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Mills DC, Huder JB, Bloemberg GV, Huber M. Comparison of three cartridge-based platforms for syndromic testing for respiratory viruses. Diagn Microbiol Infect Dis 2024; 109:116308. [PMID: 38688147 DOI: 10.1016/j.diagmicrobio.2024.116308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
Syndromic testing, the simultaneous testing for multiple pathogens causing similar symptoms, has recently gained ground in clinical diagnostics. This approach can significantly shorten time to diagnosis and speed up decision-making, leading to an improved outcome for the patient. Here, we compared three automated multiplex PCR platforms for syndromic testing of respiratory samples in a retrospective study, and assessed their relative sensitivities. The PPA between BioFire and QIAstat compared to ePlex was 98.4 % and 93.8 %, respectively, and 6 discrepant results were observed. The BioFire was identified as the platform with the highest relative sensitivity. Overall, the platforms performed similarly and are all suitable for syndromic testing of respiratory samples.
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Affiliation(s)
| | - Jon Barduot Huder
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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2
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Salachas C, Gounane C, Beduneau G, Lopinto J, Turpin M, Amiel C, Cuvelier A, Gueudin M, Voiriot G, Fartoukh M. Diagnostic yield of viral multiplex PCR during acute exacerbation of COPD admitted to the intensive care unit: a pilot study. Sci Rep 2024; 14:1057. [PMID: 38212620 PMCID: PMC10784589 DOI: 10.1038/s41598-024-51465-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024] Open
Abstract
Acute exacerbation of chronic obstructive pulmonary disease (AECOPD) is one of the leading causes of admission to the intensive care unit, often triggered by a respiratory tract infection of bacterial or viral aetiology. Managing antibiotic therapy in this context remains a challenge. Respiratory panel molecular tests allow identifying viral aetiologies of AECOPD. We hypothesized that the systematic use of a respiratory multiplex PCR (mPCR) would help antibiotics saving in severe AECOPD. Our objectives were to describe the spectrum of infectious aetiologies of severe AECOPD, using a diagnostic approach combining conventional diagnostic tests and mPCR, and to measure antibiotics exposure. The study was bicentric, prospective, observational, and included 105 critically ill patients with a severe AECOPD of presumed infectious aetiology, in whom a respiratory mPCR with a viral panel was performed in addition to conventional microbiological tests. Altogether, the microbiological documentation rate was 50%, including bacteria alone (19%), respiratory viruses alone (16%), and mixed viruses and bacterial species (16%). The duration of antibiotic therapy was shorter in patients without documented bacterial infection (5.6 vs. 9 days; P = 0.0006). This pilot study suggests that molecular tests may help for the proper use of anti-infective treatments in critically ill patients with severe AECOPD.
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Affiliation(s)
- Costa Salachas
- Assistance Publique - Hôpitaux de Paris, Service de Médecine Intensive Réanimation, Hôpital Tenon, 4, Rue de La Chine, 75020, Paris, France
| | - Cherifa Gounane
- Assistance Publique - Hôpitaux de Paris, Service de Médecine Intensive Réanimation, Hôpital Tenon, 4, Rue de La Chine, 75020, Paris, France
| | - Gaëtan Beduneau
- Département de Médecine Intensive Réanimation, Normandie Univ, UNIROUEN, UR 3830, CHU Rouen, 76000, Rouen, France
| | - Julien Lopinto
- Assistance Publique - Hôpitaux de Paris, Service de Médecine Intensive Réanimation, Hôpital Tenon, 4, Rue de La Chine, 75020, Paris, France
| | - Matthieu Turpin
- Assistance Publique - Hôpitaux de Paris, Service de Médecine Intensive Réanimation, Hôpital Tenon, 4, Rue de La Chine, 75020, Paris, France
| | - Corinne Amiel
- Assistance Publique - Hôpitaux de Paris, Département de Virologie, Hôpital Tenon, 75020, Paris, France
| | - Antoine Cuvelier
- Normandie Univ, UNIROUEN, UR 3830, CHU Rouen, Service de Soins Intensifs Respiratoires, Rouen, France
| | - Marie Gueudin
- Département de Virologie, Normandie Univ, UNIROUEN, UNICAEN, UMR1311 INSERM DYNAMICURE, CHU Rouen, Rouen, France
| | - Guillaume Voiriot
- Assistance Publique - Hôpitaux de Paris, Service de Médecine Intensive Réanimation, Hôpital Tenon, 4, Rue de La Chine, 75020, Paris, France
- Sorbonne Université, Paris, France
| | - Muriel Fartoukh
- Assistance Publique - Hôpitaux de Paris, Service de Médecine Intensive Réanimation, Hôpital Tenon, 4, Rue de La Chine, 75020, Paris, France.
- Sorbonne Université, Paris, France.
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Relich RF, Abbott AN. Syndromic and Point-of-Care Molecular Testing. Clin Lab Med 2022; 42:507-531. [PMID: 36368779 DOI: 10.1016/j.cll.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ryan F Relich
- Division of Clinical Microbiology, Indiana University Health Pathology Laboratory, Indiana University Health and Indiana University School of Medicine, Suite 6027E, 350 West 11th Street, Indianapolis, IN 46202, USA.
| | - April N Abbott
- Department of Laboratory Medicine, Deaconess Hospital, 600 Mary Street, Evansville, IN 47747, USA
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Madhu S, Ramasamy S, Choi J. Recent Developments in Electrochemical Sensors for the Detection of Antibiotic-Resistant Bacteria. Pharmaceuticals (Basel) 2022; 15:ph15121488. [PMID: 36558939 PMCID: PMC9786047 DOI: 10.3390/ph15121488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
The development of efficient point-of-care (POC) diagnostic tools for detecting infectious diseases caused by destructive pathogens plays an important role in clinical and environmental monitoring. Nevertheless, evolving complex and inconsistent antibiotic-resistant species mire their drug efficacy. In this regard, substantial effort has been expended to develop electrochemical sensors, which have gained significant interest for advancing POC testing with rapid and accurate detection of resistant bacteria at a low cost compared to conventional phenotype methods. This review concentrates on the recent developments in electrochemical sensing techniques that have been applied to assess the diverse latent antibiotic resistances of pathogenic bacteria. It deliberates the prominence of biorecognition probes and tailor-made nanomaterials used in electrochemical antibiotic susceptibility testing (AST). In addition, the bimodal functional efficacy of nanomaterials that can serve as potential transducer electrodes and the antimicrobial agent was investigated to meet the current requirements in designing sensor module development. In the final section, we discuss the challenges with contemporary AST sensor techniques and extend the key ideas to meet the demands of the next POC electrochemical sensors and antibiotic design modules in the healthcare sector.
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Liu H, Zou Q, Kim MG, Qiao Z, Nguyen DTT, Koo B, Lee HJ, Jang YO, Kim JK, Shin Y. Homobifunctional Imidoester Combined Black Phosphorus Nanosheets Used as Cofactors for Nucleic Acid Extraction. BIOCHIP JOURNAL 2022. [DOI: 10.1007/s13206-022-00046-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Schuele L, Cassidy H, Peker N, Rossen JWA, Couto N. Future potential of metagenomics in clinical laboratories. Expert Rev Mol Diagn 2021; 21:1273-1285. [PMID: 34755585 DOI: 10.1080/14737159.2021.2001329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Rapid and sensitive diagnostic strategies are necessary for patient care and public health. Most of the current conventional microbiological assays detect only a restricted panel of pathogens at a time or require a microbe to be successfully cultured from a sample. Clinical metagenomics next-generation sequencing (mNGS) has the potential to unbiasedly detect all pathogens in a sample, increasing the sensitivity for detection and enabling the discovery of unknown infectious agents. AREAS COVERED High expectations have been built around mNGS; however, this technique is far from widely available. This review highlights the advances and currently available options in terms of costs, turnaround time, sensitivity, specificity, validation, and reproducibility of mNGS as a diagnostic tool in clinical microbiology laboratories. EXPERT OPINION The need for a novel diagnostic tool to increase the sensitivity of microbial diagnostics is clear. mNGS has the potential to revolutionise clinical microbiology. However, its role as a diagnostic tool has yet to be widely established, which is crucial for successfully implementing the technique. A clear definition of diagnostic algorithms that include mNGS is vital to show clinical utility. Similarly to real-time PCR, mNGS will one day become a vital tool in any testing algorithm.
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Affiliation(s)
- Leonard Schuele
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Hayley Cassidy
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Nilay Peker
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - John W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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van Asten SAV, Boers SA, de Groot JDF, Schuurman R, Claas ECJ. Evaluation of the Genmark ePlex® and QIAstat-Dx® respiratory pathogen panels in detecting bacterial targets in lower respiratory tract specimens. BMC Microbiol 2021; 21:236. [PMID: 34445973 PMCID: PMC8390116 DOI: 10.1186/s12866-021-02289-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 07/30/2021] [Indexed: 11/26/2022] Open
Abstract
Background The ePlex® and QIAstat-Dx® respiratory pathogen panels detect multiple respiratory pathogens, mainly viruses but also Legionella pneumophila, Mycoplasma pneumoniae and Bordetella pertussis. The assays have been marketed for use in nasopharyngeal swab specimens. For diagnosing bacterial pneumonia, lower respiratory tract (LRT) specimens are indicated. Aim of this study was to evaluate the performance of these syndromic panels for these three bacterial targets in samples from the LRT. Fifty-six specimens were collected from our repositories, five negative samples and fifty-one samples which had been previously tested positive with the routine diagnostic real-time PCR assays for Legionella spp. (N = 20), Bordetella spp. (N = 16) or M. pneumoniae (N = 15). Results The QIAstat-Dx Respiratory Panel V2 (RP) assay detected all of the L. pneumophila and B. pertussis positive samples but only 11/15 (73.3 %) of the M. pneumoniae targets. The ePlex Respiratory Pathogen Panel (RPP) assay detected 10/14 (71.4 %) of the L. pneumophila targets, 8/12 (66.7 %) of the B. pertussis positive samples and 13/15 (86.7 %) of the M. pneumoniae targets. Conclusions No false-positive results were reported for all three bacterial pathogens by both assays. The clinical performance of both assays depended highly on the bacterial load in the sample and the type of specimen under investigation.
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Affiliation(s)
- Suzanne A V van Asten
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, Leiden, 2300 RC, The Netherlands.
| | - Stefan A Boers
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, Leiden, 2300 RC, The Netherlands
| | - Jolanda D F de Groot
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - R Schuurman
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Eric C J Claas
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, Leiden, 2300 RC, The Netherlands
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Steiner F, Schmutz S, Gosert R, Huder JB, Redli PM, Capaul R, Hirsch HH, Böni J, Zbinden A. Usefulness of the GenMark ePlex RPP assay for the detection of respiratory viruses compared to the FTD21 multiplex RT-PCR. Diagn Microbiol Infect Dis 2021; 101:115424. [PMID: 34111651 DOI: 10.1016/j.diagmicrobio.2021.115424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/26/2021] [Accepted: 05/01/2021] [Indexed: 11/26/2022]
Abstract
Cartridge-based multiplex panels covering numerous pathogens offer an advantage of minimal hands-on-time and short time to result to commercial RT-PCR assays. In this study, we evaluated the performance of the ePlex respiratory pathogen panel (RPP) compared to the Fast Track Diagnostics Respiratory pathogens 21 multiplex RT-PCR assay (FTD21) using 400 clinical respiratory samples. Discrepant results were further analysed by a reference nucleic acid amplification testing (NAT) and a composite reference approach was used for final interpretation. Discordant results were observed in 56 targets corresponding to 54 samples. Sensitivities and specificities were 85.5% and 99.9% for the ePlex RPP and 95.8% and 99.7% for the FTD21 system, respectively. Altogether, the ePlex RPP is a valuable tool for the rapid detection of a number of different respiratory viruses with the exception of the coronavirus family (low sensitivity ranging from 50-80%) and samples with a low pathogen load (Ct values >33).
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Affiliation(s)
- Fiona Steiner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Rainer Gosert
- Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland; Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Jon B Huder
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Patrick M Redli
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Riccarda Capaul
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Hans H Hirsch
- Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland; Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Andrea Zbinden
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
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Combined SARS-CoV-2 nucleic acid amplification testing and respiratory virus panel RT-PCR on the Hologic Panther Fusion system. J Clin Virol 2021; 138:104792. [PMID: 33770659 PMCID: PMC7944800 DOI: 10.1016/j.jcv.2021.104792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 02/07/2021] [Accepted: 03/04/2021] [Indexed: 01/08/2023]
Abstract
Background Significant overlap exists between the symptoms of SARS-CoV-2 and other respiratory viruses. This poses a serious challenge to clinical diagnosis, laboratory testing, and infection control programs. Objectives To evaluate the performance of the Hologic Panther Fusion Respiratory Assays (RA) compared to the GenMark ePlex Respiratory Pathogen Panel (RPP) and to assess the ability of the Panther Fusion to perform parallel testing of SARS-CoV-2 and other respiratory viruses from a single sample. Study design A diagnostic comparison study was carried out using 375 clinical nasopharyngeal specimens. Assay performance was assessed by overall, positive, and negative percent agreement and Cohen’s kappa coefficient. Results Overall agreement between the Fusion RA and ePlex RPP was 97.3 % (95 % CI 96.3−98.0), positive percent agreement was 97.2 % (95 % CI 93.0−99.2), negative percent agreement was 97.3 % (95 % CI 96.3−98.0), and the kappa coefficient was 0.85 (95 % CI 0.81−0.89). Forty additional viruses in 30 specimens were detected by Fusion that were not detected by ePlex. The maximum specimen throughput for parallel testing of the Fusion Respiratory Assays with SARS-CoV-2 was 275 samples in 20.7 h for Fusion SARS-CoV-2 and 350 samples in 20.0 h for Aptima Transcription Mediated Amplification SARS-CoV-2. Conclusion Fusion RA demonstrated substantial agreement compared to the ePlex RPP. However, the Fusion detected respiratory viruses not identified by ePlex, consistent with higher clinical sensitivity. Workflows for parallel testing of respiratory pathogens and SARS-CoV-2 demonstrate that the Panther Fusion instrument provides a flexible, moderate to high throughput testing option for pandemic and seasonal respiratory viruses.
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Anderson S, Hadwen B, Brown C. Thin-film-transistor digital microfluidics for high value in vitro diagnostics at the point of need. LAB ON A CHIP 2021; 21:962-975. [PMID: 33511381 DOI: 10.1039/d0lc01143f] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The latest developments in thin-film-transistor digital-microfluidics (TFT-DMF, also known by the commercial name aQdrop™) are reported, and proof of concept application to molecular diagnostics (e.g. for coronavirus disease, COVID-19) at the point-of-need demonstrated. The TFT-DMF array has 41 thousand independently addressable electrodes that are capable of manipulating large numbers of droplets of any size and shape, along any pathway to perform multiple parallel reactions. Droplets are continually tracked and adjusted through closed-loop feedback enabled by TFT based sensors at each array element. The sample-to-answer molecular in vitro diagnostic (IVD) test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) includes nucleic acid extractions from saliva, removal of dsDNA and quantitative reverse transcription polymerase chain reaction (RT-PCR). This proof of concept illustrates how the highly configurable TFT-DMF technology can perform many reactions in parallel and thus support the processing of a range of sample types followed by multiple complex multi-step assays.
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Affiliation(s)
- Sally Anderson
- Sharp Life Science (EU) Ltd, Edmund Halley Road, Oxford Science Park, OX4 4GB, UK.
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11
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[Virological diagnosis of lower respiratory tract infections]. Rev Mal Respir 2021; 38:58-73. [PMID: 33461842 DOI: 10.1016/j.rmr.2020.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 08/06/2020] [Indexed: 11/21/2022]
Abstract
INTRODUCTION The etiological diagnosis of bronchopulmonary infections cannot be assessed with clinical, radiological and epidemiological data alone. Viruses have been demonstrated to cause a large proportion of these infections, both in children and adults. BACKGROUND The diagnosis of viral bronchopulmonary infections is based on the analysis of secretions, collected from the lower respiratory tract when possible, by techniques that detect either influenza and respiratory syncytial viruses, or a large panel of viruses that can be responsible for respiratory disease. The latter, called multiplex PCR assays, allow a syndromic approach to respiratory infection. Their high cost for the laboratory raises the question of their place in the management of patients in terms of antibiotic economy and isolation. In the absence of clear recommendations, the strategy and equipment are very unevenly distributed in France. OUTLOOK Medico-economic analyses need to be performed in France to evaluate the place of these tests in the management of patients. The evaluation of the role of the different viruses often detected in co-infection, especially in children, also deserves the attention of virologists and clinicians. CONCLUSIONS The availability of new diagnostic technologies, the recent emergence of SARS-CoV-2, together with the availability of new antiviral drugs are likely to impact future recommendations for the management of viral bronchopulmonary infections.
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Commercialized diagnostic technologies to combat SARS-CoV2: Advantages and disadvantages. Talanta 2020; 225:121898. [PMID: 33592692 PMCID: PMC7713573 DOI: 10.1016/j.talanta.2020.121898] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 12/13/2022]
Abstract
The current situation of the Covid-19 pandemic is indicated by a huge number of infections, high lethality, and rapid spread. These circumstances have stopped the activity of almost the entire world, affecting severely the global economy. A rapid diagnosis of the Covid-19 and a generalized testing protocol is essential to fight against the pandemic and to maintain health control in the population. Principal biosensing and diagnostic technologies used to monitor the spread of the SARS-CoV-2 are based on specific genomic analysis and rapid immune tests, both with different technology platforms that include advantages and disadvantages. Most of the in vitro diagnosis companies are competing to be the first on validating under different regulations their technology for placing their platforms for Covid-19 detection as fast as possible in this big international market. A comprehensive analysis of the commercialized technologies for the genomic based sensing and the antibody/antigen detection methods devoted to Covid-19 diagnosis is described in this review, which have been detailed and listed under different countries regulations. The effectiveness of the described technologies throughout the different stages of the disease and a critical comparison of the emerging technologies in the market to counterattack this pandemic have been discussed.
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Thrift WJ, Ronaghi S, Samad M, Wei H, Nguyen DG, Cabuslay AS, Groome CE, Santiago PJ, Baldi P, Hochbaum AI, Ragan R. Deep Learning Analysis of Vibrational Spectra of Bacterial Lysate for Rapid Antimicrobial Susceptibility Testing. ACS NANO 2020; 14:15336-15348. [PMID: 33095005 DOI: 10.1021/acsnano.0c05693] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Rapid antimicrobial susceptibility testing (AST) is an integral tool to mitigate the unnecessary use of powerful and broad-spectrum antibiotics that leads to the proliferation of multi-drug-resistant bacteria. Using a sensor platform composed of surface-enhanced Raman scattering (SERS) sensors with control of nanogap chemistry and machine learning algorithms for analysis of complex spectral data, bacteria metabolic profiles post antibiotic exposure are correlated with susceptibility. Deep neural network models are able to discriminate the responses of Escherichia coli and Pseudomonas aeruginosa to antibiotics from untreated cells in SERS data in 10 min after antibiotic exposure with greater than 99% accuracy. Deep learning analysis is also able to differentiate responses from untreated cells with antibiotic dosages up to 10-fold lower than the minimum inhibitory concentration observed in conventional growth assays. In addition, analysis of SERS data using a generative model, a variational autoencoder, identifies spectral features in the P. aeruginosa lysate data associated with antibiotic efficacy. From this insight, a combinatorial dataset of metabolites is selected to extend the latent space of the variational autoencoder. This culture-free dataset dramatically improves classification accuracy to select effective antibiotic treatment in 30 min. Unsupervised Bayesian Gaussian mixture analysis achieves 99.3% accuracy in discriminating between susceptible versus resistant to antibiotic cultures in SERS using the extended latent space. Discriminative and generative models rapidly provide high classification accuracy with small sets of labeled data, which enormously reduces the amount of time needed to validate phenotypic AST with conventional growth assays. Thus, this work outlines a promising approach toward practical rapid AST.
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Affiliation(s)
- William John Thrift
- Department of Materials Science and Engineering, University of California, Irvine, California 92697, United States
| | - Sasha Ronaghi
- Sage Hill School, Newport Coast, California 92657, United States
| | - Muntaha Samad
- Department of Computer Science, University of California, Irvine, California 92697, United States
| | - Hong Wei
- Department of Materials Science and Engineering, University of California, Irvine, California 92697, United States
| | - Dean Gia Nguyen
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
| | | | - Chloe E Groome
- Department of Materials Science and Engineering, University of California, Irvine, California 92697, United States
| | - Peter Joseph Santiago
- Department of Materials Science and Engineering, University of California, Irvine, California 92697, United States
| | - Pierre Baldi
- Department of Computer Science, University of California, Irvine, California 92697, United States
| | - Allon I Hochbaum
- Department of Materials Science and Engineering, University of California, Irvine, California 92697, United States
- Department of Chemistry, University of California, Irvine, California 92617, United States
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Regina Ragan
- Department of Materials Science and Engineering, University of California, Irvine, California 92697, United States
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
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Meyer Sauteur PM, Krautter S, Ambroggio L, Seiler M, Paioni P, Relly C, Capaul R, Kellenberger C, Haas T, Gysin C, Bachmann LM, van Rossum AMC, Berger C. Improved Diagnostics Help to Identify Clinical Features and Biomarkers That Predict Mycoplasma pneumoniae Community-acquired Pneumonia in Children. Clin Infect Dis 2020; 71:1645-1654. [PMID: 31665253 PMCID: PMC7108170 DOI: 10.1093/cid/ciz1059] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/23/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND There are no reliable signs or symptoms that differentiate Mycoplasma pneumoniae (Mp) infection in community-acquired pneumonia (CAP) from other etiologies. Additionally, current diagnostic tests do not reliably distinguish between Mp infection and carriage. We previously determined that the measurement of Mp-specific immunoglobulin M antibody-secreting cells (ASCs) by enzyme-linked immunospot assay allowed for differentiation between infection and carriage. Using this new diagnostic test, we aimed to identify clinical and laboratory features associated with Mp infection. METHODS This is a prospective cohort study of children, 3-18 years of age, with CAP from 2016 to 2017. Clinical features and biomarkers were compared between Mp-positive and -negative groups by Mann-Whitney U test or Fisher exact test, as appropriate. Area under the receiver operating characteristic curve (AUC) differences and optimal thresholds were determined by using the DeLong test and Youden J statistic, respectively. RESULTS Of 63 CAP patients, 29 were Mp-positive (46%). Mp positivity was statistically associated with older age (median, 8.6 vs 4.7 years), no underlying disease, family with respiratory symptoms, prior antibiotic treatment, prolonged prodromal respiratory symptoms and fever, and extrapulmonary (skin) manifestations. Lower levels of C-reactive protein, white blood cell count, absolute neutrophil count, and procalcitonin (PCT), specifically PCT <0.25 μg/L, were statistically associated with Mp infection. A combination of age >5 years (AUC = 0.77), prodromal fever and respiratory symptoms >6 days (AUC = 0.79), and PCT <0.25 μg/L (AUC = 0.81) improved diagnostic performance (AUC = 0.90) (P = .05). CONCLUSIONS A combination of clinical features and biomarkers may aid physicians in identifying patients at high risk for Mp CAP.
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Affiliation(s)
- Patrick M Meyer Sauteur
- Division of Infectious Diseases and Hospital Epidemiology, University Children’s Hospital Zurich, Zurich, Switzerland
| | - Selina Krautter
- Division of Infectious Diseases and Hospital Epidemiology, University Children’s Hospital Zurich, Zurich, Switzerland
| | - Lilliam Ambroggio
- Emergency Medicine and Hospital Medicine, Children’s Hospital Colorado, Denver, Colorado, USA
| | - Michelle Seiler
- Emergency Department, University Children’s Hospital Zurich, Zurich, Switzerland
| | - Paolo Paioni
- Division of Infectious Diseases and Hospital Epidemiology, University Children’s Hospital Zurich, Zurich, Switzerland
| | - Christa Relly
- Division of Infectious Diseases and Hospital Epidemiology, University Children’s Hospital Zurich, Zurich, Switzerland
| | - Riccarda Capaul
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Christian Kellenberger
- Division of Diagnostic Imaging, University Children’s Hospital Zurich, Zurich, Switzerland
| | - Thorsten Haas
- Division of Anesthesiology, University Children’s Hospital Zurich, Zurich, Switzerland
| | - Claudine Gysin
- Division of Otolaryngology, University Children’s Hospital Zurich, Zurich, Switzerland
| | | | - Annemarie M C van Rossum
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, Erasmus MC University Medical Center–Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Christoph Berger
- Division of Infectious Diseases and Hospital Epidemiology, University Children’s Hospital Zurich, Zurich, Switzerland
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15
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Vasala A, Hytönen VP, Laitinen OH. Modern Tools for Rapid Diagnostics of Antimicrobial Resistance. Front Cell Infect Microbiol 2020; 10:308. [PMID: 32760676 PMCID: PMC7373752 DOI: 10.3389/fcimb.2020.00308] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/22/2020] [Indexed: 12/18/2022] Open
Abstract
Fast, robust, and affordable antimicrobial susceptibility testing (AST) is required, as roughly 50% of antibiotic treatments are started with wrong antibiotics and without a proper diagnosis of the pathogen. Validated growth-based AST according to EUCAST or CLSI (European Committee on Antimicrobial Susceptibility Testing, Clinical Laboratory Standards Institute) recommendations is currently suggested to guide the antimicrobial therapy. Any new AST should be validated against these standard methods. Many rapid diagnostic techniques can already provide pathogen identification. Some of them can additionally detect the presence of resistance genes or resistance proteins, but usually isolated pure cultures are needed for AST. We discuss the value of the technologies applying nucleic acid amplification, whole genome sequencing, and hybridization as well as immunodiagnostic and mass spectrometry-based methods and biosensor-based AST. Additionally, we evaluate the potential of integrated systems applying microfluidics to integrate cultivation, lysis, purification, and signal reading steps. We discuss technologies and commercial products with potential for Point-of-Care Testing (POCT) and their capability to analyze polymicrobial samples without pre-purification steps. The purpose of this critical review is to present the needs and drivers for AST development, to show the benefits and limitations of AST methods, to introduce promising new POCT-compatible technologies, and to discuss AST technologies that are likely to thrive in the future.
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Affiliation(s)
- Antti Vasala
- Protein Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Vesa P. Hytönen
- Protein Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
| | - Olli H. Laitinen
- Protein Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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16
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Kaboré B, Post A, Lompo P, Bognini JD, Diallo S, Kam BTD, Rahamat-Langendoen J, Wertheim HFL, van Opzeeland F, Langereis JD, de Jonge MI, Tinto H, Jacobs J, van der Ven AJ, de Mast Q. Aetiology of acute febrile illness in children in a high malaria transmission area in West Africa. Clin Microbiol Infect 2020; 27:590-596. [PMID: 32505586 DOI: 10.1016/j.cmi.2020.05.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/19/2020] [Accepted: 05/25/2020] [Indexed: 01/12/2023]
Abstract
OBJECTIVES Areas with declining malaria transmission in sub-Saharan Africa have recently witnessed important changes in the aetiology of childhood acute febrile illness (AFI). We describe the aetiology of AFI in a high malaria transmission area in rural Burkina Faso. METHODS In a prospective hospital-based diagnostic study, children aged 3 months to 15 years with AFI were recruited and assessed using a systematic diagnostic protocol, including blood cultures, whole blood PCR on a selection of bacterial pathogens, malaria diagnostics and a multiplex PCR on nasopharyngeal swabs targeting 21 viral and 4 bacterial respiratory pathogens. RESULTS A total of 589 children with AFI were enrolled from whom an infectious disease was considered in 575 cases. Acute respiratory tract infections, malaria and invasive bacterial infections (IBI) accounted for 179 (31.1%), 175 (30.4%) and 75 (13%) of AFI cases respectively; 16 (21.3%) of IBI cases also had malarial parasitaemia. A viral pathogen was demonstrated from the nasopharynx in 157 children (90.7%) with respiratory tract symptoms. Of all children with viral respiratory tract infections, 154 (92.4% received antibiotics, whereas no antibiotic was provided in 13 (17%) of IBI cases. CONCLUSIONS Viral respiratory infections are a common cause of childhood AFI in high malaria transmission areas, next to malaria and IBI. These findings highlight the importance of interventions to improve targeted treatment with antimicrobials. Most patients with viral infections received antibiotics unnecessarily, while a considerable number with IBI did not receive antibiotics.
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Affiliation(s)
- B Kaboré
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands; IRSS/Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso
| | - A Post
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - P Lompo
- IRSS/Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso
| | - J D Bognini
- IRSS/Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso
| | - S Diallo
- IRSS/Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso
| | - B T D Kam
- IRSS/Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso
| | - J Rahamat-Langendoen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands; Radboudumc Center for Infectious Diseases (RCI), the Netherlands
| | - H F L Wertheim
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands; Radboudumc Center for Infectious Diseases (RCI), the Netherlands
| | - F van Opzeeland
- Section of Paediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - J D Langereis
- Radboudumc Center for Infectious Diseases (RCI), the Netherlands; Section of Paediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - M I de Jonge
- Radboudumc Center for Infectious Diseases (RCI), the Netherlands; Section of Paediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - H Tinto
- IRSS/Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso; Centre Muraz, Bobo-Dioulasso, Burkina Faso
| | - J Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine (ITM), Antwerp, Belgium; Department of Microbiology, Immunology and Transplantation, University of Leuven (KU Leuven), Leuven, Belgium
| | - A J van der Ven
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands; Radboudumc Center for Infectious Diseases (RCI), the Netherlands
| | - Q de Mast
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands; Radboudumc Center for Infectious Diseases (RCI), the Netherlands.
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17
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Evaluation of Commercial Molecular Diagnostic Methods for Detection and Determination of Macrolide Resistance in Mycoplasma pneumoniae. J Clin Microbiol 2020; 58:JCM.00242-20. [PMID: 32269102 DOI: 10.1128/jcm.00242-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/01/2020] [Indexed: 12/11/2022] Open
Abstract
We evaluated six commercial molecular tests targeting Mycoplasma pneumoniae, namely, the BioFire FilmArray respiratory panel (RP), the Meridian Alethia Mycoplasma Direct, the GenMark ePlex respiratory pathogen panel (RPP), the Luminex NxTAG RPP, the ELITech ELITe InGenius Mycoplasma MGB research use only (RUO) PCR, and the SpeeDx Resistance Plus MP assays. Laboratory-developed PCR assays at the University of Alabama at Birmingham and the Centers for Disease Control and Prevention were used as reference standards. Among 428 specimens, 212 were designated confirmed positives for M. pneumoniae The highest clinical sensitivities were found with the InGenius PCR (99.5%) and the FilmArray RP (98.1%). The Resistance Plus MP identified 93.3% of the confirmed-positive specimens, whereas 83.6, 64.6, and 55.7% were identified by the ePlex RPP, NxTAG RPP, and Mycoplasma Direct assays, respectively. There was no significant difference between the sensitivity of the reference methods and that of the FilmArray RP and InGenius assays, but the remaining four assays detected significantly fewer positive specimens (P < 0.05). Specificities of all assays were 99.5 to 100%. The Resistance Plus MP assay detected macrolide resistance in 27/33 specimens, resulting in a sensitivity of 81.8%. This study provides the first large-scale comparison of commercial molecular assays for detection of M. pneumoniae in the United States and identified clear differences among their performance. Additional studies are necessary to explore the impact of various test performances on patient outcome.
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18
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Multicenter Evaluation of QIAstat-Dx Respiratory Panel V2 for Detection of Viral and Bacterial Respiratory Pathogens. J Clin Microbiol 2020; 58:JCM.01793-19. [PMID: 32229601 PMCID: PMC7269373 DOI: 10.1128/jcm.01793-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/20/2020] [Indexed: 12/01/2022] Open
Abstract
QIAstat-Dx Respiratory Panel V2 (RP) is a novel molecular-method-based syndromic test for the simultaneous and rapid (∼70-min) detection of 18 viral and 3 bacterial pathogens causing respiratory infections. This report describes the first multicenter retrospective comparison of the performance of the QIAstat-Dx RP assay to the established ePlex Respiratory Pathogen Panel (RPP) assay, for which we used 287 respiratory samples from patients suspected with respiratory infections. The QIAstat-Dx RP assay detected 312 (92%) of the 338 respiratory targets that were detected by the ePlex RPP assay. QIAstat-Dx Respiratory Panel V2 (RP) is a novel molecular-method-based syndromic test for the simultaneous and rapid (∼70-min) detection of 18 viral and 3 bacterial pathogens causing respiratory infections. This report describes the first multicenter retrospective comparison of the performance of the QIAstat-Dx RP assay to the established ePlex Respiratory Pathogen Panel (RPP) assay, for which we used 287 respiratory samples from patients suspected with respiratory infections. The QIAstat-Dx RP assay detected 312 (92%) of the 338 respiratory targets that were detected by the ePlex RPP assay. Most of the discrepant results have been observed in the low-pathogen-load samples. In addition, the QIAstat-Dx RP assay detected 19 additional targets in 19 respiratory samples that were not detected by the ePlex RPP assay. Nine of these discordant targets were considered to represent true positives after discrepancy testing by a third method. The main advantage of the QIAstat-Dx system compared to other syndromic testing systems, including the ePlex RPP assay, is the ability to generate cycle threshold (CT) values, which could help with the interpretation of results. Taking the data together, this study showed good performance of the QIAstat-Dx RP assay in comparison to the ePlex RPP assay for the detection of respiratory pathogens. The QIAstat-Dx RP assay offers a new, rapid, and accurate sample-to-answer multiplex panel for the detection of the most common viral and bacterial respiratory pathogens and therefore has the potential to direct appropriate therapy and infection control precautions.
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19
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Azhar IR, Mohraz M, Mardani M, Tavakoli MA, Afshar AE, Zamani M, Sadeghpoor S, Safari S, Dadashpoor R, Rezaee M, Shirvani F, Azimi S, Heydarifard Z, Ranjbar HH, Lotfi AH, Mosadegh F, Hashemnejad F, Jazayeri SM. Influenza species and subtypes circulation among hospitalized patients in Laleh hospital during two influenza seasonal (2016-2017 and 2017-2018) using a multiplex Real Time-Polymerase Chain Reaction. Infect Dis Rep 2020; 12:8139. [PMID: 32318254 PMCID: PMC7171471 DOI: 10.4081/idr.2020.8139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/09/2019] [Indexed: 11/24/2022] Open
Abstract
The introduction of polymerase chain reaction (PCR) techniques has improved the detection of respiratory viruses, particularly with the use of multiplex real-time technique with the capability of simultaneous detection of various pathogens in a single reaction. The aim of this study was to apply the above technology for the diagnosis of influenza infections and at the same time to differentiate between common flu species between hospitalized patients in Laleh hospital (Iran) between two flu seasons (2016-2017 and 2017-2018). Different respiratory specimens were collected from 540 patients from a period of December 2016 to May 2018 and were sent to the laboratory for molecular diagnosis. RNAs were extracted and subsequently, a multiplex real time PCR identifying flu A, flu B and typing flu A (H1N1) was carried out. The mean age of patients was 47.54±23.96. 216 (40%) and 321 (60%) of subjects were male and female, respectively. 219 out of 540 (40.5%) were positive for influenza infection including flu A (n=97, 44.3%), flu A (H1N1) (n=45, 20.7%) and flu B (n=77, 35%). Flu A was the dominant species on 2016-2017 and flu B was the major species on 2017-2018. Flu A (H1N1) was comparable in both time periods. Flu infections were most frequently diagnosed in age groups 21-40. Flu-positive patients suffered more from body pain and sore throat than flunegative patients with significant statistical difference (P values <0.001). The mean duration of hospitalization was shorter for flu-positive patients (P value = 0.016). Application of multiplex real time PCR could facilitate the influenza diagnosis in a short period of time, benefiting patients from exclusion of bacterial infections and avoiding unnecessary antibiotic therapy. Influenza diagnosis was not achieved in up to 60% of flu-like respiratory infections, suggesting the potential benefit of adopting the same methodology for assessing the involvement of other viral or/and bacterial pathogens in those patients.
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Affiliation(s)
| | - Minoo Mohraz
- Infection Control Office, Laleh Hospital, Tehran.,Internal Medicine, Gynecology and Surgery Wards Laleh Hospital, Tehran
| | - Masoud Mardani
- Infection Control Office, Laleh Hospital, Tehran.,Internal Medicine, Gynecology and Surgery Wards Laleh Hospital, Tehran
| | | | | | - Mohammad Zamani
- Genetic Laboratory and Molecular Diagnosis, Laleh Hospital, Tehran
| | | | - Saeid Safari
- Infection Control Office, Laleh Hospital, Tehran
| | | | - Mahsa Rezaee
- Genetic Laboratory and Molecular Diagnosis, Laleh Hospital, Tehran
| | - Fariba Shirvani
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Shohreh Azimi
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Heydarifard
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
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Trotter M, Borst N, Thewes R, von Stetten F. Review: Electrochemical DNA sensing – Principles, commercial systems, and applications. Biosens Bioelectron 2020; 154:112069. [DOI: 10.1016/j.bios.2020.112069] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/28/2020] [Accepted: 02/01/2020] [Indexed: 02/06/2023]
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21
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Ganzenmueller T, Kaiser R, Baier C, Wehrhane M, Hilfrich B, Witthuhn J, Flucht S, Heim A. Comparison of the performance of the Panther Fusion respiratory virus panel to R-Gene and laboratory developed tests for diagnostic and hygiene screening specimens from the upper and lower respiratory tract. J Med Microbiol 2020; 69:427-435. [DOI: 10.1099/jmm.0.001133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Introduction. Diagnosis of acute respiratory infections (ARIs) can be facilitated by the Panther Fusion (PF) automatic, random access PCR system for the detection of influenzavirus A (Flu A) and B (Flu B), parainfluenzavirus (Paraflu), respiratory syncytial virus (RSV), human metapneumovirus (hMPV), rhinovirus (RV) and human adenovirus (AdV) in nasopharyngeal swabs.
Aim. To evaluate the performance of PF in comparison with established methods, including subsets of (1) lower respiratory tract (LRT) specimens and (2) upper respiratory tract (URT) hygiene screening specimens of patients without ARI symptoms.
Methodology. The performance characteristics of PF were compared with bioMérieux R-Gene and laboratory-developed PCR tests (LDTs). Overall, 1544 specimens with 6658 individual diagnostic requests were analysed.
Results. The overall concordances of PF and LDTs for Flu A, Flu B and AdV were 98.4, 99.9 and 96.1%, respectively; by re-testing of discrepant specimens concordances increased to 99.4, 99.9 and 98.0%, respectively. Initial concordances of PF and R-Gene assays for RSV, Paraflu, hMPV and RV were 98.4, 96.3, 99.3 and 96.0%, respectively, and retest concordances were 99.7, 97.9, 99.9 and 98.9%, respectively. No differences to the overall performance were found for the subgroups of LRT and hygiene screening specimens. PCR cycle threshold (Ct) values correlated very well between methods, indicating that a semi-quantitative diagnostic approach using Ct values (e.g. highly vs. weakly positive) could augment the diagnostic information.
Conclusion. PF performed similar to R-Gene and LDTs not only for its intended use but also for LRT and hygiene screening specimens with shorter hands-on and turnaround times.
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Affiliation(s)
- Tina Ganzenmueller
- Institute for Medical Virology, University Hospital Tuebingen, Tuebingen, Germany
- Institute for Virology, Hannover Medical School, Hannover, Germany
| | - Rolf Kaiser
- Institute for Virology, University Hospital Cologne, Cologne, Germany
| | - Claas Baier
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Marlies Wehrhane
- Institute for Virology, Hannover Medical School, Hannover, Germany
| | | | - Jenny Witthuhn
- Institute for Virology, Hannover Medical School, Hannover, Germany
| | - Sandra Flucht
- Institute for Virology, Hannover Medical School, Hannover, Germany
| | - Albert Heim
- Institute for Virology, Hannover Medical School, Hannover, Germany
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22
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Meyers L, Dien Bard J, Galvin B, Nawrocki J, Niesters HGM, Stellrecht KA, St George K, Daly JA, Blaschke AJ, Robinson C, Wang H, Cook CV, Hassan F, Dominguez SR, Pretty K, Naccache S, Olin KE, Althouse BM, Jones JD, Ginocchio CC, Poritz MA, Leber A, Selvarangan R. Enterovirus D68 outbreak detection through a syndromic disease epidemiology network. J Clin Virol 2020; 124:104262. [PMID: 32007841 DOI: 10.1016/j.jcv.2020.104262] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 01/08/2020] [Accepted: 01/14/2020] [Indexed: 02/04/2023]
Abstract
BACKGROUND In 2014, enterovirus D68 (EV-D68) was responsible for an outbreak of severe respiratory illness in children, with 1,153 EV-D68 cases reported across 49 states. Despite this, there is no commercial assay for its detection in routine clinical care. BioFire® Syndromic Trends (Trend) is an epidemiological network that collects, in near real-time, deidentified. BioFire test results worldwide, including data from the BioFire® Respiratory Panel (RP). OBJECTIVES Using the RP version 1.7 (which was not explicitly designed to differentiate EV-D68 from other picornaviruses), we formulate a model, Pathogen Extended Resolution (PER), to distinguish EV-D68 from other human rhinoviruses/enteroviruses (RV/EV) tested for in the panel. Using PER in conjunction with Trend, we survey for historical evidence of EVD68 positivity and demonstrate a method for prospective real-time outbreak monitoring within the network. STUDY DESIGN PER incorporates real-time polymerase chain reaction metrics from the RPRV/EV assays. Six institutions in the United States and Europe contributed to the model creation, providing data from 1,619 samples spanning two years, confirmed by EV-D68 gold-standard molecular methods. We estimate outbreak periods by applying PER to over 600,000 historical Trend RP tests since 2014. Additionally, we used PER as a prospective monitoring tool during the 2018 outbreak. RESULTS The final PER algorithm demonstrated an overall sensitivity and specificity of 87.1% and 86.1%, respectively, among the gold-standard dataset. During the 2018 outbreak monitoring period, PER alerted the research network of EV-D68 emergence in July. One of the first sites to experience a significant increase, Nationwide Children's Hospital, confirmed the outbreak and implemented EV-D68 testing at the institution in response. Applying PER to the historical Trend dataset to determine rates among RP tests, we find three potential outbreaks with predicted regional EV-D68 rates as high as 37% in 2014, 16% in 2016, and 29% in 2018. CONCLUSIONS Using PER within the Trend network was shown to both accurately predict outbreaks of EV-D68 and to provide timely notifications of its circulation to participating clinical laboratories.
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Affiliation(s)
- Lindsay Meyers
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA 90027, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA 90039, United States.
| | - Ben Galvin
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Jeff Nawrocki
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Hubert G M Niesters
- The University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Division of Clinical Virology, Groningen, The Netherlands.
| | - Kathleen A Stellrecht
- Department of Pathology and Laboratory Medicine, Albany Medical Center, Albany, NY 12208, United States.
| | - Kirsten St George
- New York State Department of Health, Albany, NY, 12202, United States.
| | - Judy A Daly
- Department of Pathology, University of Utah, Salt Lake City, UT 84132, United States; Division of Inpatient Medicine, Primary Children's Hospital, Salt Lake City, UT 84132, United States.
| | - Anne J Blaschke
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84132, United States.
| | - Christine Robinson
- Department of Pathology and Laboratory Medicine, Children's Colorado, Aurora, CO 80045, United States.
| | - Huanyu Wang
- Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH 43205, United States.
| | - Camille V Cook
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Ferdaus Hassan
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 64108, United States.
| | - Sam R Dominguez
- Department of Pathology and Laboratory Medicine, Children's Colorado, Aurora, CO 80045, United States.
| | - Kristin Pretty
- Department of Pathology and Laboratory Medicine, Children's Colorado, Aurora, CO 80045, United States.
| | - Samia Naccache
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA 90027, United States.
| | | | - Benjamin M Althouse
- Information School, University of Washington, Seattle, WA, 98105, United States; Department of Biology, New Mexico State University, Las Cruces, NM, 88003, United States.
| | - Jay D Jones
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Christine C Ginocchio
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States; Global Medical Affairs, bioMérieux, Durham, NC 27712, United States; Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, United States.
| | - Mark A Poritz
- BioFire Defense, Salt Lake City, UT 84107, United States.
| | - Amy Leber
- Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH 43205, United States.
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 64108, United States.
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Abstract
Antimicrobial susceptibility testing (AST) technologies help to accelerate the initiation of targeted antimicrobial therapy for patients with infections and could potentially extend the lifespan of current narrow-spectrum antimicrobials. Although conceptually new and rapid AST technologies have been described, including new phenotyping methods, digital imaging and genomic approaches, there is no single major, or broadly accepted, technological breakthrough that leads the field of rapid AST platform development. This might be owing to several barriers that prevent the timely development and implementation of novel and rapid AST platforms in health-care settings. In this Consensus Statement, we explore such barriers, which include the utility of new methods, the complex process of validating new technology against reference methods beyond the proof-of-concept phase, the legal and regulatory landscapes, costs, the uptake of new tools, reagent stability, optimization of target product profiles, difficulties conducting clinical trials and issues relating to quality and quality control, and present possible solutions. This Consensus Statement presents the barriers that currently prevent the timely development and implementation of novel and rapid antimicrobial susceptibility testing platforms, including the costs involved, uptake of new tools, legal and regulatory aspects, difficulties conducting clinical trials and quality control, and presents possible solutions.
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Zanella MC, Meylan P, Kaiser L. Syndromic panels or 'panel syndrome'? A perspective through the lens of respiratory tract infections. Clin Microbiol Infect 2020; 26:665-668. [PMID: 31904564 DOI: 10.1016/j.cmi.2019.12.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/25/2019] [Accepted: 12/26/2019] [Indexed: 10/25/2022]
Affiliation(s)
- M-C Zanella
- Laboratory of Virology, Division of Laboratory Medicine and Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland; University of Geneva Medical School, Geneva, Switzerland; Laboratory of Bacteriology, Division of Laboratory Medicine and Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
| | - P Meylan
- University of Lausanne Faculty of Biology and Medicine, Lausanne, Switzerland
| | - L Kaiser
- Laboratory of Virology, Division of Laboratory Medicine and Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland; University of Geneva Medical School, Geneva, Switzerland
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Opportunities Revealed for Antimicrobial Stewardship and Clinical Practice with Implementation of a Rapid Respiratory Multiplex Assay. J Clin Microbiol 2019; 57:JCM.00861-19. [PMID: 31413077 PMCID: PMC6760939 DOI: 10.1128/jcm.00861-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/05/2019] [Indexed: 12/18/2022] Open
Abstract
Few studies assess the utility of rapid multiplex molecular respiratory panels in adult patients. Previous multiplex PCR assays took hours to days from order time to result. We analyze the clinical impact of switching to a molecular assay with a 3-h test-turnaround-time (TAT). We performed a retrospective review of adult patients who presented to our emergency departments with respiratory symptoms and had a respiratory viral panel (xTAG RVP; RVP) or respiratory pathogen panel (ePlex RP; RPP) within 48 h of presentation. The average TATs for the RVP and RPP were 27.9 and 3.0 h, respectively (P < 0.0001). In RVP-positive and RPP-positive patients, 68.9 and 44.5% of those with normal chest imaging received antibiotics (P = 0.013), while 95.4 and 89.6% of those with abnormal imaging received antibiotics, respectively (P = 0.187). There was no difference in antibiotic duration in RVP-positive and RPP-positive patients with abnormal chest imaging (6.2 and 6.0 days, respectively; P = 0.923) and normal chest imaging (4.5 and 4.3 days, respectively; P = 0.922). Fewer patients were admitted in the RPP-positive compared to the RVP-positive group (76.9 and 88.6%, respectively; P = 0.013), while the proportion of admissions were similar among RPP-negative and RVP-negative patients (85.3 and 87.1%, P = 0.726). Switching to a multiplex respiratory panel with a clinically actionable TAT is associated with reduced hospital admissions and, in admitted adults without focal radiographic findings, reduced antibiotic initiation. Opportunities to further mitigate inappropriate antibiotic use may be realized by combining rapid multiplex PCR with provider education, clinical decision-care algorithms, and active antibiotic stewardship.
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26
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Zhang HC, Ai JW, Cui P, Zhu YM, Hong-Long W, Li YJ, Zhang WH. Incremental value of metagenomic next generation sequencing for the diagnosis of suspected focal infection in adults. J Infect 2019; 79:419-425. [PMID: 31442461 DOI: 10.1016/j.jinf.2019.08.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/15/2019] [Accepted: 08/18/2019] [Indexed: 12/22/2022]
Abstract
OBJECTIVES Microbiological diagnosis is essential during clinical management of focal infections. Metagenomic next generation sequencing (mNGS) has been reported as a promising diagnostic tool in infectious diseases. However, little is known about the clinical utility of mNGS in focal infections. METHODS We conducted a single-center retrospective study to investigate impact of mNGS on focal infection diagnosis and compared it with conventional methods, including culture, pathological examination, Xpert MTB/RIF, etc. 98 suspected focal infections cases were enrolled, and medical records were reviewed to determine their rates of detection, time-to-identification, and clinical outcomes. RESULTS mNGS showed a satisfying diagnostic positive percent agreement of 86.30% (95% CI: 75.79-92.88%) in a variety of tissues, compared to 45.21% (95% CI: 33.68-57.24%) for culture and 57.53% (95% CI: 45.43-68.84%)f for conventional methods (p < 0.0125), and detected an extra 34 pathogenic microorganisms. Time requirement for pathogen identification using mNGS ranges from 31 h to 55 h, which showed an advantage over culture. (82.36 h; 95%CI: 65.83, 98.89; P < 0.05) CONCLUSIONS: mNGS showed promising potential in pathogenic diagnosis during focal infections and might enable clinicians to make more timely and targeted therapeutic decisions.
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Affiliation(s)
- Hao-Cheng Zhang
- Department of Infectious Disease, Huashan Hospital of Fudan University, 12 Wulumuqi Zhong Road, Shanghai 200040, China
| | - Jing-Wen Ai
- Department of Infectious Disease, Huashan Hospital of Fudan University, 12 Wulumuqi Zhong Road, Shanghai 200040, China
| | - Peng Cui
- Department of Infectious Disease, Huashan Hospital of Fudan University, 12 Wulumuqi Zhong Road, Shanghai 200040, China
| | - Yi-Min Zhu
- Department of Infectious Disease, Huashan Hospital of Fudan University, 12 Wulumuqi Zhong Road, Shanghai 200040, China
| | - Wu Hong-Long
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Yong-Jun Li
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Wen-Hong Zhang
- Department of Infectious Disease, Huashan Hospital of Fudan University, 12 Wulumuqi Zhong Road, Shanghai 200040, China.
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Memish ZA. Call to action for improved case definition and contact tracing for MERS-CoV. J Travel Med 2019; 26:5288009. [PMID: 30649438 PMCID: PMC7107567 DOI: 10.1093/jtm/taz001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/07/2018] [Accepted: 01/10/2019] [Indexed: 01/31/2023]
Abstract
Progress has been made in KSA in reducing the number and size of healthcare facilities outbreaks of MERS-CoV by the application of wide scope case definition leading to excessive MERS-CoV testing. Critical case definition review and application of point of care testing with revision of HCWs furlough are urgently needed.
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Affiliation(s)
- Ziad A Memish
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,Infectious Diseases Division, Department of Medicine & Department of Research, Prince Mohamed Bin Abdulaziz Hospital ('PMAH'), Ministry of Health, Riyadh, Saudi Arabia.,Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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28
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Kelly-Cirino C, Mazzola LT, Chua A, Oxenford CJ, Van Kerkhove MD. An updated roadmap for MERS-CoV research and product development: focus on diagnostics. BMJ Glob Health 2019; 4:e001105. [PMID: 30815285 PMCID: PMC6361340 DOI: 10.1136/bmjgh-2018-001105] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/13/2018] [Accepted: 10/23/2018] [Indexed: 01/12/2023] Open
Abstract
Diagnostics play a central role in the early detection and control of outbreaks and can enable a more nuanced understanding of the disease kinetics and risk factors for the Middle East respiratory syndrome-coronavirus (MERS-CoV), one of the high-priority pathogens identified by the WHO. In this review we identified sources for molecular and serological diagnostic tests used in MERS-CoV detection, case management and outbreak investigations, as well as surveillance for humans and animals (camels), and summarised the performance of currently available tests, diagnostic needs, and associated challenges for diagnostic test development and implementation. A more detailed understanding of the kinetics of infection of MERS-CoV is needed in order to optimise the use of existing assays. Notably, MERS-CoV point-of-care tests are needed in order to optimise supportive care and to minimise transmission risk. However, for new test development, sourcing clinical material continues to be a major challenge to achieving assay validation. Harmonisation and standardisation of laboratory methods are essential for surveillance and for a rapid and effective international response to emerging diseases. Routine external quality assessment, along with well-characterised and up-to-date proficiency panels, would provide insight into MERS-CoV diagnostic performance worldwide. A defined set of Target Product Profiles for diagnostic technologies will be developed by WHO to address these gaps in MERS-CoV outbreak management.
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Affiliation(s)
| | | | - Arlene Chua
- Department of Information, Evidence and Research, WHO, Geneva, Switzerland.,Medecins Sans Frontières, Geneva, Switzerland
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29
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Hasan MR, Al Mana H, Young V, Tang P, Thomas E, Tan R, Tilley P. A novel real-time PCR assay panel for detection of common respiratory pathogens in a convenient, strip-tube array format. J Virol Methods 2018; 265:42-48. [PMID: 30578898 PMCID: PMC7113679 DOI: 10.1016/j.jviromet.2018.12.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/16/2018] [Accepted: 12/18/2018] [Indexed: 12/14/2022]
Abstract
Respanel is a laboratory-developed PCR test panel for common respiratory pathogens. Strip-tube array-based assay, designed for convenience and minimal hands-on time. Specificity and accuracy of Respanel is ≥95% against two commercial assays. Sensitivity of Respanel is 94% and 88% against two commercial assays.
Commercial multiplex assays, built on different chemistries and platforms are widely available for simultaneous detection of pathogens that cause respiratory infections. However, these tests are often difficult to implement in a resource limited setting because of high cost. In this study, we developed and validated a method for simultaneous testing of common respiratory pathogens (Respanel) by real-time PCR in a convenient, strip-tube array format. Primers and probes for sixteen PCR assays were selected from the literature or newly designed. Following optimization of individual PCR assays, strip-tube arrays were prepared by dispensing primer-probe mixes (PPM) into two sets of 8-tube strips. Nucleic acid extracts from specimens were mixed with PCR master mix, and dispensed column-wise into 2 × 8-wells of a 96-well plate. PPMs from strip-tubes were then added to the wells using a multichannel pipette for real-time PCR. Individual PCR assays were optimized using previously known specimens (n = 394) with 91%–100% concordance with culture, DFA or PCR results. Respanel was then tested in a routine manner at two different sites using specimens (n = 147) previously tested by Qiagen Resplex I&II or Fast-Track Diagnostics Respiratory Pathogens 21 assays. The sensitivity, specificity and accuracy of Respanel were 94%, 95% and 95%, respectively, against Resplex and 88%, 100% and 99%, respectively, against FTDRP21. Respanel detected more pathogens (p < 0.05) than Resplex but the rate of pathogen detection was not significantly different from FTDRP21. Respanel is a convenient and inexpensive assay that is more sensitive than Resplex and comparable to FTDRP21 for the detection of common respiratory pathogens.
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Affiliation(s)
- Mohammad Rubayet Hasan
- Department of Pathology, Sidra Medicine, Doha, Qatar; Weill Cornell Medical College in Qatar, Doha, Qatar.
| | | | - Virginia Young
- Children's and Women's Health Centre of BC, Vancouver, British Columbia, Canada
| | - Patrick Tang
- Department of Pathology, Sidra Medicine, Doha, Qatar; Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Eva Thomas
- Department of Pathology, Sidra Medicine, Doha, Qatar; Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Rusung Tan
- Department of Pathology, Sidra Medicine, Doha, Qatar; Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Peter Tilley
- Children's and Women's Health Centre of BC, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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30
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Schmitz JE, Tang YW. The GenMark ePlex ®: another weapon in the syndromic arsenal for infection diagnosis. Future Microbiol 2018; 13:1697-1708. [PMID: 30547684 DOI: 10.2217/fmb-2018-0258] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
As one of the most recent additions to the syndromic testing landscape, the ePlex® platform by GenMark Diagnostics is a system that combines the manufacturer's signature electrochemical detection technology with updated microfluidics, providing a new option for multiplex testing that is both rapid and requires minimal hands-on steps. In this review, we detail the ePlex platform and its current/future syndromic panels, with a particular focus on the respiratory pathogen panel - the platform's first assay to undergo clinical trials and receive regulatory approval in the USA. By keeping informed of these ever-expanding laboratory options, clinicians and microbiologists can stay positioned at the forefront of infectious disease diagnosis.
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Affiliation(s)
- Jonathan E Schmitz
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center & School of Medicine, Nashville, TN 37232, USA
| | - Yi-Wei Tang
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA.,Department of Pathology & Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065 USA
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31
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Gosert R, Naegele K, Hirsch HH. Comparing the Cobas Liat Influenza A/B and respiratory syncytial virus assay with multiplex nucleic acid testing. J Med Virol 2018; 91:582-587. [PMID: 30345524 PMCID: PMC7166997 DOI: 10.1002/jmv.25344] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/13/2018] [Indexed: 01/21/2023]
Abstract
Influenza virus and respiratory syncytial virus (RSV) detection with short turn‐around‐time (TAT) is pivotal for rapid decisions regarding treatment and infection control. However, negative rapid testing results may come from poor assay sensitivity or from influenza‐like illnesses caused by other community‐acquired respiratory viruses (CARVs). We prospectively compared the performance of Cobas Liat Influenza A/B and RSV assay (LIAT) with our routine multiplexNAT‐1 (xTAG Respiratory Pathogen Panel; Luminex) and multiplexNAT‐2 (ePlex‐RPP; GenMark Diagnostics) using 194 consecutive nasopharyngeal swabs from patients with influenza‐like illness during winter 2017/2018. Discordant results were reanalyzed by specific in‐house quantitative nucleic acid amplification testing (NAT). LIAT was positive for influenza virus‐A, ‐B, and RSV in 18 (9.3%), 13 (6.7%), and 55 (28.4%) samples, and negative in 108 samples. Other CARVs were detected by multiplexNAT in 66 (34.0%) samples. Concordant results for influenza and RSV were seen in 190 (97.9%), discordant results in 4 (2.1%), which showed low‐level RSV (<40 000 copies/mL). Sensitivity and specificity of LIAT for influenza‐A, ‐B, and RSV were 100%, 100% and 100%, and 100%, 99.5% and 100%, respectively. The average TAT of LIAT was 20 minutes compared to 6 hours and 2 hours for the multiplexNAT‐1 and ‐2, respectively. Thus, LIAT demonstrated excellent sensitivity and specificity for influenza and RSV, which together with the simple sample processing and short TAT renders this assay suitable for near‐patient testing. Cobas Liat is highly sensitive and specific for Influenza and RSV in 86/194 children Other CARVs were detected by multiplex NAT in 66/196 children Simple processing and TAT of 20 min suitable for near‐patient testing LIAT assay shows excellent sensitivity and specificity for influenza and RSV Simple sample processing and short turn‐around‐time of 20 min render the assay suitable for near‐patient testing Barcode reading and direct transfer of results into the laboratory information system
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Affiliation(s)
- Rainer Gosert
- Division of Infection Diagnostics, Department Biomedicine, Haus Petersplatz, University of Basel, Basel, Switzerland
| | - Klaudia Naegele
- Division of Infection Diagnostics, Department Biomedicine, Haus Petersplatz, University of Basel, Basel, Switzerland
| | - Hans H Hirsch
- Division of Infection Diagnostics, Department Biomedicine, Haus Petersplatz, University of Basel, Basel, Switzerland.,Transplantation and Clinical Virology, Department Biomedicine, Haus Petersplatz, University of Basel, Basel, Switzerland.,Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
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32
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Senescau A, Kempowsky T, Bernard E, Messier S, Besse P, Fabre R, François JM. Innovative DendrisChips ® Technology for a Syndromic Approach of In Vitro Diagnosis: Application to the Respiratory Infectious Diseases. Diagnostics (Basel) 2018; 8:E77. [PMID: 30423863 PMCID: PMC6316573 DOI: 10.3390/diagnostics8040077] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/31/2018] [Accepted: 11/08/2018] [Indexed: 02/03/2023] Open
Abstract
Clinical microbiology is experiencing the emergence of the syndromic approach of diagnosis. This paradigm shift will require innovative technologies to detect rapidly, and in a single sample, multiple pathogens associated with an infectious disease. Here, we report on a multiplex technology based on DNA-microarray that allows detecting and discriminating 11 bacteria implicated in respiratory tract infection. The process requires a PCR amplification of bacterial 16S rDNA, a 30 min hybridization step on species-specific oligoprobes covalently linked on dendrimers coated glass slides (DendriChips®) and a reading of the slides by a dedicated laser scanner. A diagnostic result is delivered in about 4 h as a predictive value of presence/absence of pathogens using a decision algorithm based on machine-learning method, which was constructed from hybridization profiles of known bacterial and clinical isolated samples and which can be regularly enriched with hybridization profiles from clinical samples. We demonstrated that our technology converged in more than 95% of cases with the microbiological culture for bacteria detection and identification.
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Affiliation(s)
| | | | | | | | - Philippe Besse
- Département Génie Mathématiques et Modélisation, Fédérale Université of Toulouse, F-31077 Toulouse, France.
| | | | - Jean Marie François
- LISBP, Fédérale Université de Toulouse, CNRS, INRA, INSA, F-31077 Toulouse, France.
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33
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Bioassays: The best alternative for conventional methods in detection of Legionella pneumophila. Int J Biol Macromol 2018; 121:1295-1307. [PMID: 30219511 DOI: 10.1016/j.ijbiomac.2018.09.074] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/20/2018] [Accepted: 09/12/2018] [Indexed: 11/21/2022]
Abstract
Fastidious bacteria are group of bacteria that not only grow slowly but also have complex nutritional needs. In this review, recent progress made on development of biosensing strategies towards quantification of Legionella pneumophila as fastidious bacteria in microbiology was investigated. In coincidence with medical bacteriology, it is the most widely used bio-monitoring, biosensors based on DNA and antibody. Also, all of legionella pneumophila genosensors and immunosensors that developed in recent years were collected analyzed. This review is meant to provide an overview of the various types of bioassays have been developed for determination of Legionella Legionella, along with significant advances over the last several years in related technologies. In addition, this review described: i) Most frequently applied principles in bioassay/biosensing of Legionellaii) The aspects of fabrication in the perspective of bioassay/biosensing applications iii) The potential of various electrochemical and optical bioassay/biosensing for the determination of Legionella and the circumvention of the most serious problem in immunosensing/immunoassay was discussed. iv) Some of bioassay/biosensing has been discussed with and without labels. v) We also summarize the latest developments in the applications of bioassay/biosensing methods for detection of Legionella. vi) The development trends of optical and electrochemical based bioassay/biosensing are also introduced.
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34
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Amer H, Alqahtani AS, Alzoman H, Aljerian N, Memish ZA. Unusual presentation of Middle East respiratory syndrome coronavirus leading to a large outbreak in Riyadh during 2017. Am J Infect Control 2018; 46:1022-1025. [PMID: 29661625 PMCID: PMC7115299 DOI: 10.1016/j.ajic.2018.02.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 02/26/2018] [Accepted: 02/26/2018] [Indexed: 12/17/2022]
Abstract
Background The hallmark of Middle East respiratory syndrome coronavirus (MERS-CoV) disease is the ability to cause major health care-associated nosocomial outbreaks with superspreading events leading to massive numbers of cases and excessive morbidity and mortality. In this report, we describe a patient who presented with acute renal failure requiring hemodialysis and became a MERS-CoV superspreader, igniting a recent multihospital outbreak in Riyadh. Material and Results Between May 31 and June 15, 2017, 44 cases of MERS-CoV infection were reported from 3 simultaneous clusters from 3 health care facilities in Riyadh, Saudi Arabia, including 11 fatal cases. Out of the total reported cases, 29 cases were reported from King Saud Medical City. The cluster at King Saud Medical City was ignited by a single superspreader patient who presented with acute renal failure. After 14 hours in the open area of the emergency department and 2 hemodialysis sessions he was diagnosed with MERS-CoV. One hundred twenty contacts who had direct unprotected exposure were screened. Among those contacts, 9 out of 107 health care workers (5 nurses, 3 physicians, and 1 paramedic) and 7 out of 13 patients tested positive for MERS-CoV. Conclusions This hospital outbreak demonstrated the difficulties in diagnosing pneumonia in patients with renal and cardiac failure, which leads to delayed suspicion of MERS-CoV and hence delay in applying the proper infection control procedures. In MERS-CoV endemic countries there is an urgent need for developing rapid point-of-care testing that would assist emergency department staff in triaging suspected cases of MERS-CoV to ensure timely isolation and management of their primary illness and prevent major MERS-CoV outbreaks.
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35
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Meyers L, Ginocchio CC, Faucett AN, Nolte FS, Gesteland PH, Leber A, Janowiak D, Donovan V, Dien Bard J, Spitzer S, Stellrecht KA, Salimnia H, Selvarangan R, Juretschko S, Daly JA, Wallentine JC, Lindsey K, Moore F, Reed SL, Aguero-Rosenfeld M, Fey PD, Storch GA, Melnick SJ, Robinson CC, Meredith JF, Cook CV, Nelson RK, Jones JD, Scarpino SV, Althouse BM, Ririe KM, Malin BA, Poritz MA. Automated Real-Time Collection of Pathogen-Specific Diagnostic Data: Syndromic Infectious Disease Epidemiology. JMIR Public Health Surveill 2018; 4:e59. [PMID: 29980501 PMCID: PMC6054708 DOI: 10.2196/publichealth.9876] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/29/2018] [Accepted: 04/12/2018] [Indexed: 12/22/2022] Open
Abstract
Background Health care and public health professionals rely on accurate, real-time monitoring of infectious diseases for outbreak preparedness and response. Early detection of outbreaks is improved by systems that are comprehensive and specific with respect to the pathogen but are rapid in reporting the data. It has proven difficult to implement these requirements on a large scale while maintaining patient privacy. Objective The aim of this study was to demonstrate the automated export, aggregation, and analysis of infectious disease diagnostic test results from clinical laboratories across the United States in a manner that protects patient confidentiality. We hypothesized that such a system could aid in monitoring the seasonal occurrence of respiratory pathogens and may have advantages with regard to scope and ease of reporting compared with existing surveillance systems. Methods We describe a system, BioFire Syndromic Trends, for rapid disease reporting that is syndrome-based but pathogen-specific. Deidentified patient test results from the BioFire FilmArray multiplex molecular diagnostic system are sent directly to a cloud database. Summaries of these data are displayed in near real time on the Syndromic Trends public website. We studied this dataset for the prevalence, seasonality, and coinfections of the 20 respiratory pathogens detected in over 362,000 patient samples acquired as a standard-of-care testing over the last 4 years from 20 clinical laboratories in the United States. Results The majority of pathogens show influenza-like seasonality, rhinovirus has fall and spring peaks, and adenovirus and the bacterial pathogens show constant detection over the year. The dataset can also be considered in an ecological framework; the viruses and bacteria detected by this test are parasites of a host (the human patient). Interestingly, the rate of pathogen codetections, on average 7.94% (28,741/362,101), matches predictions based on the relative abundance of organisms present. Conclusions Syndromic Trends preserves patient privacy by removing or obfuscating patient identifiers while still collecting much useful information about the bacterial and viral pathogens that they harbor. Test results are uploaded to the database within a few hours of completion compared with delays of up to 10 days for other diagnostic-based reporting systems. This work shows that the barriers to establishing epidemiology systems are no longer scientific and technical but rather administrative, involving questions of patient privacy and data ownership. We have demonstrated here that these barriers can be overcome. This first look at the resulting data stream suggests that Syndromic Trends will be able to provide high-resolution analysis of circulating respiratory pathogens and may aid in the detection of new outbreaks.
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Affiliation(s)
| | - Christine C Ginocchio
- BioFire Diagnostics, Salt Lake City, UT, United States.,bioMérieux USA, Durham, NC, United States.,Hofstra Northwell School of Medicine, Hempstead, NY, United States
| | | | - Frederick S Nolte
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Per H Gesteland
- Departments of Pediatrics and Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Amy Leber
- Laboratory of Microbiology and Immunoserology, Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, United States
| | - Diane Janowiak
- Department of Lab Operations, South Bend Medical Foundation, South Bend, IN, United States
| | - Virginia Donovan
- Department of Pathology, New York University Winthrop Hospital, Mineola, NY, United States
| | - Jennifer Dien Bard
- Clinical Microbiology and Virology Laboratory, Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA, United States.,Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Silvia Spitzer
- Molecular Genetics Laboratory, Stony Brook University Medical Center, Stony Brook, NY, United States
| | - Kathleen A Stellrecht
- Department of Pathology and Laboratory Medicine, Albany Medical Center, Albany, NY, United States
| | - Hossein Salimnia
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Rangaraj Selvarangan
- Clinical Microbiology, Virology and Molecular Infectious Diseases Laboratory, Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO, United States
| | - Stefan Juretschko
- Department of Pathology and Laboratory Medicine, Division of Infectious Disease Diagnostics, Northwell Health, Lake Success, NY, United States
| | - Judy A Daly
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Jeremy C Wallentine
- Department of Pathology, Intermountain Medical Center, Murray, UT, United States
| | - Kristy Lindsey
- Laboratory of Microbiology, University of Massachusetts Medical School-Baystate, Springfield, MA, United States
| | - Franklin Moore
- Laboratory of Microbiology, University of Massachusetts Medical School-Baystate, Springfield, MA, United States
| | - Sharon L Reed
- Department of Pathology and Medicine, Divisions of Clinical Pathology and Infectious Diseases, UC San Diego, San Diego, CA, United States
| | - Maria Aguero-Rosenfeld
- Department of Clinical Laboratories, New York University Langone Health, New York, NY, United States
| | - Paul D Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Gregory A Storch
- Department of Pediatrics, Washington University, St. Louis, MO, United States
| | - Steve J Melnick
- Department of Pathology and Clinical Laboratories, Nicklaus Children's Hospital, Miami, FL, United States
| | - Christine C Robinson
- Department of Pathology and Laboratory Medicine, Microbiology/Virology Laboratory Section, Children's Hospital Colorado, Aurora, CO, United States
| | - Jennifer F Meredith
- Department of Laboratory Services, Microbiology Section, Greenville Health System, Greenville, SC, United States
| | | | | | - Jay D Jones
- BioFire Diagnostics, Salt Lake City, UT, United States
| | | | - Benjamin M Althouse
- University of Washington, Seattle, WA, United States.,New Mexico State University, Las Cruces, NM, United States
| | | | - Bradley A Malin
- Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN, United States
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Multicenter Evaluation of the ePlex Respiratory Pathogen Panel for the Detection of Viral and Bacterial Respiratory Tract Pathogens in Nasopharyngeal Swabs. J Clin Microbiol 2018; 56:JCM.01658-17. [PMID: 29212701 PMCID: PMC5786739 DOI: 10.1128/jcm.01658-17] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 11/20/2017] [Indexed: 12/20/2022] Open
Abstract
The performance of the new ePlex Respiratory Pathogen (RP) panel (GenMark Diagnostics) for the simultaneous detection of 19 viruses (influenza A virus; influenza A H1 virus; influenza A 2009 H1 virus; influenza A H3 virus; influenza B virus; adenovirus; coronaviruses [HKU1, OC43, NL63, and 229E]; human rhinovirus/enterovirus; human metapneumovirus; parainfluenza viruses 1, 2, 3, and 4; and respiratory syncytial virus [RSV] [RSV subtype A and RSV subtype B]) and 2 bacteria (Mycoplasma pneumoniae and Chlamydia pneumoniae) was evaluated. Prospectively and retrospectively collected nasopharyngeal swab (NPS) specimens (n = 2,908) were evaluated by using the ePlex RP panel, with the bioMérieux/BioFire FilmArray Respiratory Panel (BioFire RP) as the comparator method. Discordance analysis was performed by using target-specific PCRs and bidirectional sequencing. The reproducibility of the assay was evaluated by using reproducibility panels comprised of 6 pathogens. The overall agreement between the ePlex RP and BioFire RP results was >95% for all targets. Positive percent agreement with the BioFire RP result for viruses ranged from 85.1% (95% confidence interval [CI], 80.2% to 88.9%) to 95.1% (95% CI, 89.0% to 97.9%), while negative percent agreement values ranged from 99.5% (95% CI, 99.1% to 99.7%) to 99.8% (95% CI, 99.5% to 99.9%). Additional testing of discordant targets (12%; 349/2,908) confirmed the results of ePlex RP for 38% (131/349) of samples tested. Reproducibility was 100% for all targets tested, with the exception of adenovirus, for which reproducibilities were 91.6% at low virus concentrations and 100% at moderate virus concentrations. The ePlex RP panel offers a new, rapid, and sensitive “sample-to-answer” multiplex panel for the detection of the most common viral and bacterial respiratory pathogens.
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Clinical implications of rapid ePlex® Respiratory Pathogen Panel testing compared to laboratory-developed real-time PCR. Eur J Clin Microbiol Infect Dis 2017; 37:571-577. [PMID: 29222697 PMCID: PMC5816761 DOI: 10.1007/s10096-017-3151-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/24/2017] [Indexed: 11/04/2022]
Abstract
Rapid diagnosis of respiratory infections is of great importance for adequate isolation and treatment. Due to the batch-wise testing, laboratory-developed real-time polymerase chain reaction (PCR) assays (LDT) often result in a time to result of one day. Here, LDT was compared with rapid ePlex® Respiratory Pathogen (RP) Panel testing of GenMark Diagnostics (Carlsbad, CA, USA) with regard to time to result, installed isolation precautions, and antibacterial/antiviral treatment. Between January and March 2017, 68 specimens of 64 patients suspected of an acute respiratory infection were tested with LDT and the ePlex® RP panel. The time to result was calculated as the time between sample reception and result reporting. Information regarding isolation and antibacterial/antiviral treatment was obtained from the patient records. Thirty specimens tested LDT positive (47%) and 29 ePlex® RP panel positive (45%). The median time to result was 27.1 h (range 6.5–96.6) for LDT versus 3.4 h (range 1.5–23.6) for the RP panel, p-value < 0.001. In 14 out of 30 patients, isolation was discontinued based on the ePlex® RP panel results, saving 21 isolation days. ePlex® RP panel test results were available approximately one day ahead of the LDT results in the 19 patients receiving antiviral/antibacterial treatment. In addition, two bacterial pathogens, not requested by the physician, were detected using the RP panel. Analysis of respiratory infections with the ePlex® RP panel resulted in a significant decrease in time to result, enabling a reduction in isolation days in half of the patients. Furthermore, syndromic RP panel testing increased the identification of causative pathogens.
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Abstract
The recent development of commercial panel-based molecular diagnostics for the rapid detection of pathogens in positive blood culture bottles, respiratory specimens, stool, and cerebrospinal fluid has resulted in a paradigm shift in clinical microbiology and clinical practice. This review focuses on U.S. Food and Drug Administration (FDA)-approved/cleared multiplex molecular panels with more than five targets designed to assist in the diagnosis of bloodstream, respiratory tract, gastrointestinal, or central nervous system infections. While these panel-based assays have the clear advantages of a rapid turnaround time and the detection of a large number of microorganisms and promise to improve health care, they present certain challenges, including cost and the definition of ideal test utilization strategies (i.e., optimal ordering) and test interpretation.
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