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Aydin M, Carter-Conger J, Gao N, Gilmore DF, Ricke SC, Ahn S. Molecular identification of common Salmonella serovars using multiplex DNA sensor-based suspension array. Anal Bioanal Chem 2018; 410:2637-2646. [DOI: 10.1007/s00216-018-0938-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/25/2018] [Accepted: 02/02/2018] [Indexed: 12/15/2022]
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Chen YS, Li HR, Zhang W, Hua ZD, Lin XH, Lin MQ, Huang WS, Huang LP, Yu XL, Xu NL, Lin M, Xie BS, Shen XN, Xie JF, Wang Y, Huang M, Wu YA, Hu XL. Development of a bead-based suspension array for the detection of pathogens in acute respiratory tract infections. Exp Biol Med (Maywood) 2016; 241:1551-8. [PMID: 27190247 DOI: 10.1177/1535370216647128] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 04/06/2016] [Indexed: 01/15/2023] Open
Abstract
We developed a high-throughput bead-based suspension array for simultaneous detection of 20 respiratory tract pathogens in clinical specimens. Pathogen-specific genes were amplified and hybridized to probes coupled to carboxyl-encoded microspheres. Fluorescence intensities generated via the binding of phycoerythrin-conjugated streptavidin with biotin-labeled targets were measured by the Luminex 100 bead-based suspension array system. The bead-based suspension array detected bacteria in a significantly higher number of samples compared to the conventional culture. There was no significant difference in the detection rate of atypical pathogensatypical pathogens or viruses between the bead-based suspension array and real-time PCR. This technology can play a significant role in screening patients with pneumonia.
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Affiliation(s)
- Yu-Sheng Chen
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Hong-Ru Li
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Wei Zhang
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Zhi-Dan Hua
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Xiao-Hong Lin
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Meng-Qing Lin
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Wen-Sen Huang
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Li-Ping Huang
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Xiao-Li Yu
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Neng-Luan Xu
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Ming Lin
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Bao-Song Xie
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Xiao-Na Shen
- Department of Viral Diseases, Fujian Center for Disease Control and Prevention, Fuzhou 350001, China
| | - Jian-Feng Xie
- Department of Viral Diseases, Fujian Center for Disease Control and Prevention, Fuzhou 350001, China
| | - Yi Wang
- Shanghai Tellgen Life Science Co. Ltd, Shanghai 201203,China
| | - Meng Huang
- Department of Viral Diseases, Fujian Center for Disease Control and Prevention, Fuzhou 350001, China
| | - Yan-An Wu
- Clinical Microbiology Laboratory, Fujian Provincial Hospital, Fuzhou 350001, China
| | - Xin-Lan Hu
- Clinical Microbiology Laboratory, Fujian Provincial Hospital, Fuzhou 350001, China
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Lu X, Nie S, Xia C, Huang L, He Y, Wu R, Zhang L. A rapid two-step algorithm detects and identifies clinical macrolide and beta-lactam antibiotic resistance in clinical bacterial isolates. J Microbiol Methods 2014; 102:26-31. [PMID: 24769404 DOI: 10.1016/j.mimet.2014.04.006] [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: 02/03/2014] [Revised: 04/12/2014] [Accepted: 04/13/2014] [Indexed: 10/25/2022]
Abstract
PURPOSE Aiming to identify macrolide and beta-lactam resistance in clinical bacterial isolates rapidly and accurately, a two-step algorithm was developed based on detection of eight antibiotic resistance genes. METHODS Targeting at genes linked to bacterial macrolide (msrA, ermA, ermB, and ermC) and beta-lactam (blaTEM, blaSHV, blaCTX-M-1, blaCTX-M-9) antibiotic resistances, this method includes a multiplex real-time PCR, a melting temperature profile analysis as well as a liquid bead microarray assay. Liquid bead microarray assay is applied only when indistinguishable Tm profile is observed. RESULTS The clinical validity of this method was assessed on clinical bacterial isolates. Among the total 580 isolates that were determined by our diagnostic method, 75% of them were identified by the multiplex real-time PCR with melting temperature analysis alone, while the remaining 25% required both multiplex real-time PCR with melting temperature analysis and liquid bead microarray assay for identification. Compared with the traditional phenotypic antibiotic susceptibility test, an overall agreement of 81.2% (kappa=0.614, 95% CI=0.550-0.679) was observed, with a sensitivity and specificity of 87.7% and 73% respectively. Besides, the average test turnaround time is 3.9h, which is much shorter in comparison with more than 24h for the traditional phenotypic tests. CONCLUSIONS Having the advantages of the shorter operating time and comparable high sensitivity and specificity with the traditional phenotypic test, our two-step algorithm provides an efficient tool for rapid determination of macrolide and beta-lactam antibiotic resistances in clinical bacterial isolates.
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Affiliation(s)
- Xuedong Lu
- Department of Laboratory Medicine, Futian Hospital, Guangdong Medical College, Shenzhen 518033, China.
| | - Shuping Nie
- Department of Laboratory Medicine, Futian Hospital, Guangdong Medical College, Shenzhen 518033, China
| | - Chengjing Xia
- Department of Laboratory Medicine, Futian Hospital, Guangdong Medical College, Shenzhen 518033, China
| | - Lie Huang
- Department of Laboratory Medicine, Futian Hospital, Guangdong Medical College, Shenzhen 518033, China
| | - Ying He
- Department of Laboratory Medicine, Futian Hospital, Guangdong Medical College, Shenzhen 518033, China
| | - Runxiang Wu
- Department of Laboratory Medicine, Futian Hospital, Guangdong Medical College, Shenzhen 518033, China
| | - Li Zhang
- Department of Laboratory Medicine, Futian Hospital, Guangdong Medical College, Shenzhen 518033, China; Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden.
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van Brunschot SL, Bergervoet JHW, Pagendam DE, de Weerdt M, Geering ADW, Drenth A, van der Vlugt RAA. Development of a multiplexed bead-based suspension array for the detection and discrimination of pospiviroid plant pathogens. PLoS One 2014; 9:e84743. [PMID: 24404188 PMCID: PMC3880322 DOI: 10.1371/journal.pone.0084743] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/19/2013] [Indexed: 12/25/2022] Open
Abstract
Efficient and reliable diagnostic tools for the routine indexing and certification of clean propagating material are essential for the management of pospiviroid diseases in horticultural crops. This study describes the development of a true multiplexed diagnostic method for the detection and identification of all nine currently recognized pospiviroid species in one assay using Luminex bead-based suspension array technology. In addition, a new data-driven, statistical method is presented for establishing thresholds for positivity for individual assays within multiplexed arrays. When applied to the multiplexed array data generated in this study, the new method was shown to have better control of false positives and false negative results than two other commonly used approaches for setting thresholds. The 11-plex Luminex MagPlex-TAG pospiviroid array described here has a unique hierarchical assay design, incorporating a near-universal assay in addition to nine species-specific assays, and a co-amplified plant internal control assay for quality assurance purposes. All assays of the multiplexed array were shown to be 100% specific, sensitive and reproducible. The multiplexed array described herein is robust, easy to use, displays unambiguous results and has strong potential for use in routine pospiviroid indexing to improve disease management strategies.
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Affiliation(s)
- Sharon L. van Brunschot
- Plant Biosecurity Cooperative Research Centre, Bruce, Australian Capital Territory, Australia
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Jan H. W. Bergervoet
- Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Daniel E. Pagendam
- Commonwealth Scientific and Industrial Research Organisation Mathematics, Informatics and Statistics, Dutton Park, Queensland, Australia
| | - Marjanne de Weerdt
- Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Andrew D. W. Geering
- Plant Biosecurity Cooperative Research Centre, Bruce, Australian Capital Territory, Australia
- Centre for Plant Science, The University of Queensland, St Lucia, Queensland, Australia
| | - André Drenth
- Centre for Plant Science, The University of Queensland, St Lucia, Queensland, Australia
| | - René A. A. van der Vlugt
- Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands
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Schweighardt AJ, Battaglia A, Wallace MM. Detection of anthrax and other pathogens using a unique liquid array technology. J Forensic Sci 2013; 59:15-33. [PMID: 24147813 DOI: 10.1111/1556-4029.12283] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Revised: 09/29/2012] [Accepted: 10/07/2012] [Indexed: 11/30/2022]
Abstract
A bead-based liquid hybridization assay, Luminex(®) 100™, was used to identify four pathogenic bacteria, Bacillus anthracis, Clostridium botulinum, Francisella tularensis subsp. tularensis, and Yersinia pestis, and several close relatives. Hybridization between PCR-amplified target sequences and probe sequences (located within the 23S ribosomal RNA gene rrl and the genes related to the toxicity of each bacterium) was detected in single-probe or multiple-probe assays, depending on the organism. The lower limits of detection (LLDs) for the probes ranged from 0.1 to 10 ng. Sensitivity was improved using lambda exonuclease to digest the noncomplementary target strand. All contributors in 33 binary, ternary, and quaternary mixtures in which all components were present in a 1:1 ratio were identified with an 80% success rate. Twenty-eight binary mixtures in which the two components were combined in various ratios were further studied. All target sequences were detected, even when the minor component was overshadowed by a tenfold excess of the major component.
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Affiliation(s)
- Andrew J Schweighardt
- Graduate School and University Center, The City University of New York, 365 Fifth Avenue, New York, NY, 10016
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Schnee C, Schulsse S, Hotzel H, Ayling RD, Nicholas RAJ, Schubert E, Heller M, Ehricht R, Sachse K. A novel rapid DNA microarray assay enables identification of 37 Mycoplasma species and highlights multiple Mycoplasma infections. PLoS One 2012; 7:e33237. [PMID: 22479374 PMCID: PMC3315567 DOI: 10.1371/journal.pone.0033237] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 02/06/2012] [Indexed: 12/02/2022] Open
Abstract
Mycoplasmas comprise a conglomerate of pathogens and commensals occurring in humans and animals. The genus Mycoplasma alone contains more than 120 species at present, and new members are continuously being discovered. Therefore, it seems promising to use a single highly parallel detection assay rather than develop separate tests for each individual species. In this study, we have designed a DNA microarray carrying 70 oligonucleotide probes derived from the 23S rRNA gene and 86 probes from the tuf gene target regions. Following a PCR amplification and biotinylation step, hybridization on the array was shown to specifically identify 31 Mycoplasma spp., as well as 3 Acholeplasma spp. and 3 Ureaplasma spp. Members of the Mycoplasma mycoides cluster can be recognized at subgroup level. This procedure enables parallel detection of Mollicutes spp. occurring in humans, animals or cell culture, from mono- and multiple infections, in a single run. The main advantages of the microarray assay include ease of operation, rapidity, high information content, and affordability. The new test's analytical sensitivity is equivalent to that of real-time PCR and allows examination of field samples without the need for culture. When 60 field samples from ruminants and birds previously analyzed by denaturing-gradient gel electrophoresis (DGGE) were tested by the microarray assay both tests identified the same agent in 98.3% of the cases. Notably, microarray testing revealed an unexpectedly high proportion (35%) of multiple mycoplasma infections, i.e., substantially more than DGGE (15%). Two of the samples were found to contain four different Mycoplasma spp. This phenomenon deserves more attention, particularly its implications for epidemiology and treatment.
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Affiliation(s)
- Christiane Schnee
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-lnstitut (Federal Research Institute for Animal Health), Jena, Germany
| | - Samuel Schulsse
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-lnstitut (Federal Research Institute for Animal Health), Jena, Germany
| | - Helmut Hotzel
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-lnstitut (Federal Research Institute for Animal Health), Jena, Germany
| | - Roger D. Ayling
- Department of Bacteriology, Animal Health and Veterinary Laboratories Agency Mycoplasma Group, Addlestone, United Kingdom
| | - Robin A. J. Nicholas
- Department of Bacteriology, Animal Health and Veterinary Laboratories Agency Mycoplasma Group, Addlestone, United Kingdom
| | - Evelyn Schubert
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-lnstitut (Federal Research Institute for Animal Health), Jena, Germany
| | - Martin Heller
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-lnstitut (Federal Research Institute for Animal Health), Jena, Germany
| | | | - Konrad Sachse
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-lnstitut (Federal Research Institute for Animal Health), Jena, Germany
- * E-mail:
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