsky P, Fournier PE. Molecular Tests That Target the RTX Locus Do Not Distinguish between Kingella kingae and the Recently Described Kingella negevensis Species. J Clin Microbiol 2017; 55:3113-3122. [PMID: 28794176 PMCID: PMC5625396 DOI: 10.1128/jcm.00736-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/31/2017] [Indexed: 11/20/2022] Open
Abstract
Kingella kingae is an important invasive pathogen in early childhood. The organism elaborates an RTX toxin presumably restricted to this species. Consequently, real-time quantitative PCR (qPCR) assays targeting the RTX locus have been developed in recent years and are gaining increasing use for the molecular diagnosis of K. kingae infections. However, the present study shows that Kingella negevensis, a Kingella species newly identified in young children, harbors an identical Kingella RTX locus, raising the question of whether K. negevensis can be misidentified as K. kingae by clinical microbiology laboratories. In silico comparison of Kingella sp. RTX and groEL genes and in vitro studies provided evidence that targeting the rtxA and rtxB genes could not differentiate between strains of K. kingae and K. negevensis, whereas targeting the groEL gene could. This prompted the design of a highly specific and sensitive qPCR assay targeting K. negevensis groEL (kngroEL). Ninety-nine culture-negative osteoarticular specimens from 99 children younger than 4 years of age were tested with a conventional 16S rRNA gene-based broad-range PCR assay and Kingella-specific rtxB, K. kingae-specific groEL (kkgroEL), and kngroEL qPCR assays. Forty-two specimens were rtxB positive, including 41 that were also kkgroEL positive and 1 (the remaining one) that was kngroEL positive. Thus, this study discloses an invasive infection caused by K. negevensis in humans and demonstrates that targeting the RTX locus cannot be used for the formal diagnosis of K. kingae infections. These findings stress the need for further studies on the epidemiology of asymptomatic carriage and invasive infections caused by K. negevensis in humans.
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Affiliation(s)
- Nawal El Houmami
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Janek Bzdrenga
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France
| | - Guillaume André Durand
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Minodier
- Department of Pediatric Emergency, North Hospital, Marseille, France
| | - Hervé Seligmann
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Elsa Prudent
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Sofiane Bakour
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Stéphane Bonacorsi
- Inserm, IAME, UMR 1137, Université Paris-Diderot, Sorbonne Paris Cité, Laboratoire de Microbiologie, Hôpital Robert-Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Didier Raoult
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Pablo Yagupsky
- Clinical Microbiology Laboratory, Soroka University Medical Center, Beer-Sheva, Israel
| | - Pierre-Edouard Fournier
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
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109
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Almeida S, Dorneles EMS, Diniz C, Abreu V, Sousa C, Alves J, Carneiro A, Bagano P, Spier S, Barh D, Lage AP, Figueiredo H, Azevedo V. Quadruplex PCR assay for identification of Corynebacterium pseudotuberculosis differentiating biovar Ovis and Equi. BMC Vet Res 2017; 13:290. [PMID: 28946887 PMCID: PMC5613524 DOI: 10.1186/s12917-017-1210-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/14/2017] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Corynebacterium pseudotuberculosis is classified into two biovars, nitrate-negative biovar Ovis which is the etiologic agent of caseous lymphadenitis in small ruminants and nitrate-positive biovar Equi, which causes abscesses and ulcerative lymphangitis in equines. The aim of this study was to develop a quadruplex PCR assay that would allow simultaneous detection and biovar-typing of C. pseudotuberculosis. METHODS In the present study, genomes of C. pseudotuberculosis strains were used to identify the genes involved in the nitrate reduction pathway to improve a species identification three-primer multiplex PCR assay. The nitrate reductase gene (narG) was included in the PCR assay along with the 16S, rpoB and pld genes to enhance the diagnosis of the multiplex PCR at biovar level. RESULTS A novel quadruplex PCR assay for C. pseudotuberculosis species and biovar identification was developed. The results of the quadruplex PCR of 348 strains, 346 previously well-characterized clinical isolates of C. pseudotuberculosis from different hosts (goats, sheep, horse, cattle, buffalo, llamas and humans), the vaccine strain 1002 and the type strain ATCC 19410T, were compared to the results of nitrate reductase identification by biochemical test. The McNemar's Chi-squared test used to compare the two methods used for C. pseudotuberculosis biovar identification showed no significant difference (P = 0.75) [95% CI for odds ratio (0.16-6.14)] between the quadruplex PCR and the nitrate biochemical test. Concordant results were observed for 97.13% (338 / 348) of the tested strains and the kappa value was 0.94 [95% CI (0.90-0.98)]. CONCLUSIONS The ability of the quadruplex assay to discriminate between C. pseudotuberculosis biovar Ovis and Equi strains enhances its usefulness in the clinical microbiology laboratory.
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Affiliation(s)
- Sintia Almeida
- Instituto de Ciências Biológicas, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Elaine M. S. Dorneles
- Escola de Veterinária, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Carlos Diniz
- Instituto de Ciências Biológicas, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
- Departamento de Medicina Veterinária, Federal University of Lavras, Lavras, MG Brazil
| | - Vinícius Abreu
- Centro de Energia Nuclear na Agricultura, University of Sao Paulo, Piracicaba, SP Brazil
| | - Cassiana Sousa
- Instituto de Ciências Biológicas, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Jorianne Alves
- Instituto de Ciências Biológicas, Federal University of Para, Belém, PA Brazil
| | - Adriana Carneiro
- Instituto de Ciências Biológicas, Federal University of Para, Belém, PA Brazil
| | - Priscilla Bagano
- Instituto de Ciências Biológicas, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Sharon Spier
- Department of Medicine and Epidemiology, UC Davis School of Veterinary Medicine, Davis, CA USA
| | - Debmalya Barh
- Instituto de Ciências Biológicas, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB India
| | - Andrey P. Lage
- Escola de Veterinária, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Henrique Figueiredo
- Aquacen - National Reference Laboratory for Aquatic Animal Diseases, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Vasco Azevedo
- Instituto de Ciências Biológicas, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
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110
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Duffy D, Mottez E, Ainsworth S, Buivan TP, Baudin A, Vray M, Reed B, Fontanet A, Rohel A, Petrov-Sanchez V, Abel L, Theodorou I, Miele G, Pol S, Albert ML. An in vitro diagnostic certified point of care single nucleotide test for IL28B polymorphisms. PLoS One 2017; 12:e0183084. [PMID: 28877177 PMCID: PMC5587232 DOI: 10.1371/journal.pone.0183084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 07/29/2017] [Indexed: 01/26/2023] Open
Abstract
Numerous genetic polymorphisms have been identified as associated with disease or treatment outcome, but the routine implementation of genotyping into actionable medical care remains limited. Point-of-care (PoC) technologies enable rapid and real-time treatment decisions, with great potential for extending molecular diagnostic approaches to settings with limited medical infrastructure (e.g., CLIA certified diagnostic laboratories). With respect to resource-limited settings, there is a need for simple devices to implement biomarker guided treatment strategies. One relevant example is chronic hepatitis C infection, for which several treatment options are now approved. Single nucleotide polymorphisms (SNPs) in the IL-28B / IFNL3 locus have been well described to predict both spontaneous clearance and response to interferon based therapies. We utilized the Genedrive® platform to develop an assay for the SNP rs12979860 variants (CC, CT and TT). The assay utilizes a hybrid thermal engine, permitting rapid heating and cooling, enabling an amplification based assay with genetic variants reported using endpoint differential melting cure analysis in less than 60 minutes. We validated this assay using non-invasive buccal swab sampling in a prospective study of 246 chronic HCV patients, achieving 100% sensitivity and 100% specificity (95% exact CI: 98.8-100%)) in 50 minutes as compared to conventional lab based PCR testing. Our results provide proof of concept that precision medicine is feasible in resource-limited settings, offering the first CE-IVD (in vitro diagnostics) validated PoC SNP test. We propose that IL-28B genotyping may be useful for directing patients towards lower cost therapies, and rationing use of costly direct antivirals for use in those individuals showing genetic risk.
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Affiliation(s)
- Darragh Duffy
- Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France
- Inserm U1223, Institut Pasteur, Paris, France
- Centre for Translational Research, Institut Pasteur, Paris, France
| | - Estelle Mottez
- Centre for Translational Research, Institut Pasteur, Paris, France
- Inserm UMS20, Institut Pasteur Paris, France
| | | | - Tan-Phuc Buivan
- Centre for Translational Research, Institut Pasteur, Paris, France
- Inserm UMS20, Institut Pasteur Paris, France
- Université Paris Descartes et Département d'hépatologie, Groupe Hospitalier Cochin Hôtel- Dieu, Paris, France
| | - Aurelie Baudin
- Université Paris Descartes et Département d'hépatologie, Groupe Hospitalier Cochin Hôtel- Dieu, Paris, France
| | - Muriel Vray
- Emerging Disease Epidemiology Unit, Institut Pasteur, Paris, France
- PARCI Unit, Conservatoire National des Arts et Métiers, Paris, France
- Unit of epidemiology of infectious diseases, Institut Pasteur, Dakar, Senegal
| | - Ben Reed
- Genedrive plc, Manchester, United Kingdom
| | - Arnaud Fontanet
- Emerging Disease Epidemiology Unit, Institut Pasteur, Paris, France
- PARCI Unit, Conservatoire National des Arts et Métiers, Paris, France
| | - Alexandra Rohel
- ANRS (France REcherche Nord&Sud Sida-hiv Hépatites), Paris, France
| | | | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm U1163, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York, United States of America
| | - Ioannis Theodorou
- Department of Immunology, AP-HP, La Pitie Salpetriere, Paris, France
| | - Gino Miele
- Genedrive plc, Manchester, United Kingdom
| | - Stanislas Pol
- Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France
- Inserm U1223, Institut Pasteur, Paris, France
- Centre for Translational Research, Institut Pasteur, Paris, France
- Inserm UMS20, Institut Pasteur Paris, France
- Université Paris Descartes et Département d'hépatologie, Groupe Hospitalier Cochin Hôtel- Dieu, Paris, France
| | - Matthew L. Albert
- Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France
- Inserm U1223, Institut Pasteur, Paris, France
- Centre for Translational Research, Institut Pasteur, Paris, France
- Inserm UMS20, Institut Pasteur Paris, France
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111
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Skodvin B, Aase K, Brekken AL, Charani E, Lindemann PC, Smith I. Addressing the key communication barriers between microbiology laboratories and clinical units: a qualitative study. J Antimicrob Chemother 2017; 72:2666-2672. [PMID: 28633405 PMCID: PMC5890706 DOI: 10.1093/jac/dkx163] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 04/05/2017] [Accepted: 04/28/2017] [Indexed: 12/28/2022] Open
Abstract
Background Many countries are on the brink of establishing antibiotic stewardship programmes in hospitals nationwide. In a previous study we found that communication between microbiology laboratories and clinical units is a barrier to implementing efficient antibiotic stewardship programmes in Norway. We have now addressed the key communication barriers between microbiology laboratories and clinical units from a laboratory point of view. Methods Qualitative semi-structured interviews were conducted with 18 employees (managers, doctors and technicians) from six diverse Norwegian microbiological laboratories, representing all four regional health authorities. Interviews were recorded and transcribed verbatim. Thematic analysis was applied, identifying emergent themes, subthemes and corresponding descriptions. Results The main barrier to communication is disruption involving specimen logistics, information on request forms, verbal reporting of test results and information transfer between poorly integrated IT systems. Furthermore, communication is challenged by lack of insight into each other's area of expertise and limited provision of laboratory services, leading to prolonged turnaround time, limited advisory services and restricted opening hours. Conclusions Communication between microbiology laboratories and clinical units can be improved by a review of testing processes, educational programmes to increase insights into the other's area of expertise, an evaluation of work tasks and expansion of rapid and point-of-care test services. Antibiotic stewardship programmes may serve as a valuable framework to establish these measures.
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Affiliation(s)
- Brita Skodvin
- Norwegian Advisory Unit for Antibiotic Use in Hospitals, Department of Research and Development, Haukeland University Hospital, 5021 Bergen, Norway
| | - Karina Aase
- Department of Health Studies, University of Stavanger, 4036 Stavanger, Norway
| | - Anita Løvås Brekken
- Department of Microbiology, Stavanger University Hospital, 4068 Stavanger, Norway
| | - Esmita Charani
- National Institute of Health Research Health Protection Research Unit—Antimicrobial Resistance and Healthcare Associated Infection, Imperial College London, Hammersmith Hospital, London W12 OHS, UK
| | - Paul Christoffer Lindemann
- Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Ingrid Smith
- Norwegian Advisory Unit for Antibiotic Use in Hospitals, Department of Research and Development, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
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Abstract
Basic sciences constitute the most abundant sources of creativity and innovation, as they are based on the passion of knowing. Basic knowledge, in close and fertile contact with medical and public health needs, produces distinct advancements in applied sciences. Basic sciences play the role of stem cells, providing material and semantics to construct differentiated tissues and organisms and enabling specialized functions and applications. However, eventually processes of "practice deconstruction" might reveal basic questions, as in de-differentiation of tissue cells. Basic sciences, microbiology, infectious diseases, and public health constitute an epistemological gradient that should also be an investigational continuum. The coexistence of all these interests and their cross-fertilization should be favored by interdisciplinary, integrative research organizations working simultaneously in the analytical and synthetic dimensions of scientific knowledge.
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Affiliation(s)
- Fernando Baquero
- Biology and Evolution of Microorganisms, Ramón y Cajal Institute for Health Research (IRYCIS), Department of Microbiology, Network Center for Research in Epidemiology and Public Health (CIBERESP), Ramón y Cajal University Hospital, Madrid, Spain
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113
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Biomarker research to improve clinical outcomes of peritoneal dialysis: consensus of the European Training and Research in Peritoneal Dialysis (EuTRiPD) network. Kidney Int 2017; 92:824-835. [PMID: 28797473 DOI: 10.1016/j.kint.2017.02.037] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/16/2017] [Accepted: 02/27/2017] [Indexed: 12/15/2022]
Abstract
Peritoneal dialysis (PD) therapy substantially requires biomarkers as tools to identify patients who are at the highest risk for PD-related complications and to guide personalized interventions that may improve clinical outcome in the individual patient. In this consensus article, members of the European Training and Research in Peritoneal Dialysis Network (EuTRiPD) review the current status of biomarker research in PD and suggest a selection of biomarkers that can be relevant to the care of PD patients and that are directly accessible in PD effluents. Currently used biomarkers such as interleukin-6, interleukin-8, ex vivo-stimulated interleukin-6 release, cancer antigen-125, and advanced oxidation protein products that were collected through a Delphi procedure were first triaged for inclusion as surrogate endpoints in a clinical trial. Next, novel biomarkers were selected as promising candidates for proof-of-concept studies and were differentiated into inflammation signatures (including interleukin-17, M1/M2 macrophages, and regulatory T cell/T helper 17), mesothelial-to-mesenchymal transition signatures (including microRNA-21 and microRNA-31), and signatures for senescence and inadequate cellular stress responses. Finally, the need for defining pathogen-specific immune fingerprints and phenotype-associated molecular signatures utilizing effluents from the clinical cohorts of PD patients and "omics" technologies and bioinformatics-biostatistics in future joint-research efforts was expressed. Biomarker research in PD offers the potential to develop valuable tools for improving patient management. However, for all biomarkers discussed in this consensus article, the association of biological rationales with relevant clinical outcomes remains to be rigorously validated in adequately powered, prospective, independent clinical studies.
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114
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Kardoush MI, Ward BJ, Ndao M. Serum Carbonic Anhydrase 1 is a Biomarker for Diagnosis of Human Schistosoma mansoni Infection. Am J Trop Med Hyg 2017; 96:842-849. [PMID: 28500821 DOI: 10.4269/ajtmh.16-0021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
AbstractSchistosoma mansoni is a major public health threat in many parts of the world. The current diagnostic tests for schistosomiasis are suboptimal, particularly early in infection, when the parasite burden is low and with reinfection after treatment. We sought to identify novel biomarkers of active infection by studying serum proteins in a mouse model of schistosomiasis followed by confirmation in chronically infected patients. Acute (6 weeks) and chronic (12 weeks) sera from S. mansoni-infected C57Bl/6 mice as well as sera from chronically infected patients were assessed using two proteomic platforms: surface-enhanced, laser desorption and ionization, time-of-flight mass spectrometry and Velos Orbitrap mass spectrometry. Several candidate biomarkers were further evaluated by Western blot and/or enzyme-linked immunosorbent assay (ELISA). Among the most promising was carbonic anhydrase 1 (CA1), a host protein found primarily in red blood cells and enterocytes that proved to be a negative biomarker for schistosomiasis in both mouse and human samples. Reduced serum CA-1 levels were confirmed by both Western blot (murine and human: both P < 0.001) and ELISA (human: P < 0.01). Western blots of serial mouse sera revealed a progressive reduction in serum CA1 levels over the 12-week infection period. CA1 is a promising negative serum biomarker for the diagnosis of S. mansoni infection.
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Affiliation(s)
- Manal Ibrahim Kardoush
- Department of Parasitology, Faculty of Medicine, Benha University, Benha, Egypt.,National Reference Center for Parasitology, Research Institute of the McGill University Health Center, Montreal, Canada.,Institute of Parasitology, McGill University, Montreal, Canada
| | - Brian J Ward
- Department of Experimental Medicine, McGill University, Montreal, Canada.,National Reference Center for Parasitology, Research Institute of the McGill University Health Center, Montreal, Canada
| | - Momar Ndao
- National Reference Center for Parasitology, Research Institute of the McGill University Health Center, Montreal, Canada.,Department of Experimental Medicine, McGill University, Montreal, Canada
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115
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Hassan MM, Ranzoni A, Cooper MA. A nanoparticle-based method for culture-free bacterial DNA enrichment from whole blood. Biosens Bioelectron 2017; 99:150-155. [PMID: 28753457 DOI: 10.1016/j.bios.2017.07.057] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 07/20/2017] [Accepted: 07/22/2017] [Indexed: 01/25/2023]
Abstract
Point-of-care (POC) diagnostics are one of the quick and sensitive detection approaches used in current clinical applications, but always face a performance tradeoff between time-to-result and assay sensitivity. One critical setting where these limitations are evident is the detection of sepsis, where 6-10mL of whole blood may contain as little as one bacterial colony forming unit (cfu). The large sample volume, complex nature of the sample and low analyte concentration necessitates signal enhancement using culture-based or molecular amplification techniques. In the time-critical diagnosis of sepsis, waiting for up to 24h to produce sufficient DNA for analysis is not possible. As a consequence, there is a need for integrated sample preparation methods that could enable shorter detection times, whilst maintaining high analytical performance. We report the development of a culture-free bacterial enrichment method to concentrate bacteria from whole blood in less than 3h. The method relies on triple-enrichment steps to magnetically concentrate bacterial cells and their DNA with a 500-fold reduction in sample volume (from 10 to 0.02mL). Using this sample preparation method, sensitive qPCR detection of the extracted S. aureus bacterial DNA was achieved with a detection limit of 5±0.58cfu/mL within a total elapsed time of 4h; much faster than conventional culture-based approaches. The method could be fully automated for integration into clinical practice for point-of-care or molecular detection of bacterial DNA from whole blood.
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Affiliation(s)
- Marwa M Hassan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Andrea Ranzoni
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Matthew A Cooper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
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116
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Laboratory Workflow Analysis of Culture of Periprosthetic Tissues in Blood Culture Bottles. J Clin Microbiol 2017; 55:2817-2826. [PMID: 28701418 DOI: 10.1128/jcm.00652-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/29/2017] [Indexed: 01/16/2023] Open
Abstract
Culture of periprosthetic tissue specimens in blood culture bottles is more sensitive than conventional techniques, but the impact on laboratory workflow has yet to be addressed. Herein, we examined the impact of culture of periprosthetic tissues in blood culture bottles on laboratory workflow and cost. The workflow was process mapped, decision tree models were constructed using probabilities of positive and negative cultures drawn from our published study (T. N. Peel, B. L. Dylla, J. G. Hughes, D. T. Lynch, K. E. Greenwood-Quaintance, A. C. Cheng, J. N. Mandrekar, and R. Patel, mBio 7:e01776-15, 2016, https://doi.org/10.1128/mBio.01776-15), and the processing times and resource costs from the laboratory staff time viewpoint were used to compare periprosthetic tissues culture processes using conventional techniques with culture in blood culture bottles. Sensitivity analysis was performed using various rates of positive cultures. Annualized labor savings were estimated based on salary costs from the U.S. Labor Bureau for Laboratory staff. The model demonstrated a 60.1% reduction in mean total staff time with the adoption of tissue inoculation into blood culture bottles compared to conventional techniques (mean ± standard deviation, 30.7 ± 27.6 versus 77.0 ± 35.3 h per month, respectively; P < 0.001). The estimated annualized labor cost savings of culture using blood culture bottles was $10,876.83 (±$337.16). Sensitivity analysis was performed using various rates of culture positivity (5 to 50%). Culture in blood culture bottles was cost-effective, based on the estimated labor cost savings of $2,132.71 for each percent increase in test accuracy. In conclusion, culture of periprosthetic tissue in blood culture bottles is not only more accurate than but is also cost-saving compared to conventional culture methods.
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117
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[new multiplex PCR for species-specific diagnosis of human candidiasis]. BIOMEDICA 2017; 37:200-208. [PMID: 28527284 DOI: 10.7705/biomedica.v37i2.3202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 06/01/2016] [Indexed: 11/21/2022]
Abstract
INTRODUCTION Candidiases is a group of opportunistic infections caused by yeasts belonging to the genus Candida. Candida albicans is the most prevalent species in both superficial and deep infections, however, the clinical importance of non-albicans Candida has increased during the last decade, driving an urgent need for diagnostic tests that allow for species-level resolution and selection of the optimum therapeutic approach. OBJECTIVE To design and to optimize a new multiplex PCR assay for the simultaneous identification of the five most relevant species of Candida involved in human candidiasis etiology. MATERIALS AND METHODS For primers design, the physical and thermodynamic restrictions that affect multiplex PCR performance were analyzed using Gene Runner and Mult-PSOS. As templates, the internal transcribed region 2 (ITR2) was selected for C. albicans (AJ249486.1), and topoisomerase II (TOPII) for C. parasilopsis (AB049144.1), C. krusei (AB049139.1), C. tropicalis (AB049141.1), and C. guillermondii (AB049145.1). We used ATCC strains of all these five species and clinical isolates as templates. RESULTS We designed ten oligonucleotides for the simultaneous amplification of the Candida species. The electrophoresis band profile was: C. albicans (206 bp), C. guillermondii (244 bp), C. tropicalis (474 bp), C. parasilopsis (558 bp), and C. krusei (419 bp). CONCLUSION The new multiplex PCR assay designed in this study allowed a simultaneous and efficient amplification of the amplicons corresponding to the five species of Candida under study, with an adequate resolution in standard agarose gel.
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118
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Abstract
Optical mapping (OM) has been used in microbiology for the past 20 years, initially as a technique to facilitate DNA sequence-based studies; however, with decreases in DNA sequencing costs and increases in sequence output from automated sequencing platforms, OM has grown into an important auxiliary tool for genome assembly and comparison. Currently, there are a number of new and exciting applications for OM in the field of microbiology, including investigation of disease outbreaks, identification of specific genes of clinical and/or epidemiological relevance, and the possibility of single-cell analysis when combined with cell-sorting approaches. In addition, designing lab-on-a-chip systems based on OM is now feasible and will allow the integrated and automated microbiological analysis of biological fluids. Here, we review the basic technology of OM, detail the current state of the art of the field, and look ahead to possible future developments in OM technology for microbiological applications.
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119
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Steen Redeker E, Eersels K, Akkermans O, Royakkers J, Dyson S, Nurekeyeva K, Ferrando B, Cornelis P, Peeters M, Wagner P, Diliën H, van Grinsven B, Cleij TJ. Biomimetic Bacterial Identification Platform Based on Thermal Wave Transport Analysis (TWTA) through Surface-Imprinted Polymers. ACS Infect Dis 2017; 3:388-397. [PMID: 28388095 PMCID: PMC5432958 DOI: 10.1021/acsinfecdis.7b00037] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
This
paper introduces a novel bacterial identification assay based on thermal
wave analysis through surface-imprinted polymers (SIPs). Aluminum
chips are coated with SIPs, serving as synthetic cell receptors that
have been combined previously with the heat-transfer method (HTM)
for the selective detection of bacteria. In this work, the concept
of bacterial identification is extended toward the detection of nine
different bacterial species. In addition, a novel sensing approach,
thermal wave transport analysis (TWTA), is introduced, which analyzes
the propagation of a thermal wave through a functional interface.
The results presented here demonstrate that bacterial rebinding to
the SIP layer resulted in a measurable phase shift in the propagated
wave, which is most pronounced at a frequency of 0.03 Hz. In this
way, the sensor is able to selectively distinguish between the different
bacterial species used in this study. Furthermore, a dose–response
curve was constructed to determine a limit of detection of 1 ×
104 CFU mL–1, indicating that TWTA is
advantageous over HTM in terms of sensitivity and response time. Additionally,
the limit of selectivity of the sensor was tested in a mixed bacterial
solution, containing the target species in the presence of a 99-fold
excess of competitor species. Finally, a first application for the
sensor in terms of infection diagnosis is presented, revealing that
the platform is able to detect bacteria in clinically relevant concentrations
as low as 3 × 104 CFU mL–1 in spiked
urine samples.
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Affiliation(s)
- Erik Steen Redeker
- Maastricht Science
Programme, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Kasper Eersels
- Maastricht Science
Programme, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
- Soft-Matter
Physics and Biophysics Section, Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200 D, B-3001 Leuven, Belgium
| | - Onno Akkermans
- Maastricht Science
Programme, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Jeroen Royakkers
- Maastricht Science
Programme, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Simba Dyson
- Maastricht Science
Programme, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Kunya Nurekeyeva
- Maastricht Science
Programme, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Beniamino Ferrando
- Maastricht Science
Programme, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Peter Cornelis
- Soft-Matter
Physics and Biophysics Section, Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200 D, B-3001 Leuven, Belgium
| | - Marloes Peeters
- Faculty of Science and
Engineering, School of Science and the Environment, Division of Chemistry
and Environmental Science, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, United Kingdom
| | - Patrick Wagner
- Soft-Matter
Physics and Biophysics Section, Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200 D, B-3001 Leuven, Belgium
| | - Hanne Diliën
- Maastricht Science
Programme, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Bart van Grinsven
- Maastricht Science
Programme, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Thomas Jan Cleij
- Maastricht Science
Programme, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
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120
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Opota O, Greub G. Mentor-mentee relationship in clinical microbiology. Clin Microbiol Infect 2017; 23:448-453. [PMID: 28478239 DOI: 10.1016/j.cmi.2017.04.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/25/2017] [Accepted: 04/27/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND Clinical microbiology is a field in constant evolution, with increasing technological opportunities and a growing emphasis on human and social issues. Maintaining knowledge and skills and anticipating future changes is challenging both for laboratory managers and for all the co-workers. Training and succession preparation represents a unique opportunity to adapt/prepare future generations according to the evolutions of the field. AIMS The aim of this review is to provide to clinical microbiologists a reflection on ongoing technological and social changes in their field and a deepening of the central role of preparing future generations to these changes through a fruitful mentor-mentee relationship. SOURCES This narrative review relies on selected publications addressing mentor-mentee interactions in various academic fields, on interview with our colleagues and pairs, as well as on our personal experience. CONTENT From the qualities and aspects that emerged as necessary for a productive mentor-mentee interaction, we selected and discuss five of them for the mentor: the role and responsibility, the positioning, the vision, the scientific credibility, and the moral credibility, as well as five for the mentee: creativity, flexibility, energy, responsibility, and self evaluation. IMPLICATIONS This review emphasizes the importance of both the scientific and the ethical credibility of the mentor and the mentee as well as the importance of human and social values such as solidarity, equality, equity, respectfulness, and empathy, and might support mentor and mentee in the field of clinical microbiology and also in the field of infectious disease in their intent for a fruitful interaction.
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Affiliation(s)
- O Opota
- Institute of Microbiology University of Lausanne and University Hospital Centre, Lausanne, Switzerland.
| | - G Greub
- Institute of Microbiology University of Lausanne and University Hospital Centre, Lausanne, Switzerland.
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121
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Das S, Shibib DR, Vernon MO. The new frontier of diagnostics: Molecular assays and their role in infection prevention and control. Am J Infect Control 2017; 45:158-169. [PMID: 28159066 PMCID: PMC7115290 DOI: 10.1016/j.ajic.2016.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 08/19/2016] [Accepted: 08/19/2016] [Indexed: 01/05/2023]
Abstract
Recent advances in technology over the last decade have propelled the microbiology laboratory into a pivotal role in infection prevention and control. The rapid adaptation of molecular technologies to the field of clinical microbiology now greatly influences infectious disease management and significantly impacts infection control practices. This review discusses recent developments in molecular techniques in the diagnosis of infectious diseases. It describes the basic concepts of molecular assays, discusses their advantages and limitations, and characterizes currently available commercial assays with respect to cost, interpretive requirements, and clinical utility.
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122
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Frickmann H, Zautner AE, Moter A, Kikhney J, Hagen RM, Stender H, Poppert S. Fluorescence in situ hybridization (FISH) in the microbiological diagnostic routine laboratory: a review. Crit Rev Microbiol 2017; 43:263-293. [PMID: 28129707 DOI: 10.3109/1040841x.2016.1169990] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Early identification of microbial pathogens is essential for rational and conservative antibiotic use especially in the case of known regional resistance patterns. Here, we describe fluorescence in situ hybridization (FISH) as one of the rapid methods for easy identification of microbial pathogens, and its advantages and disadvantages for the diagnosis of pathogens in human infections in the laboratory diagnostic routine. Binding of short fluorescence-labeled DNA or nucleic acid-mimicking PNA probes to ribosomes of infectious agents with consecutive analysis by fluorescence microscopy allows identification of bacterial and eukaryotic pathogens at genus or species level. FISH analysis leads to immediate differentiation of infectious agents without delay due to the need for microbial culture. As a microscopic technique, FISH has the unique potential to provide information about spatial resolution, morphology and identification of key pathogens in mixed species samples. On-going automation and commercialization of the FISH procedure has led to significant shortening of the time-to-result and increased test reliability. FISH is a useful tool for the rapid initial identification of microbial pathogens, even from primary materials. Among the rapidly developing alternative techniques, FISH serves as a bridging technology between microscopy, microbial culture, biochemical identification and molecular diagnostic procedures.
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Affiliation(s)
- Hagen Frickmann
- a German Armed Forces Hospital of Hamburg, Department of Tropical Medicine at the Bernhard Nocht Institute , Hamburg , Germany
| | - Andreas Erich Zautner
- b Department of Medical Microbiology, University Medical Center Göttingen , Göttingen , Germany
| | - Annette Moter
- c University Medical Center Berlin, Biofilmcenter at the German Heart Institute Berlin , Berlin , Germany
| | - Judith Kikhney
- c University Medical Center Berlin, Biofilmcenter at the German Heart Institute Berlin , Berlin , Germany
| | - Ralf Matthias Hagen
- a German Armed Forces Hospital of Hamburg, Department of Tropical Medicine at the Bernhard Nocht Institute , Hamburg , Germany
| | | | - Sven Poppert
- e Institute for Medical Microbiology, Justus-Liebig-University Giessen , Giessen , Germany
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123
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Vásquez G, Rey A, Rivera C, Iregui C, Orozco J. Amperometric biosensor based on a single antibody of dual function for rapid detection of Streptococcus agalactiae. Biosens Bioelectron 2017; 87:453-458. [DOI: 10.1016/j.bios.2016.08.082] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 08/15/2016] [Accepted: 08/25/2016] [Indexed: 11/30/2022]
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124
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Huang KT, Ludy S, Calligaris D, Dunn IF, Laws E, Santagata S, Agar NYR. Rapid Mass Spectrometry Imaging to Assess the Biochemical Profile of Pituitary Tissue for Potential Intraoperative Usage. Adv Cancer Res 2016; 134:257-282. [PMID: 28110653 DOI: 10.1016/bs.acr.2016.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pituitary adenomas are relatively common intracranial neoplasms that are frequently treated with surgical resection. Rapid visualization of pituitary tissue remains a challenge as current techniques either produce little to no information on hormone-secreting function or are too slow to practically aid in intraoperative or even perioperative decision-making. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) represents a powerful method by which molecular maps of tissue samples can be created, yielding a two-dimensional representation of the expression patterns of small molecules and proteins from biologic samples. In this chapter, we review the use of MALDI MSI, its application to the characterization of the pituitary gland, and its potential applications for guiding the management of pituitary adenomas.
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Affiliation(s)
- K T Huang
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - S Ludy
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - D Calligaris
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - I F Dunn
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - E Laws
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - S Santagata
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
| | - N Y R Agar
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States.
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125
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Optimal Periprosthetic Tissue Specimen Number for Diagnosis of Prosthetic Joint Infection. J Clin Microbiol 2016; 55:234-243. [PMID: 27807152 DOI: 10.1128/jcm.01914-16] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/01/2016] [Indexed: 01/16/2023] Open
Abstract
We recently demonstrated improved sensitivity of prosthetic joint infection (PJI) diagnosis using an automated blood culture bottle system for periprosthetic tissue culture [T. N. Peel et al., mBio 7(1):e01776-15, 2016, https://doi.org/10.1128/mBio.01776-15]. This study builds on the prior research by examining the optimal number of periprosthetic tissue specimens required for accurate PJI diagnosis. Current guidelines recommend five to six, which is impractical. We applied Bayesian latent class modeling techniques for estimating diagnostic test properties of conventional culture techniques (aerobic and anaerobic agars and thioglycolate broth) compared to inoculation into blood culture bottles. Conventional, frequentist receiver operating characteristic curve analysis was conducted as a sensitivity analysis. The study was conducted at Mayo Clinic, Rochester, MN, from August 2013 through April 2014 and included 499 consecutive patients undergoing revision arthroplasty from whom 1,437 periprosthetic tissue samples were collected and processed. For conventional periprosthetic tissue culture techniques, the greatest accuracy was observed when four specimens were obtained (91%; 95% credible interval, 77 to 100%), whereas when using inoculation of periprosthetic tissues into blood culture bottles, the greatest accuracy of diagnosis was observed when three specimens were cultured (92%; 95% credible intervals, 79 to 100%). Results of this study show that the greatest accuracy of PJI diagnosis is obtained when three periprosthetic tissue specimens are obtained and inoculated into blood culture bottles or four periprosthetic tissue specimens are obtained and cultured using standard plate and broth cultures. Increasing the number of specimens to five or more, per current recommendations, does not improve accuracy of PJI diagnosis.
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126
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Guthrie JL, Gardy JL. A brief primer on genomic epidemiology: lessons learned from Mycobacterium tuberculosis. Ann N Y Acad Sci 2016; 1388:59-77. [PMID: 28009051 DOI: 10.1111/nyas.13273] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/02/2016] [Accepted: 09/13/2016] [Indexed: 12/13/2022]
Abstract
Genomics is now firmly established as a technique for the investigation and reconstruction of communicable disease outbreaks, with many genomic epidemiology studies focusing on revealing transmission routes of Mycobacterium tuberculosis. In this primer, we introduce the basic techniques underlying transmission inference from genomic data, using illustrative examples from M. tuberculosis and other pathogens routinely sequenced by public health agencies. We describe the laboratory and epidemiological scenarios under which genomics may or may not be used, provide an introduction to sequencing technologies and bioinformatics approaches to identifying transmission-informative variation and resistance-associated mutations, and discuss how variation must be considered in the light of available clinical and epidemiological information to infer transmission.
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Affiliation(s)
- Jennifer L Guthrie
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer L Gardy
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada.,Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
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127
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Abstract
Point-of-care (POC) laboratories that deliver rapid diagnoses of infectious diseases were invented to balance the centralization of core laboratories. POC laboratories operate 24 h a day and 7 days a week to provide diagnoses within 2 h, largely based on immunochromatography and real-time PCR tests. In our experience, these tests are conveniently combined into syndrome-based kits that facilitate sampling, including self-sampling and test operations, as POC laboratories can be operated by trained operators who are not necessarily biologists. POC laboratories are a way of easily providing clinical microbiology testing for populations distant from laboratories in developing and developed countries and on ships. Modern Internet connections enable support from core laboratories. The cost-effectiveness of POC laboratories has been established for the rapid diagnosis of tuberculosis and sexually transmitted infections in both developed and developing countries.
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128
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Abat C, Colson P, Chaudet H, Rolain JM, Bassene H, Diallo A, Mediannikov O, Fenollar F, Raoult D, Sokhna C. Implementation of Syndromic Surveillance Systems in Two Rural Villages in Senegal. PLoS Negl Trop Dis 2016; 10:e0005212. [PMID: 27926917 PMCID: PMC5167408 DOI: 10.1371/journal.pntd.0005212] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 12/19/2016] [Accepted: 11/28/2016] [Indexed: 12/14/2022] Open
Abstract
Infectious diseases still represent a major challenge for humanity. In this context, their surveillance is critical. From 2010 to 2016, two Point-Of-Care (POC) laboratories have been successfully implemented in the rural Saloum region of Senegal. In parallel, a homemade syndromic surveillance system called EPIMIC was implemented to monitor infectious diseases using data produced by the POC laboratory of the Timone hospital in Marseille, France. The aim of this study is to describe the steps necessary for implementing EPIMIC using data routinely produced by two POC laboratories (POC-L) established in rural Senegal villages. After improving EPIMIC, we started to monitor the 15 pathogens routinely diagnosed in the two POC-L using the same methodology we used in France. In 5 years, 2,577 deduplicated patients-samples couples from 775 different patients have been tested in the Dielmo and Ndiop POC-L. 739 deduplicated patients-samples couples were found to be positive to at least one of the tested pathogens. The retrospective analysis of the Dielmo and Ndiop POC data with EPIMIC allowed to generate 443 alarms. Since January 2016, 316 deduplicated patients-samples couples collected from 298 different patients were processed in the Niakhar POC laboratory. 56 deduplicated patients-samples couples were found to be positive to at least one of the tested pathogens. The retrospective analysis of the data of the Niakhar POC laboratory with EPIMIC allowed to generate 14 alarms. Although some improvements are still needed, EPIMIC has been successfully spread using data routinely produced by two rural POC-L in Senegal, West Africa.
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Affiliation(s)
- Cédric Abat
- Aix-Marseille Univ., URMITE UM 63 CNRS 7278 IRD 198 INSERM U1095, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, 27 boulevard Jean Moulin, Marseille CEDEX 05, France
- Campus IRD d' Hann Maristes, Dakar, Sénégal
| | - Philippe Colson
- Aix-Marseille Univ., URMITE UM 63 CNRS 7278 IRD 198 INSERM U1095, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, 27 boulevard Jean Moulin, Marseille CEDEX 05, France
| | - Hervé Chaudet
- Aix-Marseille Univ., URMITE UM 63 CNRS 7278 IRD 198 INSERM U1095, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, 27 boulevard Jean Moulin, Marseille CEDEX 05, France
| | - Jean-Marc Rolain
- Aix-Marseille Univ., URMITE UM 63 CNRS 7278 IRD 198 INSERM U1095, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, 27 boulevard Jean Moulin, Marseille CEDEX 05, France
| | | | | | - Oleg Mediannikov
- Aix-Marseille Univ., URMITE UM 63 CNRS 7278 IRD 198 INSERM U1095, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, 27 boulevard Jean Moulin, Marseille CEDEX 05, France
| | - Florence Fenollar
- Aix-Marseille Univ., URMITE UM 63 CNRS 7278 IRD 198 INSERM U1095, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, 27 boulevard Jean Moulin, Marseille CEDEX 05, France
| | - Didier Raoult
- Aix-Marseille Univ., URMITE UM 63 CNRS 7278 IRD 198 INSERM U1095, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, 27 boulevard Jean Moulin, Marseille CEDEX 05, France
| | - Cheikh Sokhna
- Aix-Marseille Univ., URMITE UM 63 CNRS 7278 IRD 198 INSERM U1095, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, 27 boulevard Jean Moulin, Marseille CEDEX 05, France
- Campus IRD d' Hann Maristes, Dakar, Sénégal
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129
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Xu B, Du Y, Lin J, Qi M, Shu B, Wen X, Liang G, Chen B, Liu D. Simultaneous Identification and Antimicrobial Susceptibility Testing of Multiple Uropathogens on a Microfluidic Chip with Paper-Supported Cell Culture Arrays. Anal Chem 2016; 88:11593-11600. [PMID: 27934103 DOI: 10.1021/acs.analchem.6b03052] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Banglao Xu
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
- Clinical Molecular Medicine and Molecular Diagnosis Key Laboratory of Guangdong Province, Guangzhou 510180, China
| | - Yan Du
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
| | - Jinqiong Lin
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
| | - Mingyue Qi
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
| | - Bowen Shu
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
- Clinical Molecular Medicine and Molecular Diagnosis Key Laboratory of Guangdong Province, Guangzhou 510180, China
| | - Xiaoxia Wen
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
| | - Guangtie Liang
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
- Clinical Molecular Medicine and Molecular Diagnosis Key Laboratory of Guangdong Province, Guangzhou 510180, China
| | - Bin Chen
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
- Clinical Molecular Medicine and Molecular Diagnosis Key Laboratory of Guangdong Province, Guangzhou 510180, China
| | - Dayu Liu
- Department
of Laboratory Medicine, Guangzhou First People’s Hospital, Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
- Clinical Molecular Medicine and Molecular Diagnosis Key Laboratory of Guangdong Province, Guangzhou 510180, China
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130
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Ruhaak LR, van der Burgt YE, Cobbaert CM. Prospective applications of ultrahigh resolution proteomics in clinical mass spectrometry. Expert Rev Proteomics 2016; 13:1063-1071. [DOI: 10.1080/14789450.2016.1253477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- L. Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Yuri E.M. van der Burgt
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Christa M. Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
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131
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Proteomics progresses in microbial physiology and clinical antimicrobial therapy. Eur J Clin Microbiol Infect Dis 2016; 36:403-413. [PMID: 27812806 PMCID: PMC5309286 DOI: 10.1007/s10096-016-2816-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/16/2016] [Indexed: 02/05/2023]
Abstract
Clinical microbial identification plays an important role in optimizing the management of infectious diseases and provides diagnostic and therapeutic support for clinical management. Microbial proteomic research is aimed at identifying proteins associated with microbial activity, which has facilitated the discovery of microbial physiology changes and host–pathogen interactions during bacterial infection and antimicrobial therapy. Here, we summarize proteomic-driven progresses of host–microbial pathogen interactions at multiple levels, mass spectrometry-based microbial proteome identification for clinical diagnosis, and antimicrobial therapy. Proteomic technique progresses pave new ways towards effective prevention and drug discovery for microbial-induced infectious diseases.
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132
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Formisano N, Bhalla N, Heeran M, Reyes Martinez J, Sarkar A, Laabei M, Jolly P, Bowen CR, Taylor JT, Flitsch S, Estrela P. Inexpensive and fast pathogenic bacteria screening using field-effect transistors. Biosens Bioelectron 2016; 85:103-109. [DOI: 10.1016/j.bios.2016.04.063] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 04/03/2016] [Accepted: 04/20/2016] [Indexed: 01/24/2023]
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133
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Wieser A, Schubert S. MALDI-TOF MS entering the microbiological diagnostic laboratory – from fast identification to resistance testing. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.05.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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134
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Cimmino T, Le Page S, Raoult D, Rolain JM. Contemporary challenges and opportunities in the diagnosis and outbreak detection of multidrug-resistant infectious disease. Expert Rev Mol Diagn 2016; 16:1163-1175. [PMID: 27690721 DOI: 10.1080/14737159.2016.1244005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION The dissemination of multi-drug resistant bacteria (MDRB) has become a major public health concern worldwide because of the increase in infections caused by MDRB, the difficulty in treating them, and expenditures in patient care. Areas covered: We have reviewed challenges and contemporary opportunities for rapidly confronting infections caused by MDRB in the 21st century, including surveillance, detection, identification of resistance mechanisms, and action steps. Expert commentary: In this context, the first critical point for clinical microbiologists is to be able to rapidly detect an abnormal event, an outbreak and/or the spread of a MDRB with surveillance tools so that healthcare policies and therapies adapted to a new stochastic event that will certainly occur again in the future can be implemented.
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Affiliation(s)
- Teresa Cimmino
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Stéphanie Le Page
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Didier Raoult
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Jean-Marc Rolain
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
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135
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Microfluidic cantilever detects bacteria and measures their susceptibility to antibiotics in small confined volumes. Nat Commun 2016; 7:12947. [PMID: 27698375 PMCID: PMC5059454 DOI: 10.1038/ncomms12947] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 08/18/2016] [Indexed: 12/21/2022] Open
Abstract
In the fight against drug-resistant bacteria, accurate and high-throughput detection is essential. Here, a bimaterial microcantilever with an embedded microfluidic channel with internal surfaces chemically or physically functionalized with receptors selectively captures the bacteria passing through the channel. Bacterial adsorption inside the cantilever results in changes in the resonance frequency (mass) and cantilever deflection (adsorption stress). The excitation of trapped bacteria using infrared radiation (IR) causes the cantilever to deflect in proportion to the infrared absorption of the bacteria, providing a nanomechanical infrared spectrum for selective identification. We demonstrate the in situ detection and discrimination of Listeria monocytogenes at a concentration of single cell per μl. Trapped Escherichia coli in the microchannel shows a distinct nanomechanical response when exposed to antibiotics. This approach, which combines enrichment with three different modes of detection, can serve as a platform for the development of a portable, high-throughput device for use in the real-time detection of bacteria and their response to antibiotics. Analysis of bacteria and their response to antibiotics in real time is challenging. Here the authors report a microcantilever based system that can detect and discriminate between bacteria species and, due to the ability to discriminate between alive and dead samples, measure response to antibiotics.
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136
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Sanguinetti M, Posteraro B. Mass spectrometry applications in microbiology beyond microbe identification: progress and potential. Expert Rev Proteomics 2016; 13:965-977. [DOI: 10.1080/14789450.2016.1231578] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | - Brunella Posteraro
- Institute of Public Health (Section of Hygiene), Università Cattolica del Sacro Cuore, Rome, Italy
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137
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The rapid detection of cefotaxime-resistant Enterobacteriaceae by HPLC. Future Sci OA 2016; 2:FSO142. [PMID: 28116124 PMCID: PMC5242201 DOI: 10.4155/fsoa-2016-0042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/05/2016] [Indexed: 12/02/2022] Open
Abstract
Aim: Antibiotic resistance mediated by extended-spectrum β-lactamases (ESBL) and AmpC β-lactamases is widespread and increasingly common, often rendering empiric antibiotic therapy ineffective. In septicemia, delays in initiating effective antibiotic therapy are associated with worse clinical outcomes. With current phenotypic antimicrobial susceptibility testing methods, there is often a delay of 18–24 h before the susceptibility of an isolate is known. Results: Using an HPLC assay, breakdown of the third-generation cephalosporin cefotaxime by ESBL- and AmpC- β-lactamase-producing organisms could be detected within 90 min with 86.4% sensitivity and 100% specificity; sensitivity for ESBL detection was 100%. Conclusion: This assay could be readily established in any clinical laboratory with an HPLC to rapidly detect ESBL-producing Enterobacteriaceae. In bloodstream infections, early initiation of effective antibiotics is critical. However, with increasing antimicrobial resistance empirical therapy may not be effective. Therefore rapid identification of resistant bacteria is required. Here we describe an assay that can detect resistant gram-negative bacteria within 90 min. Enteric gram-negative bacteria, including Escherichia coli, resistant to the extended-spectrum cephalosporin cefotaxime, could rapidly be identified by using HPLC to detect the breakdown of cefotaxime. This assay could reduce the time to detect resistant bacterial strains by almost a day.
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138
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Abstract
Drug analysis represents a large field in different disciplines. Plasma is commonly considered to be the biosample of choice for that purpose. However, concentrations often do not represent the levels present within deeper compartments and therefore cannot sufficiently explain efficacy or toxicology of drugs. MALDI-MS in drug analysis is of great interest for high-throughput quantification and particularly spatially resolved tissue imaging. The current perspective article will deal with challenges and opportunities of MALDI-MS drug analysis in different biological samples. A particular focus will be on hair samples. Recent applications were included, reviewed for their instrumental setup and sample preparation and pros and cons as well as future perspectives are critically discussed.
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139
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Rahi P, Prakash O, Shouche YS. Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists. Front Microbiol 2016; 7:1359. [PMID: 27625644 PMCID: PMC5003876 DOI: 10.3389/fmicb.2016.01359] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 08/17/2016] [Indexed: 12/29/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) based biotyping is an emerging technique for high-throughput and rapid microbial identification. Due to its relatively higher accuracy, comprehensive database of clinically important microorganisms and low-cost compared to other microbial identification methods, MALDI-TOF MS has started replacing existing practices prevalent in clinical diagnosis. However, applicability of MALDI-TOF MS in the area of microbial ecology research is still limited mainly due to the lack of data on non-clinical microorganisms. Intense research activities on cultivation of microbial diversity by conventional as well as by innovative and high-throughput methods has substantially increased the number of microbial species known today. This important area of research is in urgent need of rapid and reliable method(s) for characterization and de-replication of microorganisms from various ecosystems. MALDI-TOF MS based characterization, in our opinion, appears to be the most suitable technique for such studies. Reliability of MALDI-TOF MS based identification method depends mainly on accuracy and width of reference databases, which need continuous expansion and improvement. In this review, we propose a common strategy to generate MALDI-TOF MS spectral database and advocated its sharing, and also discuss the role of MALDI-TOF MS based high-throughput microbial identification in microbial ecology studies.
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Affiliation(s)
- Praveen Rahi
- Microbial Culture Collection, National Centre for Cell Science Pune, India
| | - Om Prakash
- Microbial Culture Collection, National Centre for Cell Science Pune, India
| | - Yogesh S Shouche
- Microbial Culture Collection, National Centre for Cell Science Pune, India
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140
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van Grinsven B, Eersels K, Akkermans O, Ellermann S, Kordek A, Peeters M, Deschaume O, Bartic C, Diliën H, Steen Redeker E, Wagner P, Cleij TJ. Label-Free Detection of Escherichia coli Based on Thermal Transport through Surface Imprinted Polymers. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00435] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Bart van Grinsven
- Maastricht University, Maastricht Science Programme, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Kasper Eersels
- KU Leuven, Soft-Matter Physics and Biophysics
Section, Department of Physics and Astronomy, Celestijnenlaan 200 D, B-3001 Leuven, Belgium
| | - Onno Akkermans
- Maastricht University, Maastricht Science Programme, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Sophie Ellermann
- Maastricht University, Maastricht Science Programme, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Aleksandra Kordek
- Maastricht University, Maastricht Science Programme, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Marloes Peeters
- Faculty
of Science and Engineering, School of Science and the Environment,
Division of Chemistry and Environmental Science, Manchester Metropolitan University, Chester Street, Manchester M1 5GD, United Kingdom
| | - Olivier Deschaume
- KU Leuven, Soft-Matter Physics and Biophysics
Section, Department of Physics and Astronomy, Celestijnenlaan 200 D, B-3001 Leuven, Belgium
| | - Carmen Bartic
- KU Leuven, Soft-Matter Physics and Biophysics
Section, Department of Physics and Astronomy, Celestijnenlaan 200 D, B-3001 Leuven, Belgium
| | - Hanne Diliën
- Maastricht University, Maastricht Science Programme, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Erik Steen Redeker
- Maastricht University, Maastricht Science Programme, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Patrick Wagner
- KU Leuven, Soft-Matter Physics and Biophysics
Section, Department of Physics and Astronomy, Celestijnenlaan 200 D, B-3001 Leuven, Belgium
| | - Thomas J. Cleij
- Maastricht University, Maastricht Science Programme, P.O. Box 616, 6200 MD Maastricht, The Netherlands
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141
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Pazos-Perez N, Pazos E, Catala C, Mir-Simon B, Gómez-de Pedro S, Sagales J, Villanueva C, Vila J, Soriano A, García de Abajo FJ, Alvarez-Puebla RA. Ultrasensitive multiplex optical quantification of bacteria in large samples of biofluids. Sci Rep 2016; 6:29014. [PMID: 27364357 PMCID: PMC4929498 DOI: 10.1038/srep29014] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/10/2016] [Indexed: 12/29/2022] Open
Abstract
Efficient treatments in bacterial infections require the fast and accurate recognition of pathogens, with concentrations as low as one per milliliter in the case of septicemia. Detecting and quantifying bacteria in such low concentrations is challenging and typically demands cultures of large samples of blood (~1 milliliter) extending over 24–72 hours. This delay seriously compromises the health of patients. Here we demonstrate a fast microorganism optical detection system for the exhaustive identification and quantification of pathogens in volumes of biofluids with clinical relevance (~1 milliliter) in minutes. We drive each type of bacteria to accumulate antibody functionalized SERS-labelled silver nanoparticles. Particle aggregation on the bacteria membranes renders dense arrays of inter-particle gaps in which the Raman signal is exponentially amplified by several orders of magnitude relative to the dispersed particles. This enables a multiplex identification of the microorganisms through the molecule-specific spectral fingerprints.
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Affiliation(s)
- Nicolas Pazos-Perez
- Universitat Rovira i Virgili and Centro de Tecnología Química de Catalunya, Carrer de Marcel·lí Domingo s/n, 43007 Tarragona, Spain.,Medcom Advance S.A., Av. Roma, 08840 Barcelona, Spain
| | - Elena Pazos
- Medcom Advance S.A., Av. Roma, 08840 Barcelona, Spain
| | - Carme Catala
- Universitat Rovira i Virgili and Centro de Tecnología Química de Catalunya, Carrer de Marcel·lí Domingo s/n, 43007 Tarragona, Spain.,Medcom Advance S.A., Av. Roma, 08840 Barcelona, Spain
| | - Bernat Mir-Simon
- Medcom Advance S.A., Av. Roma, 08840 Barcelona, Spain.,Department of Surgery, UD-Vall d'Hebron School of Medicine, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | | | - Juan Sagales
- Medcom Advance S.A., Av. Roma, 08840 Barcelona, Spain
| | - Carlos Villanueva
- Medcom Advance S.A., Av. Roma, 08840 Barcelona, Spain.,Department of Surgery, Hospital el Pilar, 08006 Barcelona, Spain
| | - Jordi Vila
- Department of Clinical Microbiology, Hospital Clinic and School of Medicine, University of Barcelona, Barcelona, Spain.,Barcelona Center for International Health Research (CRESIB), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Alex Soriano
- Department of Infectious Diseases, Hospital Clínic and School of Medicine, University of Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - F Javier García de Abajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain.,ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Ramon A Alvarez-Puebla
- Universitat Rovira i Virgili and Centro de Tecnología Química de Catalunya, Carrer de Marcel·lí Domingo s/n, 43007 Tarragona, Spain.,Medcom Advance S.A., Av. Roma, 08840 Barcelona, Spain.,ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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142
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Palama TL, Canard I, Rautureau GJP, Mirande C, Chatellier S, Elena-Herrmann B. Identification of bacterial species by untargeted NMR spectroscopy of the exo-metabolome. Analyst 2016; 141:4558-61. [PMID: 27349704 DOI: 10.1039/c6an00393a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Identification of bacterial species is a crucial bottleneck for clinical diagnosis of infectious diseases. Quick and reliable identification is a key factor to provide suitable antibiotherapies and avoid the development of multiple-drug resistance. We propose a novel nuclear magnetic resonance (NMR)-based metabolomics strategy for rapid discrimination and identification of several bacterial species that relies on untargeted metabolic profiling of supernatants from bacterial culture media. We show that six bacterial species (Gram negative: Escherichia coli, Pseudomonas aeruginosa, Proteus mirabilis; Gram positive: Enterococcus faecalis, Staphylococcus aureus, and Staphylococcus saprophyticus) can be well discriminated from multivariate statistical analysis, opening new prospects for NMR applications to microbial clinical diagnosis.
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Affiliation(s)
- T L Palama
- Université de Lyon, Institut des Sciences Analytiques (CNRS/ENS Lyon/UCB Lyon1), Centre de RMN à Très Hauts Champs, 69100 Villeurbanne, France.
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143
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Clavel T, Lagkouvardos I, Hiergeist A. Microbiome sequencing: challenges and opportunities for molecular medicine. Expert Rev Mol Diagn 2016; 16:795-805. [DOI: 10.1080/14737159.2016.1184574] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Thomas Clavel
- ZIEL Institute for Food and Health, Technical University of Munich, Munich, Germany
| | - Ilias Lagkouvardos
- ZIEL Institute for Food and Health, Technical University of Munich, Munich, Germany
| | - Andreas Hiergeist
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
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144
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Fleurbaaij F, Kraakman MEM, Claas ECJ, Knetsch CW, van Leeuwen HC, van der Burgt YEM, Veldkamp KE, Vos MC, Goessens W, Mertens BJ, Kuijper EJ, Hensbergen PJ, Nicolardi S. Typing Pseudomonas aeruginosa Isolates with Ultrahigh Resolution MALDI-FTICR Mass Spectrometry. Anal Chem 2016; 88:5996-6003. [PMID: 27123572 DOI: 10.1021/acs.analchem.6b01037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The introduction of standardized matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) platforms in the medical microbiological practice has revolutionized the way microbial species identification is performed on a daily basis. To a large extent, this is due to the ease of operation. Acquired spectra are compared to profiles obtained from cultured colonies present in a reference spectra database. It is fast and reliable, and costs are low compared to previous diagnostic approaches. However, the low resolution and dynamic range of the MALDI-TOF profiles have shown limited applicability for the discrimination of different bacterial strains, as achieved with typing based on genetic markers. This is pivotal in cases where certain strains are associated with, e.g., virulence or antibiotic resistance. Ultrahigh resolution MALDI-FTICR MS allows the measurement of small proteins at isotopic resolution and can be used to analyze complex mixtures with increased dynamic range and higher precision than MALDI-TOF MS, while still generating results in a similar time frame. Here, we propose to use ultrahigh resolution 15T MALDI-Fourier transform ion cyclotron resonance (FTICR) MS to discriminate clinically relevant bacterial strains after species identification performed by MALDI-TOF MS. We used a collection of well characterized Pseudomonas aeruginosa strains, featuring distinct antibiotic resistance profiles, and isolates obtained during hospital outbreaks. Following cluster analysis based on amplification fragment length polymorphism (AFLP), these strains were grouped into three different clusters. The same clusters were obtained using protein profiles generated by MALDI-FTICR MS. Subsequent intact protein analysis by electrospray ionization (ESI)-collision-induced dissociation (CID)-FTICR MS was applied to identify protein isoforms that contribute to the separation of the different clusters, illustrating the additional advantage of this analytical platform.
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Affiliation(s)
- Frank Fleurbaaij
- Department of Medical Microbiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Margriet E M Kraakman
- Department of Medical Microbiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Eric C J Claas
- Department of Medical Microbiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Cornelis W Knetsch
- Department of Medical Microbiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Hans C van Leeuwen
- Department of Medical Microbiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Yuri E M van der Burgt
- Center for Proteomics and Metabolomics, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Karin Ellen Veldkamp
- Department of Medical Microbiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Margreet C Vos
- Department of Medical Microbiology and Infectious Disease, Erasmus MC , 3015 CN Rotterdam, The Netherlands
| | - Wil Goessens
- Department of Medical Microbiology and Infectious Disease, Erasmus MC , 3015 CN Rotterdam, The Netherlands
| | - Bart J Mertens
- Department of Medical Statistics, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Paul J Hensbergen
- Center for Proteomics and Metabolomics, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Simone Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
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145
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Tsalik EL, Li Y, Hudson LL, Chu VH, Himmel T, Limkakeng AT, Katz JN, Glickman SW, McClain MT, Welty-Wolf KE, Fowler VG, Ginsburg GS, Woods CW, Reed SD. Potential Cost-effectiveness of Early Identification of Hospital-acquired Infection in Critically Ill Patients. Ann Am Thorac Soc 2016; 13:401-13. [PMID: 26700878 DOI: 10.1513/annalsats.201504-205oc] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
RATIONALE Limitations in methods for the rapid diagnosis of hospital-acquired infections often delay initiation of effective antimicrobial therapy. New diagnostic approaches offer potential clinical and cost-related improvements in the management of these infections. OBJECTIVES We developed a decision modeling framework to assess the potential cost-effectiveness of a rapid biomarker assay to identify hospital-acquired infection in high-risk patients earlier than standard diagnostic testing. METHODS The framework includes parameters representing rates of infection, rates of delayed appropriate therapy, and impact of delayed therapy on mortality, along with assumptions about diagnostic test characteristics and their impact on delayed therapy and length of stay. Parameter estimates were based on contemporary, published studies and supplemented with data from a four-site, observational, clinical study. Extensive sensitivity analyses were performed. The base-case analysis assumed 17.6% of ventilated patients and 11.2% of nonventilated patients develop hospital-acquired infection and that 28.7% of patients with hospital-acquired infection experience delays in appropriate antibiotic therapy with standard care. We assumed this percentage decreased by 50% (to 14.4%) among patients with true-positive results and increased by 50% (to 43.1%) among patients with false-negative results using a hypothetical biomarker assay. Cost of testing was set at $110/d. MEASUREMENTS AND MAIN RESULTS In the base-case analysis, among ventilated patients, daily diagnostic testing starting on admission reduced inpatient mortality from 12.3 to 11.9% and increased mean costs by $1,640 per patient, resulting in an incremental cost-effectiveness ratio of $21,389 per life-year saved. Among nonventilated patients, inpatient mortality decreased from 7.3 to 7.1% and costs increased by $1,381 with diagnostic testing. The resulting incremental cost-effectiveness ratio was $42,325 per life-year saved. Threshold analyses revealed the probabilities of developing hospital-acquired infection in ventilated and nonventilated patients could be as low as 8.4 and 9.8%, respectively, to maintain incremental cost-effectiveness ratios less than $50,000 per life-year saved. CONCLUSIONS Development and use of serial diagnostic testing that reduces the proportion of patients with delays in appropriate antibiotic therapy for hospital-acquired infections could reduce inpatient mortality. The model presented here offers a cost-effectiveness framework for future test development.
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Affiliation(s)
- Ephraim L Tsalik
- 1 Emergency Medicine Service, and
- 2 Department of Medicine
- 3 Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina
| | | | - Lori L Hudson
- 2 Department of Medicine
- 3 Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina
| | - Vivian H Chu
- 2 Department of Medicine
- 4 Duke Clinical Research Institute, and
| | | | - Alex T Limkakeng
- 5 Department of Surgery, Duke University School of Medicine, Durham, North Carolina
| | - Jason N Katz
- 6 Department of Medicine, University of North Carolina Health Care, Chapel Hill, North Carolina; and
| | - Seth W Glickman
- 7 Department of Emergency Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Micah T McClain
- 8 Medicine Service, Durham Veterans Affairs Medical Center, Durham, North Carolina
- 2 Department of Medicine
- 3 Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina
| | - Karen E Welty-Wolf
- 8 Medicine Service, Durham Veterans Affairs Medical Center, Durham, North Carolina
- 2 Department of Medicine
| | | | - Geoffrey S Ginsburg
- 2 Department of Medicine
- 3 Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina
| | - Christopher W Woods
- 8 Medicine Service, Durham Veterans Affairs Medical Center, Durham, North Carolina
- 2 Department of Medicine
- 3 Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina
| | - Shelby D Reed
- 2 Department of Medicine
- 4 Duke Clinical Research Institute, and
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146
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Saini S, Dewan L. Application of discrete wavelet transform for analysis of genomic sequences of Mycobacterium tuberculosis. SPRINGERPLUS 2016; 5:64. [PMID: 26839757 PMCID: PMC4722049 DOI: 10.1186/s40064-016-1668-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 01/04/2016] [Indexed: 12/04/2022]
Abstract
This paper highlights the potential of discrete wavelet transforms in the analysis and comparison of genomic sequences of Mycobacterium tuberculosis (MTB) with different resistance characteristics. Graphical representations of wavelet coefficients and statistical estimates of their parameters have been used to determine the extent of similarity between different sequences of MTB without the use of conventional methods such as Basic Local Alignment Search Tool. Based on the calculation of the energy of wavelet decomposition coefficients of complete genomic sequences, their broad classification of the type of resistance can be done. All the given genomic sequences can be grouped into two broad categories wherein the drug resistant and drug susceptible sequences form one group while the multidrug resistant and extensive drug resistant sequences form the other group. This method of segregation of the sequences is faster than conventional laboratory methods which require 3–4 weeks of culture of sputum samples. Thus the proposed method can be used as a tool to enhance clinical diagnostic investigations in near real-time.
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Affiliation(s)
- Shiwani Saini
- Department of Electrical Engineering, National Institute of Technology, Kurukshetra, Haryana 136119 India
| | - Lillie Dewan
- Department of Electrical Engineering, National Institute of Technology, Kurukshetra, Haryana 136119 India
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147
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Discovery of Novel MLSB Resistance Methylase Genes and Their Associated Genetic Elements in Staphylococci. CURRENT CLINICAL MICROBIOLOGY REPORTS 2016. [DOI: 10.1007/s40588-016-0030-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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148
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Dinarelli S, Girasole M, Kasas S, Longo G. Nanotools and molecular techniques to rapidly identify and fight bacterial infections. J Microbiol Methods 2016; 138:72-81. [PMID: 26806415 DOI: 10.1016/j.mimet.2016.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/13/2016] [Accepted: 01/13/2016] [Indexed: 12/22/2022]
Abstract
Reducing the emergence and spread of antibiotic-resistant bacteria is one of the major healthcare issues of our century. In addition to the increased mortality, infections caused by multi-resistant bacteria drastically enhance the healthcare costs, mainly because of the longer duration of illness and treatment. While in the last 20years, bacterial identification has been revolutionized by the introduction of new molecular techniques, the current phenotypic techniques to determine the susceptibilities of common Gram-positive and Gram-negative bacteria require at least two days from collection of clinical samples. Therefore, there is an urgent need for the development of new technologies to determine rapidly drug susceptibility in bacteria and to achieve faster diagnoses. These techniques would also lead to a better understanding of the mechanisms that lead to the insurgence of the resistance, greatly helping the quest for new antibacterial systems and drugs. In this review, we describe some of the tools most currently used in clinical and microbiological research to study bacteria and to address the challenge of infections. We discuss the most interesting advancements in the molecular susceptibility testing systems, with a particular focus on the many applications of the MALDI-TOF MS system. In the field of the phenotypic characterization protocols, we detail some of the most promising semi-automated commercial systems and we focus on some emerging developments in the field of nanomechanical sensors, which constitute a step towards the development of rapid and affordable point-of-care testing devices and techniques. While there is still no innovative technique that is capable of completely substituting for the conventional protocols and clinical practices, many exciting new experimental setups and tools could constitute the basis of the standard testing package of future microbiological tests.
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Affiliation(s)
- S Dinarelli
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - M Girasole
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - S Kasas
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Physique de la Matière Vivante, Lausanne, Switzerland; Département des Neurosciences Fondamentales, Université de Lausanne, Lausanne, Switzerland
| | - G Longo
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche, Rome, Italy.
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149
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Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing. J Clin Microbiol 2016; 54:919-27. [PMID: 26763966 DOI: 10.1128/jcm.03050-15] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/06/2016] [Indexed: 12/12/2022] Open
Abstract
Next-generation sequencing (NGS) technology has shown promise for the detection of human pathogens from clinical samples. However, one of the major obstacles to the use of NGS in diagnostic microbiology is the low ratio of pathogen DNA to human DNA in most clinical specimens. In this study, we aimed to develop a specimen-processing protocol to remove human DNA and enrich specimens for bacterial and viral DNA for shotgun metagenomic sequencing. Cerebrospinal fluid (CSF) and nasopharyngeal aspirate (NPA) specimens, spiked with control bacterial and viral pathogens, were processed using either a commercially available kit (MolYsis) or various detergents followed by DNase prior to the extraction of DNA. Relative quantities of human DNA and pathogen DNA were determined by real-time PCR. The MolYsis kit did not improve the pathogen-to-human DNA ratio, but significant reductions (>95%;P< 0.001) in human DNA with minimal effect on pathogen DNA were achieved in samples that were treated with 0.025% saponin, a nonionic surfactant. Specimen preprocessing significantly decreased NGS reads mapped to the human genome (P< 0.05) and improved the sensitivity of pathogen detection (P< 0.01), with a 20- to 650-fold increase in the ratio of microbial reads to human reads. Preprocessing also permitted the detection of pathogens that were undetectable in the unprocessed samples. Our results demonstrate a simple method for the reduction of background human DNA for metagenomic detection for a broad range of pathogens in clinical samples.
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150
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Restricted Identification of Clinical Pathogens Categorized as Biothreats by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol 2016; 54:816. [PMID: 26763958 DOI: 10.1128/jcm.03250-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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