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A Molecular Tool for Rapid Detection and Traceability of Cyclospora cayetanensis in Fresh Berries and Berry Farm Soils. Foods 2020; 9:foods9030261. [PMID: 32121643 PMCID: PMC7142967 DOI: 10.3390/foods9030261] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/16/2020] [Accepted: 02/23/2020] [Indexed: 02/07/2023] Open
Abstract
Due to recent outbreaks of cyclosporiasis associated with consumption of fresh berries, producers are demanding modern microbiological tools for the rapid and accurate identification of the human pathogen Cyclospora cayetanensis in berries and environmental samples. The aim of the present work was to develop a molecular tool based on a PCR approach for the rapid and accurate detection of C. cayetanensis. A nested PCR assay was validated for the amplification of a 294 bp size region of the 18S rRNA gene from C. cayetanensis. The limit of detection for the nested PCR assay was validated using 48 berry samples spiked with ~0, 10, 100, and 1000 oocyst per gram of sample. With this assay, it was possible to detect as few as 1 oocyst per gram of berry, in a 50 g sample. Sanger DNA sequencing and phylogenetic analysis were carried out to confirm the presence of C. cayetanensis in berry (n = 17) and soil (n = 5) samples. The phylogenetic analysis revealed that the C. cayetanensis sequences obtained from Mexico clustered within a group recovered from China, Peru, Guatemala-Haiti, and Japan. The PCR protocol designed in the present study could be an important tool for the rapid and accurate detection of this human pathogen in environmental and food samples.
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van de Groep K, Bos MP, Savelkoul PHM, Rubenjan A, Gazenbeek C, Melchers WJG, van der Poll T, Juffermans NP, Ong DSY, Bonten MJM, Cremer OL. Development and first evaluation of a novel multiplex real-time PCR on whole blood samples for rapid pathogen identification in critically ill patients with sepsis. Eur J Clin Microbiol Infect Dis 2018; 37:1333-1344. [PMID: 29700761 PMCID: PMC6015113 DOI: 10.1007/s10096-018-3255-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 04/06/2018] [Indexed: 12/19/2022]
Abstract
Molecular tests may enable early adjustment of antimicrobial therapy and be complementary to blood culture (BC) which has imperfect sensitivity in critically ill patients. We evaluated a novel multiplex real-time PCR assay to diagnose bloodstream pathogens directly in whole blood samples (BSI-PCR). BSI-PCR included 11 species- and four genus-specific PCRs, a molecular Gram-stain PCR, and two antibiotic resistance markers. We collected 5 mL blood from critically ill patients simultaneously with clinically indicated BC. Microbial DNA was isolated using the Polaris method followed by automated DNA extraction. Sensitivity and specificity were calculated using BC as reference. BSI-PCR was evaluated in 347 BC-positive samples (representing up to 50 instances of each pathogen covered by the test) and 200 BC-negative samples. Bacterial species-specific PCR sensitivities ranged from 65 to 100%. Sensitivity was 26% for the Gram-positive PCR, 32% for the Gram-negative PCR, and ranged 0 to 7% for yeast PCRs. Yeast detection was improved to 40% in a smaller set-up. There was no overall association between BSI-PCR sensitivity and time-to-positivity of BC (which was highly variable), yet Ct-values were lower for true-positive versus false-positive PCR results. False-positive results were observed in 84 (4%) of the 2200 species-specific PCRs in 200 culture-negative samples, and ranged from 0 to 6% for generic PCRs. Sensitivity of BSI-PCR was promising for individual bacterial pathogens, but still insufficient for yeasts and generic PCRs. Further development of BSI-PCR will focus on improving sensitivity by increasing input volumes and on subsequent implementation as a bedside test.
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Affiliation(s)
- Kirsten van de Groep
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands. .,Department of Intensive Care Medicine, University Medical Center Utrecht, Utrecht University, Room F06.149, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands.
| | | | - Paul H M Savelkoul
- Microbiome, Amsterdam, the Netherlands.,Department of Medical Microbiology & Infection Control, VU University Medical Center, Amsterdam, the Netherlands.,Department of Medical Microbiology, Maastricht University Medical Center, Maastricht, the Netherlands
| | | | | | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tom van der Poll
- Center of Experimental and Molecular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.,Division of Infectious Diseases, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Nicole P Juffermans
- Department of Intensive Care, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - David S Y Ong
- Department of Intensive Care Medicine, University Medical Center Utrecht, Utrecht University, Room F06.149, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Marc J M Bonten
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Olaf L Cremer
- Department of Intensive Care Medicine, University Medical Center Utrecht, Utrecht University, Room F06.149, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
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Ferreira FP, Honorato-Castro AC, da Silva JV, Orellana SC, Oliveira GC, Madurro JM, Brito-Madurro AG. A novel polymer-based genosensor for the detection and quantification of Streptococcus pneumoniae
in genomic DNA sample. POLYM ENG SCI 2017. [DOI: 10.1002/pen.24707] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Fábio P. Ferreira
- Institute of Chemistry; Federal University of Uberlândia; Uberlândia 38400902 Minas Gerais Brazil
| | - Ana C. Honorato-Castro
- Institute of Genetics and Biochemistry; Federal University of Uberlândia; Uberlândia 38400902 Minas Gerais Brazil
| | - Jussara Vieira da Silva
- Institute of Chemistry; Federal University of Uberlândia; Uberlândia 38400902 Minas Gerais Brazil
| | | | | | - João M. Madurro
- Institute of Chemistry; Federal University of Uberlândia; Uberlândia 38400902 Minas Gerais Brazil
| | - Ana G. Brito-Madurro
- Institute of Genetics and Biochemistry; Federal University of Uberlândia; Uberlândia 38400902 Minas Gerais Brazil
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Salieb-Beugelaar GB, Zhang B, Nigo MM, Frischmann S, Hunziker PR. Improving diagnosis of pneumococcal disease by multiparameter testing and micro/nanotechnologies. EUROPEAN JOURNAL OF NANOMEDICINE 2016. [DOI: 10.1515/ejnm-2016-0012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
AbstractThe diagnosis and management of pneumococcal disease remains challenging, in particular in children who often are asymptomatic carriers, and in low-income countries with a high morbidity and mortality from febrile illnesses where the broad range of bacterial, viral and parasitic cases are in contrast to limited, diagnostic resources. Integration of multiple markers into a single, rapid test is desirable in such situations. Likewise, the development of multiparameter tests for relevant arrays of pathogens is important to avoid overtreatment of febrile syndromes with antibiotics. Miniaturization of tests through use of micro- and nanotechnologies combines several advantages: miniaturization reduces sample requirements, reduces the use of consumables and reagents leading to a reduction in costs, facilitates parallelization, enables point-of-care use of diagnostic equipment and even reduces the amount of potentially infectious disposables, characteristics that are highly desirable in most healthcare settings. This critical review emphasizes our vision on the importance of multiparametric testing for diagnosing pneumococcal infections in patients with fever and examines recent relevant developments in micro/nanotechnologies to achieve this goal.
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