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Dąbrowska J, Karamon J, Kochanowski M, Sroka J, Zdybel J, Cencek T. Comparison Study of Four Extraction Methods Combined with PCR and LAMP for Feline Tritrichomonas foetus Detection in Fecal Samples. Pathogens 2022; 11:604. [PMID: 35631125 PMCID: PMC9143749 DOI: 10.3390/pathogens11050604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/26/2022] Open
Abstract
Feline trichomonosis occurs worldwide, with gastrointestinal symptoms such as chronic large-bowel diarrhea and abdominal pain. The inclusion of molecular methods in diagnostic and epidemiological studies has necessitated an effective method for extracting DNA from feces. We tested four extraction commercial kits: ZR Fecal DNA MiniPrep (50 preps) (Zymo Research, Irvine, CA, USA), QIAamp® DNA Stool Mini Kit (Qiagen Inc., Valencia, CA, USA), UltraClean Fecal DNA Kit (50 preps) (MO BIO, San Diego, CA, USA), and Sherlock AX/100 isolations (A&A Biotechnology, Gdynia, Poland). We assessed the sensitivity of detection of Tritrichomonas foetus in spiked fecal samples for the four kits combined with two molecular assays: PCR and LAMP. The extraction efficacy was quantified using defined aliquots of fecal samples spiked with 5 μL of suspensions containing serial dilutions of trophozoites (0.1; 1; 10; 100; 1000; 10,000), with six replicates for each concentration. In our study, we proved that the ZR Fecal DNA MiniPrep (50 preps) kit combined with LAMP and PCR had the highest efficiency among all the compared methods for the detection of feline T. foetus from fecal samples.
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Luka G, Samiei E, Tasnim N, Dalili A, Najjaran H, Hoorfar M. Comprehensive review of conventional and state-of-the-art detection methods of Cryptosporidium. J Hazard Mater 2022; 421:126714. [PMID: 34325293 DOI: 10.1016/j.jhazmat.2021.126714] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 07/06/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Cryptosporidium is a critical waterborne protozoan pathogen found in water resources that have been a major cause of death and serious illnesses worldwide, costing millions of dollars annually for its detection and treatment. Over the past several decades, substantial efforts have been made towards developing techniques for the detection of Cryptosporidium. Early diagnostic techniques were established based on the existing tools in laboratories, such as microscopes. Advancements in fluorescence microscopy, immunological, and molecular techniques have led to the development of several kits for the detection of Cryptosporidium spp. However, these methods have several limitations, such as long processing times, large sample volumes, the requirement for bulky and expensive laboratory tools, and the high cost of reagents. There is an urgent need to improve these existing techniques and develop low-cost, portable and rapid detection tools for applications in the water quality industry. In this review, we compare recent advances in nanotechnology, biosensing and microfluidics that have facilitated the development of sophisticated tools for the detection of Cryptosporidium spp.Finally, we highlight the advantages and disadvantages, of these state-of-the-art detection methods compared to current analytical methodologies and discuss the need for future developments to improve such methods for detecting Cryptosporidium in the water supply chain to enable real-time and on-site monitoring in water resources and remote areas.
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Affiliation(s)
- George Luka
- School of Engineering, University of British Columbia, 3333 University Way, Kelowna, BC V1V1V7, Canada.
| | - Ehsan Samiei
- Department of Mechanical & Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada.
| | - Nishat Tasnim
- School of Engineering, University of British Columbia, 3333 University Way, Kelowna, BC V1V1V7, Canada.
| | - Arash Dalili
- School of Engineering, University of British Columbia, 3333 University Way, Kelowna, BC V1V1V7, Canada.
| | - Homayoun Najjaran
- School of Engineering, University of British Columbia, 3333 University Way, Kelowna, BC V1V1V7, Canada.
| | - Mina Hoorfar
- School of Engineering, University of British Columbia, 3333 University Way, Kelowna, BC V1V1V7, Canada.
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Luka GS, Nowak E, Toyata QR, Tasnim N, Najjaran H, Hoorfar M. Portable on-chip colorimetric biosensing platform integrated with a smartphone for label/PCR-free detection of Cryptosporidium RNA. Sci Rep 2021; 11:23192. [PMID: 34853388 PMCID: PMC8636559 DOI: 10.1038/s41598-021-02580-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
Cryptosporidium, a protozoan pathogen, is a leading threat to public health and the economy. Herein, we report the development of a portable, colorimetric biosensing platform for the sensitive, selective and label/PCR-free detection of Cryptosporidium RNA using oligonucleotides modified gold nanoparticles (AuNPs). A pair of specific thiolated oligonucleotides, complementary to adjacent sequences on Cryptosporidium RNA, were attached to AuNPs. The need for expensive laboratory-based equipment was eliminated by performing the colorimetric assay on a micro-fabricated chip in a 3D-printed holder assembly. A smartphone camera was used to capture an image of the color change for quantitative analysis. The detection was based on the aggregation of the gold nanoparticles due to the hybridization between the complementary Cryptosporidium RNA and the oligonucleotides immobilized on the AuNPs surface. In the complementary RNA's presence, a distinctive color change of the AuNPs (from red to blue) was observed by the naked eye. However, in the presence of non-complementary RNA, no color change was observed. The sensing platform showed wide linear responses between 5 and 100 µM with a low detection limit of 5 µM of Cryptosporidium RNA. Additionally, the sensor developed here can provide information about different Cryptosporidium species present in water resources. This cost-effective, easy-to-use, portable and smartphone integrated on-chip colorimetric biosensor has great potential to be used for real-time and portable POC pathogen monitoring and molecular diagnostics.
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Affiliation(s)
- George S Luka
- School of Engineering, Faculty of Applied Science, The University of British Columbia, Kelowna, BC, V1V 1V7, Canada
| | - Ephraim Nowak
- School of Engineering, Faculty of Applied Science, The University of British Columbia, Kelowna, BC, V1V 1V7, Canada
| | - Quin Robert Toyata
- School of Engineering, Faculty of Applied Science, The University of British Columbia, Kelowna, BC, V1V 1V7, Canada
| | - Nishat Tasnim
- School of Engineering, Faculty of Applied Science, The University of British Columbia, Kelowna, BC, V1V 1V7, Canada
| | - Homayoun Najjaran
- School of Engineering, Faculty of Applied Science, The University of British Columbia, Kelowna, BC, V1V 1V7, Canada
| | - Mina Hoorfar
- School of Engineering, Faculty of Applied Science, The University of British Columbia, Kelowna, BC, V1V 1V7, Canada.
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Demonchy J, Cordier C, Fréalle E, Demarquette H, Herbaux C, Escure G, Willaume A, Van De Wyngaert Z, Noel MP, Facon T, Faure K, Caro J, Morgan G, Davies FE, Alfandari S, Bories C, Boyle EM. Case Report: Two Cases of Cryptosporidiosis in Heavily Pretreated Patients With Myeloma. Clin Lymphoma Myeloma Leuk 2021; 21:e545-e547. [PMID: 33642203 DOI: 10.1016/j.clml.2021.01.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 11/26/2022]
Affiliation(s)
- Jordane Demonchy
- Department of Haematology Lille University Hospital, Lille, France
| | - Camille Cordier
- Department of Parasitology-Mycology, Lille University Hospital, Lille, France
| | - Emilie Fréalle
- Department of Parasitology-Mycology, Lille University Hospital, Lille, France
| | - Hélène Demarquette
- Department of Haematology, Dunkirk District General Hospital, Dunkirk, France
| | - Charles Herbaux
- Department of Haematology Lille University Hospital, Lille, France
| | - Guillaume Escure
- Department of Haematology Lille University Hospital, Lille, France
| | | | - Zoé Van De Wyngaert
- Department of Haematology Lille University Hospital, Lille, France; Department of Haematology, Saint Antoine Hospital, Sorbonne University, INSERM UMRs 938, Paris, France
| | | | - Thierry Facon
- Department of Haematology Lille University Hospital, Lille, France
| | - Karine Faure
- Department of Infectious Diseases, Lille University Hospital, Lille, France
| | - Jessica Caro
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone, New York, NY
| | - Gareth Morgan
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone, New York, NY
| | - Faith E Davies
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone, New York, NY
| | - Serge Alfandari
- Department of Haematology Lille University Hospital, Lille, France; Department of Infectious Diseases, Gustave Dron Hospital, Tourcoing, France
| | - Claire Bories
- Department of Haematology, Lens District General Hospital, Lens, France
| | - Eileen M Boyle
- Department of Haematology Lille University Hospital, Lille, France; Myeloma Research Program, Perlmutter Cancer Center, NYU Langone, New York, NY.
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Claudel L, Valeix N, Basmaciyan L, Pereira B, Costa D, Vincent A, Valot S, Favennec L, Dalle F. Comparative Study of Eleven Mechanical Pretreatment Protocols for Cryptosporidium parvum DNA Extraction from Stool Samples. Microorganisms 2021; 9:297. [PMID: 33540520 DOI: 10.3390/microorganisms9020297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/20/2021] [Accepted: 01/26/2021] [Indexed: 12/21/2022] Open
Abstract
Nowadays, many commercial kits allow the polymerase chain reaction (PCR) detection of Cryptosporidium deoxyribonucleic acid (DNA) in stool samples, the efficiency of which relies on the extraction method used. Mechanical pretreatment of the stools using grinding beads has been reported to greatly improve this extraction step. However, optimization of this key step remains to be carried out. Indeed, many parameters could influence the pretreatment performances, among which the modulation of the speed and duration of the grinding step, in addition to the physicochemical features of the grinding beads, have never been evaluated to date. In this study, eleven commercial mechanical pretreatment matrixes (Lysis matrix tubes®, MP Biomedical, Irvine, CA, USA) composed of beads with different sizes, shapes, and molecular compositions, were evaluated for their performances in improving Cryptosporidium parvum oocyst DNA extraction before amplification by using our routinely used real-time PCR method. As expected, the eleven commercial mechanical pretreatment matrixes showed varying performances depending on the composition, size, and shape. All in all, the best performances were obtained when using the Lysing matrix, including ceramic beads with a median size (diameter of 1.4 mm).
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Abstract
Cryptosporidium spp. are one of the most important waterborne pathogens worldwide and a leading cause of mortality from waterborne gastrointestinal diseases. Detection of Cryptosporidium spp. in water can be very challenging due to their low numbers and the complexity of the water matrix. This review describes the biology of Cryptosporidium spp. and current methods used in their detection with a focus on C. parvum and C. hominis. Among the methods discussed and compared are microscopy, immunology-based methods using monoclonal antibodies, molecular methods including PCR (polymerase chain reaction)-based assays, and emerging aptamer-based methods. These methods have different capabilities and limitations, but one common challenge is the need for better sensitivity and specificity, particularly in the presence of contaminants. The application of DNA aptamers in the detection of Cryptosporidium spp. oocysts shows promise in overcoming these challenges, and there will likely be significant developments in aptamer-based sensors in the near future.
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Affiliation(s)
- Eman M Hassan
- Department of Civil and Environmental Engineering, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, Canada E-mail:
| | - Banu Örmeci
- Department of Civil and Environmental Engineering, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, Canada E-mail:
| | - Maria C DeRosa
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Canada, K1S 5B6
| | - Brent R Dixon
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, Canada, K1A 0K9
| | - Syed A Sattar
- Department of Civil and Environmental Engineering, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, Canada E-mail: ; C.R.E.M. Co Labs, Units 1-2, 3403 American Drive, Mississauga, ON, Canada, L4V 1T4
| | - Asma Iqbal
- C.R.E.M. Co Labs, Units 1-2, 3403 American Drive, Mississauga, ON, Canada, L4V 1T4
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Valeix N, Costa D, Basmaciyan L, Valot S, Vincent A, Razakandrainibe R, Robert-Gangneux F, Nourrisson C, Pereira B, Fréalle E, Poirier P, Favennec L, Dalle F. Multicenter Comparative Study of Six Cryptosporidium parvum DNA Extraction Protocols Including Mechanical Pretreatment from Stool Samples. Microorganisms 2020; 8:E1450. [PMID: 32971858 PMCID: PMC7564494 DOI: 10.3390/microorganisms8091450] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/13/2020] [Accepted: 09/20/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Nowadays, many commercial kits allow the detection of Cryptosporidium sp. in stool samples after deoxyribonucleic acid (DNA) extraction. Protocols of stool pretreatment have been proposed to optimize oocysts' DNA extraction. Among them, mechanical grinding was reported to improve the performance of Cryptosporidium oocysts' DNA extraction. METHODS A multicenter comparative study was conducted within the framework of the French National Reference Center-Expert Laboratory for Cryptosporidiosis. Six extraction systems (i.e., manual or automated) associated with various mechanical pretreatment protocols, were compared for the Cryptosporidium parvum oocyst' DNA extraction, before amplification using the same real-time PCR method targeting. RESULTS The sensitivity of real-time PCR assay was unequally impacted by the pretreatment/extraction protocol. We observed significant differences for the lowest concentrations of C. parvum oocysts (i.e., 0-94.4% and 33.3-100% respectively for 10 and 50 oocysts/mL). All in all, the protocol using Quick DNA Fecal/Soil Microbe-Miniprep® manual kit showed the best performances. In addition, optimal performances of mechanical pretreatment were obtained by combining a grinding duration of 60 s with a speed of 4 m/s using Fastprep24® with Lysing Matrix E®. CONCLUSIONS Sample pretreatment, as well as the extraction method, needs to be properly adapted to improve the diagnostic performances of the C. parvum DNA amplification methods.
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Affiliation(s)
- Nicolas Valeix
- Laboratoire de Parasitologie-Mycologie, Plateforme de Biologie Hospitalo-Universitaire, 2 rue A. Ducoudray, BP 37013, CEDEX, 21070 Dijon, France; (N.V.); (L.B.); (S.V.); (A.V.)
| | - Damien Costa
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalo-Universitaire C. Nicolle de Rouen, 76000 Rouen, France; (D.C.); (R.R.); (L.F.)
- Centre National de Référence–Laboratoire Expert des Cryptosporidioses, Institut de Biologie Clinique, Centre Hospitalo-Universitaire C. Nicolle de Rouen, 76000 Rouen, France
| | - Louise Basmaciyan
- Laboratoire de Parasitologie-Mycologie, Plateforme de Biologie Hospitalo-Universitaire, 2 rue A. Ducoudray, BP 37013, CEDEX, 21070 Dijon, France; (N.V.); (L.B.); (S.V.); (A.V.)
- UMR PAM, University Bourgogne Franche-Comté-AgroSup Dijon-Equipe Vin, Aliment, Microbiologie, Stress, CEDEX, 21078 Dijon, France
| | - Stéphane Valot
- Laboratoire de Parasitologie-Mycologie, Plateforme de Biologie Hospitalo-Universitaire, 2 rue A. Ducoudray, BP 37013, CEDEX, 21070 Dijon, France; (N.V.); (L.B.); (S.V.); (A.V.)
| | - Anne Vincent
- Laboratoire de Parasitologie-Mycologie, Plateforme de Biologie Hospitalo-Universitaire, 2 rue A. Ducoudray, BP 37013, CEDEX, 21070 Dijon, France; (N.V.); (L.B.); (S.V.); (A.V.)
| | - Romy Razakandrainibe
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalo-Universitaire C. Nicolle de Rouen, 76000 Rouen, France; (D.C.); (R.R.); (L.F.)
- Centre National de Référence–Laboratoire Expert des Cryptosporidioses, Institut de Biologie Clinique, Centre Hospitalo-Universitaire C. Nicolle de Rouen, 76000 Rouen, France
| | - Florence Robert-Gangneux
- Univ. Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé Environnement Travail), UMR_S 1085, 35000 Rennes, France;
| | - Céline Nourrisson
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalo-Universitaire de Clermont-Ferrand, 63000 Clermont-Ferrand, France; (C.N.); (B.P.); (P.P.)
| | - Bruno Pereira
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalo-Universitaire de Clermont-Ferrand, 63000 Clermont-Ferrand, France; (C.N.); (B.P.); (P.P.)
| | - Emilie Fréalle
- CHU Lille, Laboratoire de Parasitologie-Mycologie, F-59000 Lille, France;
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019–UMR8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Philippe Poirier
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalo-Universitaire de Clermont-Ferrand, 63000 Clermont-Ferrand, France; (C.N.); (B.P.); (P.P.)
| | - Loic Favennec
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalo-Universitaire C. Nicolle de Rouen, 76000 Rouen, France; (D.C.); (R.R.); (L.F.)
- Centre National de Référence–Laboratoire Expert des Cryptosporidioses, Institut de Biologie Clinique, Centre Hospitalo-Universitaire C. Nicolle de Rouen, 76000 Rouen, France
| | - Frederic Dalle
- Laboratoire de Parasitologie-Mycologie, Plateforme de Biologie Hospitalo-Universitaire, 2 rue A. Ducoudray, BP 37013, CEDEX, 21070 Dijon, France; (N.V.); (L.B.); (S.V.); (A.V.)
- UMR PAM, University Bourgogne Franche-Comté-AgroSup Dijon-Equipe Vin, Aliment, Microbiologie, Stress, CEDEX, 21078 Dijon, France
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Morio F, Poirier P, Le Govic Y, Laude A, Valot S, Desoubeaux G, Argy N, Nourrisson C, Pomares C, Machouart M, Dalle F, Botterel F, Bourgeois N, Cateau E, Leterrier M, Beser J, Lavergne RA, Le Pape P. Assessment of the first commercial multiplex PCR kit (ParaGENIE Crypto-Micro Real-Time PCR) for the detection of Cryptosporidium spp., Enterocytozoon bieneusi, and Encephalitozoon intestinalis from fecal samples. Diagn Microbiol Infect Dis 2019; 95:34-37. [DOI: 10.1016/j.diagmicrobio.2019.04.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/06/2019] [Accepted: 04/08/2019] [Indexed: 10/27/2022]
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Ahmed SA, Karanis P. Comparison of current methods used to detect Cryptosporidium oocysts in stools. Int J Hyg Environ Health 2018; 221:743-63. [PMID: 29776848 DOI: 10.1016/j.ijheh.2018.04.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 04/17/2018] [Accepted: 04/17/2018] [Indexed: 01/12/2023]
Abstract
In this review all of the methods that are currently in use for the investigation of Cryptosporidium in stool material are highlighted and critically discussed. It appears that more qualifications and background knowledge in this field regarding the diagnosis of the Cryptosporidium parasite is required. Furthermore, there is no standardization for the protocols that are commonly used to either detect oocysts in faeces or to diagnose the Cryptosporidium infection. It is therefore necessary to initiate further education and research that will assist in improving the accuracy of the diagnosis of Cryptosporidium oocysts in the faecal micro-cosmos. Where ambient concentrations of oocysts are low in stool material, detection becomes a formidable task. Procedures for ring tests and the standardization of multi-laboratory testing are recommended. It is also necessary to enhance the routine surveillance capacity of cryptosporidiosis and to improve the safety against it, considering the fact that this disease is under diagnosed and under reported. This review is intended to stimulate research that could lead to future improvements and further developments in monitoring the diagnostic methodologies that will assist in harmonizing Cryptosporidium oocysts in stool diagnosis.
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